An inventive mechanism - AgnosticWeb.com

DAVID: (under Spider Silk) What is being found in genomes all over the animal kingdom is a repeated use to the same genomic mechanisms in a large variety of species and families. I think this implies that there is strong evidence for theistic evolution as the proper theory. Why should the genome be that way unless planned to cover the inventive needs of life as it advances from single cells to us?-Let's confine the discussion to the theistic interpretation of my hypothesis. The inventive mechanism within the cells/cell communities is therefore your God's way of enabling life to advance from single cells to us.-DAVID: To avoid that thought, dhw has invented intelligent cells, but cannot tell us where the intelligence came from.-No-one knows where intelligence comes from: God's, yours, or that which may reside in the cells. That is not the point of my hypothesis, which is to explain how evolution may have happened. I did not invent intelligent cells: the term intelligent is explicitly used by experts such as Margulis, Shapiro and Albrecht-Buehler, along with cognitive, sentient, cooperative, communicative, decision-making etc. Apparently what I've invented is the hypothesis that this intelligence might be responsible for the innovations that drive evolution. DAVID: He has forsaken chance as a mechanism. He wants to create whole new phenotypes by having them cooperate, and won't tell us where the plans come from that they must cooperatively follow. -As I've said repeatedly, just as the human cell community we call the brain comes up with plans, so too does the inventive mechanism (intelligence) within the cells/cell communities.-DAVID: That dosn't answer the huge fossil gaps I have pointed out.-Innovation by intelligent organisms explains the gaps. If the changes hadn't worked, the organisms wouldn't have survived. You are back in your trap: did God dabble? You don't think so. Did God preprogramme every innovation into the first cells? You don't think so. Then the mechanism for change has to be in the cell communities themselves. See below for your attempt to avoid the implications.-DAVID: The idea of cells cooperating into planning a new body form de nova, fully functional in all organs is beyond belief. They have to be given a plan. That is why I raised the issue of a God-given inventive mechanism.-Re "body form de novo", see my reply to Tony's polymorphism analogy. As usual, you separate the mechanism from the cells. It's absurd to argue that cells are not inventive but contain an inventive mechanism. We do not say humans are not inventive but contain an inventive mechanism (the brain). You did not raise this issue. It has been the subject of debate between us since I first proposed the hypothesis of the intelligent cell/cell communities being responsible for innovations (= an inventive intelligence within the cell). You rubbished the idea, and insisted that the only alternatives were preprogramming or God dabbling. Your epiphany seemed to come on Sunday 17 August: -Dhw: ...the idea that God programmed the very first cells to pass on intricate plans for spider silk, fire ant rafting, eyes, kidneys [...]seems to me to require a great deal more faith than the idea that he invented a mechanism that would do its own inventing as and when conditions demanded or allowed.-DAVID: Your latter suggestion makes more sense. He used a self-inventing mechanism is a great idea. Your help in proposing a most reasonable explanation for a God-guided evolution process is much appreciated.-So what happened since 17 August?-DAVID(under Dragonfly): You are totally blind to the complex biology behind all of this problem we are discussing.-The complex biology is one of the main reasons why I cannot accept atheism. Please don't insult my intelligence.-DAVID: Tell me how cooperating cells do it. Where did they get the plans and information? We see no tiny experimental steps, only huge jumps in fossils.[..] Your only escape from this problem is if you recognize that an inventive mechanism in cells comes with full-blown plans.-Suddenly, you are preaching my own sermon at me, with one huge exception. An inventive mechanism in the cells is the hypothesis I have been putting forward for months, but an inventive mechanism would not come WITH full-blown plans, it would INVENT plans. That is why it is an INVENTIVE mechanism. Once more, the hypothesis: your God provided the first living cells with an inventive mechanism (intelligence, brain') which without preprogramming or dabbling enabled them and their increasingly complex descendants to devise innovations that would cope with or exploit environmental changes. What you are proposing is no different from your earlier insistence on total preprogramming, with dabbling as your creationist alternative, both of which you doubted on 17 August. Back to Square One.

DHW: (under Spider Silk): I agree that we can only speculate, as we cannot observe the arrival of eyes, kidneys etc. However, adaptation is an observable fact, and it's not unreasonable to suppose that since cell communities can change themselves to cope with environmental threats, there is an internal mechanism for change. The question then becomes how inventive that mechanism might be. TONY: Limited adaptation. That is the keyword that seems to be missing from most statements when we discuss this. See the analogy above.-Thank you for the dog example, which is beautifully organized and expressed. However, it does only deal with limited adaptation, and the point that I am making is that if the cell communities contain a mechanism that can organize such minor changes, it may be possible that the same mechanism can organize major changes when the environment demands or allows it. That is why I suggested that perhaps (it's always perhaps) there have been no major environmental changes since the Cambrian to allow for further inventions (as opposed to adaptations).-TONY: I give you Polymorphism. To me, this concept is what bridges the gaps between all of these discussions. It is where adaptation, variation, epigenetics, and to a limited extent, evolution meet. Let me pose a question. What if all life didn't evolve from a common ancestor, but instead was created from the same source code? Note, this differs from Darwinian evolution in that individual programs still have to be written individually, but they are all built upon the same framework until you get down to a level of abstraction that can handle all of the variants without further modification. DAVID: Wow, this fits what I have been looking for, a code at the beginning of life that leads to a bush of life, not a tree. That could be the 'inventive mechanism'. I wish I knew more about programming, but it is obvious to me the genome is the most sophisticated program ever written, and we will take many more years picking it apart to understand it. At that point atheism will have little to support it.-QUOTE: "In effect, polymorphism trims down the work of the developer because he can now create a sort of general class with all the attributes and behaviors that he envisions for it. When the time comes for the developer to create more specific subclasses with certain unique attributes and behaviors, the developer can simply alter code in the specific portions where the behaviors will differ. All other portions of the code can be left as is."-If I've understood this correctly, it means God separately creating different species (in the sense of totally different organisms, as opposed to different species of dogwhich are all dogs). In that case, David's enthusiasm suggests a return to creationism.***- ***Your latest posts confirm a mixture of preplanning and dabbling. There is no inventive mechanism: only a mechanism that implements the plans of the developer.-My alternative is evolution driven by interaction between organism and environment. The theistic version of my hypothesis is your God (the developer) has created a mechanism which from within can of its own accord (i.e. without preprogramming) alter specific portions of an organism in order to change its attributes or behaviour, while all other portions of the organism remain as they were, other than adapting themselves to the new cell combinations. (The process would apply as much to innovation as to adaptation.) Same story, but different approach by the developer. This obviates the need for your God specifically to create the spider and the dragonfly, the alligator and the eagle one by one (or two by two), even if in your hypothesis he might only have to fiddle here and there rather than start de novo.

TONY: Limited adaptation. That is the keyword that seems to be missing from most statements when we discuss this. See the analogy above. > >DHW: Thank you for the dog example, which is beautifully organized and expressed. However, it does only deal with limited adaptation, and the point that I am making is that if the cell communities contain a mechanism that can organize such minor changes, it may be possible that the same mechanism can organize major changes when the environment demands or allows it. That is why I suggested that perhaps (it's always perhaps) there have been no major environmental changes since the Cambrian to allow for further inventions (as opposed to adaptations). > -Except that the historical/fossil record is against your argument. When there are drastic environmental changes such that they override the blueprints ability to cope, creatures go extinct, they do not adapt and overcome. If they did, the only cause for extinction would be over hunting by humans.--> TONY: I give you Polymorphism.... > > DHW: QUOTE: "In effect, polymorphism trims down the work of the developer because he can now create a sort of general class with all the attributes and behaviors that he envisions for it. When the time comes for the developer to create more specific subclasses with certain unique attributes and behaviors, the developer can simply alter code in the specific portions where the behaviors will differ. All other portions of the code can be left as is." > > If I've understood this correctly, it means God separately creating different species (in the sense of totally different organisms, as opposed to different species of dogwhich are all dogs). In that case, David's enthusiasm suggests a return to creationism.*** > -Creationism with limited adaptation, yes. -- >DHW: My alternative is evolution driven by interaction between organism and environment. The theistic version of my hypothesis is your God (the developer) has created a mechanism which from within can of its own accord (i.e. without preprogramming) alter specific portions of an organism in order to change its attributes or behaviour, while all other portions of the organism remain as they were, other than adapting themselves to the new cell combinations. (The process would apply as much to innovation as to adaptation.) Same story, but different approach by the developer. This obviates the need for your God specifically to create the spider and the dragonfly, the alligator and the eagle one by one (or two by two), even if in your hypothesis he might only have to fiddle here and there rather than start de novo.- Unfortunately, it does not. To use your examples of the spider and the dragonfly, the differences between the two are too great to be covered by polymorphism in the code. If you had said between two members of the arachnid family, I likely would have agreed, though. Let's put it this way, I would agree that the mechanism for change is there, but I disagree on the scope that the mechanism allows. This is born out by our observations where, despite all of our watching, waiting, and even our attempts to tamper, "a dog is still a dog is still a dog". No matter what, we will never see a dog become a cat, or a mouse, or a turtle. In fact, we will never see a canine be anything other than a canine, regardless of which variety of canine it polymorphs into. Polymorphism allows the change within kinds, not invention.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: Polymorphism allows the change within kinds, not invention.-That still leaves us with pre-planning, dabbling or the inventive mechanism has pre-set plans within it.

Tony: Polymorphism allows the change within kinds, not invention. > > David: That still leaves us with pre-planning, dabbling or the inventive mechanism has pre-set plans within it.- Programs can not invent. Period. They can implement anything within the scope of their design, but they can not create new information from whole-cloth. That is the sort of adaptation that we actually observe in nature. It is not inventive. It may move within a broad range of possible values, and different combinations of those value types might give the appearance of invention, but it is not invention.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: Polymorphism allows the change within kinds, not invention. > > > > David: That still leaves us with pre-planning, dabbling or the inventive mechanism has pre-set plans within it. > Tony:Programs can not invent. Period. They can implement anything within the scope of their design, but they can not create new information from whole-cloth. That is the sort of adaptation that we actually observe in nature. It is not inventive. It may move within a broad range of possible values, and different combinations of those value types might give the appearance of invention, but it is not invention.-I know programs can only do what they are set to do.But that does not exclude God from putting future plans into the genome for later action. This is what I meant by an inventive mechanism.

Tony: Polymorphism allows the change within kinds, not invention. > > > > > > David: That still leaves us with pre-planning, dabbling or the inventive mechanism has pre-set plans within it. > > > > Tony:Programs can not invent. Period. They can implement anything within the scope of their design, but they can not create new information from whole-cloth. That is the sort of adaptation that we actually observe in nature. It is not inventive. It may move within a broad range of possible values, and different combinations of those value types might give the appearance of invention, but it is not invention. > > David: I know programs can only do what they are set to do.But that does not exclude God from putting future plans into the genome for later action. This is what I meant by an inventive mechanism.-I guess it is the word "inventive" that throws me. Inventive to me means creating something new, an increase in the available information.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

David: I know programs can only do what they are set to do.But that does not exclude God from putting future plans into the genome for later action. This is what I meant by an inventive mechanism. > > Tony: I guess it is the word "inventive" that throws me. Inventive to me means creating something new, an increase in the available information.-Your point is the fact dhw always misses. A new activity, a new ability, a new form in evolution always requires additional new information to support the change. I'm simply saying the information is already there to be tapped when needed. That gives me pre-planning, a concept I've always preferred over dabbling. And the program techniques you have described (polymorphism created by classes in programs) helps me understand the enormous diversity in life, the bushiness.

DHW: ...if the cell communities contain a mechanism that can organize such minor changes, it may be possible that the same mechanism can organize major changes when the environment demands or allows it. That is why I suggested that perhaps (it's always perhaps) there have been no major environmental changes since the Cambrian to allow for further inventions (as opposed to adaptations).-TONY: Except that the historical/fossil record is against your argument. When there are drastic environmental changes such that they override the blueprints ability to cope, creatures go extinct, they do not adapt and overcome. If they did, the only cause for extinction would be over hunting by humans.-We simply don't know the full history of environmental changes, but since the planet was initially hostile to life, and since life forms proliferated, there must have been some major changes that were beneficial. In any case, changes that destroy one form of life may be beneficial to another. The fossil record shows that the Cambrian produced an explosion of new organisms. One theory is that there was an increase in oxygen. It's not unreasonable to suppose that something in the environment changed to allow for new inventions, but we can only speculate what. It's obvious, though, that these new forms could not have come into being if they hadn't been able to cope with the environment. God suddenly having a huge dabble? God's billions of computer programmes suddenly coming into operation? Or God's inventive mechanisms experimenting under new conditions? TONY: To use your examples of the spider and the dragonfly, the differences between the two are too great to be covered by polymorphism in the code. [...] I would agree that the mechanism for change is there, but I disagree on the scope that the mechanism allows. [...] we will never see a canine be anything other than a canine, regardless of which variety of canine it polymorphs into. Polymorphism allows the change within kinds, not invention.-Then polymorphism is irrelevant to our discussion, which is about invention, although it would be the same intelligence that produced both micro and macroevolution. Your hypothesis presumably is separate creation of spider and dragonfly. Mine is that if all organisms descended from earlier organisms (= evolution), the spider and the dragonfly are products of different directions taken by the inventive mechanisms in earlier cells. As an analogy: Shakespeare's inventive mechanism produced King Lear, and Carl Benz's produced the motor car. Neither could have taken place if earlier generations had not invented language or the wheel. When individual cells linked up to create multicellular organisms, their inventive mechanisms were able progressively to create an ever wider range of combinations, as and when the environment demanded or allowed, with their respective inventive mechanisms giving instructions to the other parts of their cell community. DAVID: I know programs can only do what they are set to do.But that does not exclude God from putting future plans into the genome for later action. This is what I meant by an inventive mechanism.-The mechanism you are describing is not inventive. You have gone back to preprogramming, as you make clear below. TONY: I guess it is the word "inventive" that throws me. Inventive to me means creating something new, an increase in the available information. DAVID: Your point is the fact dhw always misses. A new activity, a new ability, a new form in evolution always requires additional new information to support the change. I'm simply saying the information is already there to be tapped when needed. That gives me pre-planning, a concept I've always preferred over dabbling.-Do you really think I don't know the meaning of inventive? The information is knowledge accumulated from the experiences of earlier inventions all the way back to the first cells, and the inventiveness is the product of an intelligence that is cognitive, sentient, communicative etc. The combination enables SOME organisms to cope with or exploit new information emanating from a changed environment. On 17 August you wrote: ...dabbling has always bothered me. I like your self-inventing built into the mechanism. On 20 August, I wrote: So too would you be haunted by the extraordinary concept of the first few cells being programmed with every single wonder and innovation throughout the history of evolution. To this you replied: That does bother me. The idea of an inventive mechanism being present makes sense.. Now, however, your God once more preplanned every innovation and wonder, and over billions of years, generations and organisms, the cell communities implemented God's vast variety of plans inherited from the first cells. And inventiveness means automatically obeying God's built-in instructions. Plenty here to be bothered about!

dhw: Do you really think I don't know the meaning of inventive? - I am still formulating a God-arranged process for speciation. I initially misused the concept of inventive mechanism as I was thinking out loud. I have defined it now as a set of pre-planned instructions for a new species in some still hidden area of the genome. I expect it to be found.-> dhw:The information is knowledge accumulated from the experiences of earlier inventions all the way back to the first cells, and the inventiveness is the product of an intelligence that is cognitive, sentient, communicative etc.-Let's take your view of cells: 'cognitive": calls can chemically recognize signals and follow genomic instructions as to appropriate responses; 'sentient': cells recognize signals by chemical reactions, and give genomic guided responses; 'communicative': cells send messages to each other by different biochemical molecules which are recognizable as signals. How much mentation, as implied by your use of those words is really involved? None. Cells are primarily automatons. There is no escaping that fact. -One of the best examples of epigentics is 25 years old: Reznick's guppies change size when threatened by predators. They are still guppies. No answer to speciation. This is what your cell community theory is capable of, no more than that.-> dhw: Plenty here to be bothered about!-Agreed. Please find a better theory for speciation. I'm stuck with mine.

dhw: The complex biology is one of the main reasons why I cannot accept atheism. Please don't insult my intelligence.-This quote set me to thinking. Your intelligence is just fine. The problem is you do not understand how I view things. You and I think of functioning cells from very different viewpoints. The unicellular organisms that Shapiro studies are very much on their own. They have to take care of their whole 'self' and have more latitude from their genome in adaptations than cells in a complex multicellular organism. What Shapiro studies is primarily much different than looking at a kidney cell.-> dhw: An inventive mechanism in the cells is the hypothesis I have been putting forward for months, but an inventive mechanism would not come WITH full-blown plans, it would INVENT plans.-I view the inventive mechanism as coming with plans at the multicellular level of evoltion. At the single cell stage, baceria remain bacteria and modify. The jump to complex multicellularity probably still requires God's preplanning or dabbling.-The variety of cells in a human are not independent. They are responsible to their brothers in an organ and also to outside signals for cooperative changes in cellular product output for the whole organism with its different parts. -A cell in this circumstance is not like a human with a brain. This is a comparison you keep using. It is not a true comparison. The cell in a multicellular animal is a tightly controlled factory, just like an auto factory run by computers. The computer is in the genome and its translation parts. Feedback controls are in place to reduce error to almost zero. These cells have very little latitude. In this instance, it is impossible to understand the appearance of a new species through cell community action.-This exchange between Tony and I fits the discussion:-> by Balance_Maintained , U.S.A., Saturday, August 30, 2014, 08:15 (14 hours, 5 minutes ago) @ David Turell Tony: It would have to be from within. My point was that polymorphism doesn't mean that a subclass creates its own implementation of a method. That implementation still has to be 'written', as it were, by the programmer before it is implemented.-> David: Your version then of the 'inventive mechanism' would be written into the genome at the beginning of life? That would equate to pre-planning with built-in dabbling. > Tony: Yes, precisely. And that actually lines up with the biblical account.-Your comment on Aug 30 12:11 leads to my point: -> dhw: Let's confine the discussion to the theistic interpretation of my hypothesis. The inventive mechanism within the cells/cell communities is therefore your God's way of enabling life to advance from single cells to us.-Not exactly. If my interpretation of cell activity is correct, unicellular forms have more leeway to use a pre-planned inventive mechanism for adaptation, while complex multicellular forms have apparently much less leeway and Tony's polymorphism plays a larger role. This does not help to explain the Cambrian, because the jump to complexity is so large, unless we go back to pre-planning and dabbling at that juncture, before Tony's programming of 'classes of polymorphism' are employed in complex organisms.- Conclusion: I think the inventive mechanism in bacteria has somewhat more latitude at that stage of evolution for invention, and polymorphism is more at play in the inventive mechanism of complex animals and plants. Tony's explanation is the best partial approach to my dilemma of how God guides evolution. And your 'intelligent cell communities' is still a non-answer for my search. It may provide some answer for very simple multicellular sheets of cooperative cells, but nothing more complex.

DAVID: The problem is you do not understand how I view things. You and I think of functioning cells from very different viewpoints. The unicellular organisms that Shapiro studies are very much on their own. They have to take care of their whole 'self' and have more latitude from their genome in adaptations than cells in a complex multicellular organism. What Shapiro studies is primarily much different than looking at a kidney cell.-This is a misunderstanding of the whole concept. It is believed that evolution started out with single cells. At some point these combined to form multicellular organisms. Of course single cells only have to look after themselves (though actually they also help one another), and multicellular organisms need to cooperate, which is why I have always bracketed cells and cell communities together. If you begin with the premise that single cell organisms have a built-in intelligence (which embraces sentience, cognition, information processing, decision-making, cooperativeness), once they get together in communities they will use all of those attributes to enable their communities to function. The cells in the kidney implement the programme invented by the inventive mechanism within the community of cells that first recognized the need for kidneys. This would have taken place within an existing organism (if you believe in evolution), which means that all the cell communities within the whole organism would have had to reshuffle themselves, in the same way as any community has to adapt to changes within itself. A dabbling God would have had to perform exactly the same operation, unless he created every new organism separately from scratch, i.e. he would have had to insert his readymade kidney into an organism, and adjust the rest of the creature's body accordingly. Preprogramming would have had to follow precisely the same course. All the cell communities would have had to be preprogrammed to accommodate the new invention. Your objections on grounds of complexity apply to all the hypotheses, once you try to work out how God did it. DAVID: The variety of cells in a human are not independent. They are responsible to their brothers in an organ and also to outside signals for cooperative changes in cellular product output for the whole organism with its different parts.-Agreed. The intelligence within the cells/cell communities enables ALL the cell communities to work together. That is what is meant by cooperation, a key term for this whole concept.-DAVID: A cell in this circumstance is not like a human with a brain. This is a comparison you keep using. It is not a true comparison. The cell in a multicellular animal is a tightly controlled factory, just like an auto factory run by computers. The computer is in the genome and its translation parts. Feedback controls are in place to reduce error to almost zero. These cells have very little latitude. In this instance, it is impossible to understand the appearance of a new species through cell community action.-In a multicellular animal like a human, you cannot talk of the cell alone, because the animal is a collection of different cell communities. The vast majority of the cells in cell communities are exactly as you describe: they obey instructions. The inventive mechanism (if it exists - I am offering a hypothesis) is what you are calling the computer, which is in the genome, and the genome is the genetic complement of the cell or the cell community. But I don't like the computer image, because computers have to be programmed. I call it intelligence, and I do not understand why you insist on talking of it as if it were not part of the cell/cell community. If it's within the genome, it's part of the cell community! That is where the instructions come from, in the same way as instructions come from the human brain to the rest of the community that constitutes a human being.-To pursue the analogy one step further: you believe your God gave man free will, so presumably man was not preprogrammed to invent the motor car. Maybe man has inherited that inventive freedom from the intelligence your God built into our first ancestors - he gave them the ability to invent. We invent machines outside ourselves, and cells/cell communities invent things inside themselves. I shall try to answer the points re polymorphism in my response to Tony.

dhw: This is a misunderstanding of the whole concept. .....Your objections on grounds of complexity apply to all the hypotheses, once you try to work out how God did it.-No, I don't misunderstand your theory. I think it is impossible based on what we now know about genomic function. And yes, I am trying to work out a process, employed by God, by which speciation occurs, based on discussion with you and Tony. > > dhw: The inventive mechanism (if it exists - I am offering a hypothesis) is what you are calling the computer, which is in the genome, and the genome is the genetic complement of the cell or the cell community. But I don't like the computer image, because computers have to be programmed. -And that is part of our diffference. Both Tony and I view the genome as a computer program. What else can you call the code in DNA? We see that the organism (as whole) can respond to challenges by methylation in the genome to adapt genes to slightly different responses. These slight differences do not make a new species. You want your cell communities to gain intelligence from experience and then use that intelligence to make changes. Just where is any of that 'intelligence' stored? Cells don't have brains (as humans do) and all they can do is slight genomic epigentic modifications. Your theory invents an abilty for cells they cannot have. It is very apparent to me (and Tony) that speciation requires the input of new information in the genome. Either the information is already there, ready to be tapped when required by environmental changes, or there is directed input. I favor the former. Polymorphism classes is an explanation for bushiness. > > dhw: Maybe man has inherited that inventive freedom from the intelligence your God built into our first ancestors - he gave them the ability to invent. We invent machines outside ourselves, and cells/cell communities invent things inside themselves.-Once again, cells and cell communities do not have the 'brain' power to invent. Your analogy just doesn't work. My view of the inventive mechansim is that it contains in the genome elements for a new species, basically preplanned. Cells cannot construct a new form of complex living organism from past experience. That must be collated into a workable plan in advance of any changes. Darwin used itty-bitty advances to support his theory, because he recognized the huge jump between species. He predicted the fossil record would support his idea. It hasn't. Your cell communities don't answer the problem either.

dhw: The inventive mechanism (if it exists - I am offering a hypothesis) is what you are calling the computer, which is in the genome, and the genome is the genetic complement of the cell or the cell community. But I don't like the computer image, because computers have to be programmed. -Like it or not, DNA has been used in computing since papers in 2003. The genome uses a computer code. It requires new information for advancements. The genome is really a computer program system. -http://en.wikipedia.org/wiki/DNA_computing-I see no way your theory can work around this issue. And yes, I do not think the genome is separate from the cells themselves. It is within the cells and it runs the cells. And the whole organism can make some epigentic modifications, but whole species change is beyond that modest capacity, as current research sees it. Epigenetic changes are very modest steps, a la Darwin and his itty-bitty. As I see it, your theory requires itty-bitty, which has never been in the fossil record. Remember, I started as an agnostic. There are reasons why I am a theist, and this is a major one.

Rather than reproduce all your interesting statements, I'll select those I feel require comment.-DAVID: I don't misunderstand your theory. I think it is impossible based on what we now know about genomic function. [...] I am still formulating a God-arranged process for speciation. I initially misused the concept of inventive mechanism as I was thinking out loud. I have defined it now as a set of pre-planned instructions for a new species in some still hidden area of the genome. I expect it to be found.-Firstly, I don't think you should use inventive of a mechanism that invents nothing and merely carries out pre-planned instructions. Preplanning and preprogramming are far clearer.-Secondly, these two statements together show double standards. My theory may seem impossible based on what we now know, but your theory is based on a hidden area of the genome which you expect to be found. What's the difference? Current knowledge sheds no light on the mystery of innovation. Therefore there are gaps in our knowledge, and your theory depends just as much as mine on speculation as to what lies in those gaps. -DAVID: Let's take your view of cells: 'cognitive": calls can chemically recognize signals and follow genomic instructions as to appropriate responses; 'sentient': cells recognize signals by chemical reactions, and give genomic guided responses; 'communicative': cells send messages to each other by different biochemical molecules which are recognizable as signals. How much mentation, as implied by your use of those words is really involved? None. Cells are primarily automatons. -You are following the same line as neuroscientists who trace the chemical and electrical processes that accompany human thought. All our activities can be described in such terms, but we don't know the nature of the thought that triggers the physical actions. Different forms of life may think differently from us. You recognize that with our fellow animals, because we have so much in common. But other forms of life, including plants and bacteria, do their own thinking, and if they didn't, they wouldn't survive. -DAVID: It is very apparent to me (and Tony) that speciation requires the input of new information in the genome. Either the information is already there, ready to be tapped when required by environmental changes, or there is directed input. I favor the former. This is your preprogramming versus your dabbling. Here are the implications. Evolution requires information being passed from one generation to another, from the beginning of life to the present. Therefore according to you every innovation, whether of organs or of modes of behaviour, had to be programmed into the first cells, allowing for every environmental change that was to trigger those innovations: kidneys, eyes, spider's silk, fire-ant's raft - all to be passed down through billions of organisms and generations and years and environments. Of course we shall never find those first computers, so what do you expect to find in, say, the spider's genome? A little chip, perhaps, saying not to be used till the year 400 million BC? The dabble theory is just as fanciful. Your infinite God of pure energy somehow contriving - perhaps through psychokinesis - to manipulate the microscopic globules of material in such a way that they will form kidneys in, say, half a dozen kidneyless organisms to make sure at least two of them survive to promulgate kidneydom. And personally planting chemicals and instructions into the spider to make sure it spins its silk. You called this intricate planning, so how else could God have planned it, if not by dabbling or popping a heritable silk-spinning chip into the computer section of the first living cells? DAVID: As I see it, your theory requires itty-bitty, which has never been in the fossil record. Remember, I started as an agnostic. There are reasons why I am a theist, and this is a major one.-My theory does not require itty-bitty. Intelligent men tried to fly, and a lot of them got killed when their contraptions didn't work. But other intelligent men put various bits and pieces together, using the knowledge acquired from their predecessors, and were able to fly. Either the invention succeeds or it fails. That is the process I envisage with intelligent cell communities cooperating. Many of the organisms will die. But some will get the formula right (innovations can only take place within existing organisms), and then you will have speciation. It's only a hypothesis. And it does depend on us finding that cells/cell communities can think intelligently and inventively, to a degree beyond what is now known. Your two theories (preprogramming and dabbling) seem to me to depend on our finding something a few million degrees beyond what is now known. Remember, I started as a theist, and then an atheist. There are reasons why I am an agnostic, and this is a major one.

DHW: My theory may seem impossible based on what we now know, but your theory is based on a hidden area of the genome which you expect to be found. What's the difference? Current knowledge sheds no light on the mystery of innovation. Therefore there are gaps in our knowledge, and your theory depends just as much as mine on speculation as to what lies in those gaps. > -The idea of progressive evolution through innovation is also just speculation without evidence. Let me rephrase this argument:-We are trying to explain something that we have not observed but speculate about with theoretical processes that we have not observed but speculate about.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

DHW: ...according to you every innovation, whether of organs or of modes of behaviour, had to be programmed into the first cells, allowing for every environmental change that was to trigger those innovations...all to be passed down through billions of organisms and generations and years and environments. Of course we shall never find those first computers, so what do you expect to find in, say, the spider's genome? ..-When we see a multitude of examples that are virtually unchanged since the Cambrian, just exactly which part of this is fanciful? It is only fanciful if you believe in species divergence via evolution, which we have absolutely no evidence for, only speculation.- >DHW: The dabble theory is just as fanciful. Your infinite God of pure energy somehow contriving - perhaps through psychokinesis - to manipulate the microscopic globules of material in such a way that they will form kidneys in, say, half a dozen kidneyless organisms to make sure at least two of them survive to promulgate kidneydom. And personally planting chemicals and instructions into the spider to make sure it spins its silk. You called this intricate planning, so how else could God have planned it, if not by dabbling or popping a heritable silk-spinning chip into the computer section of the first living cells? > -Well, it is less fanciful than saying that a cluster of cells first conceived the concept of a string/web, then the concept of shooting said web out their rears, then invented the concept of silk that is stronger than steel, then performed the chemical engineering to figure out how to make it, and then the biological engineering to figure out how to upgrade the spider, and at the very least reprogramed the genetic material so that the NEXT generation has that ability, all within the lifespan of a single spider...Because that is exactly what would be required by your cellular intelligence. The process of silk is a very poor choice to argue cellular intelligence on due to it's sheer complexity.- ->DHW: My theory does not require itty-bitty. Intelligent men tried to fly, and a lot of them got killed when their contraptions didn't work. But other intelligent men put various bits and pieces together, using the knowledge acquired from their predecessors, and were able to fly. Either the invention succeeds or it fails. That is the process I envisage with intelligent cell communities cooperating. Many of the organisms will die. But some will get the formula right (innovations can only take place within existing organisms), and then you will have speciation. It's only a hypothesis. And it does depend on us finding that cells/cell communities can think intelligently and inventively, to a degree beyond what is now known. Your two theories (preprogramming and dabbling) seem to me to depend on our finding something a few million degrees beyond what is now known. Remember, I started as a theist, and then an atheist. There are reasons why I am an agnostic, and this is a major one.- I see a critical flaw here, and I am curious how you envision it being overcome. Those men that tried to fly shared their knowledge. They experimented repeatedly, and failed, leaving evidence of their experiments for others to learn from. Through the accumulation of knowledge over centuries, they eventually figured it out. That could not happen without some means to transmit that knowledge and experiment. Where is the mechanism for transmitting knowledge of failed experiments, and where is the evidence of the failed experiments?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: I see a critical flaw here, and I am curious how you envision it being overcome. Those men that tried to fly shared their knowledge. They experimented repeatedly, and failed, leaving evidence of their experiments for others to learn from..... Where is the mechanism for transmitting knowledge of failed experiments, and where is the evidence of the failed experiments?-You have answered dhw beautifully, better than my poor attempts. That is why I said his theory calls for itty-bitty advances. Where do his cell communities store the knowledge of the failures, and then finally achiedve success. As I have pointed out to him, he is humaninzing those cels with a brain somewhere.

TONY: Those men that tried to fly shared their knowledge. They experimented repeatedly, and failed, leaving evidence of their experiments for others to learn from.[...] Where is the mechanism for transmitting knowledge of failed experiments, and where is the evidence of the failed experiments?-You are quite right. A failed experiment will have resulted in death, and so the knowledge could not have been passed on. Thank you. (As for evidence, I don't know what sort of fossil a failed experiment would leave behind.) However, a bad analogy doesn't invalidate the general hypothesis. David's cry: As I have pointed out to him, he is humaninzing those cels with a brain somewhere is a travesty, as I've repeatedly warned against anthropomorphization, and I use the human brain as an analogy. We don't know how your God thinks, or how other organisms think, and David's efforts to trace the chemical processes of cellular thought are no different from neuroscientists attempting to explain human thought in the same terms. TONY: The idea of progressive evolution through innovation is also just speculation without evidence. [...] We are trying to explain something that we have not observed but speculate about with theoretical processes that we have not observed but speculate about. -Agreed, and speculation applies just as much to your theories about God as it does to any other hypotheses. This is where it gets interesting. David believes evolution happened through innovation (so do I), and for him that means God preprogramming every single innovation into the first living cells. You clearly favour dabbling (= creationism). I'll go along with theism for the sake of this discussion, and offer a third option: God created a mechanism capable of doing its own inventing. (I have the same objection to your creative, David, as to your inventive. A creative mechanism does not simply obey instructions. Why not stick to preprogramming?) I presume neither of you consider your God incapable of creating such a mechanism, since you believe he's already done so: in David's case, by preprogramming human intelligence into the first living cells, along with spiders' webs and every other multicellular organism and apparatus you can think of, and presumably Tony, you think he created humans separately, along with different species (spider/dragonfly/dog/alligator). Perhaps you and David can explain why you don't like each other's speculative hypotheses.-TONY: When we see a multitude of examples that are virtually unchanged since the Cambrian, just exactly which part of this [= David's preprogramming of every single innovation] is fanciful? It is only fanciful if you believe in species divergence via evolution, which we have absolutely no evidence for, only speculation.-It's the Cambrian that we are trying to explain, and you don't believe David's explanation either, since you reject evolution by innovation. I'll leave you to fight that out between you. DHW: The dabble theory is just as fanciful. TONY: Well, it is less fanciful than saying that a cluster of cells first conceived the concept of a string/web, then the concept of shooting said web out their rears, then invented the concept of silk that is stronger than steel, then performed the chemical engineering to figure out how to make it [etc.] -I'd like to reproduce this in its entirety because it's so beautiful, but space is limited. Thank you. The complexity of all living things is a major factor in my inability to embrace atheism. But even if I believed in God, (a)I would find it difficult to conceive of such a programme being inserted into the first living cells, along with the zillions of other programmes that have led from single cells to humans (David's preferred hypothesis). I have equal difficulty imagining your God painstakingly and - presumably - psychokinetically manipulating globules of matter to separately create the process you've so beautifully described, along with every other such process and every different species (although apparently he did install a mechanism to allow cell communities to organize variations within the same species). You may argue that what I can imagine is no test of truth - but where's the evidence for these hypotheses? All three explanations are speculations, and I'm the only one of us three who doesn't actually believe in any of them. dhw: Therefore there are gaps in our knowledge, and your theory depends just as much as mine on speculation as to what lies in those gaps. DAVID: True, but my problem with your theory is that you are giving properties to cells taht I know they do not have and are not capable of using. -You do not know this. You believe it, just as you believe your God's all-encompassing computer programme will be found hidden somewhere in the cells: "You have sidestepped the issue of is the genome really a computer or not. Tony and I say it is. It is programmed [...] You have said roughly, your theory can't work if the genome is a computer. Agreed, but I have not sidestepped it. I have proposed a mechanism that does its own inventing, and a computer that merely obeys instructions cannot do its own inventing. Your theory attempts to explain evolution by preprogrammed innovation, which Tony does not believe in, so I don't see how you can claim he is on your side. But he will certainly speak for himself.-.

DHW: You are quite right. A failed experiment will have resulted in death, and so the knowledge could not have been passed on. .... > -Typically engineers/designers leave their notes, and even if they don't leave notes, others analyze the events surrounding their demise to construct how the failure occurred. Do you think cells have this ability, either the ability to leave notes with remarks about what failed and why, or the ability to conceptually construct why another organism failed in its experiment??- > TONY: The idea of progressive evolution through innovation is also just speculation without evidence. [...] We are trying to explain something that we have not observed but speculate about with theoretical processes that we have not observed but speculate about. > > Agreed, and speculation applies just as much to your theories about God as it does to any other hypotheses. This is where it gets interesting. David believes evolution happened through innovation (so do I), and for him that means God preprogramming every single innovation into the first living cells. You clearly favour dabbling (= creationism). I'll go along with theism for the sake of this discussion, and offer a third option: God created a mechanism capable of doing its own inventing.... I presume neither of you consider your God incapable of creating such a mechanism, since you believe he's already done so: ... presumably Tony, you think he created humans separately, along with different species (spider/dragonfly/dog/alligator). Perhaps you and David can explain why you don't like each other's speculative hypotheses. >-Sorry, I thought I had been clear on that. I do not believe in divergence through gradual evolution beyond the species level. As for how God did it, I can't say, only speculate as we so often do. -I think of creation as a giant computer program. (Quantum) Physics acts as a native instructions for the machine logic, applying the required force to operate the components. On top of that you have Chemistry, which acts like a sort of "assembly" language, under and interfacing with the rules of physics. On top of that, you have the basic rules of biology, that work as an operating system, using the language of Chemistry. Within this framework you have DNA which acts like C++, a compilation of digital "libraries", bits of programs that are known to work very efficiently and can be organized in numerous different ways to create any possible program you can conceive of by arranging them in different ways. Just like a master engineer/programmer could create a computer starting with nothing but sand (silicon), time, and energy, I think God used pretty much the same methodology. - > TONY: Well, it is less fanciful than saying that a cluster of cells first conceived the concept of a string/web, then the concept of shooting said web out their rears, then invented the concept of silk that is stronger than steel, then performed the chemical engineering to figure out how to make it [etc.] > >DHW: I'd like to reproduce this in its entirety because it's so beautiful, but space is limited. Thank you. -You're welcome. :)->DHW: The complexity of all living things is a major factor in my inability to embrace atheism. But even if I believed in God, (a)I would find it difficult to conceive of such a programme being inserted into the first living cells, along with the zillions of other programmes that have led from single cells to humans (David's preferred hypothesis). I have equal difficulty imagining your God painstakingly and - presumably - psychokinetically manipulating globules of matter to separately create the process you've so beautifully described, along with every other such process and every different species (although apparently he did install a mechanism to allow cell communities to organize variations within the same species). You may argue that what I can imagine is no test of truth - but where's the evidence for these hypotheses? All three explanations are speculations, and I'm the only one of us three who doesn't actually believe in any of them. >-The evidence is in the DNA, the laws of Chemistry, and the laws of Physics and Quantum Physics. Further, if we assume that there is a God, and that God exists as some form of energy, then it is only logical that he could manipulate energy as easily as we manipulate matter being material creatures. Since all matter is comprised of energy, his creating matter is no different kind than our creating buildings or other constructions out of raw matter. - > dhw: Therefore there are gaps in our knowledge, and your theory depends just as much as mine on speculation as to what lies in those gaps. > DAVID: True, but my problem with your theory is that you are giving properties to cells taht I know they do not have and are not capable of using. > >DHW: You do not know this. You believe it, just as you believe your God's all-encompassing computer programme will be found hidden somewhere in the cells.-The program has already been found. Multitudes of programs have been found. The all encompassing program, the operating system if you will, is in the laws of biochemistry, its hardware platform is the material world, and it, just like a computer, requires energy input in order to carry out it's instructions. It's circuits are controlled according to the laws of physics which govern energy.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

DHW: You are quite right. A failed experiment will have resulted in death, and so the knowledge could not have been passed on. .... TONY: Typically engineers/designers leave their notes, and even if they don't leave notes, others analyze the events surrounding their demise to construct how the failure occurred. Do you think cells have this ability, either the ability to leave notes with remarks about what failed and why, or the ability to conceptually construct why another organism failed in its experiment??-Hey, I've already agreed that it was a bad analogy! Do I have to agree twice? TONY: The idea of progressive evolution through innovation is also just speculation without evidence. [...] Dhw: This is where it gets interesting. David believes evolution happened through innovation (so do I), and for him that means God preprogramming every single innovation into the first living cells. You clearly favour dabbling (= creationism). [...]Perhaps you and David can explain why you don't like each other's speculative hypotheses.-TONY: Sorry, I thought I had been clear on that. I do not believe in divergence through gradual evolution beyond the species level. As for how God did it, I can't say, only speculate as we so often do. Yes, you made it very clear, as quoted above, that you do not believe in progressive evolution through innovation. (None of us three believe in gradualism.) But David does believe in it, so I asked you to explain why you didn't like David's speculative hypothesis. And since you believe in separate creation of the species (in the broader sense - spiders/dragonflies/dogs) I asked David to explain why he didn't like your speculative hypothesis. I thought we might all learn something from such an exchange. You have both been quick to attack my own speculative hypothesis, so why the sudden coyness?!-TONY: I think of creation as a giant computer program. (Quantum) Physics acts as a native instructions for the machine logic, applying the required force to operate the components. On top of that you have Chemistry, which acts like a sort of "assembly" language, under and interfacing with the rules of physics. On top of that, you have the basic rules of biology, that work as an operating system, using the language of Chemistry. Within this framework you have DNA which acts like C++, a compilation of digital "libraries", bits of programs that are known to work very efficiently and can be organized in numerous different ways to create any possible program you can conceive of by arranging them in different ways. Just like a master engineer/programmer could create a computer starting with nothing but sand (silicon), time, and energy, I think God used pretty much the same methodology. -Another strikingly written account, for which again many thanks. My guess is that atheists would agree with most of this, apart from your finale. You have later referred to the laws of chemistry, biochemistry, physics, quantum physics etc. and that is the answer one so often gets from atheists: it's all a matter of natural laws. And theists cry: Who made the natural laws? And atheists cry: Who made your God? But this is not the problem we are investigating on the thread called An Inventive Mechanism. The idea of a mechanism that can change itself or be changed into virtually any form one can imagine lies at the heart of evolution. The great question, apart from how such a mechanism came into being (= the existence or not of God), is how it functions. You are a careful writer, and I assume when you say can be organized, your use of the passive is a reference to God dabbling. David doesn't much like that. He thinks God's programmes, handed down from the first tiny cells of 3.7 billion years ago, automatically switch themselves on when the environment provides the trigger. You don't like that, because it entails progressive evolution through innovation. That's why I hoped you would both exchange views on the subject. TONY: Further, if we assume that there is a God, and that God exists as some form of energy, then it is only logical that he could manipulate energy as easily as we manipulate matter being material creatures. Since all matter is comprised of energy, his creating matter is no different kind than our creating buildings or other constructions out of raw matter. -Nicely put again, and I didn't make myself clear. I don't doubt that an omnipotent God could do it, just as I don't doubt that he could create an inventive mechanism that would do the same thing without his interference, but I can't imagine him spending billions of years painstakingly and personally making the first clockwork trilobites etc. etc. and popping the instructions in so that they can reproduce a few zillion more clockwork trilobytes (till they disappear) while he goes on to manufacture the first few clockwork spiders etc. etc. The idea bothers David too. I'm sure we would all learn a lot if only you would exchange views on the subject.

Not off topic. Life appears programmed to do the same thing in different ways. Caffeine in plants is caused by different enzymes:-http://www.scientificamerican.com/article/coffee-s-caffeine-buzz-evolved-separately-from-tea-s/?&WT.mc_id=SA_DD_20140905

TONY: Sorry, I thought I had been clear on that. I do not believe in divergence through gradual evolution beyond the species level. As for how God did it, I can't say, only speculate as we so often do. > >DHW: Yes, you made it very clear, as quoted above, that you do not believe in progressive evolution through innovation. (None of us three believe in gradualism.) But David does believe in it, so I asked you to explain why you didn't like David's speculative hypothesis. And since you believe in separate creation of the species (in the broader sense - spiders/dragonflies/dogs) I asked David to explain why he didn't like your speculative hypothesis. I thought we might all learn something from such an exchange. You have both been quick to attack my own speculative hypothesis, so why the sudden coyness?! > -I am going to go out on a limb and say that David doesn't like my reasoning for two reasons. A) David is a trained scientist, B) Though a theist, David is not (to my knowledge) a Christian, and prefers his God a little less "human" (and I use the term VERY loosely). Whereas I see God as an individual, powerful though he is, with thoughts and feelings similar in kind with ours, David sees him(it) without any personification. There are certain things that, to me at least, make more sense when you accept that personification. For example, why could love not be the motivating factor for the time spent painstakingly crafting the universe. --> TONY: I think of creation as a giant computer program. (Quantum) Physics acts as a native instructions for the machine logic, applying the required force to operate the components. On top of that you have Chemistry, which acts like a sort of "assembly" language, under and interfacing with the rules of physics. On top of that, you have the basic rules of biology, that work as an operating system, using the language of Chemistry. Within this framework you have DNA which acts like C++, a compilation of digital "libraries", bits of programs that are known to work very efficiently and can be organized in numerous different ways to create any possible program you can conceive of by arranging them in different ways. Just like a master engineer/programmer could create a computer starting with nothing but sand (silicon), time, and energy, I think God used pretty much the same methodology. > > DHW: The idea of a mechanism that can change itself or be changed into virtually any form one can imagine lies at the heart of evolution. The great question, apart from how such a mechanism came into being (= the existence or not of God), is how it functions. You are a careful writer, and I assume when you say can be organized, your use of the passive is a reference to God dabbling. David doesn't much like that. He thinks God's programmes, handed down from the first tiny cells of 3.7 billion years ago, automatically switch themselves on when the environment provides the trigger. You don't like that, because it entails progressive evolution through innovation. That's why I hoped you would both exchange views on the subject.->....I don't doubt that an omnipotent God could do it, just as I don't doubt that he could create an inventive mechanism that would do the same thing without his interference, but I can't imagine him spending billions of years painstakingly and personally making the first clockwork trilobites etc. etc. and popping the instructions in so that they can reproduce a few zillion more clockwork trilobytes (till they disappear) while he goes on to manufacture the first few clockwork spiders etc. etc. The idea bothers David too. I'm sure we would all learn a lot if only you would exchange views on the subject.- "Can be organized" is a reference to the creation process, yes. When you write a computer program, you might write:-int a; int b; int c; a = 9; b = 22;-If(a >= B) then c = a*b;- But what is "int", why are their ";, >=, =" and what do they mean. Each of those 'operators' requires another bit of code somewhere in the library to explain just how they work as well some other code somewhere to translate them. Once that code is written however, you can use and reuse it at will, so every bit of code that you write, can be reused anywhere that it would work. -This would greatly reduce the amount of time and effort needed to create each species. Humans can mass produce things once we have the right recipe for them, even things that vary slightly from one instance of them to the next. When you "zoom" out far enough, you can see that this mass production is sort of what has happened. Designing the rules that govern things and then setting them in motion takes far less time and energy than hand-crafting each and every particle.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

DHW: Yes, you made it very clear, as quoted above, that you do not believe in progressive evolution through innovation. (None of us three believe in gradualism.) But David does believe in it, so I asked you to explain why you didn't like David's speculative hypothesis. -TONY: I am going to go out on a limb and say that David doesn't like my reasoning for two reasons. A) David is a trained scientist, B) Though a theist, David is not (to my knowledge) a Christian, and prefers his God a little less "human" (and I use the term VERY loosely). Whereas I see God as an individual, powerful though he is, with thoughts and feelings similar in kind with ours, David sees him(it) without any personification. There are certain things that, to me at least, make more sense when you accept that personification. For example, why could love not be the motivating factor for the time spent painstakingly crafting the universe.-I'm sure all this is true, but David is probably better qualified to explain why he doesn't like your reasoning. My question to you was why you didn't like his reasoning, which is that God preprogrammed every innovation and wonder into the first living cells, to be passed down through billions of years until each one was triggered by a changed environment, thereby leading to evolution by innovation. However, we may be able to move on from this, thanks to the next section of your post: -TONY: Once that code is written however, you can use and reuse it at will, so every bit of code that you write, can be reused anywhere that it would work. This would greatly reduce the amount of time and effort needed to create each species. [...] Designing the rules that govern things and then setting them in motion takes far less time and energy than hand-crafting each and every particle.-Do forgive me for leaving out the rest of your post, most of which is incomprehensible to me. (I'm sorry, but computer language, like most other specialized languages of science and technology, is way beyond my horribly limited range.) What I have quoted suggests a possible compromise between your beliefs and David's, so I too will go out on a limb and put a new theistic hypothesis to you both, based on your two different sets of beliefs:-Cells are miniature computers, as David claims, and - as I have learned recently - an outside operator can get inside my computer and do what he/she likes with it. Your God is the operator, working by psychokinesis, as he has always done. He set up the first living cells with a first, comparatively simple programme (e.g. just carry on reproducing), and then proceeded to transmit programme after programme to enable his mechanism to expand to multicellularity, and incorporate one innovation after another. Each innovation entailed signals to the cells to create different combinations and, if necessary, different functions depending on their place in, or in relationship to, the new community. Advantages of this hypothesis: 1) it removes the necessity for God to have preprogrammed the first living cells with every single innovation and wonder to be passed down through 3.7 billion years; 2) it allows for evolution, since the succession of new programmes would clearly have been progressive and would have taken place within existing organisms; 3) it also allows for God dabbling, which has hitherto been a problem for theistic evolutionists. The dabbling comes with his altering existing cell combinations through new programmes without having to create new species from scratch; 4) it precludes the necessity for God to factor in environmental changes from the very beginning. -We now have six hypotheses, bearing in mind that evolution entails common descent (i.e. all organisms have descended from earlier organisms): 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God.-What have I missed out?

dhw: We now have six hypotheses, bearing in mind that evolution entails common descent (i.e. all organisms have descended from earlier organisms): 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God. > > What have I missed out?-I totally reject any possibility of your 1,2,3, and especially 6. 4 & 5 are the only possibilities I accept. If you will study this explanation you will see why:-The reason I so strongly oppose dhw's cell community theory is that it faces a statistical nightmare. The key issue is the understanding of the organic chemistry of life, once established. Life consists of interactive protein molecules which must work together when any inventive improvement is added to any current station in time in evolution. For a new function new molecules have to be found to do the new work together. -A simple protein molecule is 150-200 or more amino acids strung together. They must be in a certain order and have a certain folding pattern to produce the desired function. Folding reduces choice by its required specificity. From the possible landscape of protein combinations available, choice is limited by life to left-handed amino acids and right-handed sugars, cutting the landscape in half. -An example of a 'chance' calculation:-"The probability of one amino acid being correct is 1/20. The probability of two amino acids being correct is 1/20 x 1/20. So the probability of a sequence of 287 amino acids being correct is 1/20 raised to the power of 287 or one in 10 raised to the power of 373. In everyday terms, this is the same chance as tossing a die and getting 479 sixes in a row"- http://www.changinglivesonline.org/questions-and-answers/item/880-could-a-protein-molec... problem: protein chemistry reactions are exceedingly slow, thousands of years, unless enzymes are present. Enzymes have lock and key areas that hold specific molecules in place and literally force them to react. Enzymes are giant molecules of amino acids (a-a), often with two or three different patterns of organization as coils, straight and jumbles, with 3-4,000 a-a's or more involved again with specific folding and twisting. Think of the odds to find one of these that works, and they are throughout living organs each specific enzyme doing a very specific job. -Then there is the issue of a construction plan. The embryology of a new part of an organ has to develop a plan of construction, changed from the plan that preceded it to produce the new function. -What I am describing is complex specific forms to create a new function. All of this requires complex specific informational planning, especially since we have agreed chance does not work. A community of cells cannot make a number of these steps all at once. They do not have the planning capacity. It has to be trial and error. Darwin evolution is trial and error. For me a designing agent is the only logical answer. -Tony's suggestions about God handling the DNA computer program makes perfect sense

I have suggested six hypotheses to explain the different forms of life that occupy our planet: 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: but God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God.-David has described in intricate detail the immense complexity of the organic chemistry of life. Thank you for this highly educational post. As always, it makes a mockery of hypothesis 1. (Incidentally, the chief aim of the website article you quote seems to be to discredit the theory of evolution, disregarding the fact that theistic evolution is perfectly feasible.) Your main aim, however, seems to be to discredit 6. As an evolutionist, you do not doubt that the innovations happened, but you believe they were preprogrammed into the very first cells (4) or progressively directed by God (5). Prior to this latest phase of our discussion, your only alternative to (4) was God dabbling (3), which caused you problems as it entailed rejecting evolution. (We must always remember that evolution entails innovations taking place within existing organisms.) While firmly believing that God's 3.7-billion-year-old computer programmes will be found somewhere in the genome of living organisms, you categorically reject the possibility that God could have programmed cellular communities to make the changes on their own initiative (6).-In order to clarify this, I would like to go back, not to an innovation, but to one of Nature's Wonders which I love to use as an analogy. Fire ants cooperate to make themselves into a floating raft, which enables them to survive floods. A simple question: do you believe that your God preprogrammed this action into the very first living cells, to be passed down to the fire ants billions of years later? Or do you believe that God installed a new computer programme, let's say in the queen ant of the first rafting colony (later colonies would have learnt the trick from their predecessors), when he saw that the colony was in trouble? Or do you believe that the ant community devised the strategy on the spot? (If it hadn't worked, of course, they would have drowned.) Not to be compared to the complexity of cells, but I am now trying to understand how you think your own hypotheses might work in practice. -Coming closer to the question of cellular intelligence, I was also fascinated by your reference to a man born without a corpus callosum in his brain. Apparently this has disastrous effects on some people, but it didn't on him. How do you think his brain cells were able to organize their way round the problem? Did your God prepare a programme to deal with an absent corpus callosum 3.7 billion years ago, to be passed on to some humans but not to others? Or did he notice this particular man had something wrong, and juggle the programme just for him? We are coming very close to religion here, since many people believe in a personal God who takes a personal interest in each and every one of us. You don't go that far, but my question to you is how you think this extraordinary adjustment fits in with your concept of cells as automatons capable only of obeying instructions from God.

Tony, September 08, 2014, 21:13 : Cellular communication does NOT mean cellular planning, however, and that communication is very, very limited. Special creation/pre-planning solves this problem neatly because the intelligence behind the creation can plan.-This is the key point that Tony and I keep pounding. One major issue is a definition of "cellular communities" (CC's) needs to be carefully delineated and your use of it seems amorphous to me. As an example, if a primitive kidney needs to add a new function, do the kidney community cells do the planning? You have rejected chance so trial cannot be the method for your cells. Or by CC's do you intend to mean whole organisms with all their organs and brains? We know that whole guppies can change size when necessary. Can they change their kidneys by themselves. I doubt it.-> dhw, September 08, 2014, 12:15: David has described in intricate detail the immense complexity of the organic chemistry of life. Thank you for this highly educational post. As always, it makes a mockery of hypothesis 1...... Your main aim, however, seems to be to discredit 6. As an evolutionist, you do not doubt that the innovations happened, but you believe they were preprogrammed into the very first cells (4) or progressively directed by God (5)-Yes, I was severely discrediting 6. And I think epigenetic mechanisms can make some modifications, probably fairly minimal. I still hope an inventive or more complex modification mechanism will be found to get me out of my dilemma, but it all may be up to God all the time.-> dhw:you categorically reject the possibility that God could have programmed cellular communities to make the changes on their own initiative (6). >In order to clarify this, I would like to go back, not to an innovation, but to one of Nature's Wonders which I love to use as an analogy. Fire ants cooperate to make themselves into a floating raft, which enables them to survive floods. -Not clumps of cells. I use instinct of whole animals. These comments bring up the need for another clarification. What is instinctual behavior and how does it happen? I put the rafting of ants at the instinct level. It has to be with learned patterns of behavior from living experience, much like we train dogs to be housebroken and baby horses from losing their fear of us. My theory about instinct is that when the pattern is learned over and over, eventually brain plasticity allows it to stick, and it is somehow put into the neuron's DNA as instinct. This actually is the general theory of how it works.-So, ants live on the ground; they get flooded over and over; ants are a cooperative society, and while swimming around several of them try to save each other and while they are clinging together they discover they float easily. They have brains and learn by experience.-On the other hand an isolated organ cell community without a planning brain can do almost nothing. For much of evolution the huge jumps in complexity, which you fully recognize, require planning from a brain or a consciousness. Back to the need for God.-> dhw: I was also fascinated by your reference to a man born without a corpus callosum in his brain. Easy answer: God gave our brains plasticity. We know that. Many young children who have their brain separated like this fellow, to cure severe epilepsy, often function perfectly well. The same is true of some children born with a shell of the brain, can function at high levels of IQ.

dhw, September 08, 2014, 12:15: David has described in intricate detail the immense complexity of the organic chemistry of life. Thank you for this highly educational post. ...... Your main aim, however, seems to be to discredit 6. > David: Yes, I was severely discrediting 6.-I'd like to add to this. Some of the complexity that cellular committees cannot plan are the automatic protein folding proceses in cells. These are highly complex maneuvers that must have exact results, and to be properly understood cells are like automated auto factories. These are very exact highly controlled processes. A mistakec and the cell kills itself.:- http://www.scientificamerican.com/article/map-of-body-s-protein-folding-machinery-wins-...

DAVID: One major issue is a definition of "cellular communities" (CC's) needs to be carefully delineated and your use of it seems amorphous to me. As an example, if a primitive kidney needs to add a new function, do the kidney community cells do the planning? [...]. Or by CC's do you intend to mean whole organisms with all their organs and brains? We know that whole guppies can change size when necessary. Can they change their kidneys by themselves. I doubt it.-Organs are cell communities, and organisms like ourselves are a community of cell communities. When innovations occur, all the cell communities within an organism must change and cooperate in order to accommodate the new community. Where does the planning come from? Tell me where in the genome your God has hidden his 3.7-billion-year-old computer programme, and I'll tell you where the planning comes from. ALL these hypotheses are pure speculation. Yes, guppies adapt. And whatever mechanism enables this to happen has not created totally new species within the period of human observation. Does this mean your God has stopped messing about with his computer programmes (hypothesis 5), or his 3.7-billion-year-old programme has come to a temporary halt (hypothesis 4), or the inventive mechanism he may have planted in the first cells has stopped inventing (hypothesis 6)? (Please see also my response to Tony.)-dhw, As an evolutionist, you do not doubt that the innovations happened, but you believe they were preprogrammed into the very first cells (4) or progressively directed by God (5) DAVID: I still hope an inventive or more complex modification mechanism will be found to get me out of my dilemma, but it all may be up to God all the time.-An inventive mechanism is hypothesis 6. Hypotheses 4 and 5 involve God and not the mechanism doing the inventing. We all have a dilemma, and I'm sure all believers and non-believers hope their hypotheses will prove correct. dhw: I would like to go back, not to an innovation, but to one of Nature's Wonders which I love to use as an analogy. Fire ants cooperate to make themselves into a floating raft, which enables them to survive floods. DAVID: Not clumps of cells.-No, I said it was an analogy.-DAVID: I use instinct of whole animals. These comments bring up the need for another clarification. What is instinctual behavior and how does it happen? [...] My theory about instinct is that when the pattern is learned over and over, eventually brain plasticity allows it to stick, and it is somehow put into the neuron's DNA as instinct. This actually is the general theory of how it works.-But it is not a theory about how new forms of behaviour are invented.-DAVID: So, ants live on the ground; they get flooded over and over; ants are a cooperative society, and while swimming around several of them try to save each other and while they are clinging together they discover they float easily. They have brains and learn by experience.-Yes, they have brains, and yes, they learn, and yes they pass on what they learn. And so according to your explanation, God did not preprogramme them and God did not intervene. They worked it out for themselves. That is why I like the analogy!-DAVID: On the other hand an isolated organ cell community without a planning brain can do almost nothing. For much of evolution the huge jumps in complexity, which you fully recognize, require planning from a brain or a consciousness. Back to the need for God.-I agree that organs can't function without some kind of a brain, but that should not be equated with the human brain. I prefer intelligence. And I agree that the huge jumps require intelligence and cooperation between all the cell communities in the organism in which the jumps take place. Just like my ants, eh? So we're back to your 37-billion-year programme, your God messing about with his programmes, or your God having installed an inventive mechanism within the cells themselves. I know you discount the latter, but you are not really happy with your own alternatives, are you? Just hoping... -dhw: I was also fascinated by your reference to a man born without a corpus callosum in his brain. DAVID: Easy answer: God gave our brains plasticity. We know that. Many young children who have their brain separated like this fellow, to cure severe epilepsy, often function perfectly well. The same is true of some children born with a shell of the brain, can function at high levels of IQ.-Easy when you say it quickly. What does brain plasticity mean? The brain is composed of cells. If the behaviour of those cells is flexible enough in some cases to compensate for abnormalities, but not flexible enough in other cases to cope with the same abnormalities, doesn't that suggest that the brain cells themselves vary from one organism to the next, and doesn't it suggest that brain cells do not respond to a given programme but somehow make their own decisions?

dhw:I agree that organs can't function without some kind of a brain, but that should not be equated with the human brain. I prefer intelligence. And I agree that the huge jumps require intelligence and cooperation between all the cell communities in the organism in which the jumps take place.-The intelligence has to be a sophisticated planner which included the planning for cellular functional cooperation. you look at it backwards. Cells and groups of cells alone have no capacity for this planning.-> > dhw:Easy when you say it quickly. What does brain plasticity mean?..... and doesn't it suggest that brain cells do not respond to a given programme but somehow make their own decisions?-Einstein's brain had an area in the temporal lobe almost 1/2 inch thicker than normal. It was a conceptual area. We know that we can affect and raise brain IQ by certain techniques. Brain neurons are programmed to respond to intelletual activity, and areas of the brain grow new neurons and connections. The brain changes all through a lifetime, modified by the person's attempts at mental activity. We do not know if Einstein grew the area or was born with it. But what we are learning now suggests he grew it. He said he always saw problems in pictures and diagrams. He was a left-handed dyslectic. Repeat: brain neurons come programmed to increase intellectual capacity.

DHW: My question to you was why you didn't like his reasoning, which is that God preprogrammed every innovation and wonder into the first living cells, to be passed down through billions of years until each one was triggered by a changed environment, thereby leading to evolution by innovation. However, we may be able to move on from this, thanks to the next section of your post: > -Well, aside from the fact that we have exactly 0 observations of species divergence, there is also the fact that the Bible directly states God "dabbled" after the fact, on a couple of occasions, actually. -- >DHW: Cells are miniature computers, as David claims, and - as I have learned recently - an outside operator can get inside my computer and do what he/she likes with it. Your God is the operator, working by psychokinesis, as he has always done. He set up the first living cells with a first, comparatively simple programme (e.g. just carry on reproducing), and then proceeded to transmit programme after programme to enable his mechanism to expand to multicellularity, and incorporate one innovation after another. Each innovation entailed signals to the cells to create different combinations and, if necessary, different functions depending on their place in, or in relationship to, the new community. Advantages of this hypothesis: 1) it removes the necessity for God to have preprogrammed the first living cells with every single innovation and wonder to be passed down through 3.7 billion years; 2) it allows for evolution, since the succession of new programmes would clearly have been progressive and would have taken place within existing organisms; 3) it also allows for God dabbling, which has hitherto been a problem for theistic evolutionists. The dabbling comes with his altering existing cell combinations through new programmes without having to create new species from scratch; 4) it precludes the necessity for God to factor in environmental changes from the very beginning. > > We now have six hypotheses, bearing in mind that evolution entails common descent (i.e. all organisms have descended from earlier organisms): 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God. > > What have I missed out?- What you have missed out on is the "big picture". No life, or program, exists in a bubble, and climate/chemical changes are the least of its worries. We have discussed numerous examples of life that depends on other life in order to exist. This utterly rules out 1 & 6 because it requires communication and planning between cells, not only of different species, but of completely different types of life. (Floura & Fauna simultaneously.) -That leaves 2-5. Basic biochemistry, logic, and ironically the bible itself rules out 2, leaving us with 3-5. Of these, 4 has 0 observations to support it, in terms of speciation, and without speciation reverts back to 2,3, or 5. -3 & 5 however are not mutually exclusive, and a combination of limited versions of 3-5 would actually be closer to the truth, I think, as I have gone on about at some length in older posts.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony:3 & 5 however are not mutually exclusive, and a combination of limited versions of 3-5 would actually be closer to the truth, I think, as I have gone on about at some length in older posts.-Note, of course, I've picked out 4 & 5.

TONY: Well, aside from the fact that we have exactly 0 observations of species divergence [...] (Hypothesis] 4 has 0 observations to support it, in terms of speciation....-You think 3 and 5*** may be closer to the truth. May I ask how often these have been observed? If we had first-hand observation of new species (broad sense - not different types of dog) being created, then there'd be no discussion. Nobody knows how it happened, and that's why we have to speculate, so non-observation can hardly be regarded as a reason for rejecting any of the hypotheses.-TONY: What you have missed out on is the big picture. No life, or program, exists in a bubble, and climate/chemical change are the least of its worries. [Well, not if climate/chemical change leads to starvation, or the inability to breathe, or to reproduce!] ...life depends on other life in order to exist. This utterly rules out 1 & 6 because it requires communication and planning between cells, not only of different species, but of completely different types of life. (Flora & Fauna simultaneously.) -I'm not so sure that cows need to communicate and plan anything with grass, but I agree that there is interdependence between different organisms. My apologies if I'm being dense here, but I don't see how this rules out 6 but rules in 3 and 5*** (let's forget 1, since none of us like it). If life depends on other life in order to exist, and this requires communication and planning between cells etc., then cells must be able to communicate and plan. In that case, 6 remains extremely relevant. If you are saying, as David does, that cells are not capable of communicating and planning, how does separate creation (3) explain the interdependence and ability to cooperate and plan? And how does a change of computer programme in one organism (5) explain the ability of other organisms to cooperate and plan with the newcomer? -*** The six hypotheses are: 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: but God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God.

TONY: Well, aside from the fact that we have exactly 0 observations of species divergence [...] (Hypothesis] 4 has 0 observations to support it, in terms of speciation.... > > You think 3 and 5*** may be closer to the truth. May I ask how often these have been observed? If we had first-hand observation of new species (broad sense - not different types of dog) being created, then there'd be no discussion. Nobody knows how it happened, and that's why we have to speculate, so non-observation can hardly be regarded as a reason for rejecting any of the hypotheses. > - 3 Could not have been observed by humans, because we were among the last created (which ironically is also backed up by scientific observations). 5 however, has been observed many times in the DNA of living creatures.-- >DHW I'm not so sure that cows need to communicate and plan anything with grass, but I agree that there is interdependence between different organisms. My apologies if I'm being dense here, but I don't see how this rules out 6 but rules in 3 and 5*** (let's forget 1, since none of us like it). If life depends on other life in order to exist, and this requires communication and planning between cells etc., then cells must be able to communicate and plan. In that case, 6 remains extremely relevant. If you are saying, as David does, that cells are not capable of communicating and planning, how does separate creation (3) explain the interdependence and ability to cooperate and plan? And how does a change of computer programme in one organism (5) explain the ability of other organisms to cooperate and plan with the newcomer? > - Life depends on life. True. Life depends on cellular communication. True. Cellular communication does NOT mean cellular planning, however, and that communication is very, very limited. Special creation/pre-planning solves this problem neatly because the intelligence behind the creation can plan. I can write programs that depend on each other very easily. When you read this you are are using dozens of such programs. Concept 3 does not require cells to plan, so there is no need to explain something that does not happen. -When I said that there was a limited version of 5 in play, it means that there aren't any "new comers" in terms of new types of creatures popping up out of no where. The few points in history where life got the reset button, it reset. There was not really a lot of left overs for the new creatures to have to interact with. The old guard dies when the new arrives. --- > *** The six hypotheses are: 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: but God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Six hypotheses concerning evolution: 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: but God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God.-Dhw: If we had first-hand observation of new species (broad sense - not different types of dog) being created, then there'd be no discussion. Nobody knows how it happened, and that's why we have to speculate, so non-observation can hardly be regarded as a reason for rejecting any of the hypotheses. TONY: 3 Could not have been observed by humans, because we were among the last created (which ironically is also backed up by scientific observations). 5 however, has been observed many times in the DNA of living creatures.-Um, yes...all the innovations that led to humans preceded humans and could not have been observed by humans! Changes in DNA may have been observed, but has anyone seen God directing evolution through innovations caused by his inserting new computer programmes etc.? My question seems absurd to me, but my point is that those of us who believe evolution happened through innovations can only speculate on HOW it happened. One should therefore not reject any hypothesis simply on the grounds that no-one has observed it happening.-DHW If life depends on other life in order to exist, and this requires communication and planning between cells etc., then cells must be able to communicate and plan. In that case, 6 remains extremely relevant. If you are saying, as David does, that cells are not capable of communicating and planning, how does separate creation (3) explain the interdependence and ability to cooperate and plan? And how does a change of computer programme in one organism (5) explain the ability of other organisms to cooperate and plan with the newcomer? TONY: Life depends on life. True. Life depends on cellular communication. True. Cellular communication does NOT mean cellular planning, however, and that communication is very, very limited.-That is David's argument too. But it is limited to programmes already devised. There is no innovating going on at present - this is an unpunctuated period of equilibrium - and so there is no evidence now that cells can create something totally new. However, there is plenty of evidence that they can adapt, which might suggest an autonomous mechanism that can work out different ways of coping with different environments. There is likewise no evidence of your God separately creating new species, or devising new programmes. All three hypotheses remain speculation.-TONY: Special creation/pre-planning solves this problem neatly because the intelligence behind the creation can plan. I can write programs that depend on each other very easily. [...] Concept 3 does not require cells to plan... -In that case, your God would also have to change the programmes in the other organisms, to ensure compatibility. Why is an autonomous inventive mechanism a problem? In the name of Occam, wouldn't it be simpler for God to create a mechanism that can devise its own programmes as and when they're needed throughout 3.7.billion years so far of changing environments (see below)? Concept 3, of course, excludes evolution. I do hope David will explain to you why he is so against it. TONY: When I said that there was a limited version of 5 in play, it means that there aren't any "new comers" in terms of new types of creatures popping up out of no where. That is why we cannot reject hypotheses on the grounds that no-one has observed the arrival of new species (general definition, as opposed to different dogs).-TONY: The few points in history where life got the reset button, it reset. There was not really a lot of left overs for the new creatures to have to interact with. The old guard dies when the new arrives. -So interaction isn't much of a problem anyway. If I were a 4 or 5 theist, I'd be more bothered about why God programmed the obliteration of so many of his programmes. But let's return to innovation. If 90% of species are killed off by a new environment, maybe those that survive do so because their inventive mechanism is able not only to adapt to it but also to exploit it. After all, a dabbling God (3) would also exploit the new possibilities. I'd be interested to know if you believe your God a) deliberately changed the environments as he went along, b) preplanned each change from the beginning, or c) adapted his programmes and/or separately created his new species to fit in with each unplanned change.

Six hypotheses concerning evolution: 1) Evolution happened through innovations caused by random mutations; 2) Evolution didn't happen: God made every species independently at the same time; 3) Evolution didn't happen: but God made every species separately at different times; 4) Evolution happened: God preprogrammed the first cells to pass on every stage of it; 5) Evolution happened: God directed it through innovations, as he inserted sequences of new computer programmes into different existing cell communities; 6) Evolution happened through innovations created by intelligent cell communities, whose intelligence may or may not have been created by a God. > > DHW If life depends on other life in order to exist, and this requires communication and planning between cells etc., then cells must be able to communicate and plan. In that case, 6 remains extremely relevant. -> TONY: Life depends on life. True. > Life depends on cellular communication. True. > Cellular communication does NOT mean cellular planning, however, and that communication is very, very limited. > > dhw: That is David's argument too. All three hypotheses remain speculation.-Your cell planning is simply wild speculation, because you continue to ignore the complex specificity of life, as Tony and I point out. Cells cannot plan for major change. Look at the whale series, giant changes requiring major engineering. Only advanced intelligence can. This is one of the major reasons I became a theist.-> dhw:Concept 3, of course, excludes evolution. I do hope David will explain to you why he is so against it.-I don't follow the Bible. God is mentally powerful enough to not need 3.-> dhw:If 90% of species are killed off by a new environment, maybe those that survive do so because their inventive mechanism is able not only to adapt to it but also to exploit it.-That has happened. The Permian extinction killed off 90%, but life came back and diversified again. Doesn't tell us how.

DHW: One should therefore not reject any hypothesis simply on the grounds that no-one has observed it happening. > -Direct observation is not a requirement, no. However, indirect observation IS a requirement or your speculations become wilder and wilder, which is exactly what has happened with the theory of evolution. Change within limits is very reasonable, and have been observed repeatedly. Extrapolating those minute changes to serve as an explanation for everything that ever lived is a fairy tale.--> TONY: Life depends on life. True. > Life depends on cellular communication. True. > Cellular communication does NOT mean cellular planning, however, and that communication is very, very limited. > > DHW: That is David's argument too. But it is limited to programmes already devised. There is no innovating going on at present - this is an unpunctuated period of equilibrium - and so there is no evidence now that cells can create something totally new. However, there is plenty of evidence that they can adapt, which might suggest an autonomous mechanism that can work out different ways of coping with different environments. There is likewise no evidence of your God separately creating new species, or devising new programmes. All three hypotheses remain speculation. > -The evolutionary version of Punctuated equilibrium you refer to, as an idea, only has value if evolution is true in the commonly accept form. (i.e. we all crawled out of the slime) But, at least you acknowledge "there is no evidence now that cells can create something totally new." However, then you go on to state: "There is likewise no evidence of your God separately creating new species." I would like examine this for a moment. -If separate creation were true:-

We would observe no definitive transition between species in the fossil record. (Observed)
We would observe that extreme environmental changes wiped out the majority of existing life because it lacked enough freedom and flexibility in its code to adapt. (Observed)
We would observe no new species spontaneously cropping up. (Observed)
We would observe species remaining remarkably unchanged over time. (Observed)
When new species DID crop up, we would observe them coming into existence fully formed and fully functional.(Observed)
We would observe some mechanism that prevented creatures from deviating too far, a self-correcting function to ensure their stability.(Observed)
We would be able to discern designed patterns and commonalities for all creatures of a given environment.[Observed]
We would likely see highly efficient patterns repeatedly used for the same purpose.[Observed]
The observed elements of life, once understood, would make logical sense and lack random messiness of random chance evolution.[observed]
-Now, you tell me which one has less evidence from observations, evolution or creation. - > >DHW: In the name of Occam, wouldn't it be simpler for God to create a mechanism that can devise its own programmes as and when they're needed throughout 3.7.billion years so far of changing environments (see below)? > -As David has repeatedly said, life, even the so-called 'simple' forms of life, are still incredibly complex. How much latitude and freedom to deviate could be given if that life were going to remain stable? If your inventive mechanisms were true, why did ANYTHING remain virtually unchanged for billions of years? Logically, there wouldn't be any simple life left on earth. All we would observe would be cell communities constantly growing in complexity. Yet, in every domain we see creatures that are virtually identical to their far ancient ancestors. -> >DHW: So interaction isn't much of a problem anyway. If I were a 4 or 5 theist, I'd be more bothered about why God programmed the obliteration of so many of his programmes. -Would you be bothered by an architect removing braces that he had constructed to support a building until the free-standing framework was completed? Does the fact that airplanes use hydraulics now instead of pulley systems bother you? (When the Wright brothers made their plane, there did not exist any infrastructure to support hydraulics.) Does it bother you that we no longer use CRT monitors for our computers?-One of the key points of being a theist is trusting that God knows what he is doing. Giving even a cursory thought to the way that biological history has played out tells us WHY some events had to happen. When you stop treating god like Houdini or a Djinn that snaps his fingers or twitches his nose to make galaxies *poof* into existence, then what he has done makes perfect sense. -Unlike the Djinn, God didn't twitch his nose and make things poof into existence. Things had to be prepared at each and ever step, and he used life to do that. Sometimes it was the simple machines (single-celled organisms), at others it was more complex life. Regardless, each necessary step was planned and implemented in such a way that it achieved the desired results, whether those results were terraforming the land, altering the atmosphere, or filling a niche in the ecosystem that needed to be filled in order to maintain homeostasis.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: Unlike the Djinn, God didn't twitch his nose and make things poof into existence. Things had to be prepared at each and ever step, and he used life to do that. Sometimes it was the simple machines (single-celled organisms), at others it was more complex life. Regardless, each necessary step was planned and implemented in such a way that it achieved the desired results, whether those results were terraforming the land, altering the atmosphere, or filling a niche in the ecosystem that needed to be filled in order to maintain homeostasis.-Recognizing that Tony and I come from very different religious childhoods, and therefore biases, I think Tony's reasoning makes the bible inconsisent. If the Bible's God is as all-powerful and all-knowing as implied, why did He have to do so much planning? That is why I feel God could create an evolutionary system that could do a great deal of its own advancement planning. My stumbling block is deciding if the plan were perfect as the Bible would imply, and not requiring dabbling, or did it have imperfections? So I've not used the Bible and tried from just the science discovery standpoint. Certainly, evolution looks like there was a process in place that God could have started. It ended in humans, and that is extremely significant. Based on Darwinoid thinking, humans are not a required result, and the gap to consciousness compared to other living forms is gigantic.

Tony: Unlike the Djinn, God didn't twitch his nose and make things poof into existence. Things had to be prepared at each and ever step, and he used life to do that. Sometimes it was the simple machines (single-celled organisms), at others it was more complex life. Regardless, each necessary step was planned and implemented in such a way that it achieved the desired results, whether those results were terraforming the land, altering the atmosphere, or filling a niche in the ecosystem that needed to be filled in order to maintain homeostasis. > >David: Recognizing that Tony and I come from very different religious childhoods, and therefore biases, I think Tony's reasoning makes the bible inconsisent. If the Bible's God is as all-powerful and all-knowing as implied, why did He have to do so much planning? ...if the plan were perfect as the Bible would imply, and not requiring dabbling, or did it have imperfections?-Firstly, I am not sure how my reasoning makes the bible inconsistent. If you would care to point that out to me, I could probably clarify. As to why he had to do so much planning, I have a counter question. From a biblical standpoint, God created his son directly, and then all other things were created according to God's will/design BY his Son, and to make it all happen they employed "myriads upon myriads" of angels(spirit creatures). My question is this, if you were a infinitely wise, all powerful, all knowing god, would you twitch your nose and produce this vast universe and all its life in the blink of an eye?-To me, that is not only a tremendous undertaking, but it would be monumentally foolish as everything would die the instant it was created. Science tells us that in the first seconds after the big bang, the universe was excruciatingly hot. It tells us that the early earth was toxic to all life. Why did god have to plan it all out? Because he created the laws of physics that govern all matter, the laws which allow all of this to work. If he then created all of us with a twitch of his nose, those laws say that tremendous amounts of heat would see us still born everything destroyed. That doesn't sound wise. He may not have to operate within the laws of physics, but whatever is created within the universe does, not just when the nose twitches but in the first few seconds after and for the rest of its days.-Why did he have to plan so much for the variation in life? He didn't. He could have gotten away with leaving the world with nothing but squishy little single celled organisms on it, or no life at all, for that matter. If you want life, though. If you want animal life, human life, plant life, on a planet in the goldilocks zone with sweet waters and sweater air that can maintain itself for billions of years and maintain the lives of the creatures living upon it, then you have to plan out the systems to make sure they are correct.-As for the imperfection, no. Unless of course you count free will as an imperfection.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony; Firstly, I am not sure how my reasoning makes the bible inconsistent. If you would care to point that out to me, I could probably clarify. As to why he had to do so much planning, I have a counter question. From a biblical standpoint, God created his son directly, and then all other things were created according to God's will/design BY his Son,-We are discussing apples and oranges. I noted our different backgrounds. I was born a Jew and use only the OT. That is what I reference in my analysis. -> > Tony;To me, that is not only a tremendous undertaking, but it would be monumentally foolish as everything would die the instant it was created. Science tells us that in the first seconds after the big bang, the universe was excruciatingly hot. It tells us that the early earth was toxic to all life. Why did god have to plan it all out? Because he created the laws of physics that govern all matter, the laws which allow all of this to work. If he then created all of us with a twitch of his nose, those laws say that tremendous amounts of heat would see us still born everything destroyed. -I didn't interpret the 'nose twitch' to mean instantaneous creation of everything. Genesis says there were six stages. I assumed your plannng by God to be a sequential series of events. That has been my problem in thinking about dabbling.-> Tony: Why did he have to plan so much for the variation in life? He didn't. .....If you want animal life, human life, plant life, on a planet in the goldilocks zone with sweet waters and sweater air that can maintain itself for billions of years and maintain the lives of the creatures living upon it, then you have to plan out the systems to make sure they are correct.-Agreed, but God, as described, should have been able to do all the planning from the beginning, or he had to step in and adjust. Again, my dilemma. > > Tony: As for the imperfection, no. Unless of course you count free will as an imperfection.-Free will is what we have and it allows for the human imperfections and the evil, and I think god intended it that way.

Tony; Firstly, I am not sure how my reasoning makes the bible inconsistent. If you would care to point that out to me, I could probably clarify. As to why he had to do so much planning, I have a counter question. From a biblical standpoint, God created his son directly, and then all other things were created according to God's will/design BY his Son, > > We are discussing apples and oranges. I noted our different backgrounds. I was born a Jew and use only the OT. That is what I reference in my analysis. -Ok. From Proverbs 8:-22 Jehovah produced me as the beginning of his way,+ The earliest of his achievements of long ago.+ 23 From ancient times* I was installed,+ From the start, from times earlier than the earth.+ ...... 27 When he prepared the heavens,+ I was there; When he marked out the horizon* on the surface of the waters,+ 28 When he established* the clouds above, When he founded the fountains of the deep, 29 When he set a decree for the sea That its waters should not pass beyond his order,+ When he established* the foundations of the earth, 30 Then I was beside him as a master worker.+ I was the one he was especially fond of+ day by day; I rejoiced before him all the time-- > >David: I didn't interpret the 'nose twitch' to mean instantaneous creation of everything. Genesis says there were six stages. I assumed your plannng by God to be a sequential series of events. That has been my problem in thinking about dabbling. > -The problem is that you are holding the planning and action to be the same thing, and they are not. Doesn't an architect draw up blueprints long before the workers start construction? Once the construction starts, does he do everything at once, or does each thing have an appointed time and order in which it must occur? When building something, don't you sometime have to build up scaffolding or supports that you later tear down when they are no longer needed? Wouldn't failing to do so at the appropriate time prevent you from doing other things, all according to the plan laid out before the first stone was laid? A wise builder starts with a plan, and a plan starts with a goal, a destination, and everything in that plan leads towards that goal, step by step. If something comes up that tries to derail his plan, does he give up, or does he work around it, determined to see his plan through to completion? God is not foolish enough to not have a plan, and is is capable enough to deal with any issues of "time and unforeseen circumstances." -And one last thing about the nature of God as applied to this conversation. We have free will, something we both agreed on. Free will, by its very nature introduces uncertainty. ->In Hebrew, the name Jehovah comes from a verb that means to become, and a number of scholars feel that it reflects the causative form of that Hebrew verb. Thus, the understanding .. is that God's name means He Causes to Become. .. this definition well fits Jehovah's(YHWH) role as the Creator of all things and the Fulfiller of his purpose. He not only caused the physical universe and intelligent beings to exist, but as events unfold, he continues to cause his will and purpose to be realized.-The point is that he doesn't have to be able to predict the future and no every single event that will ever happen(that would violate free will), but rather, like the skilled architect, when something tries to derail his purpose he has the ability to work around it and fulfill his purpose through other avenues. - > > Tony: Why did he have to plan so much for the variation in life? He didn't. .....If you want animal life, human life, plant life, on a planet in the goldilocks zone with sweet waters and sweater air that can maintain itself for billions of years and maintain the lives of the creatures living upon it, then you have to plan out the systems to make sure they are correct. > >David: Agreed, but God, as described, should have been able to do all the planning from the beginning, or he had to step in and adjust. Again, my dilemma.-They are not mutually exclusive, nor should they be. (See Above)

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony;The problem is that you are holding the planning and action to be the same thing, and they are not. Doesn't an architect draw up blueprints long before the workers start construction? Once the construction starts, does he do everything at once, or does each thing have an appointed time and order in which it must occur? ...... God is not foolish enough to not have a plan, and is is capable enough to deal with any issues of "time and unforeseen circumstances." -I admire your knowledge and scholarship re the OT. I'm no where near that ability. On the other hand my self-education after the smattering in childhood is partially with Gerald Schroeder' books on science and the OT, and Adler's "How to think about God". Both authors attribute much more power to God than you do above, and I feel your description is very anthropomorphic, and God is much more than what you have attributed to him. That is why I view him as the universal consciousness with near infinite intellectual capacities.-> > Tony: And one last thing about the nature of God as applied to this conversation. We have free will, something we both agreed on. Free will, by its very nature introduces uncertainty. -Agreed. > > > Tony:In Hebrew, the name Jehovah comes from a verb that means to become, and a number of scholars feel that it reflects the causative form of that Hebrew verb. Thus, the understanding .. is that God's name means He Causes to Become. .. this definition well fits Jehovah's(YHWH) role as the Creator of all things and the Fulfiller of his purpose. He not only caused the physical universe and intelligent beings to exist, but as events unfold, he continues to cause his will and purpose to be realized.-Very reasonable > > Tony; The point is that he doesn't have to be able to predict the future and no every single event that will ever happen(that would violate free will), but rather, like the skilled architect, when something tries to derail his purpose he has the ability to work around it and fulfill his purpose through other avenues.-I don't think this limited interpretation necessarily follows the paragraph above. Free will in humans cannot block the works of God. What we do to ourselves is our problem. > > > >David: Agreed, but God, as described, should have been able to do all the planning from the beginning, or he had to step in and adjust. Again, my dilemma. > > They are not mutually exclusive, nor should they be. (See Above)-Under your interpretation of God that is true, under mine no.

Tony;The problem is that you are holding the planning and action to be the same thing, and they are not. Doesn't an architect draw up blueprints long before the workers start construction? Once the construction starts, does he do everything at once, or does each thing have an appointed time and order in which it must occur? ...... God is not foolish enough to not have a plan, and is is capable enough to deal with any issues of "time and unforeseen circumstances." > >David: I admire your knowledge and scholarship re the OT. I'm no where near that ability. On the other hand my self-education after the smattering in childhood is partially with Gerald Schroeder' books on science and the OT, and Adler's "How to think about God". Both authors attribute much more power to God than you do above, and I feel your description is very anthropomorphic, and God is much more than what you have attributed to him. That is why I view him as the universal consciousness with near infinite intellectual capacities. > > > -> > > > > >David: God...should have been able to do all the planning from the beginning, or he had to step in and adjust. Again, my dilemma. > > > > They are not mutually exclusive, nor should they be. (See Above) > > Under your interpretation of God that is true, under mine no.- Simple question, do you think a) God knows the future in every minute detail, or b) do you think that God has a purpose and shapes events to his will as they unfold in order to fulfill his purpose? As a Jew, this question should be near and dear to your heart. Can you give examples from the OT where YHWH adjusted things in order to fulfill his purpose? I can think of several. How can you believe in free will and still believe in version A, how can you believe in the OT and not believe in version B?

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: Simple question, do you think a) God knows the future in every minute detail, or b) do you think that God has a purpose and shapes events to his will as they unfold in order to fulfill his purpose? As a Jew, this question should be near and dear to your heart. Can you give examples from the OT where YHWH adjusted things in order to fulfill his purpose? I can think of several. How can you believe in free will and still believe in version A, how can you believe in the OT and not believe in version B?-Your questions to me I think imply a very personal God. God gave us free will, so that means He can't anticipate the things humans do, but that was His choice. In that sense I view us on our own. It we get into a nuclear war in my opinion He will not step in to save us, if He can. I don't think God answers personal prayers, but belief in God gives a strength to solve your own problems. So, (a) God knows his future and His plans and how they will work out, but hopes we will work out our problems. (b) As I explain below some of God's interventions in the OT are not accepted as real history, but are stories, accepted by Reform Judaism, to make a moral point. Therefore, I stay with my dilemma, and tend to feel God does not intervene. -I rely on Karen Armstrong's "A History of God" to analyze the three Bibles: the OT is somewhat primative in its picture of God, made fun of by Richard Dawkins as vengeful,vindictive, etc. I've listened to Rabbi's sermons based on Talmudic reasoning which accept much of this as allegory and have heard the deeper reasoning that change the words to a softened view. The OT is a book of love. The Quran has its nasty parts also, but it views God primarily through His works, which I view as a very mature way to find God, the path I have followed.-I consider these three books as man-made attempts to understand our religious feeling, feelings we seem to be born with. I do not 'believe in the OT', but I use aspects of it in my thinking. One God, no Trinity.-I deeply appreciate our discussion.

->David: Your questions to me I think imply a very personal God. -I view him as very personal. Not only is that the view given throughout the bible, it is also the view that have witnessed in my own life. Suffice to say that I should have been dead, quite literally, two dozen times over, both in war and peace. I've seen things manipulated in a way that is inexplicable by mere coincidence. I think this is one of the major differences in our thinking, though.- >David: God gave us free will, so that means He can't anticipate the things humans do, but that was His choice. In that sense I view us on our own. It we get into a nuclear war in my opinion He will not step in to save us, if He can. I don't think God answers personal prayers, but belief in God gives a strength to solve your own problems.- Despite my comment above, I actually agree with this, to an extent. I don't agree with the part about prayer. We are left to our own devices if we choose to be left to our own devices, just like a petulant teen that runs away from home. - >David: So, (a) God knows his future and His plans and how they will work out, but hopes we will work out our problems. (b) As I explain below some of God's interventions in the OT are not accepted as real history, but are stories, accepted by Reform Judaism, to make a moral point. Therefore, I stay with my dilemma, and tend to feel God does not intervene. - This is where your thought on all of it and mine truly depart. People pick and choose what they want to believe for the same reason atheists disbelieve entirely: because on the surface it's easier, or at the very least more fun. - > >David: I rely on Karen Armstrong's "A History of God" to analyze the three Bibles: the OT is somewhat primative in its picture of God, made fun of by Richard Dawkins as vengeful,vindictive, etc. I've listened to Rabbi's sermons based on Talmudic reasoning which accept much of this as allegory and have heard the deeper reasoning that change the words to a softened view. The OT is a book of love. The Quran has its nasty parts also, but it views God primarily through His works, which I view as a very mature way to find God, the path I have followed. > -I haven't read her assessment, and quite honestly I don't think I will. Anyone that thinks that the OT's God is primitive is not an authority on the Bible. Even the OT paints him as a god of love, and as an immensely complicated figure. "The OT is a book of love." I could not agree more with anything you have said. The OT is a book of love, and most often a book of unrequited love. Reading through it I can FEEL the pain and anger that God must have felt at the steady stream of betrayals. Because I do view god as personal, and because I am empathetic to the way humanity has treated him, I am more conscious of my own actions.- >David: I consider these three books as man-made attempts to understand our religious feeling, feelings we seem to be born with. I do not 'believe in the OT', but I use aspects of it in my thinking. One God, no Trinity. > -Believe it or not, I believe in "One God, no Trinity" as well. The bible never says Christ was god. Christ never claimed to be god. And the trinity doctrine is not, and never was, supported in the bible. Neither was the hell doctrine, for that matter. I will be first in line to admit that Christendom has twisted and perverted the Bibles teachings, but then, it happened just as the bible said it would happen.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

Tony: Believe it or not, I believe in "One God, no Trinity" as well. The bible never says Christ was god. Christ never claimed to be god. And the trinity doctrine is not, and never was, supported in the bible. Neither was the hell doctrine, for that matter. I will be first in line to admit that Christendom has twisted and perverted the Bibles teachings, but then, it happened just as the bible said it would happen.-You sound just like my wife, a born-again Christian. The Bible never insisted we had to have religious organizations. The OT justs asks for 10 people to get together in fellowship to pray ,although personal prayer was certainly expected.

David: You sound just like my wife, a born-again Christian. -Since you are talking about your wife, I am going to assume that is a compliment. Don't know about the whole born again thing, but it is a saying I suppose. ->David: The Bible never insisted we had to have religious organizations. The OT justs asks for 10 people to get together in fellowship to pray ,although personal prayer was certainly expected.-That is actually a bit misleading. In the OT YHWH was depicted as a god of organization. Look at the way the tribes of Israel were laid out as they marched through the wilderness. Numbers is quite detailed on the organizational side, and perhaps more tellingly, it lays out the specification for a priesthood which does indeed mean organized religion in a fashion. I don't disagree with the concept of an organized religion in general. Where I get burnt is when dealing with organizations that are morally bankrupt and think that their traditions override biblical teachings. That kind of hypocrisy really gets on my nerves.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

David: You sound just like my wife, a born-again Christian. > > Tony:Since you are talking about your wife, I am going to assume that is a compliment. Don't know about the whole born again thing, but it is a saying I suppose.-It is a type of beliving, Bible-based. -> Tony: Where I get burnt is when dealing with organizations that are morally bankrupt and think that their traditions override biblical teachings. That kind of hypocrisy really gets on my nerves.-That is what a "born-again Christian" is, someone who believes in Bible-based beliefs, without the trappings and traditions of religion. Jesus never asked for a religion about him.

Tony: Where I get burnt is when dealing with organizations that are morally bankrupt and think that their traditions override biblical teachings. That kind of hypocrisy really gets on my nerves. > > David: That is what a "born-again Christian" is, someone who believes in Bible-based beliefs, without the trappings and traditions of religion. Jesus never asked for a religion about him.-True. For him, it was all about his Father, YHWH of the OT.

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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

DAVID: Your cell planning is simply wild speculation, because you continue to ignore the complex specificity of life, as Tony and I point out. Cells cannot plan for major change. Look at the whale series, giant changes requiring major engineering. Only advanced intelligence can. This is one of the major reasons I became a theist.-Then as an evolutionist, you seem to have no choice: 3.7 billion years ago, your God implanted the very first living cells with programmes for every single innovation leading from single cells to whales and humans, and all the different species in between. I suspect some people would call that wild speculation. Your alternative is to reject evolution and opt for separate creation. But you are against that. Dhw (to Tony:) Concept 3***, of course, excludes evolution. I do hope David will explain to you why he is so against it. [***Evolution didn't happen: but God made every species separately at different times.] DAVID: I don't follow the Bible. God is mentally powerful enough to not need 3. -Why does separate creation require more mental power than creating a computer programme to be passed down through billions of species over billions of years? Meanwhile, Tony has posted a detailed defence of his creationist theory, which I will try to answer tomorrow.-I asked you how, if cells were automatons, the brain cells of one person could work their way round an abnormality while someone else's couldn't. You said it was easy: brain plasticity.-dhw: What does brain plasticity mean?..... and doesn't it suggest that brain cells do not respond to a given programme but somehow make their own decisions? DAVID: Einstein's brain had an area in the temporal lobe almost 1/2 inch thicker than normal. It was a conceptual area. We know that we can affect and raise brain IQ by certain techniques. Brain neurons are programmed to respond to intelletual activity, and areas of the brain grow new neurons and connections. [...]-None of this explains why some brain cell communities can cope with abnormality and others can't, if all them are automatons merely obeying God's instructions. -DAVID: Some of the complexity that cellular committees cannot plan are the automatic protein folding proceses in cells. These are highly complex maneuvers that must have exact results, and to be properly understood cells are like automated auto factories. These are very exact highly controlled processes. A mistakec and the cell kills itself.: http://www.scientificamerican.com/article/map-of-body-s-protein-folding-machinery-wins-... are some quotes: You now have cells that may inappropriately signal and become rogue cells that could become a danger to the organism. Rather than doing that, the cells try to establish equilibrium and then establish a balance between capacity and need. If that balance cannot be achieved, the cell submits to apoptosis - cell death.-We wanted to find the molecular machinery that allows one component of the cell to talk to another. [...] We [...] asked the question how does one part of the cell know what is going on in another part.-We are trying to figure out the molecular pathways by which the cells make the decisions and decide if they need to kill themselves.-I am puzzled by the fact that your God (so mentally powerful that he doesn't need to create species separately) has invented a programme which makes some automated cells become rogue, other automated cells and parts of cells talk to one another, and automated cells take decisions as to whether or not they should kill themselves, though you say none of them can do anything except obey God's instructions. Do you not also find it confusing?-DAVID: How a small number of genes can make a complex human: There are a finite number of genes in the genome, and changing which of those gets turned on or off gives you a certain level of complexity, Calarco said. What alternative splicing does is add another layer of complexity, allowing an organism to diversify a cell type even more  we think this contributes a great deal to an organism's ability to diversify its cellular function and cellular architecture.-http://news.harvard.edu/gazette/story/2014/08/neurons-at-work/-This may explain some of the innovations-Strange that Calarco talks of an organism's ability to diversify its cellular function etc. It's almost as if he's saying that there is some mechanism within the organism that takes such decisions. -In your post earlier today, there were two very striking sentences: ...I feel God could create an evolutionary system that could do a great deal of its own advancement planning. And Certainly, evolution looks like there was a process in place that God could have started. An evolutionary system can't plan. Living organisms can plan, thereby creating a system. And so you are actually saying that living organisms could do a great deal of their own advancement planning. And if evolution is a process that God started, but he did NOT do all the advancement planning, he would have had to implant some kind of planning mechanism within the organisms he created. Organisms are made of cells. Where would he have put the mechanism for advancement planning?

dhw: Then as an evolutionist, you seem to have no choice: 3.7 billion years ago, your God implanted the very first living cells with programmes for every single innovation ... I suspect some people would call that wild speculation. Your alternative is to reject evolution and opt for separate creation. But you are against that.-It is just my dilemma. I just don't know how God managed evolution. Since I believe a type of evolutionary But evolution could not have occurred without intelligent planning, once chance is excluded.-> > dhw; Why does separate creation require more mental power than creating a computer programme to be passed down through billions of species over billions of years? -You have misintrepreted. Separate creation, stepwise, requires less mental power than doing it all from beginning plans. > > dhw: I asked you how, if cells were automatons, the brain cells of one person could work their way round an abnormality while someone else's couldn't. You said it was easy: brain plasticity.-Each individual has a brain plasticity on a bell curve, some more facile than others. > > dhw: None of this explains why some brain cell communities can cope with abnormality and others can't, if all them are automatons merely obeying God's instructions.-Explained above. Biology in individuals has much variation.- > dhw:We are trying to figure out the molecular pathways by which the cells make the decisions and decide if they need to kill themselves.-Note in the quote 'moleclar pathways'. How much thought do you think moleculs have? These are standarized biochemical reactions in cells.-> > dhw:I am puzzled by the fact that your God (so mentally powerful that he doesn't need to create species separately) has invented a programme which makes some automated cells become rogue, other automated cells and parts of cells talk to one another, and automated cells take decisions as to whether or not they should kill themselves, though you say none of them can do anything except obey God's instructions. Do you not also find it confusing?-Not a bit. God did not invent "rogue cell programs". Cells are 99.99+% perfect in avoiding error, but they are making molecules at splint second timing and occasionally that editing process makes an error. So there is a program for self-destruction. That is what is provided by God > > dhw: Strange that Calarco talks of an organism's ability to diversify its cellular function etc. It's almost as if he's saying that there is some mechanism within the organism that takes such decisions.-Again, I'm looking for a way to have speciation as part of the evolutionary program written by god. > > dhw: In your post earlier today, there were two very striking sentences: ...I feel God could create an evolutionary system that could do a great deal of its own advancement planning. And Certainly, evolution looks like there was a process in place that God could have started. An evolutionary system can't plan. Living organisms can plan, thereby creating a system. And so you are actually saying that living organisms could do a great deal of their own advancement planning.-No, I am not. -> dhw: And if evolution is a process that God started, but he did NOT do all the advancement planning, he would have had to implant some kind of planning mechanism within the organisms he created. .. Where would he have put the mechanism for advancement planning?-An evolutionary system can plan if programmed properly. An evolutionary program can include a planning section for more complexity, and it is probably a layer in the genome. Again, chance doesn't work. Living cells are controlled by the genome, but have the ability to make small modifications: i.e., Darwin's finch beaks.

Dhw: Then as an evolutionist, you seem to have no choice: 3.7 billion years ago, your God implanted the very first living cells with programmes for every single innovation ... I suspect some people would call that wild speculation. Your alternative is to reject evolution and opt for separate creation. But you are against that. DAVID: It is just my dilemma. I just don't know how God managed evolution. Since I believe a type of evolutionary But evolution could not have occurred without intelligent planning, once chance is excluded.-Tony says that One of the key points of being a theist is trusting that God knows what he is doing. Is it possible that this is part of your dilemma? Supposing creating life was a new experience for God, he hadn't a clue where it was leading, let it do its own thing (the bit you refuse to countenance), but then occasionally dabbled, and eventually decided to enhance simian intelligence into human intelligence a bit like his own? You would then have your mixture of guided and non-guided evolution, without separate creation. Only trying to be helpful. But you are already heading that way (see later).-I asked you how, if cells were automatons that could only obey God's instructions, the brain cells of one person could work their way round an abnormality while someone else's couldn't. -DAVID: Each individual has a brain plasticity on a bell curve, some more facile than others. [...] Biology in individuals has much variation-What does brain plasticity mean if not the flexibility of cell behaviour? The more variation you have, the less rigid the programming. I can't believe you're saying that every community of human brain cells consists of automatons obeying a separate programme God has devised for each individual. And if not, then each set of brain cells must be able to take its own decisions. (Remember in this case, the patient didn't know he had the condition, so the cells worked independently of his control - whatever his control might consist of.) dhw:We are trying to figure out the molecular pathways by which the cells make the decisions and decide if they need to kill themselves. DAVID: Note in the quote 'moleclar pathways'. How much thought do you think moleculs have? These are standarized biochemical reactions in cells.-I have not been talking of molecular intelligence. If cells make decisions, the decision-making mechanism must be within the cells, and the chemical processes, as in human brains, tell us what happens when intelligence is at work.-dhw: Strange that Calarco talks of an organism's ability to diversify its cellular function etc. It's almost as if he's saying that there is some mechanism within the organism that takes such decisions. DAVID: Again, I'm looking for a way to have speciation as part of the evolutionary program written by god.-So are we all. Speciation is the whole point of evolutionary theory. How did single cell organisms develop into whales and humans? All these scientists keep talking of the cells processing information, communicating, cooperating, taking decisions....I wonder why they don't simply talk of cells being preprogrammed by God to do what he tells them. dhw: In your post earlier today, there were two very striking sentences: ...I feel God could create an evolutionary system that could do a great deal of its own advancement planning. And Certainly, evolution looks like there was a process in place that God could have started. An evolutionary system can't plan. Living organisms can plan, thereby creating a system. And so you are actually saying that living organisms could do a great deal of their own advancement planning. And if evolution is a process that God started, but he did NOT do all the advancement planning, he would have had to implant some kind of planning mechanism within the organisms he created. Where would he have put the mechanism for advancement planning?-DAVID: An evolutionary system can plan if programmed properly. -That is like saying a plan can plan if it's properly planned. Plans don't plan. Plans are planned by planners like your God, humans or other organisms.-DAVID: An evolutionary program can include a planning section for more complexity, and it is probably a layer in the genome. -Yes, a programme can INCLUDE a plan, and that would be the 3.7-billion-year-old programme for all innovations you think your God inserted into the first living cells. However, you think your God could create a SYSTEM that could do a great deal of its own planning. And yet you don't think he could create a MECHANISM that could do a great deal of its own planning. And the system that plans plans is probably a layer in the genome, which of course is situated in the cells, but the cells couldn't possibly contain a mechanism that plans plans. Does this make sense? -DAVID: Again, chance doesn't work. Living cells are controlled by the genome, but have the ability to make small modifications: i.e., Darwin's finch beaks.-We keep agreeing that chance doesn't work. We agree there is a mechanism within the genome, which is within the cells, that can make small modifications. We don't know how large those modifications might become, since we are going through a period of evolutionary stasis.

DAVID(on a different thread that's disappeared from view): I posted an article recently re the first fossil brain found in the Cambrian: Cambrian Explosion: early brains (Introduction) by David Turell , Thursday, July 17, 2014, 15:35 (59 days ago) @ David Turell-A jump from no brains in the Ediacarans to simple brains is a massive leap for evolution:-http://www.sciencedaily.com/releases/2014/07/140716131628.htm-QUOTE: An international team of paleontologists has identified the exquisitely preserved brain in the fossil of one of the world's first known predators that lived in the Lower Cambrian, about 520 million years ago. The discovery revealed a brain that is surprisingly simple and less complex than those known from fossils of some of the animal's prey.-I think you have slightly misinterpreted this article. If the animal's prey already had brains, this is not the first brain. It's the first predator brain they've found, and it opens up an absolutely fascinating field of evolutionary speculation, summarized in the conclusion:-QUOTE: The fact that the brain of the earliest known predator appears much simpler in shape than the previously unearthed brains of its contemporaries begs intriguing questions, according to Strausfeld, one of which is whether it is possible that predators drove the evolution of more complex brains. "With the evolution of dedicated and highly efficient predators, the pressure was on other animals to be able to detect and recognize potential danger and rapidly coordinate escape movements. These requirements may have driven the evolution of more complex brain circuitry," Strausfeld said.-In an earlier post on this thread(10 September at 19.44), you wrote: Brain neurons are programmed to respond to intellectual activity, and areas of the brain grow new neurons and connections. This ties in perfectly with the above, and with evolution. DAVID: Darwin cannot explain its appearance. What nest of "cell community" invented it, when it appears from no precursor?-It's not the first brain, but somewhere along the line there must have been a first brain. According to our last exchange on the subject, you had modified your 3.7-billion-year computer programme that covered every innovation and wonder throughout the history of life, and now suggested that your God had created a system that could do a great deal of its own planning, and the system was probably a layer in the genome. I have suggested a mechanism that can do a great deal of its own planning, and the mechanism is in the cell/cell community (of which, of course the genome is a part). Perhaps you can explain why you believe in a system but not in a mechanism that can do its own planning.

David: A jump from no brains in the Ediacarans to simple brains is a massive leap for evolution[/i]: > > http://www.sciencedaily.com/releases/2014/07/140716131628.htm-> I think you have slightly misinterpreted this article. If the animal's prey already had brains, this is not the first brain. It's the first predator brain they've found, and it opens up an absolutely fascinating field of evolutionary speculation, summarized in the conclusion:-> > DAVID: Darwin cannot explain its appearance. What nest of "cell community" invented it, when it appears from no precursor? > > dhw: It's not the first brain, but somewhere along the line there must have been a first brain. I have suggested a mechanism that can do a great deal of its own planning, and the mechanism is in the cell/cell community (of which, of course the genome is a part). Perhaps you can explain why you believe in a system but not in a mechanism that can do its own planning.-We need a definition of your cell communities' abilities. I view the cells as run by the genome rather automatically; the genome of course resides in the cells, but is expressed differently in different cells. You make it seem as though the cells can manipulate, of their own volition, the major codes of the genome to make major changes. Who is running the show, the genome as I envision it, or the cells running changes in the genome? All we see at this juncture in research is minor variation created by organisms. The gaps in evolution are so complex cells have to have guidance, which must be in the genome.

dhw: It's not the first brain, but somewhere along the line there must have been a first brain. I have suggested a mechanism that can do a great deal of its own planning, and the mechanism is in the cell/cell community (of which, of course the genome is a part). Perhaps you can explain why you believe in a system but not in a mechanism that can do its own planning.-DAVID: We need a definition of your cell communities' abilities. I view the cells as run by the genome rather automatically; the genome of course resides in the cells, but is expressed differently in different cells. You make it seem as though the cells can manipulate, of their own volition, the major codes of the genome to make major changes. Who is running the show, the genome as I envision it, or the cells running changes in the genome? All we see at this juncture in research is minor variation created by organisms. The gaps in evolution are so complex cells have to have guidance, which must be in the genome.-I only refer to the cell because researchers such as Margulis, Shapiro and Albrecht-Buehler talk of the intelligent cell and not the intelligent genome. The point of the hypothesis is the existence of an autonomous form of intelligence, i.e. a mechanism that does its own planning, and if you think it's within the genome, that's absolutely fine with me. Can we therefore now say goodbye to the 3.7-billion-year-old computer programme with which your God organized every innovation and wonder in the history of life?

dhw: I only refer to the cell because researchers such as Margulis, Shapiro and Albrecht-Buehler talk of the intelligent cell and not the intelligent genome. The point of the hypothesis is the existence of an autonomous form of intelligence, i.e. a mechanism that does its own planning, and if you think it's within the genome, that's absolutely fine with me. Can we therefore now say goodbye to the 3.7-billion-year-old computer programme with which your God organized every innovation and wonder in the history of life?-Certainly not. Whatever program is in the genome runs the cells, not the other way around. The cells have a minimal epigentic adaptation ability. Cells cannot plan major species alterations to new species.

dhw: I only refer to the cell because researchers such as Margulis, Shapiro and Albrecht-Buehler talk of the intelligent cell and not the intelligent genome. The point of the hypothesis is the existence of an autonomous form of intelligence, i.e. a mechanism that does its own planning, and if you think it's within the genome, that's absolutely fine with me. Can we therefore now say goodbye to the 3.7-billion-year-old computer programme with which your God organized every innovation and wonder in the history of life?-DAVID: Certainly not. Whatever program is in the genome runs the cells, not the other way around. The cells have a minimal epigentic adaptation ability. Cells cannot plan major species alterations to new species.-No problem for me. So now we have a mechanism that can do a great deal of its own advancement planning (you: 11 September), is situated in the genome, and directs cellular activity. This is all part of the evolutionary process that God could have started (you: 11 September). Agreement at last. Except that if it can do its own planning, the mechanism in the genome is obviously not simply obeying instructions programmed into it 3.7 billion years ago.

dhw: No problem for me. So now we have a mechanism that can do a great deal of its own advancement planning (you: 11 September), is situated in the genome, and directs cellular activity. This is all part of the evolutionary process that God could have started (you: 11 September). Agreement at last. Except that if it can do its own planning, the mechanism in the genome is obviously not simply obeying instructions programmed into it 3.7 billion years ago.-Remembering that I don't know how God managed evolution but I presume He used it, I suggest an inventive mechanism emplanted by God as a special layer in the genome can respond to new environmental changes, which changes may or may not be planned by God. Did God hurl the Chicxulub asteroid, or did it just happen as an independent event in an evolving universe not entirely controlled by God? There is no way of knowing. -So my view of Shapiro, et. al. is that the genome is in control, and the cells really bend to genome control, while being allowed some attempts at adaptation by self-methylation of the DNA. And latest research shows that methylation is lasting thru generations, but in no sense that speciation occurs by that mechanism.

dhw: So now we have a mechanism that can do a great deal of its own advancement planning (you: 11 September), is situated in the genome, and directs cellular activity. This is all part of the evolutionary process that God could have started (you: 11 September). Agreement at last. Except that if it can do its own planning, the mechanism in the genome is obviously not simply obeying instructions programmed into it 3.7 billion years ago.-DAVID: Remembering that I don't know how God managed evolution but I presume He used it, I suggest an inventive mechanism emplanted by God as a special layer in the genome can respond to new environmental changes, which changes may or may not be planned by God. Did God hurl the Chicxulub asteroid, or did it just happen as an independent event in an evolving universe not entirely controlled by God? There is no way of knowing.-There is no way of knowing whether ANY of our hypotheses are correct - including the existence of God! Meanwhile, I'm delighted that here you have shifted your planning hypothesis from a programme implanted in the first cells to changes in the environment. Personally (still wearing my theist's hat), I doubt if 3.7 billion years ago God said to himself, 3.6 billion years from now, I'm gonna chuck an asteroid. I'd say it's more likely he decided 60-100 million years ago that he'd had enough of them thar dinos and would try something else. Or, having set the evolutionary and the randomly changing environmental mechanisms in motion, he just let it all happen. DAVID: So my view of Shapiro, et. al. is that the genome is in control, and the cells really bend to genome control, while being allowed some attempts at adaptation by self-methylation of the DNA. And latest research shows that methylation is lasting thru generations, but in no sense that speciation occurs by that mechanism. -We need to recap on your dilemma. You believe evolution happened, i.e. God did not separately create every single innovation that led from bacteria to humans. You proposed a theory that he installed a computer programme in the first living cells that would be passed down though 3.7 billion years to implement every innovation when the environment allowed (or when God preprogrammed every environmental change to happen). The alternative I have proposed is that there is a mechanism within the cells - you have placed it more precisely within the genome, which I'm happy to accept - that responds to environmental changes not only by adapting but also by inventing. In your first paragraph you have accepted the idea of an inventive mechanism in the genome. In your second paragraph you only allow for some attempts at adaptation and say there is no evidence that speciation occurs by that mechanism. Then what does the inventive mechanism invent? Are you still adhering to your preprogramming hypothesis, or are you acknowledging the possibility that innovations are created autonomously through an internal mechanism which your God may have installed? Your only alternatives are random mutations and separate creation of every innovation. Resolve your dilemma. Make a firm decision. And instead of predicting that science will discover a 3.7-billion-year-old computer programme in the genome, join me in predicting that it will uncover a mechanism capable not only of adaptation but also of invention. Commit yourself. And I'll let you have half my Nobel Prize money.

DAVID: So my view of Shapiro, et. al. is that the genome is in control, and the cells really bend to genome control, while being allowed some attempts at adaptation by self-methylation of the DNA. And latest research shows that methylation is lasting thru generations, but in no sense that speciation occurs by that mechanism. > > > dhw: We need to recap on your dilemma. You believe evolution happened, i.e. God did not separately create every single innovation that led from bacteria to humans. You proposed a theory that he installed a computer programme in the first living cells that would be passed down though 3.7 billion years to implement every innovation when the environment allowed (or when God preprogrammed every environmental change to happen). The alternative I have proposed is that there is a mechanism within the cells - you have placed it more precisely within the genome, which I'm happy to accept - that responds to environmental changes not only by adapting but also by inventing. -It seems to me we are stating the same possibility, except you seem to want the cells to run the genome and it is the other way around.--> dhw: In your first paragraph you have accepted the idea of an inventive mechanism in the genome. In your second paragraph you only allow for some attempts at adaptation and say there is no evidence that speciation occurs by that mechanism. Then what does the inventive mechanism invent? Are you still adhering to your preprogramming hypothesis, or are you acknowledging the possibility that innovations are created autonomously through an internal mechanism which your God may have installed? -I am struggling with what we know now about genomics and what we might find to explain the advances by speciation.-dhw: Your only alternatives are random mutations and separate creation of every innovation. Resolve your dilemma. Make a firm decision. And instead of predicting that science will discover a 3.7-billion-year-old computer programme in the genome, join me in predicting that it will uncover a mechanism capable not only of adaptation but also of invention. -My three possibilities, to recap: (1) pre-planning, every step to humans is programmed into the genome; (2) dabbling, God steps in to change things, organisms or environment or both; (3) inventive mechanism, which is a variation of pre-programming and can create the new complex species by analysis and planning, following given guidelines. -On thinking about (3) it would have to be an extremely complex computer code, and perhaps not beyond God's capabilities to create it. DNA is a complex code beyond what we humans use now. Note you use the word 'mechanism'without describing it. Fuzzy concept. It has to be a code like DNA. I can't imagine anything else. I've gotten you to recognize what ever and where ever it is, it must be part of the genome. Now unfuzzy your theory, recognize the power of the codes in the genome and forget the stupid cells. You fell for scientists' hyperbole. We are not far apart, but Nobel will probably credit me more, if and when my prediction is found.-Here is a study on tilapia sub-species that is an attempt to explain variations:-http://phys.org/news/2014-09-cichlid-fish-genome-story-evolution.html-Involving gene duplications and microRNA activities

dhw: The alternative I have proposed is that there is a mechanism within the cells - you have placed it more precisely within the genome, which I'm happy to accept - that responds to environmental changes not only by adapting but also by inventing. -DAVID: It seems to me we are stating the same possibility, except you seem to want the cells to run the genome and it is the other way around.-I have never in my life, let alone on this forum, suggested that the cells run the genome. I took the concept of the intelligent cell from several researchers, and a year or two ago, on one of those occasions when you quite liked the idea, you said the intelligence must lie within the genome, which I accepted. (The genome is within the cell, and would therefore be the equivalent of the brain within the body.) It's not the cell that's the focal point of the hypothesis but the intelligent, inventive mechanism. However, whenever we get close to agreement, you continually scurry back to preprogramming. Here is an exchange between us under How epigenetics works, Jan 8 & Jan 9 2013 (yep, we've been gnawing this bone for a long time) :-D hw: Unless your god preprogrammed the original genome structure to come up specifically with legs, wings, penises, vaginas, noses, eyes, livers, kidneys, teeth, tongue, brains etc., there has to be an inventive mechanism with takes its own decisions as and when environmental conditions are favourable for the introduction of such organs. -I then asked if you thought it possible that innovation was caused by the inventive intelligence of the genome. You replied: Yes I think God designed a genome mechanism to respond in a rather automatic and autonomic fashion to environmental changes. The cells are not intelligent...do not wilfully make changes of their own. They are programmed to do so.-Notice, it was you and not me who switched from the genome to the cells, and of course automatic and autonomic are a far, far cry from autonomous decision-making. On 22 March 2013 under Trilobite eyes you wrote: My intelligent genome is not your intelligent genome. My genome has underlying information and intelligent application of that information, planned to be that way. [...] Your intelligence' has no characteristics of anything recognizable as a conscious planning mind I replied: ...In your version the genome is an automaton programmed by God to adapt and innovate when it has to. [This was a quote, but I can't find it.] In my version it is not an automaton, but is able to make its own decisions.-That has always been the difference between us: your automatic and my autonomous, and you continue to climb on and off your own evolutionary picket fence. On 17 August you expressed doubts about your 3.7-billion-year computer programme and about your dabbling God theory, and wrote: I like your self-inventing built into the mechanism and The idea of an inventive mechanism being present makes sense. On September 1st you scurried away again: I initially misused the concept of inventive mechanism as I was thinking out loud. I have defined it now as a set of preplanned instructions for a new species in some still hidden area of the genome. I expect it to be found. You know as well as I do that inventive' does not mean following preplanned instructions.-In your latest post, you have at least incorporated it as a third possibility (previously, you were confined to two: preprogramming versus God dabbling). However, you now define it as: inventive mechanism, which is a variation of pre-programming and can create the new complex species by analysis and planning, following given guidelines. And you think my concept is fuzzy! How can an inventive mechanism be a variation of preprogramming? What given guidelines? You are playing with words. (And no, I can't describe the mechanism. How do you describe a mechanism that has yet to be discovered and may not even be there? It's a hypothesis, not a scientific thesis.) There are restrictions, but these are not guidelines: the organism must be able to cope with its environment, and a worm is unlikely to be able to change itself into an eagle, or a crocodile, or a human. -The hypothesis, once more, is that along the route from bacteria to humans, cell combinations (directed by the intelligent, inventive mechanism your God may have installed within the genome) have over millions of years autonomously, independently, intelligently, without any preprogramming, without any given instructions, and in accordance with prevailing environmental conditions, created each innovation that has led to this vast diversity. If you insist on these nebulous, preprogramming dilutions, I definitely shan't share the prize money with you. Unless, of course, you are able to use your scientific knowledge to describe precisely how my inventive mechanism or your 3.7 billion-year-old computer programme or your God's dabbling works. If you can, the prize is all yours. If you can't, please don't expect me to!

dhw; That has always been the difference between us: your automatic and my autonomous, and you continue to climb on and off your own evolutionary picket fence. In your latest post, you have at least incorporated it as a third possibility (previously, you were confined to two: preprogramming versus God dabbling). However, you now define it as: inventive mechanism, which is a variation of pre-programming and can create the new complex species by analysis and planning, following given guidelines. And you think my concept is fuzzy! -I agree I'm fuzzy. I don't know what I don't know. The research hasn't made God's method of evolution obvious to me, and I may never get a clear answer. > > dhw: The hypothesis, once more, is that along the route from bacteria to humans, cell combinations (directed by the intelligent, inventive mechanism your God may have installed within the genome) have over millions of years autonomously, independently, intelligently, without any preprogramming, without any given instructions, and in accordance with prevailing environmental conditions, created each innovation that has led to this vast diversity.-This is an approach as one of the three I can accept sort of. Such a mechanism must have some guiding instructions as to the changes to adapt to new conditions. At least, as I interpreted your initial intelligent cell hypothesis, you are now clear about the supremacy of the genome over the cells, which are in general automatic factories, that have some small feedback to the genome. The DNA is already in recent research showing another layer of coding, but nothing so far that suggests how speciation is created. We don't know how phenotype is created. We are still at the level of understanding the production of protein and alterations in that production, nothing more!

dhw; That has always been the difference between us: your automatic and my autonomous, and you continue to climb on and off your own evolutionary picket fence. [...] In your latest post, you have at least incorporated it as a third possibility (previously, you were confined to two: preprogramming versus God dabbling). However, you now define it as: inventive mechanism, which is a variation of pre-programming and can create the new complex species by analysis and planning, following given guidelines. And you think my concept is fuzzy! DAVID: I agree I'm fuzzy. I don't know what I don't know. The research hasn't made God's method of evolution obvious to me, and I may never get a clear answer.-None of us know. We can only look for explanations that make sense to us. But you continue to fuzz up my hypothesis with your next response :-D AVID: This is an approach as one of the three I can accept sort of. Such a mechanism must have some guiding instructions as to the changes to adapt to new conditions.-Guiding instructions as to the changes... means preprogramming, i.e. your God anticipating every single environmental change and response throughout the history of life. Totally opposed to my hypothesis! No preprogramming, no instructions, no guidelines. An autonomous, inventive intelligence, possibly created by your God. How it might work is fuzzy, but the concept itself is not.-DAVID: At least, as I interpreted your initial intelligent cell hypothesis, you are now clear about the supremacy of the genome over the cells, which are in general automatic factories, that have some small feedback to the genome. -The genome is part of the cell. Generally the Turell organs work automatically and feed back to the intelligent, inventive mechanism inside the Turell head. Does that make you an automatic factory? The intelligent cell hypothesis does not specify the location of the mechanism, but if you say it's in the genome, that's fine with me. It doesn't make the slightest difference to the hypothesis itself (see below, re multicellularity). DAVID: The DNA is already in recent research showing another layer of coding, but nothing so far that suggests how speciation is created. We don't know how phenotype is created. We are still at the level of understanding the production of protein and alterations in that production, nothing more!-Agreed. We don't know how. That's why we offer hypotheses. DAVID (under Very early multicellularity) http://www.sciencedaily.com/releases/2014/09/140924211827.htm-QUOTE: The discovery sheds light on how and when solo cells began to cooperate with other cells to make a single, cohesive life form. -Cooperation between cells (all hail, Lynn Margulis!) lies at the heart of the hypothesis concerning evolutionary innovations. These can only come about through intelligent communication, cell to cell or genome to genome if you like. Every single one preprogrammed 3.7 billion years ago, or personally manipulated by your God? If not, and since we dismiss random mutations, there has to be an autonomous, intelligent, inventive mechanism guiding the cells. No more fuzz, please!

dhw: The genome is part of the cell.-It is the brains of the cell. -> dhw:Generally the Turell organs work automatically and feed back to the intelligent, inventive mechanism inside the Turell head. Does that make you an automatic factory? The intelligent cell hypothesis does not specify the location of the mechanism, but if you say it's in the genome, that's fine with me.-I don't know about your body, but all of my body and most other folks have an automatically functioning body with the brain that is mostly on its own and highly controlled by ones' self. I can become aware of that autonomous function by voluntarily thinking about it. A single cell in no different. Its production is monitored by feedback mechanisms provided by its genome.-http://www2.uah.es/farmamol/New_Science_Press/nsp-protein-3.pdf > dhw: Cooperation between cells (all hail, Lynn Margulis!) lies at the heart of the hypothesis concerning evolutionary innovations. These can only come about through intelligent communication, cell to cell or genome to genome if you like. Every single one preprogrammed 3.7 billion years ago, or personally manipulated by your God? If not, and since we dismiss random mutations, there has to be an autonomous, intelligent, inventive mechanism guiding the cells. No more fuzz, please!-The fuzz is yours. If cells were not programmed to coooperate there would be no life. Cells cooperate because they are instructed toc do so by their genomes. Starting with one DNA in the zygote, the DNA is modified for varying functions so that kidney cells are not liver cells. The 'autonomous intelligent mechanism guiding the cells' is the genome invented by an autonomous intelligent agent, God! I just puzzle over how He did the speciation issue. The key is in the genome that the animal or plant receives at conception. Variation is inherited from various epigentic alerations made by preceding generations, which does not get us to a mechanism for speciation. And we have agreed Darwin doesn't work.

dhw: The genome is part of the cell. DAVID: It is the brains of the cell.-Exactly. It's taken best part of two years for you to accept that cells have the equivalent of a brain. dhw: Generally the Turell organs work automatically and feed back to the intelligent, inventive mechanism inside the Turell head. Does that make you an automatic factory? The intelligent cell hypothesis does not specify the location of the mechanism, but if you say it's in the genome, that's fine with me.-DAVID: I don't know about your body, but all of my body and most other folks have an automatically functioning body with the brain that is mostly on its own and highly controlled by ones' self. I can become aware of that autonomous function by voluntarily thinking about it. A single cell in no different. Its production is monitored by feedback mechanisms provided by its genome.-I presume the typing error (in no different) = is no different. Of course we are not talking here about human levels of self-awareness. The point of the analogy is that cells are not automatons because they have an autonomous brain that takes its own decisions and is not preprogrammed. dhw: Cooperation between cells (all hail, Lynn Margulis!) lies at the heart of the hypothesis concerning evolutionary innovations. These can only come about through intelligent communication, cell to cell or genome to genome if you like. Every single one preprogrammed 3.7 billion years ago, or personally manipulated by your God? If not, and since we dismiss random mutations, there has to be an autonomous, intelligent, inventive mechanism guiding the cells. No more fuzz, please! -DAVID: The fuzz is yours. If cells were not programmed to coooperate there would be no life. Cells cooperate because they are instructed toc do so by their genomes. Starting with one DNA in the zygote, the DNA is modified for varying functions so that kidney cells are not liver cells. The 'autonomous intelligent mechanism guiding the cells' is the genome invented by an autonomous intelligent agent, God!-No fuzz, apart possibly from your reference to programmes and instructions, though at long last you are attributing these to the inventive "brain" of the cell (the genome) instead of to your God's 3.7-billion-year-old computer programme. You have now agreed that the cell is not an automaton - its body automatically obeys its brain (although some feedback will go the other way, since the brain also needs the material provided by the rest of the body). As regards its source, I have said all along that the inventive mechanism may have been designed by your God. That is a different hypothesis, as mine is only meant to explain the course of evolution. So which do you now think is most likely: 1) God's 3.7-billion-year old computer programme? 2) God personally creating every innovation and wonder? 3) God creating an autonomous, intelligent mechanism that does its own inventing?-DAVID: I just puzzle over how He did the speciation issue. The key is in the genome that the animal or plant receives at conception. Variation is inherited from various epigentic alerations made by preceding generations, which does not get us to a mechanism for speciation. And we have agreed Darwin doesn't work.-Agreed on all counts. Margulis called for further research on the nature of the cell, because she realized that every cell is a sentient, intelligent, cooperative, communicative being, and evolution depends on cooperation. My hypothesis that innovation (and hence speciation) is the product of cooperation between intelligent and inventive mechanisms within the cells, which initially you dismissed as a load of nonsense, is simply an extension of her ideas, and since it was you who introduced me to her, Shapiro and others in the first place, you shall have half the Nobel Prize money after all.

dhw: Exactly. It's taken best part of two years for you to accept that cells have the equivalent of a brain.-I did not accept the idea of 'brain' the way you have interpreted it. I should have stated it more clearly. The genome runs the cell. The cell does not run the genome, but can introduce minor adaptations. I used a slang way of referring to the genome as a brain . Computers are the 'brains' of many items, but they are not thinking and planning brains like we have. I have, in the past, referred to the cell as if it was an automated car factory. That is exactly what it is.Run by computers, but the few workers can make minior steps on their own, and also by plan. > > dhw: The intelligent cell hypothesis does not specify the location of the mechanism, but if you say it's in the genome, that's fine with me.[/i]-I still keep the concept of the cell as being almost totally controlled by the genome. If there is an invented section of the genome, we have yet to find it, but I suspect we will. > > dhw; The point of the analogy is that cells are not automatons because they have an autonomous brain that takes its own decisions and is not preprogrammed.-Your presumption is not what I intended to impart. The cells are basically automatons. > > dhw: Cooperation between cells (all hail, Lynn Margulis!) lies at the heart of the hypothesis concerning evolutionary innovations. These can only come about through intelligent communication, cell to cell or genome to genome if you like. -Cells have to communicate for life to be life. That communication is intelligently set up by the instructions in the genome. The communication is highly controlled by the genome. > > dhw: You have now agreed that the cell is not an automaton - its body automatically obeys its brain (although some feedback will go the other way, since the brain also needs the material provided by the rest of the body).-This seems to be your wish that is so strong, you have grossly misintepreted me. When I discuused the autonomic functions of the body, it is analagous to a modern car. There is a computer onboard which takes care of fuel mixture supply and other functions while the driver is the brain that navigates the trip and stays out of accidents by steering and braking the car. The driver functions without awareness of the computer's role, unless he thinks about it or dwells on it. > > dhw: My hypothesis that innovation (and hence speciation) is the product of cooperation between intelligent and inventive mechanisms within the cells, which initially you dismissed as a load of nonsense, is simply an extension of her [Margulis] ideas. -And you are still extrapolating her thoughts over the rainbow. The closest you and I have gotten together is the possibility of an inventive mechanism in the genome which might possibly account for speciation. As far as research shows, the body of the cell has influence on the genome through epigenetic effects. It is the genome that decides to methylate based on influence from the cells' experiences. Without exception, the genome is in charge of cell function. The genome itself within established species is also mostly very automatic. This is a major reason why we have no theory of speciation. By now you must realize that I view life as mostly automatic biologicly functioning machines. The only difference is in brain function, where our thoughts can modify brain function and structure. The lesser animals' brains have a small amount of that capacity for brain plasticity.

Dhw: The genome is part of the cell. DAVID: It is the brains of the cell. dhw: Exactly. It's taken best part of two years for you to accept that cells have the equivalent of a brain.-DAVID: I did not accept the idea of 'brain' the way you have interpreted it. I should have stated it more clearly. The genome runs the cell. The cell does not run the genome [...]. -That is exactly the way I interpret it. The genome runs the cell as the brain runs the body.-DAVID: I used a slang way of referring to the genome as a brain. Computers are the 'brains' of many items, but they are not thinking and planning brains like we have.-It's not slang, it's a simple analogy. I wrote that it was the equivalent of a brain, not that it was a brain like ours. I also wrote: Of course we are not talking here about human levels of self-awareness. However, if you are now saying that the brain in the genome is a computer that is not capable of autonomous invention, then you are back again with your divine 3.7-billion-year programme to cover every single innovation and wonder in the history of life, and probably including every environmental change as well, since one damned asteroid could have done for the lot - a hypothesis which, very understandably, you say bothers you.-dhw: Cooperation between cells (all hail, Lynn Margulis!) lies at the heart of the hypothesis concerning evolutionary innovations. These can only come about through intelligent communication, cell to cell or genome to genome if you like. -DAVID: Cells have to communicate for life to be life. That communication is intelligently set up by the instructions in the genome. The communication is highly controlled by the genome.-Highly controlled by the genome is fine with me. Instructions IN the genome yet again = your 3.7-billion-year-old computer programme as above. Instructions WORKED OUT AND GIVEN BY the genome makes the genome the author of the instructions. Which of these seems to you more likely? Do please answer.-dhw: You have now agreed that the cell is not an automaton - its body automatically obeys its brain (although some feedback will go the other way, since the brain also needs the material provided by the rest of the body).-DAVID: This seems to be your wish that is so strong, you have grossly misintepreted me. When I discuused the autonomic functions of the body, it is analagous to a modern car. There is a computer onboard which takes care of fuel mixture supply and other functions while the driver is the brain that navigates the trip and stays out of accidents by steering and braking the car. The driver functions without awareness of the computer's role, unless he thinks about it or dwells on it. -Our subject is not the automatic functions of the body or human self-awareness, but the source of the innovations that drive evolution. The only analogy here would be the driver (inventive mechanism within the genome) deciding to take a new route. The car (the rest of the cell/cell community) will go wherever he steers it. The theistic version would be that your God gave the driver the autonomous ability to choose his route and steer the car. But I find the hypothesis itself far clearer than this analogy.-DAVID: Without exception, the genome is in charge of cell function. The genome itself within established species is also mostly very automatic.-Of course it is. That's why species remain the same. But evolution is the history of innovations, and your MOSTLY very automatic is crucial to my hypothesis. Mostly does not mean always. Innovations would occur when the genome is NOT automatic, i.e. when it is confronted with new conditions which demand or allow new organs, functions, and/or modes of behaviour.-DAVID: The closest you and I have gotten together is the possibility of an inventive mechanism in the genome which might possibly account for speciation. -And that is all I have ever asked of you: to accept the possibility. Only inventive does not mean obeying instructions. It means creating new things and performing new actions without being preprogrammed.

dhw: That is exactly the way I interpret it. The genome runs the cell as the brain runs the body.-Well, at least we generally agree here. There are many parts of the body and of a cell that run on autopilot, with the brain or the genome simply keeping out an eye for problems. -> > dhw: if you are now saying that the brain in the genome is a computer that is not capable of autonomous invention, then you are back again with your divine 3.7-billion-year programme to cover every single innovation and wonder in the history of life, ..... a hypothesis which, very understandably, you say bothers you.-Yes it bothers me. But we have agreed that the genome may well contain an inventive mechanism which can take the organism beyond mere adaptation and create a new species.-What you have not accepted is a cause for the presence of intelligent information in the genome. It will need lots of intelligent information to change an organism into an entirely new species. Invention requires thought an planning to intergrate all the new parts so they work together. Again, the whale series is a great example. > > dhw: [cells] Highly controlled by the genome is fine with me. Instructions IN the genome yet again = your 3.7-billion-year-old computer programme as above. Instructions WORKED OUT AND GIVEN BY the genome makes the genome the author of the instructions. Which of these seems to you more likely? Do please answer.-I think the genome has previously received guidelines and instructions to accomplish speciation. As I noted above, living architecture is quite complex and requires planning and coodination of the new parts. I suspect there is some byplay between environment and genome responsiveness. > > dhw: The theistic version would be that your God gave the driver the autonomous ability to choose his route and steer the car. But I find the hypothesis itself far clearer than this analogy.-Only because your position has to avoid a universal consciousness. If you don't accept chance where did the genome get its intelligent information in the first place? > > DAVID: Without exception, the genome is in charge of cell function. The genome itself within established species is also mostly very automatic. > > dhw:Of course it is. ....... Innovations would occur when the genome is NOT automatic, i.e. when it is confronted with new conditions which demand or allow new organs, functions, and/or modes of behaviour.-Agreed, but new architecture requires an architectural plan that coordinate the new parts. Darwinian itty-bitty advances aren't apparent. And, I repe, we have discarded chance. What is left? For you, your nebulous concept is that cells can conjure up a new species, by influencing their genomes. > > DAVID: The closest you and I have gotten together is the possibility of an inventive mechanism in the genome which might possibly account for speciation. > > dhw: And that is all I have ever asked of you: to accept the possibility. Only inventive does not mean obeying instructions. It means creating new things and performing new actions without being preprogrammed.-NO WAY! It invents with knowledge of instructions and consideration of coordination of parts. Did your architect design your house (which I have seen) to make it work the way you wanted it to, or is it a hodgepodge? Species work because they have to work. They have to be designed to work or their attempt at life doesn't work. Natural selection's job is to discard, something the Darwinists have forgotten. Your house worked for you and I found it pleasently designed. Your architect didn't work at random. It seems he knew what he was doing. For me there is no way to avoid design.

Note how long elements of DNA can hop around and are under a variety of controls. How this mechanism could create a Cambrian organism in all its parts requires integrated information in the coded messages.-http://www.the-scientist.com//?articles.view/articleNo/40861/title/A-Long-Line-of-LINEs/

DAVID: [...] we have agreed that the genome may well contain an inventive mechanism which can take the organism beyond mere adaptation and create a new species.-Such an agreement is meaningless if you insist that inventive means obeying God's instructions as opposed to making autonomous decisions.-DAVID: What you have not accepted is a cause for the presence of intelligent information in the genome. It will need lots of intelligent information to change an organism into an entirely new species. Invention requires thought an planning to intergrate all the new parts so they work together. -Of course I accept all of this. Any innovation requires collecting, processing and integrating information, and working out new ways of using it. How this is done is the mystery we're trying to solve. Leaving aside your dabbling God, what you have apparently not accepted is the possibility that instead of him putting plans into the very first forms of life for every single innovation, natural "wonder" and probably environmental change to cover the next 3.7 billion years - a hypothesis which unsurprisingly you admit does bother you - he may have equipped those first sentient beings with an autonomous, intelligent mechanism that would in due course enable their descendants spontaneously (i.e. without instructions) to combine and collaborate in exchanging information and working out new ways to cope with or exploit new conditions. DAVID:[...] I suspect there is some byplay between environment and genome responsiveness.-Since all organisms must cope with their environment, and environments change, I'd have thought byplay was putting it mildly. dhw: The theistic version would be that your God gave the driver the autonomous ability to choose his route and steer the car. But I find the hypothesis itself far clearer than this analogy. DAVID: Only because your position has to avoid a universal consciousness. If you don't accept chance where did the genome get its intelligent information in the first place? -The issue we are discussing is not First Cause but evolutionary innovation. In any case, my position allows for a universal consciousness. The intelligent information your God may have provided in the first place is everything that goes to make up the cell, including its inventive mechanism' or brain'. DAVID: The genome itself within established species is also mostly very automatic. dhw: Innovations would occur when the genome is NOT automatic, i.e. when it is confronted with new conditions which demand or allow new organs, functions, and/or modes of behaviour. DAVID: Agreed, but new architecture requires an architectural plan that coordinate the new parts. Darwinian itty-bitty advances aren't apparent. And, I repe, we have discarded chance. What is left? For you, your nebulous concept is that cells can conjure up a new species, by influencing their genomes.-I repeat: My hypothesis dispenses with itty-bitty advances, because the innovation must work at once or it won't survive. I repeat: I have never ever said that cells conjure up new species by influencing their genomes. I repeat: The genome, the brain' of the cell/cell community, coordinates the information gathered by the cell/cell community and works out the new combination. DAVID: The closest you and I have gotten together is the possibility of an inventive mechanism in the genome which might possibly account for speciation. dhw: And that is all I have ever asked of you: to accept the possibility. Only inventive does not mean obeying instructions. It means creating new things and performing new actions without being preprogrammed. DAVID: NO WAY! It invents with knowledge of instructions and consideration of coordination of parts.-Knowledge of instructions can only = doing what God has told it to do. That makes God, not the mechanism, the inventor. In my hypothesis, your God's role would have been to invent the inventive mechanism, just as you might say your God invented the human brain, but humans invented the motor car. DAVID: Did your architect design your house (which I have seen) to make it work the way you wanted it to, or is it a hodgepodge? Species work because they have to work. They have to be designed to work or their attempt at life doesn't work. Natural selection's job is to discard, something the Darwinists have forgotten. Your house worked for you and I found it pleasently designed. Your architect didn't work at random. It seems he knew what he was doing. For me there is no way to avoid design.-Thank you. I like my house too, and it was a memorable pleasure to welcome you to it. Unfortunately, this warm memory has no bearing on our discussion, since my hypothesis does not avoid design. It proposes that evolutionary innovation is designed by an inventive mechanism in the genome, and it allows for that mechanism to have been designed by your God.

DAVID: [...] we have agreed that the genome may well contain an inventive mechanism which can take the organism beyond mere adaptation and create a new species. > > dhw: Such an agreement is meaningless if you insist that inventive means obeying God's instructions as opposed to making autonomous decisions.-We are agreeing as to location only, not underlying mechanisms. There we are far apart. > > DAVID: What you have not accepted is a cause for the presence of intelligent information in the genome. It will need lots of intelligent information to change an organism into an entirely new species. Invention requires thought an planning to intergrate all the new parts so they work together. > > dhw: Of course I accept all of this. Any innovation requires collecting, processing and integrating information, and working out new ways of using it. How this is done is the mystery we're trying to solve.-Of course the process of information gathering and planning are needed, but you persist in leaving out the pre-existing information which is part of any mechanism that is collating the requirements (new information)for a new species. -> > dhw: In any case, my position allows for a universal consciousness. The intelligent information your God may have provided in the first place is everything that goes to make up the cell, including its inventive mechanism' or brain'.-Fair enough, up to a point: the brain has information which guides its decision-making function- > > dhw: I repeat: I have never ever said that cells conjure up new species by influencing their genomes.-But so far in research, the only DNA changes we know about are influences from cells. We don't know of other mechanisms that have been proven. We are theorizing.-> dhw: I repeat: The genome, the brain' of the cell/cell community, coordinates the information gathered by the cell/cell community and works out the new combination.-Again, based on collating with information already existing in the genome as to how to shape a phenotype, coordinate organs and organs' functions. Current genomes already do this, but we don't know how. > > dhw: Knowledge of instructions can only = doing what God has told it to do. That makes God, not the mechanism, the inventor. In my hypothesis, your God's role would have been to invent the inventive mechanism, just as you might say your God invented the human brain, but humans invented the motor car.-And just how did the first car appear? The first ones looked like wagons with simple motors. The human brain ( Ford and others) took previous experience, which was in their brains, and with reasoning and inventiveness combined the gasoline engine to the wagon. In the fossil world, new species come across better than the first autos. In our world natural selection by buyers quickly demanded better products which rapidly appeared. So we see the steps in the modern world, but those steps are not present in the fossil world. Darwin's itty-bitty steps don't exist. It seems to me those speciation jumps had a great deal of guidance to explain them, i.e., the Cambrian explosion.-> dhw: my hypothesis does not avoid design. It proposes that evolutionary innovation is designed by an inventive mechanism in the genome, and it allows for that mechanism to have been designed by your God.-Which could then have included some instructions for future planning. I can see no other way for the mechanism to work, from the evidence we have from the gaps in the fossil record. For your approach to work, you have to make the assumption, per Darwin, that the gaps will be filled.

Doubling genes might be a way to speciation:-http://www.sciencedaily.com/releases/2014/09/140930090636.htm-Abstract:-"Polyploidy has long been considered a major force in plant evolution. G. Ledyard Stebbins, Jr., an architect of the Modern Synthesis, elegantly addressed a broad range of topics, from genes to chromosomes to deep phylogeny, but some of his most lasting insights came in the study of polyploidy. Here, we review the immense impact of his work on polyploidy over more than 60 years, from his entrance into this fledgling field in the 1920s until the end of his career. Stebbins and his contemporaries developed a model of polyploid evolution that persisted for nearly half a century. As new perspectives emerged in the 1980s and new genetic tools for addressing key aspects of polyploidy have become available, a new paradigm of polyploidy has replaced much of the Stebbinsian framework. We review that paradigm shift and emphasize those areas in which the ideas of Stebbins continue to propel the field forward, as well as those areas in which the field was held back; we also note new directions that plant geneticists and evolutionists are now exploring in polyploidy research. Perhaps the most important conclusion from recent and ongoing studies of polyploidy is that, following Levin and others, polyploidy may propel a population into a new adaptive sphere given the myriad changes that accompany genome doubling."-And another, but similar way, reduplication:-http://phys.org/news/2014-09-geneticists-year-old-dilemma-duplicate-genes.html-"Gene duplication is a biological phenomenon that leads to the sudden emergence of new genetic material. 'Sister' genes - the products of gene duplication - can survive across long evolutionary timescales, and allow organisms to tolerate otherwise lethal mutations. "The Trinity geneticists have now identified and described the mechanism underlying this increased tolerance, which is known as 'mutational robustness'. "By experimentally demonstrating that this robustness is important for yeast cells to adapt to novel conditions, including those that are stressful to the cells, they have underlined the likely reason for the existence of gene duplication."

dhw: Any innovation requires collecting, processing and integrating information, and working out new ways of using it. How this is done is the mystery we're trying to solve. DAVID: Of course the process of information gathering and planning are needed, but you persist in leaving out the pre-existing information which is part of any mechanism that is collating the requirements (new information)for a new species.-I already answered this: "The intelligent information your God may have provided in the first place is everything that goes to make up the cell, including its inventive mechanism' or brain'". What other pre-existing information are you thinking of? -dhw: I repeat: I have never ever said that cells conjure up new species by influencing their genomes. DAVID: But so far in research, the only DNA changes we know about are influences from cells. We don't know of other mechanisms that have been proven. We are theorizing.-At this stage we can ONLY theorize. But you are juggling with what conjures up what, and what influences what. The information gathered by the cells influences the genome in so far as without it, the genome has nothing to work on. But the genome (the brain' of the cell) conjures up new species, based on the information it has about the make-up of the cell community itself and the environment with which it has to cope. This must also apply to your 3.7 billion-year-old computer-brain hypothesis, so I don't know why you're querying it. dhw: In my hypothesis, your God's role would have been to invent the inventive mechanism, just as you might say your God invented the human brain, but humans invented the motor car. DAVID: And just how did the first car appear? The first ones looked like wagons with simple motors. The human brain ( Ford and others) took previous experience, which was in their brains, and with reasoning and inventiveness combined the gasoline engine to the wagon. In the fossil world, new species come across better than the first autos. In our world natural selection by buyers quickly demanded better products which rapidly appeared. So we see the steps in the modern world, but those steps are not present in the fossil world. Darwin's itty-bitty steps don't exist. It seems to me those speciation jumps had a great deal of guidance to explain them, i.e., the Cambrian explosion.-My analogy simply demonstrated two stages of invention: 1) the invention of the mechanism (= the human brain), and 2) the evolutionary innovations invented by the mechanism (= the things invented by the human brain). However, if you insist on extending the analogy, the equivalent would be the variations and adaptations demanded or allowed by changes in the environment. That's why we have so many different species of species, once the prototype has established itself. The intelligent genome invents, and then goes on modifying the invention. Of course there are no itty-bitty steps. Each change has to work or it won't survive. -dhw: My hypothesis does not avoid design. It proposes that evolutionary innovation is designed by an inventive mechanism in the genome, and it allows for that mechanism to have been designed by your God. DAVID: Which could then have included some instructions for future planning. I can see no other way for the mechanism to work, from the evidence we have from the gaps in the fossil record. For your approach to work, you have to make the assumption, per Darwin, that the gaps will be filled.-Could have... some instructions... You cannot have it both ways. Either the mechanism is capable of working out what to do, or it has to have full instructions. And if you believe in evolution, you have no choice: the instructions had to be there from the word go. I don't know why you refuse to register my constantly repeated argument that if the mechanism works, there ARE no gaps. Once again: an innovation must function straight away if it is to survive. But I'm not denying that my hypothesis requires astonishing feats of engineering by the cell communities that create the innovations (much as the first ant communities performed amazing feats when they built the first ant cities). However, the engineering did happen, and it can only have happened because cells cooperated to make it happen. If you believe in evolution, and if every single instance of innovative cooperation, not to mention environmental change, was not planned in intricate detail 3.7 billion years ago - a hypothesis that bothers you, and which should not be fuzzed with expressions like some instructions - what alternative explanation can you think of for this cooperation?

dhw: I already answered this: "The intelligent information your God may have provided in the first place is everything that goes to make up the cell, including its inventive mechanism' or brain'". What other pre-existing information are you thinking of? -Going to the heart of the information issue: DNA is a complex code, according to Gates (Windows), himself, much more complex than anything invented by humans. That code contains information, according to estimates which would fill 600 large-sized books. DNA was present in early life, if not at the very beginning. The DNA in amoebas is larger than ours! You don't think chance could have created it, and neither do I. Where did the information come from? You have never given me an answer. It is the background of that coded information that leads somehow to new species. Is speciation done by absorbing new information from the environment and collating it with existing information, and guided somehow into new species. I'm stuck with no answer. We have no evidence as to how this all works. You glibly grant my God at work. Don't put it on my ideas about God. I want you to tell me how you think it all happened to start life with DNA functioning. And then go on to arrange for new species to develop, and leave out chance.-> > dhw: That's why we have so many different species of species, once the prototype has established itself. The intelligent genome invents, and then goes on modifying the invention. Of course there are no itty-bitty steps. Each change has to work or it won't survive.-I agree. That is why there are huge gaps in the fossil record. Each speciation event must obviously be an excellent plan if the species is developed, produced and prospers. That is clearly why cooperating cells are required, but you haven't offered me any sense of how the planning is developed, other than cells cooperate. There has to be basic information to start with. Without chance what other mechanism would you employ other than cooperating sentient cells. And what 'sentient cells' means in biology is simply that they respond to stimuli, no more. > > dhw: My hypothesis does not avoid design. It proposes that evolutionary innovation is designed by an inventive mechanism in the genome, and it allows for that mechanism to have been designed by your God....... Once again: an innovation must function straight away if it is to survive. But I'm not denying that my hypothesis requires astonishing feats of engineering by the cell communities that create the innovations (much as the first ant communities performed amazing feats when they built the first ant cities). However, the engineering did happen, and it can only have happened because cells cooperated to make it happen.- You have't explained what you mean by 'design'. Is it what I believe, or how did design appear in the first place in DNA coding. DNA forces the cells to cooperate. And speciation does require 'astonishing feats of engineering'. So partially from incredulity, I am convinced there is a God who did this, and you call Him my God. I just don't know how He did it, and in my view your approach dodges the issue by your trying to give cells stupendous powers and at this point we have not shown in research that they have such enormous capabilities. Dawkins says life appears designed, but is not. I say it is designed. Your position, please!

dhw: "The intelligent information your God may have provided in the first place is everything that goes to make up the cell, including its inventive mechanism' or brain'". What other pre-existing information are you thinking of? -DAVID: Going to the heart of the information issue: DNA is a complex code, according to Gates (Windows), himself, much more complex than anything invented by humans.[...]. DNA was present in early life, if not at the very beginning. [...] Where did the information come from? You have never given me an answer. [...] Is speciation done by absorbing new information from the environment and collating it with existing information, and guided somehow into new species. I'm stuck with no answer. We have no evidence as to how this all works. [...] I want you to tell me how you think it all happened to start life with DNA functioning. And then go on to arrange for new species to develop, and leave out chance. [My bold]-Once again you are shifting the focus of this discussion from how evolution might work to the origin of life and of whatever mechanisms have led to evolution. Your answer is that God did it, but you don't know how, and then you expect me to tell you how it was done! I don't know. I can only consider different possibilities: some sort of god; some sort of panpsychist process (see the thread on that subject, which we have discussed at length); chance, which I cannot leave out. For various reasons, I find NONE of these convincing, and so just like you, I am stuck with no answer. I do, however, believe that speciation is done by absorbing new information from the environment and collating it with existing information... A good summing up of the evolutionary process that followed on after life had started. And that is the point at which this discussion begins. You have suggested that God preprogrammed the first living cells with all the innovations over the following 3.7 billion years. You take this seriously, though research has provided no evidence for it and you don't know how it works, but you dismiss out of hand my own hypothesis because there is no evidence for it and I don't know how it works. Ah, there's no justice in Texan philosophy! Do you think your God is incapable of designing an autonomously inventive mechanism (even though you believe he has done so with the human brain)? Please answer.-dhw: My hypothesis does not avoid design. It proposes that evolutionary innovation is designed by an inventive mechanism in the genome, and it allows for that mechanism to have been designed by your God....... DAVID: You have't explained what you mean by 'design'. -By design, I mean the deliberate creation of an object as opposed to its having come about by chance. In this case, God may have created the mechanism, and the mechanism may have created the innovations that led to speciation.-DAVID: Dawkins says life appears designed, but is not. I say it is designed. Your position, please!-Once again the subject of this thread is how evolution proceeds and not how life began. However, after nearly seven years of discussion, I'd have thought you would have known by now that my position is on the picket fence. I agree that life appears designed, and so I refuse to say it is not. But just as I have problems believing in chance, I have problems believing in any kind of designer, whether it's a single mind, plural minds, or a vast collection of minds that have evolved through experience of changing matter...and so I cannot go beyond the statement that life appears designed. That is why I am an agnostic. Now please tell me why your comprehensive 3.7-billion-year computer programme bothers you, and what evolutionary alternative you can think of.

dhw: Once again you are shifting the focus of this discussion from how evolution might work to the origin of life and of whatever mechanisms have led to evolution. Your answer is that God did it, but you don't know how, and then you expect me to tell you how it was done! I don't know.-And, of course, neither do I. But in discussiong evolution it is not possible to exclude from such discussion the start of life, since DNA is implanted with the startup information which is then continuously used as experience and new information is added. It is all one continuum. My first problem is not accepting the idea that any form of chance could create reliably functional information in DNA codes. Fully functional first life had to run on those codes. -> dhw: I can only consider different possibilities: some sort of god; some sort of panpsychist process ; chance, which I cannot leave out. For various reasons, I find NONE of these convincing, and so just like you, I am stuck with no answer. I do, however, believe that speciation is done by absorbing new information from the environment and collating it with existing information... A good summing up of the evolutionary process that followed on after life had started. And that is the point at which this discussion begins.- No, the discussion must begin with the start of life. It is a continuum from the first fuctional life to now, using the first coded information of the first fully functional life and adding to that information as life is experienced and as it became more complex. Old information collated with new information from experience as it is developed. > > dhw: Do you think your God is incapable of designing an autonomously inventive mechanism (even though you believe he has done so with the human brain)? Please answer.-The human brain can continuously transform its functional abilities simply from the experience of it being used in different ways. That is an magnificent example of autonomous inventiveness. So we have an example of an existing organ that can do it. As a result I strongly feel that God might have implanted a mechanism for speciation in the genome, as I have mentioned before. > > By design, I mean the deliberate creation of an object as opposed to its having come about by chance. In this case, God may have created the mechanism, and the mechanism may have created the innovations that led to speciation. I think we might find such a mechanism in the genome. > > DAVID: Dawkins says life appears designed, but is not. I say it is designed. Your position, please! > > dhw: Once again the subject of this thread is how evolution proceeds and not how life began.-As noted above, I look at life as an unbroken continuum from first life to now. All of it looks actually designed to me.-> dhw: However, after nearly seven years of discussion, I'd have thought you would have known by now that my position is on the picket fence.-I know I put you on that fence in the past. Still not painful?-> dhw: I agree that life appears designed, and so I refuse to say it is not. But just as I have problems believing in chance, I have problems believing in any kind of designer,...and so I cannot go beyond the statement that life appears designed. That is why I am an agnostic. Now please tell me why your comprehensive 3.7-billion-year computer programme bothers you, and what evolutionary alternative you can think of.-I'm bothered only by not seeing a clear way to guess the correct possibility: (1) 3.7- billion-year coded program, (2) stepping in to dabble, or (3) an offshoot of the 3.7-b-y program, an inventive speciation code which steps in as needed. Accepting God-driven evolution requires one of these to be correct. It is posible for me to imagine that all three are possible at different junctures in the evolutionary process to reach humans. And I think that there may not be further evolution than where we are right now.

It can start at the beginning. No reason, at all, it can't. think quantum mech and patters. God does not "have to be before" but can be right "after". Think Witten if you need "before".-its all over in less than 1 second ... we were going to be here at that point. - :-) ;-)

GK : It can start at the beginning. No reason, at all, it can't. think quantum mech and patters. God does not "have to be before" but can be right "after". Think Witten if you need "before". > > its all over in less than 1 second ... we were going to be here at that point. > > -I wish you would expand on these comments.

GK: It can start at the beginning. No reason, at all, it can't. think quantum mech and patters. God does not "have to be before" but can be right "after". Think Witten if you need "before". > > its all over in less than 1 second ... we were going to be here at that point. > > -I was hoping you would expand on your post. I know Witten is one of the world's leading theoretical physicists, but how do you think his work applies to the biology of evolution?

How it may have developed. Note the comments about brain plasticity which brings up the issue of how does the brain learn to interpret new signals from the retina, if the retinal signals of color are suddenly changed by a mutation?-http://www.the-scientist.com//?articles.view/articleNo/41055/title/The-Rainbow-Connection/-"This suggested that the animals' brains were making use of the new opsin. I think that's the cool part of it, that [plasticity] is just an intrinsic property of a sophisticated nervous system like a mammal's, says Nathans."

dhw: Once again you are shifting the focus of this discussion from how evolution might work to the origin of life and of whatever mechanisms have led to evolution. Your answer is that God did it, but you don't know how, and then you expect me to tell you how it was done! I don't know. DAVID: And, of course, neither do I. But in discussing evolution it is not possible to exclude from such discussion the start of life, since DNA is implanted with the startup information which is then continuously used as experience and new information is added. It is all one continuum. -Agreed, but you keep hammering away at First Cause: Where did the information come from? I want you to tell me how you think it all happened to start life. Dawkins says life appears designed, but is not. I say it is designed. Your position, please! I am happy purely for the sake of this discussion to say God did it, because my focus is on the nature of the mechanism that runs evolution, not on how the mechanism got here. Hence the heading of this thread.-dhw: Do you think your God is incapable of designing an autonomously inventive mechanism (even though you believe he has done so with the human brain)? Please answer. DAVID: The human brain can continuously transform its functional abilities simply from the experience of it being used in different ways. That is an magnificent example of autonomous inventiveness. So we have an example of an existing organ that can do it. As a result I strongly feel that God might have implanted a mechanism for speciation in the genome, as I have mentioned before.-This is the sort of equivocation that leads to so many misunderstandings. The question is whether the mechanism is autonomously inventive or preprogrammed. Yet again you appear to be agreeing with me, but you do not actually say God might have implanted an AUTONOMOUS mechanism. Whenever you appear to agree with me and I stress autonomy, you cry (29 September) NO WAY! Then you refer to instructions and blur the borders between the information that your God provided in order to create the mechanism itself, and the information that an autonomous mechanism must process in order to innovate. I hasten to add that I don't think this is a deliberate ploy. Having worked with you, met you, and discussed things with you for so long, I have total respect for your integrity. But the above statement requires clarification. You have repeatedly mentioned the mechanism for speciation only in so far as it contains God's plans for 3.7 billion years' worth of innovations. Do you or don't you now accept the possibility that speciation may be the product of an autonomous inventive mechanism (possibly created by your God) which takes its own unpreprogrammed decisions?-Dhw: Now please tell me why your comprehensive 3.7-billion-year computer programme bothers you, and what evolutionary alternative you can think of. DAVID: I'm bothered only by not seeing a clear way to guess the correct possibility: (1) 3.7- billion-year coded program, (2) stepping in to dabble, or (3) an offshoot of the 3.7-b-y program, an inventive speciation code which steps in as needed. -Thank you for answering. Once again, though, (3) equivocates. How can an autonomous inventive mechanism be an offshoot of (1)? Either the genome has an autonomous mechanism or it doesn't. You have consistently defined inventive in terms of obeying God's instructions, instead of creating new things and performing new actions without being preprogrammed (the definition to which you responded with NO WAY!). I hope you will now settle this with a direct answer to the question I have asked above.-********-(I'll watch the video tomorrow. Thank you for posting it)

DAVID: since DNA is implanted with the startup information which is then continuously used as experience and new information is added. It is all one continuum. [/i] > > dhw; Agreed, ..... I am happy purely for the sake of this discussion to say God did it, because my focus is on the nature of the mechanism that runs evolution, not on how the mechanism got here. Hence the heading of this thread.-But you must recognize the start of the evolutionary process for life must include its beginning as well ss its subsequent events and mechanisms. They are intimately related. > > dhw: Do you think your God is incapable of designing an autonomously inventive mechanism (even though you believe he has done so with the human brain)? Please answer.-Yes, but. I feel (do not know) taht the wevidence for God's power is strong enough to assume that such a mechanism contains guidelines for speciation. Just as a computer program can write a new program, it does so under the guidance of guiding instructions.-> > dhw: This is the sort of equivocation that leads to so many misunderstandings. The question is whether the mechanism is autonomously inventive or preprogrammed. Yet again you appear to be agreeing with me, but you do not actually say God might have implanted an AUTONOMOUS mechanism. .... Do you or don't you now accept the possibility that speciation may be the product of an autonomous inventive mechanism (possibly created by your God) which takes its own unpreprogrammed decisions?-No. As stated above I can only envision a guided inventive program, and think the guidance is writen into the inventive program, since it must take into account the many possible environmental and preditory challenges that may well be unexpected. Life is not only dealing with its own evolution and the evolution of rival animals, but also dealing an evolving uiniverse and Earth. > > dhw: Either the genome has an autonomous mechanism or it doesn't. You have consistently defined inventive in terms of obeying God's instructions, instead of creating new things and performing new actions without being preprogrammed-I've answered above. I don't think it is possible to create a new species without intergrating the past programming of life with the new experiences the genome finds or is told.-******** -> dhw:(I'll watch the video tomorrow. Thank you for posting it)-Just trying to show yhou that the cells are primarily automated factories. But not is the brain wwith the plasticity found.

dhw: Do you or don't you now accept the possibility that speciation may be the product of an autonomous inventive mechanism (possibly created by your God) which takes its own unpreprogrammed decisions? DAVID: No. As stated above I can only envision a guided inventive program, and think the guidance is writen into the inventive program, since it must take into account the many possible environmental and preditory challenges that may well be unexpected. Life is not only dealing with its own evolution and the evolution of rival animals, but also dealing an evolving uiniverse and Earth.-Thank you for this clear answer. The problems you have listed show why it is so difficult to believe in your evolutionary scenario. Your God's programme, implanted in the very first living organisms and consisting of billions of innovations and Nature's Wonders to be passed down over billions of years, had to take into account every single environmental change, not to mention the possibility that it could be wiped out by an oops-that-was-unexpected global catastrophe. (I'd have thought predators would be part of the 3.7-billion-year-old programme, but whaddo I know?) If you believe God's programme had a purpose, why would he leave ANYTHING to chance, since he presumably has the power to control the conditions you believe he created in the first place? But that means preprogramming the challenges as well as the responses. Perhaps for this reason you are also unsure to what extent your God may have dabbled, but dabbling would surely imply that either his programme wasn't working, or he was making it all up as he went along. And dabbling smacks of creationism rather than evolution. I have no problem accepting your reservations about my own hypothesis regarding an autonomous inventive mechanism, but perhaps you will understand why I am seeking an alternative (even a theistic one) to what you are offering. dhw: Either the genome has an autonomous mechanism or it doesn't. You have consistently defined inventive in terms of obeying God's instructions, instead of creating new things and performing new actions without being preprogrammed DAVID: I've answered above. I don't think it is possible to create a new species without intergrating the past programming of life with the new experiences the genome finds or is told.-Apart perhaps from the word programming I agree. Evolution is based on the theory that new species arise out of existing organisms. It seems likely that they change when they are confronted with new experiences. Your explanation of such changes is that every single one is preprogrammed, which implies that every single new experience is also preprogrammed, as above. -******** -dhw:(I'll watch the video tomorrow. Thank you for posting it) DAVID: Just trying to show yhou that the cells are primarily automated factories. But not is the brain wwith the plasticity found.-I like the word primarily. We too are primarily automated factories. Some materialists would argue that we are nothing but automated factories. But you believe there is something else. Perhaps that something else emerges from the interaction between our cells, and in particular our brain cells. Perhaps something else also emerges from the interaction between cells of other organisms, and in particular between their brain cells or between mechanisms of what may be the equivalent of the brain. Perhaps. The significance of the video for me is not the automation. The vocabulary leaves me numb, but the complexity confirms just how difficult it is to put one's faith in chance.

dhw: Thank you for this clear answer. The problems you have listed show why it is so difficult to believe in your evolutionary scenario. ...... If you believe God's programme had a purpose, why would he leave ANYTHING to chance, since he presumably has the power to control the conditions you believe he created in the first place? But that means preprogramming the challenges as well as the responses.-You are welcome. We don't know just how powerful God is. We presume it is very,very. It is therefore possible everything imaginable is pre-programmed. But perhaps not. That is why it is possible to imagine an evolutionary inventive mechanism that is sort of on its own. But if the DNA of life is viewed as a continuum, the inventive mechanism must be supplied with appropriate guidelines that are cognizant of the past construction to arrange for new speciation. > > dhw: Perhaps for this reason you are also unsure to what extent your God may have dabbled, but dabbling would surely imply that either his programme wasn't working, or he was making it all up as he went along. And dabbling smacks of creationism rather than evolution.-Your point is exactly why dabbling bothers me. If God is that powerful, he shouldn't have to dabble. But an inventive mechanism gets around that, but introduces the issue of deism vs. theism, and I prefer theism (without proof) which, of course, means God remains interested, watching and perhaps taking part.-> dhw: I have no problem accepting your reservations about my own hypothesis regarding an autonomous inventive mechanism, but perhaps you will understand why I am seeking an alternative (even a theistic one) to what you are offering.-I fully understand your problem. But that is why I have presented you with such strong evidence of the way cells work under very full DNA controlls. The inventive mechanism must be built the same way, but with the latitude in the instructions to allow for the very inventive bush of life.. > > dhw: Apart perhaps from the word programming I agree. Evolution is based on the theory that new species arise out of existing organisms. It seems likely that they change when they are confronted with new experiences. Your explanation of such changes is that every single one is preprogrammed, which implies that every single new experience is also preprogrammed, as above.- I view the instructions as offering latitude with constraints. Again, think of life as a changing continuum. Under this approach, as stated above, there is not absolutely tight pre-programming, much as I reminded you, you used your architect's expertese to shape the house to your desires. > dhw: The significance of the video for me is not the automation. The vocabulary leaves me numb, but the complexity confirms just how difficult it is to put one's faith in chance.-That is my point in prestning the video. Every process in the cell is like this. Each molecule acts as if it were individualy alive and thinking, just like workers in a factory. But they are simply following biochemical instructions

It is long, but clearly thought out. The supplemental box at the end is also long but an exact description of the inventive mechanism that is beginning to appear in our research of the genetic mechanisms of organisms. Simply, non-life does not make life, life brings life, life manages most genetic changes, fitness cannot be defined or described, and purpose is everywhere.-http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness-I have mentioned Talbott's other essays in the past. I love the way he logically disses Dawkins and Dennett.-"In fact, we are no longer free to imagine that evolution waits around for accidents to knock genes askew so as to provide new material for natural selection to work on. The genome of every organism is actively and insistently remodeled as an expression of its context. Genetic sequences get rewritten, reshuffled, duplicated, turned backward, invented from scratch, and otherwise revised in a way that prominently advertises the organism's accomplished skill in matters of genomic change. The illustrations of this skill are so extensive in the contemporary literature that there is no way to review it adequately here. (For some examples, see the supplement Natural Genome Engineering [below], which contains the bulk of the evidence for my contentions here.)"-But note, he never uses 'design', nor does he ever try to explain how this deeper quality of life controlling life came to be. For him it just IS.:-"Such, then, is the living reality that Dawkins refers to as the appearance of design or the illusion of design and planning.[6]- "It is also what Dennett has in mind when he writes, All the Design in the universe can be explained as the product of a process that is ultimately bereft of intelligence, in other words an algorithmic process that weds randomness and selection to produce ... all the intelligence that exists.[7]-" (Dawkins and Dennett sometimes seem fixated upon design, presumably as a result of their severely constraining preoccupation with religion and with the creationism or intelligent design promulgated by some religious folks. Although the word has its legitimate uses, you will not find me speaking of design, simply because  as I've made abundantly clear in previous articles  organisms cannot be understood as having been designed, machine-like, whether by an engineer-God or a Blind Watchmaker elevated to god-like status. If organisms participate in a higher life, it is a participation that works from within  at a deep level the ancients recognized as that of the logos informing all things. It is a sharing of the springs of life and being, not a mere receptivity to some sort of external mechanical tinkering modeled anthropocentrically on human engineering.)"

DAVID: The supplemental box at the end is also long but an exact description of the inventive mechanism that is beginning to appear in our research of the genetic mechanisms of organisms. Simply, non-life does not make life, life brings life, life manages most genetic changes, fitness cannot be defined or described, and purpose is everywhere.-http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness-Once again, thank you for recommending an illuminating article, especially since it supports so many ideas you disagree with. I am going to reshuffle some of your quotes and a few others in order to show a clear line of argument. First the autonomy of the organism (all bold lettering is mine): [We must overlook, first of all,] the fact that organisms are masterful participants in, and revisers of, their own genomes, taking a leading position in the most intricate, subtle, and intentional genomic dance one could possibly imagine. And then we must overlook the way the organism responds intelligently, and in accord with its own purposes, to whatever it encounters in its environment, including the environment of its own body, and including what we may prefer to view as accidents.-" Genetic sequences get rewritten, reshuffled, duplicated, turned backward, invented from scratch, and otherwise revised in a way that prominently advertises the organism's accomplished skill in matters of genomic change. The illustrations of this skill are so extensive in the contemporary literature that there is no way to review it adequately here.-The organism pursues its own genomic alterations with remarkable insistence and subtlety. -Next, the cooperation between individual organisms:-There is a consensus today that entire organelles of the cell originated in evolutionary history through a kind of cooperative fusion of distinct microorganisms, a process requiring an almost unimaginable degree of intricate coordination among previously independent life processes. [This is precisely how I envisage innovation coming about through cooperation between cells/cell communities.]-Third, and a truly devastating rebuttal of your opposition to the concept of the intelligent cell: In her 1983 Nobel address, geneticist Barbara McClintock cited various ways an organism responds to stress by, among other things, altering its own genome. Some sensing mechanism must be present in these instances to alert the cell to imminent danger, she said, adding that a goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged. Subsequent research has shown how far-seeing she was.-Fourth, an observation which will teach me not to be too dependent on my dear friend's superior knowledge of science. You have persuaded me that any inventive mechanism has to be located in the genome, which controls and is not controlled by the rest of the cell. Not according to Talbott:-Crucially, genetic change is almost always the result of cellular action on the genome.-Recent studies have revealed novel cellular mechanisms and environmental cues that influence genomic rearrangements.-Fifth, a shattering dismissal of your own divine hypotheses, which you have quoted without seeming to relate it to your theories:-...you will not find me speaking of design, simply because  as I've made abundantly clear in previous articles  organisms cannot be understood as having been designed, machine-like, whether by an engineer-God or a Blind Watchmaker elevated to god-like status.-Instead, the following:-If organisms participate in a higher life, it is a participation that works from within  at a deep level the ancients recognized as that of the logos informing all things. It is a sharing of the springs of life and being, not a mere receptivity to some sort of external mechanical tinkering modeled anthropocentrically on human engineering.-No divine preprogramming, and no dabbling/tinkering, but something working from within. He calls it the logos informing all things. The panpsychist hypothesis asserts that all things have a mental or inner aspect, with varying degrees of subjectivity and quasi-consciousness. Of course it still depends on an if, and none of this means that Talbott knows more than you, but you have recommended his article. And so perhaps you will find my own less dogmatic but not dissimilar musings a little more convincing in the light of the above.

dhw: Once again, thank you for recommending an illuminating article, especially since it supports so many ideas you disagree with.-You have missed the point,as always, as to why I present this material. It is not magnanimously to help you. ;>)) I find it by following ID folks who interpret it as I do, not as the author does. He is committed to a materialistic and naturalistic interpretation. We are not. His is an atheist or agnostic view of these findings. > > dhw: No divine preprogramming, and no dabbling/tinkering, but something working from within. He calls it the logos informing all things. The panpsychist hypothesis asserts that all things have a mental or inner aspect, with varying degrees of subjectivity and quasi-consciousness. Of course it still depends on an if, and none of this means that Talbott knows more than you, but you have recommended his article. And so perhaps you will find my own less dogmatic but not dissimilar musings a little more convincing in the light of the above.-Of course, no divine preprogramming, but his point of view and yours mimic each other, so of course you feel supported, and I think his findings can be interpreted as supporting mine.-How? First of all I look more than genome/cell relationships. I don't accept chance as having any possibility of creating such an intricate genome and genome/cellular dance. It is all way too complex for chance. And that is exactly what his essay shows in my mind and with the ID folks. Secondly, I am very aware of the plasticity of the DNA, which starts out as a zygote with a single code and in order to make various organs, which cooperate together, and is modified by its own plasticity to make 'kidney' DNA or 'liver' DNA, or most spectacularly 'brain neuron' DNA. Even the myocardium and skeletal muscles are very differentiated as to structure and metabolites used for energy. This ability of DNA must be very useful in speciation, however it occurs. Therefore, I accept that there is an intense interplay between genome and cells as Talbott describes. The genome does not receive sensory input directly, but through the cells tht make up the organism. This is the ultimate feedback mechanism leading to speciation, if it occurs through an IM. Remember that life is built on simple feedbacks covering levels of product output, temperature control, etc. Speciation is the most complex of all feedbacks, if it occurs by IM.-Note that I have given cells lots of credit in consideration of a speciation mechanism. But I will not give up the knowledge that they are tighly controlled by the genome. They automatically ferry information to the genome, and as with any architectural process, past experience must be employed in setting up modified plans for a new structure. Therefore, the requirement for continuity and guidelines in the genome. After all it is changes in the genome that produces the modified organism. The genome modifies how the cells are newly employed in the new structures. The genome is the final arbiter. Simply, the cells supply information and the genome creates.

dhw: Once again, thank you for recommending an illuminating article, especially since it supports so many ideas you disagree with. DAVID: You have missed the point,as always, as to why I present this material. It is not magnanimously to help you. ;>)) I find it by following ID folks who interpret it as I do, not as the author does. He is committed to a materialistic and naturalistic interpretation. We are not. His is an atheist or agnostic view of these findings. -You wrote: It is long, but clearly thought out. The supplemental box at the end is also long but an exact description of the inventive mechanism that is beginning to appear in our research of the genetic mechanisms of organisms. The points relating to the inventive mechanism, which is the subject of this thread, are (a) its autonomy, and (b) Talbott's claim that subsequent research endorses McClintock's references to the knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged. In the past, you have been resolutely opposed to both concepts. You think his findings can be interpreted as supporting yours. In this context, his findings run explicitly contrary to yours. I shan't repeat your next paragraph, which relates (a) to chance (Talbott agrees with both of us that this is a non-starter), and (b) to interplay between genome and cells. I still dislike this separation - as if the genome were not part of the cell - but it doesn't make any difference to the hypothesis that the cells contain an inventive mechanism. DAVID: Note that I have given cells lots of credit in consideration of a speciation mechanism. But I will not give up the knowledge that they are tighly controlled by the genome. [...] After all it is changes in the genome that produces the modified organism. The genome modifies how the cells are newly employed in the new structures. The genome is the final arbiter. Simply, the cells supply information and the genome creates.-I note it well, and am quite happy with it. You are now talking in terms of the inventive mechanism creating as opposed to being preprogrammed. This is very much in line with Talbott's argument as well as my own. -DAVID: What is the 'logos', the 'mental or inner aspects', the elan vital of organisms? If the chemicals I've mentioned are under a central direction then the 'logos' appears. The central directing conductor of the living orchestra is the genome, reading all the feedback loops from the cell communities.-Again, I am happy with this. Cells/cell communities are under the central direction of an intelligent, inventive mechanism. All you need to do now is choose between the genome as an automaton obeying instructions implanted 3.7 billion years ago, or as an autonomous mechanism formulating and issuing its own instructions. DAVID: I view Talbott like I view Nagel and his problem with consciousness. They are struggling because they cannot let a divine foot in the door, a la Lewonton. [...] They can't get from inorganic 'no life' forms to living forms. They can only start their analysis after life has started.-Our concern here has been how evolution might work, and we have discussed it only from a theistic angle (i.e. how your God might have set things up). But First Cause itself is a different subject. I don't think you urged me to read the essay in order to emphasize Talbott's refusal to tackle the issue of a divine foot in the door. -DAVID: Your intellectual battle with me has been of great help to me. I've come to a concept of an inventive mechanism I can live with. It has to be nebulous at this stage, because we don't know enough to go further. I'm still betting on something like an IM is present and will be found as part of the genome.-This is very important for me. Thank you. Our discussions often go round in circles, but you provide a wealth of information, and I think the exchanges gradually broaden and/or deepen our views. It was, after all, you who in the first place put me onto Margulis and others who believe the cell to be a cognitive being, and onto the role of cooperation in evolution. Our battle is far from over, since autonomy remains the key issue, but I'm delighted that you now take this hypothesis seriously as a possible explanation for how evolution might work.

dhw: The points relating to the inventive mechanism, which is the subject of this thread, are (a) its autonomy, and (b) Talbott's claim that subsequent research endorses McClintock's references to the knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged. In the past, you have been resolutely opposed to both concepts. You think his findings can be interpreted as supporting yours. In this context, his findings run explicitly contrary to yours.-That is because you stretch the concept of cellular 'thoughtful'-ness beyond the actual case when cells are studied. Cells receive stimuli and respond and tell their genomes, but the genome is still in charge. Cells are not thoughtful. They are automatic reporters. Talbott is making a point to overcome the Darwinian mantras. He must get rid of the chance mutation theory. It just doesn't work that way as he points out. You don't see that ID folks and I have a totally different analysis. It is not just me. The genome, as part of the cell, gets the message and methylates or or transposes or whatever to make changes in gene expression. Remember in embryology one DNA becomes many DNA's. The genome is very plastic like the brain. -> dhw: You are now talking in terms of the inventive mechanism creating as opposed to being preprogrammed. This is very much in line with Talbott's argument as well as my own.-Yes, that is what i've tried to find. > dhw: Cells/cell communities are under the central direction of an intelligent, inventive mechanism. All you need to do now is choose between the genome as an automaton obeying instructions implanted 3.7 billion years ago, or as an autonomous mechanism formulating and issuing its own instructions.-I've explained above my 'third way'. > > dhw: Our concern here has been how evolution might work, and we have discussed it only from a theistic angle (i.e. how your God might have set things up). -But continue to recognize that evolution starts with the appearnce of first life, and that start is part of a continuum. Current life is based on whatever first life looked like.-> dhw: It was, after all, you who in the first place put me onto Margulis and others who believe the cell to be a cognitive being, and onto the role of cooperation in evolution. Our battle is far from over, since autonomy remains the key issue, but I'm delighted that you now take this hypothesis seriously as a possible explanation for how evolution might work.-The cell recognizes stimuli and simply reports them to the genome. Just how 'cognitive' is that? I still view the genome as the brains of the cell. And the genomic solutions are semi-autonomous, as I have proposed. Remember I look at teleology not chance. Do you have a third alternative? Design of living things has the purpose of surviving. Since the time of Darwin and Wallace, only two choices have existed. Darwin chose chance and Wallace chose design.

It occurred to me today that your review of Talbott mysteriously left out a comment on his huge section discussing fitness, and the inability to define it. Since in this discussion somewhere, recently, and I can't find your quote, you pointed out very rightly that the Darwin theory depends on the concept of survivability, I wondered why you skipped commenting on that aspect of Talbott's critical points. We know that what is 'fit' is then supposed to 'survive', and you have admitted, rightly so, that the whole concept is a tautology.-I am not sure that the basis of evolution is survivability. And that is why the Darwinian attempts to quantify fitness may be so important to them but not to me. I look at the obvious drive for complexity, the appearance of advances in complexity without a driving necessity, and with a possible IM producing a bush of living weirdness with some of the strange lifestyles I've shown in natures wonders, and Darwin's theory may not be on the mark. Is life in competition with itself and the environment the only reason for evolution? I strongly doubt it.

dhw: > If organisms participate in a higher life, it is a participation that works from within  at a deep level the ancients recognized as that of the logos informing all things. It is a sharing of the springs of life and being, not a mere receptivity to some sort of external mechanical tinkering modeled anthropocentrically on human engineering. > > No divine preprogramming, and no dabbling/tinkering, but something working from within. He calls it the logos informing all things. The panpsychist hypothesis asserts that all things have a mental or inner aspect, with varying degrees of subjectivity and quasi-consciousness.-Another thought. If you look at glucose in the dry form it just sits there and nothing happens. In the blood it supplies energy to the body. The amlyase in your siliva does nothing until starch appears and then it acts to begin digestion of starch. When fat hits the small intestine lipase in bile begins tio break down the fat. The pancreas produces trypsin when it recognizes protein coming its way.If you put together all the biochemicals of the human body (many thousands) in a pot some enzymes will automatically act on some of the chemicals. That is their nature. But really nothing at all will happen. In the body, when a chemical meets another that requires some activity, it generally knows exactly what to do, amd will do it automatically or under direction. What is the 'logos', the 'mental or inner aspects', the elan vital of organisms? If the chemicals I've mentioned are under a central direction then the 'logos' appears. The central directing conductor of the living orchestra is the genome, reading all the feedback loops from the cell communities. -I view Talbott like I view Nagel and his problem with consciousness. They are struggling because they cannot let a divine foot in the door, a la Lewonton. All that panting over how vital the living body is. Of course it is, and too complex for chance to develop it. Each of the proteins have to have a very specific form to function. There are literally millions of organic protein molecules possible to employ in life. Each living being has exactly the right ones working together in concert. How did chance find them in just the right proportions and arrangements? Talbott and Nagel ignore this. They step in after the fact and look at the marvel of life and wonder. They can't get from inorganic 'no life' forms to living forms. They can only start their analysis after life has started. Too bad they avoid that gap in their thinking. Just as forceful an argument as Darwin's gaps seem to me. -Your intellectual battle with me has been of great help to me. I've come to a concept of an inventive mechanism I can live with. It has to be nebulous at this stage, because we don't know enough to go further. I'm still betting on something like an IM is present and will be found as part of the genome.

dhw: If you believe God's programme had a purpose, why would he leave ANYTHING to chance, since he presumably has the power to control the conditions you believe he created in the first place? But that means preprogramming the challenges as well as the responses. DAVID: We don't know just how powerful God is. We presume it is very,very. It is therefore possible everything imaginable is pre-programmed. But perhaps not. That is why it is possible to imagine an evolutionary inventive mechanism that is sort of on its own. But if the DNA of life is viewed as a continuum, the inventive mechanism must be supplied with appropriate guidelines that are cognizant of the past construction to arrange for new speciation.-Of course the DNA of life has to be a continuum if you believe in evolution, and if an existing organism changes its structure or its patterns of behaviour, its inventive mechanism has to be cognizant of its present construction, of the new conditions that demand or allow for change, and also of its own constraints. But that does not mean preprogramming going back 3.7 billion years! Sort of on its own means (sort of) autonomous. So does latitude in the instructions to allow for the very inventive bush of life. Latitude = freedom of choice = autonomy. (The bush is not inventive anyway. It's your God or the organisms themselves that are inventive.) Then you go on to say there is not absolutely tight pre-programming. All of this amounts to autonomy, but the very idea that inventive = able to create new things and perform new actions that have not been preprogrammed (i.e. autonomous creativity) elicits the horrified cry from you of NO WAY! The schism in your thinking is also clear from your final comment as regards the cell :-D AVID: Every process in the cell is like this. Each molecule acts as if it were individualy alive and thinking, just like workers in a factory. But they are simply following biochemical instructions-So where is the latitude, the sort of autonomy, the non-tight pre-programming? In other words, what issues the biochemical instructions if it's not the 3.7-billion-year programme? It would have to be the autonomous brain of the cell. You seem to be constantly dipping your toe in the water, and then pulling it out again, as if some nasty crocodawkins might come along and bite it off. You offer an example of the problem on your often breathtaking thread of Nature's Wonders, for which I can only go on thanking you :-D AVID: These little guys sneak into the ant colonies, have changed to be of a pretty look-alike body, and live the 'life of Riley'. Are the ants fooled or accepting?:-http://www.sciencedaily.com/releases/2014/10/141002123635.htm-QUOTE: "But pulling off this way of life means undergoing drastic morphological changes."-So do you think your God preplanned these drastic morphological changes 3.7 billion years ago? Did he dabble personally in order to change the beetles' morphology? Or did some damn smart beetles autonomously work it out for themselves, and start up a whole new line of myrmecophilously Clever Clavigeritae? Is the latter hypothesis possible or not?-**********-Thank you for the very important Talbott essay. I will get back to it tomorrow.

dhw: It's your God or the organisms themselves that are inventive.) Then you go on to say there is not absolutely tight pre-programming. All of this amounts to autonomy, but the very idea that inventive = able to create new things and perform new actions that have not been preprogrammed ...The schism in your thinking is also clear from your final comment as regards the cell: > > DAVID: Every process in the cell is like this. Each molecule acts as if it were individualy alive and thinking, just like workers in a factory. But they are simply following biochemical instructions-What I am describing is contrained autonomy, changes under guidelines tying the future to the past. I will never believe in complete autonomy of cells to do their own thing. > > dhw: So where is the latitude, the sort of autonomy, the non-tight pre-programming? -Explained above as best I can. Innovation under constraint.-> dhw: You offer an example of the problem on your often breathtaking thread of Nature's Wonders, for which I can only go on thanking you:-> > So do you think your God preplanned these drastic morphological changes 3.7 billion years ago? Did he dabble personally.-No and no. Invention under provided guidelines. --> > ********** > > dhw:Thank you for the very important Talbott essay. I will get back to it tomorrow.-He sounds a lot like Shapiro, whom he quotes.

DAVID: What I am describing is constrained autonomy, changes under guidelines tying the future to the past. I will never believe in complete autonomy of cells to do their own thing. [...] Innovation under constraint. [...] Invention under provided guidelines.-The last of these was in answer to my question whether your God preplanned the beetles' drastic morphological changes 3.7 billion years ago, or dabbled personally, those being the hypotheses you favour. You have rejected them with a clear no. The qualifications that you now add to your acceptance of a sort of autonomy apply to all inventions. You might as well say that no invention/innovation can achieve the impossible: Nature provides constraints and guidelines. Our friend the beetle may try as hard as he likes, but he'll never be able to turn himself into an elephant or an eagle. Guidelines tying the future to the past have nothing to do with preplanning or divine dabbling. An organism that changes itself has to change from what it was to what it will be. That is evolution. The environment constitutes an unbreakable constraint. If the innovation can't cope with it, then the organism won't survive. You have always criticized my hypothesis for being nebulous, because I can't explain how it works. I find your objections nebulous. What constraints and guidelines are you referring to, other than the obvious ones I've mentioned? And finally, back to our beetles: since you now firmly reject the very idea that God preprogrammed or separately invented their myrmecophily, do you agree that they autonomously worked it out for themselves?

DAVID: What I am describing is constrained autonomy, changes under guidelines tying the future to the past. I will never believe in complete autonomy of cells to do their own thing. [...] Innovation under constraint. [...] Invention under provided guidelines. > > dhw: The last of these was in answer to my question whether your God preplanned the beetles' drastic morphological changes 3.7 billion years ago, or dabbled personally, those being the hypotheses you favour. You have rejected them with a clear no. The qualifications that you now add to your acceptance of a sort of autonomy apply to all inventions. You might as well say that no invention/innovation can achieve the impossible: Nature provides constraints and guidelines.-Lets review: we are trying to reach a conclusive view of how a hypothetical inventive mechanism (IM) might work to achieve speciation. I have trouble accepting without reservation the two approaches of total preplanning vs. dabbling. I look at speciation as defined by the whale series, in which each step is vastly different than the last. This recognizes the gaps in Darwinian evolution as defined by the fossils we find. Yes, Nature provides constraints, but not guidelines. The guidelines must be in innovation instructions in the genome, just as in my example of building a new house (different than all others), with the new owner describing his desires and the architect, using his knowledge and experience forms the new set of plans, and they must include design of structure (partially new morphology) and plan of construction (embryology). -> dhw: Guidelines tying the future to the past have nothing to do with preplanning or divine dabbling. An organism that changes itself has to change from what it was to what it will be. That is evolution. The environment constitutes an unbreakable constraint. If the innovation can't cope with it, then the organism won't survive.-I think you have confused your understanding of my reasoning. In my attempt to find a reasonable IM, I am trying to bind my concept of genome control, whose methods of creating phenotypes and morphology is not at all as yet understood, with the gap issue and with continuity in evolution. My barn cat looks just like an African lion (which I have seen up close and personal). The continuity is there in form and in hunting ability. Both survive in very different environments. Life is very inventive and can handle environmental constraints with many novel inventions as I show in Natures wonders.-> dhw:You have always criticized my hypothesis for being nebulous, because I can't explain how it works. I find your objections nebulous.-Your original hypothesis stretches celluler abilities beyond what is shown they can possibility create. Once you agreed with me to place the IM in the genome, we have come much closer together in our thinking.-> dhw: What constraints and guidelines are you referring to, other than the obvious ones I've mentioned?-I have explained my constraints as part of genomic guidelines and also environmental challenges.-> dhw: And finally, back to our beetles: since you now firmly reject the very idea that God preprogrammed or separately invented their myrmecophily, do you agree that they autonomously worked it out for themselves?-I have never fully rejected 'pre-pro' or 'dabb'. These are reasonable possibilities, if one accepts theistic evolution. I just don't like them as stand-alone concepts of God's abilities. An IM is a strong possibility to get around my uneasiness, but I am content with it, only if it follows my architect analogy, as the genome guides the new production of a species.

For the sake of brevity, I am editing quotes in order to highlight the salient points of the discussion.-dhw: The qualifications that you now add to your acceptance of a sort of autonomy apply to all inventions. You might as well say that no invention/innovation can achieve the impossible: Nature provides constraints and guidelines. DAVID: Yes, Nature provides constraints, but not guidelines. The guidelines must be in innovation instructions in the genome, just as in my example of building a new house (different than all others), with the new owner describing his desires and the architect, using his knowledge and experience forms the new set of plans, and they must include design of structure (partially new morphology) and plan of construction (embryology). -One expression stands between us: innovation instructions. The question is whether the genome-architect itself designs the new house, or your God drew up all the plans 3.7 billion years ago and the genome automatically switches onto that particular programme. You cannot get round this alternative.-dhw: You have always criticized my hypothesis for being nebulous, because I can't explain how it works. I find your objections nebulous. DAVID: Your original hypothesis stretches celluler abilities beyond what is shown they can possibility create. Once you agreed with me to place the IM in the genome, we have come much closer together in our thinking.-The genome is part of the cell. The inventive mechanism is a hypothesis to explain the course of evolution, and the all-important question is not location but autonomy. (See also our discussion on Talbott). dhw: What constraints and guidelines are you referring to, other than the obvious ones I've mentioned? DAVID: I have explained my constraints as part of genomic guidelines and also environmental challenges.-Genomic guidelines would be the plans drawn up by the inventive mechanism, in response to environmental challenges. No need for a 3.7-billion-year programme or for God to dabble. dhw: And finally, back to our beetles: since you now firmly reject the very idea that God preprogrammed or separately invented their myrmecophily, do you agree that they autonomously worked it out for themselves? DAVID: I have never fully rejected 'pre-pro' or 'dabb'. -I asked: So do you think your God preplanned these drastic morphological changes 3.7 billion years ago? Did he dabble personally in order to change the beetles' morphology? And you answered: No and no. Invention under provided guidelines. As an old-fashioned English gentleman, when I hear a no, I understand it as a no. The guidelines, you have now explained, are provided by the inventive mechanism in the genome. In your heart of hearts you don't really believe your God preprogrammed myrmecophily into the first living cells, do you?-DAVID: These [divine preprogramming and dabbling] are reasonable possibilities, if one accepts theistic evolution. I just don't like them as stand-alone concepts of God's abilities. An IM is a strong possibility to get around my uneasiness, but I am content with it, only if it follows my architect analogy, as the genome guides the new production of a species.-Let me repeat: If your architect is the genome, you are acknowledging the autonomy of the inventive mechanism. If the genome is merely implementing plans drawn up by an architect 3.7 billion years ago, you are back in the uneasy position you started with.

dhw: One expression stands between us: innovation instructions. The question is whether the genome-architect itself designs the new house, or your God drew up all the plans 3.7 billion years ago and the genome automatically switches onto that particular programme. You cannot get round this alternative.-Of course I can. Either you are not thinking it through or I'm not explaining it well enough. There is the third way I am trying to put across. Sticking with the architecture analogy: imagine a suspension bridge to be built across a river in a deep valley. The structural engineer must account for the weight of the bridge, the weight of the traffic count in figuring the size and number of support cables. But considering what happened in Tacoma, Washington years ago, nature's challenges must be considered. Don't forget wind velocity in a valley. They did in Tacoma. In a wild unexpected storm the bridge swayed and collapsed. New bridges took that into account. I view the genome the same way. It knows from the past what works, and with a new challenge, looks for guidelines for a way to answer it. The genome must contain similar guidelines from the past to create a truly modified new species, not exact instructions, because that might not cover new unexpected environmental issues (Chicxulub), but suggestive solutions. If a program can write a program (and they can) the genome should be able to take cellular information and propose solutions. This is where natural selection steps in the arbitrate. > > dhw: Let me repeat: If your architect is the genome, you are acknowledging the autonomy of the inventive mechanism. If the genome is merely implementing plans drawn up by an architect 3.7 billion years ago, you are back in the uneasy position you started with.-In my view, not fully autonomous, but limited by guidelines. Still those gidelines I am proposing seem quite liberal and inventive, considering all the weird living forms we find in the bush of life.

This story is an exact representation of evolutionary speciation among man-made objects. The original event: -http://en.wikipedia.org/wiki/Tacoma_Narrows_Bridges#Westbound_bridge-The new Tacoma narrows bridge in the article from Wiki is a new species of bridge, based ln the old design with modifications. In NY city a sister-designed bridge, the Whitestone from Northern Queens to the North shore of Long Island Sound was put in about the same time. Since NY is subject to hurricanes with their high winds, the Tacoma event caused NY engineers to put a heavy steel scaffolding along both sides of the suspended roadway to stop it from any harmonic waves in a high wind. It is still in place after several hurricanes.-This is an exact analogy to evolutionary speciations. Both the NY and the Tacoma bridges are new species of bridges, responding to natural threats. The engineers followed stress-enginering guidelines in the new structures. Granted the engineers plans were now correct for wind stress the first time. In parallel to the bridges example, in evolution, my thought is that the genome tries new forms, using guidelines, and natural selection chooses.-Against that thought is the apparent drive for complexity in evolution. New species without a causative challenge. As I have pointed out in my books, bacteria are still bacteria and still successful 3.7 years later. They did not need to advance to complicated multicellular life, nor is there any evidence that they were driven to advance by adverse conditions. In fact extremeophiles love adversity. The same is true for hominin development. Leaving trees and upright posture go together. The silly Darwinian idea that the forest turned to savannah and forced the changes, is answered by simply imagining arborial-living creatures obviously following the retreating forest to where ever it ends up. Africa has never been totally deforested. And finally, the giant human brain wasn't forced to happen, but it did. Much of speciation advancement is not related to stress.

dhw: One expression stands between us: innovation instructions. The question is whether the genome-architect itself designs the new house, or your God drew up all the plans 3.7 billion years ago and the genome automatically switches onto that particular programme. You cannot get round this alternative.-DAVID: Of course I can. Either you are not thinking it through or I'm not explaining it well enough. There is the third way I am trying to put across. Sticking with the architecture analogy: imagine a suspension bridge to be built across a river in a deep valley. The structural engineer must account for the weight of the bridge [etc....] I view the genome the same way. It knows from the past what works, and with a new challenge, looks for guidelines for a way to answer it. The genome must contain similar guidelines from the past to create a truly modified new species, not exact instructions, because that might not cover new unexpected environmental issues (Chicxulub), but suggestive solutions. If a program can write a program (and they can) the genome should be able to take cellular information and propose solutions. This is where natural selection steps in the arbitrate.-You are putting across to me what I have been trying to put across to you ever since this discussion began. You started out with two hypotheses: 1) God preprogrammed all innovations and Nature's Wonders 3.7 billion years ago; 2) God dabbled. My third way is an inventive mechanism within the cells, which initially you rejected outright. You have now agreed that there is such a mechanism and have placed it in the genome, which is fine with me (so long as we don't lose sight of the fact that the genome is part of the cell), because I am only concerned with the existence of the mechanism, not with its location. Yes, it has to know its own past - though that does not have to stretch back over 3.7 billion years! - since it needs to know what, as an individual organism, it can and can't do, and relate that to the new conditions which demand or allow new structures or modes of behaviour. Those factors constitute guidelines for the genome, just as they do for the bridge-builder. And if the solution is not preprogrammed, the genome has the same autonomy as the bridge builder.-DAVID: The cell recognizes stimuli and simply reports them to the genome. Just how 'cognitive' is that? I still view the genome as the brains of the cell.-As I have said many times, I am quite happy with this. In the past you have vehemently denied that the cell had the equivalent of a brain (my bold): You want your cell communities to gain intelligence from experience and then use that intelligence to make changes. Just where is any of that intelligence' stored? Cells don't have brains (as humans do)... (1 Sep. at 18.39 on this thread). That was in the days when you only gave yourself a choice between a 3.7-billion-year programme and your God dabbling. -DAVID: And the genomic solutions are semi-autonomous, as I have proposed. Remember I look at teleology not chance. Do you have a third alternative? Design of living things has the purpose of surviving. Since the time of Darwin and Wallace, only two choices have existed. Darwin chose chance and Wallace chose design.1) -1) Re semi-autonomy, as I said above, if the solutions are not preprogrammed, the inventive mechanism has the same degree of autonomy as the bridge-builder, who also has to follow guidelines as to what he can and can't do. 2) As for teleology, Darwin chose survival as the purpose of evolution. Previously you have always insisted that its purpose was the production of humans, which ran counter to the higgledy-piggledy nature of the evolutionary bush. 3) Our discussion is not about chance v. design, since we are now debating the nature of the mechanism your God may have designed. -dhw: You are now talking in terms of the inventive mechanism creating as opposed to being preprogrammed. This is very much in line with Talbott's argument as well as my own. DAVID: Yes, that is what i've tried to find.-That is what I have been proposing to you throughout this discussion. On 1 September you wrote (my bold): I initially misused the concept of inventive mechanism as I was thinking out loud. I have defined it now as a set of pre-planned instructions for a new species in some still hidden area of the genome. I expect it to be found. Perhaps you will now accept my definition of inventive as creating new things and performing new actions without being preprogrammed.

From Nature, a battle for relevence of outside ideas about evolution:-http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080?WT.ec_id=NATURE-20141009-No firm answers for how speciation occurs. Shapiro and his ilk are avoided.

DAVID: From Nature, a battle for relevence of outside ideas about evolution:-http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080?WT.ec_id=NAT...-No firm answers for how speciation occurs. Shapiro and his ilk are avoided.-I was naturally disappointed that there was no mention of the crucial need for more research into what McClintock called knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged. I suppose phenotypic plasticity is the nearest the authors come, but they don't seem to consider its implications. It's as if they had never heard of McClintock, Margulis, or Shapiro and his ilk, but otherwise I like the call for a broader approach, and one item particularly caught my attention, as it is directly relevant to our discussions:-Such legacies can even generate macro-evolutionary patterns. For instance, evidence suggests that sponges oxygenated the ocean and by doing so created opportunities for other organisms to live on the seabed. Accumulating fossil data indicate that inherited modifications of the environment by species has repeatedly facilitated, sometimes after millions of years, the evolution of new species and ecosystems.-The authors seem to take it for granted that once there are new opportunities, organisms will simply turn themselves into new species. We're not expected to ask how. Random mutations don't fit in, since the link with environmental changes can hardly be called random, but plasticity isn't much use unless there's some sort of intelligent mechanism to mould it. However, on the plus side I would interpret the above findings as support for the hypothesis that even the Cambrian can be explained by a change in the environment offering new opportunities for inventive mechanisms to cooperate in producing new forms of life.

David No firm answers for how speciation occurs. Shapiro and his ilk are avoided. > > dhw:I was naturally disappointed that there was no mention of the crucial need for more research into what McClintock called knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged.-Overintrepreting McClintock as usual. Shapiro, her acolyte, describes how the genome is changed by methylation, etc. The genome of the cells is in charge. Remember the genome is in the nucleus which has a semipermeable membrane and it receives molecular information from the rest of the cell which reports stimuli it is receiving from its outer membrane to the nucleus. There is a hierarchy of control I'm trying to get you to recognize. You are lumping and I am splitting tp follow the lines of control.-> dhw: The authors seem to take it for granted that once there are new opportunities, organisms will simply turn themselves into new species. We're not expected to ask how. Random mutations don't fit in, since the link with environmental changes can hardly be called random, but plasticity isn't much use unless there's some sort of intelligent mechanism to mould it. However, on the plus side I would interpret the above findings as support for the hypothesis that even the Cambrian can be explained by a change in the environment offering new opportunities for inventive mechanisms to cooperate in producing new forms of life.-Yes, intelligence is needed. Did you read the other part of the reference in which old-time Darwinists are agast at their proposal and they almost fully reject it? And you bring up the subject of environmental change. Perhaps evolution is simply a method of overcoming vast changes in nature. What was present on Earth 3.7 byo is not today's Earth. Vast changes. Perhaps life's responses, as an evolutionary mechanism, are totally driven by nature. Chicxulub and the dinos!

dhw: I was naturally disappointed that there was no mention of the crucial need for more research into what McClintock called knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged.-DAVID: Overintrepreting McClintock as usual. Shapiro, her acolyte, describes how the genome is changed by methylation, etc. The genome of the cells is in charge. Remember the genome is in the nucleus which has a semipermeable membrane and it receives molecular information from the rest of the cell which reports stimuli it is receiving from its outer membrane to the nucleus. There is a hierarchy of control I'm trying to get you to recognize. You are lumping and I am splitting tp follow the lines of control.-There is no interpretation let alone overinterpretation here. I am simply quoting McClintock, who used the term cell, whereas presumably you want her to use the term genome. Yes, there is a hierarchy, yes the brain is in control of the cell, but when someone says humans are inventive, have knowledge of themselves, and utilize their knowledge, we don't protest and say the brain is in charge, there is a hierarchy of control, and therefore you can't say humans are inventive, you must say human brains are inventive. I have recognized the hierarchy of control. When I first suggested that cells may have an intelligent, autonomous, inventive mechanism which was the equivalent of the brain, I was aware of the fact that this mechanism would direct operations. It must be about eighteen months ago that I even drew your attention to the work of Guenter Albrecht-Buehler, who said that the centrosome was the control centre or brain of the cell, but in those days you were still insisting that the cell was an automaton with no brain of its own. You may be splitting to follow the lines of control. You are also splitting hairs and, to mix metaphors, flogging dead horses. Time to move on. DAVID: Yes, intelligence is needed. Did you read the other part of the reference in which old-time Darwinists are agast at their proposal and they almost fully reject it? And you bring up the subject of environmental change. Perhaps evolution is simply a method of overcoming vast changes in nature. What was present on Earth 3.7 byo is not today's Earth. Vast changes. Perhaps life's responses, as an evolutionary mechanism, are totally driven by nature. Chicxulub and the dinos!-Atheistic Darwinists will always cling to randomness and will be aghast at any suggestion of intelligence, just as some theistic Darwinists will always cling to their version of divine purpose and will be aghast at any suggestion that their God might not have been in complete control of evolution. But I don't think evolution is a matter solely of overcoming vast changes in Nature. The whole point of an inventive mechanism would be that it can exploit the opportunities offered by change, so broadly speaking I'd say evolution is a mixture of overcoming changes (adaptation) and making use of them to invent new forms of life (innovation).

dhw: I have recognized the hierarchy of control. When I first suggested that cells may have an intelligent, autonomous, inventive mechanism which was the equivalent of the brain, I was aware of the fact that this mechanism would direct operations. Time to move on.-Fine-> dhw: Atheistic Darwinists will always cling to randomness and will be aghast at any suggestion of intelligence, just as some theistic Darwinists will always cling to their version of divine purpose and will be aghast at any suggestion that their God might not have been in complete control of evolution. But I don't think evolution is a matter solely of overcoming vast changes in Nature. The whole point of an inventive mechanism would be that it can exploit the opportunities offered by change, so broadly speaking I'd say evolution is a mixture of overcoming changes (adaptation) and making use of them to invent new forms of life (innovation).-Great summary.

dhw: You are putting across to me what I have been trying to put across to you ever since this discussion began. You have now agreed that there is such a mechanism and have placed it in the genome, which is fine with me (so long as we don't lose sight of the fact that the genome is part of the cell), because I am only concerned with the existence of the mechanism, not with its location...... And if the solution is not preprogrammed, the genome has the same autonomy as the bridge builder.-It seems we are in agreement, now that we are discussing the IM as part of the genome. > > DAVID: The cell recognizes stimuli and simply reports them to the genome. Just how 'cognitive' is that? I still view the genome as the brains of the cell. > > dhw: As I have said many times, I am quite happy with this. In the past you have vehemently denied that the cell had the equivalent of a brain (my bold): You want your cell communities to gain intelligence from experience and then use that intelligence to make changes. Just where is any of that intelligence' stored? Cells don't have brains (as humans do)... -I view the DNA of a cell as a local control center, not a fully active 'brain' as we have. Remember that DNA from the zygote is very plastic and adapted to each cell for its particular function. What controls the IM is the totality of all the DNA in the whole organism in speciation.-> > DAVID: And the genomic solutions are semi-autonomous, as I have proposed. Remember I look at teleology not chance. -> dhw: As for teleology, Darwin chose survival as the purpose of evolution. Previously you have always insisted that its purpose was the production of humans, which ran counter to the higgledy-piggledy nature of the evolutionary bush.-It is not counter to a bush, if the IM is somewhat on its own in originating changes.-> dhw; Our discussion is not about chance v. design, since we are now debating the nature of the mechanism your God may have designed. -But it is. I am not bound to Dariwn's survival approach. i see design and teleology as Wallaace did, from the same evidence/ > > dhw: You are now talking in terms of the inventive mechanism creating as opposed to being preprogrammed. This is very much in line with Talbott's argument as well as my own.-> DAVID: Yes, that is what i've tried to find.-> > dhw: That is what I have been proposing to you throughout this discussion.-And I have gotten you into recognizing the central control in the many layers of the genome, some of which are still to be discovered. Note the discussion from the journal Nature I have put into our forum topics.

dhw: You are putting across to me what I have been trying to put across to you ever since this discussion began. You have now agreed that there is such a mechanism and have placed it in the genome, which is fine with me (so long as we don't lose sight of the fact that the genome is part of the cell), because I am only concerned with the existence of the mechanism, not with its location...... And if the solution is not preprogrammed, the genome has the same autonomy as the bridge builder.-DAVID: It seems we are in agreement, now that we are discussing the IM as part of the genome.-This is good news. May I also take it that you now accept inventive as meaning creating new things and performing new actions without being preprogrammed? If so, and still recognizing that my autonomous, intelligent, inventive mechanism is only a hypothesis, perhaps we can move on, and so with my fingers crossed I am opening a new thread on the subject of purpose. Just a couple of loose ends to tie up: DAVID: I view the DNA of a cell as a local control center, not a fully active 'brain' as we have. Remember that DNA from the zygote is very plastic and adapted to each cell for its particular function. What controls the IM is the totality of all the DNA in the whole organism in speciation.-I use the human brain as an analogy. That is why I was careful to say the equivalent of a brain. I was pleased to see you using the same analogy when you wrote I still view the genome as the brains of the cell. As regards totality, I have always been equally carefully to bracket cells and cell communities. Once cells had merged to create multicellularity, there had to be cooperation between them, and clearly that means all the cell communities that constitute the whole organism must integrate their many mechanisms. Once again we are in agreement. dhw: As for teleology, Darwin chose survival as the purpose of evolution. Previously you have always insisted that its purpose was the production of humans, which ran counter to the higgledy-piggledy nature of the evolutionary bush.-DAVID: It is not counter to a bush, if the IM is somewhat on its own in originating changes.-I will deal with this, and the Talbott section on fitness, under "Does evolution have a purpose?"

dhw: Once cells had merged to create multicellularity, there had to be cooperation between them, and clearly that means all the cell communities that constitute the whole organism must integrate their many mechanisms. Once again we are in agreement.-Not completely. I won't let you go back to cells integrating on their own. They are controlled by the genome of the multicellular organism and it manages their integration. Yes, each cell has genes, tailored for that cell, but there has to be central control with a centrally controlling genome.

With tongue, slightly in cheek, bugs can create adaptations to bug killers. Lots of resistence to chemical killers. New species, no! But lots of problems for us:-http://www.the-scientist.com//?articles.view/articleNo/41005/title/Sleep-Tight/

dhw: Once cells had merged to create multicellularity, there had to be cooperation between them, and clearly that means all the cell communities that constitute the whole organism must integrate their many mechanisms. Once again we are in agreement.-DAVID: Not completely. I won't let you go back to cells integrating on their own. They are controlled by the genome of the multicellular organism and it manages their integration. Yes, each cell has genes, tailored for that cell, but there has to be central control with a centrally controlling genome.-Of course there does. After initially refusing to countenance the idea that cells/cell communities might have the equivalent of a brain, you decided that they do have one after all and it is situated in the genome. The brain controls the cell/cell community, but it would be as impossible for cells/cell communities to integrate without their brains as for the brains to integrate without the rest of their cells. Would it really make sense to say that genomes merged to create multigenomity and genome communities constitute the whole organism and must integrate their many mechanisms? Please can we move on. (See also under ...another outside discussion.) -May I once again ask if you now accept that inventive means creating new things and performing new actions without being preprogrammed?

dhw: May I once again ask if you now accept that inventive means creating new things and performing new actions without being preprogrammed?-I do with guidelines. Semiautonomous means new things and new actions. Let us move on.

dhw: May I once again ask if you now accept that inventive means creating new things and performing new actions without being preprogrammed?-DAVID: I do with guidelines. Semiautonomous means new things and new actions. Let us move on.-Guidelines, yes (i.e. what the mechanism can and can't do in the given circumstances). Semiautonomous, no. Inventive = new things and new actions.

DAVID: I do with guidelines. Semiautonomous means new things and new actions. Let us move on. > > dhw: Guidelines, yes (i.e. what the mechanism can and can't do in the given circumstances). Semiautonomous, no. Inventive = new things and new actions.-We are quibbling over a definition:-http://www.oxforddictionaries.com/us/definition/english/semi-autonomous-Evolution is a continuum and the guidelines fix some limits as contrasted to totally free inventiveness. Constrained invention is the way I look at it.

dhw: May I once again ask if you now accept that inventive means creating new things and performing new actions without being programmed?-DAVID: I do with guidelines. Semiautonomous means new things and new actions. Let us move on.-dhw: Guidelines, yes (i.e. what the mechanism can and can't do in the given circumstances). Semiautonomous, no. Inventive = new things and new actions.-DAVID: We are quibbling over a definition:http://www.oxforddictionaries.com/us/definition/english/semi-autonomous Evolution is a continuum and the guidelines fix some limits as contrasted to totally free inventiveness. Constrained invention is the way I look at it.-I asked if you accepted my definition of inventive, and you wrote that semiautonomous means new things and new actions! You have changed the subject and referred me to a definition of semiautonomous (= acting independently to some degree). However, let's deal with this point too. We have agreed that evolution is a continuum, and we have agreed that ALL inventiveness is subject to limitations - not even your bridge-builder can do what he cannot do, and if his bridge is to be successful, it has to cope with conditions that are beyond his control. There is nothing in this world that is totally free from such constraints and guidelines, and so according to you there is no such thing as autonomy. None of this has anything to do with my original question, which was necessary in view of your earlier revised definition of the inventive mechanism as a set of pre-programmed instructions for a new species (which of course took you straight back to your 3.7-billion-year all-inclusive computer programme). So let me repeat my question: Do you agree that the word inventive in the term inventive mechanism means creating new things and performing new actions without being preprogrammed

Dhw: We have agreed that evolution is a continuum, and we have agreed that ALL inventiveness is subject to limitations - not even your bridge-builder can do what he cannot do, and if his bridge is to be successful, it has to cope with conditions that are beyond his control. There is nothing in this world that is totally free from such constraints and guidelines, and so according to you there is no such thing as autonomy.-As long as we are sticking to the IM, there are limitations. I agree. > > dhw: Do you agree that the word inventive in the term inventive mechanism means creating new things and performing new actions without being preprogrammed-As our concept has developed, yes. It offers a way out of my total pre-programming and dabbling dilemma.

Dhw: We have agreed that evolution is a continuum, and we have agreed that ALL inventiveness is subject to limitations - not even your bridge-builder can do what he cannot do, and if his bridge is to be successful, it has to cope with conditions that are beyond his control. There is nothing in this world that is totally free from such constraints and guidelines, and so according to you there is no such thing as autonomy. -DAVID: As long as we are sticking to the IM, there are limitations. I agree. -dhw: Do you agree that the word inventive in the term inventive mechanism means creating new things and performing new actions without being preprogrammed DAVID: As our concept has developed, yes. It offers a way out of my total pre-programming and dabbling dilemma.-Thank you. Then we can examine your dilemma in more detail on the "purpose" thread.

Trying to find a way to get to multicellularity, a tiny step:-"Beginning with single cells, the researchers show how simple cooperating groups of bacteria can reproduce via a life cycle that incorporates 'cheating' cells as a primitive germ line.-Cheats are cells that do not contribute to the integrity of the group, but still take advantage of the benefits of being part of a collective. An over abundance of cheating cells can cause the group to collapse."- Read more at: http://phys.org/news/2014-11-multicellular-life.html#jCp

Not sure what to make of this. The article is interesting, but it seems like a lot is being assumed, something are being said that aren't, and some things aren't being said that are.-"When cheats were embraced we discovered something surprising," Dr Rose says. "Evolution saw a new kind of entitya group comprised of two different cell states: cheating and cooperating cells. Evolution couldn't focus on just one state or the other; for lineages to persist, evolution had to see both typesit had to work on a developmental programme."-"Little is known", explains Professor Rainey, "but life cycles involving at least two different states are almost universal in the world of multicellular organisms. I suspect that this is because multiphase life cycles generate an organismal configuration that delivers to natural selection a machine-like entity with which it can really work.-One interesting there is, that is slightly off-topic, is the personification of Evolution being used here, as well as the contradictory assumptions. I also find the mention of links to Cancer interesting, because that would mean that this effect is overall deleterious to the organisms over time.

--
What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.

DAVID: Trying to find a way to get to multicellularity, a tiny step: "Beginning with single cells, the researchers show how simple cooperating groups of bacteria can reproduce via a life cycle that incorporates 'cheating' cells as a primitive germ line. Read more at: -http://phys.org/news/2014-11-multicellular-life.html#jCp-QUOTE: "When cheats were embraced we discovered something surprising," Dr Rose says. "Evolution saw a new kind of entitya group comprised of two different cell states: cheating and cooperating cells. Evolution couldn't focus on just one state or the other; for lineages to persist, evolution had to see both typesit had to work on a developmental programme.""-TONY: One interesting there is, that is slightly off-topic, is the personification of Evolution being used here, as well as the contradictory assumptions. I also find the mention of links to Cancer interesting, because that would mean that this effect is overall deleterious to the organisms over time.-Like Tony, I'm not sure what to make of this, but I agree that the personification of evolution is a fudge. I'm grateful to David for the article and for putting it on the inventive mechanism thread. In the context of my hypothesis, it's the cells themselves that have to work on a developmental programme. If they fail to embrace the cheats, they will not survive. This may apply to cancer, but it doesn't mean that the cheats always win, so over time, when the cheats have been successfully embraced, the organism will flourish, as follows: QUOTE: "Dr Hammerschmidt explains: "When this happened, the groups became better adapted, but they did so at the expense of the individual cells that made up the groups. This might seem nonsensical, but it is precisely what is thought to happen during major evolutionary transitions: the higher (group) level subsumes the lower (cell) level, with the lower level eventually coming to work for the good of the collective. Nothing so remarkable happened when we performed the same experiment, but with a life cycle in which we got rid of cheats.""-In the context of the inventive mechanism (origin unknown, but let us for argument's sake assume God designed it), I see this as yet another instance of cells as sentient, cognitive beings that cooperate in order to form increasingly complex, smoothly functioning units. (I always think of the analogy with ants.) The unit will fail to function if the cheats dominate. There is a wonderful moral and social parallel to be drawn here! But I don't know what to make of that final sentence. Could it be that instead of cheats, these are rebels. Too much rebellion leads to disorder, but rebels bring new ideas. And so maybe during major evolutionary transitions (which we have never witnessed) it's not a matter of higher subsuming lower, but of existing systems adopting new ideas for the good of the collective. In other words, the rebels are not always the baddies, and their inventive mechanism takes beneficial control of the organism's genome.

dhw: Like Tony, I'm not sure what to make of this, but I agree that the personification of evolution is a fudge. I'm grateful to David for the article and for putting it on the inventive mechanism thread. In the context of my hypothesis, it's the cells themselves that have to work on a developmental programme. If they fail to embrace the cheats, they will not survive.-Thank you for the compliment.The article demonstrates to me the great difficulty in understanding the advent of multicellularity.

Tony: Not sure what to make of this. The article is interesting, but it seems like a lot is being assumed, something are being said that aren't, and some things aren't being said that are. > One interesting there is, that is slightly off-topic, is the personification of Evolution being used here, as well as the contradictory assumptions. I also find the mention of links to Cancer interesting, because that would mean that this effect is overall deleterious to the organisms over time.-We cannot relive history, and they are just as far from understanding multicellularity as they every were. This is hunt and peck research hoping to stumble into an insight.

A discussion of theoretical possibilities, which doesn't mean we are any closer to an answer:-http://phys.org/news/2015-02-multicellular-life-evolve.html

Here is an example of bacteria working together in a multicellular way, actually repairing each other:-http://www.sciencedaily.com/releases/2015/05/150521133738.htm-"A University of Wyoming faculty member led a research team that discovered a certain type of soil bacteria can use their social behavior of outer membrane exchange (OME) to repair damaged cells and improve the fitness of the bacteria population as a whole.-"Daniel Wall, a UW associate professor in the Department of Molecular Biology, and others were able to show that damaged sustained by the outer membrane (OM) of a myxobacteria cell population was repaired by a healthy population using the process of OME. The research revealed that these social organisms benefit from group behavior that endows favorable fitness consequences among kin cells.-"'During nutrient depletion, myxobacteria cooperate to build a macroscopic structure called a fruiting body," Vassallo says. "The structure resembles a tree or mushroom in appearance."-"A fruiting body is essentially a multicellular organism that produces dormant spores that are resistant to environmental stresses.-"These myxobacterial cells, in their native environments, must cope with factors that compromise the integrity of the cell, Wall says. Rather than looking out only for themselves like other bacterial species, the individual myxobacteria cells band together as a social group to assist their kin that become damaged.-"'Myxobacteria are unusual for bacteria in that they have a true multicellular life," Wall says. "Researchers are interested in how the evolutionary transition occurred toward multi-cellularity; that is, how cooperation develops and single cells are not just interested in themselves. The Darwinian view is that each individual is out for themselves; 'survival of the fittest.'"-"'When environmental cells come together, they compete with each other," Wall continues. "With OME, we think it allows myxobacteria cells to transition from a heterogeneous single cellular life to a more harmonious multicellular life.'"

tis article is technically showing multicellularity in that groups of similar cells are clumped together, but they all do the same thing, none have differing function which is the definition of true multicellularity:-http://www.newscientist.com/article/dn27762-one-gene-may-drive-leap-from-single-cell-to-multicellular-life.html#.VZYNPGDbK1u-"This time, instead of daughter cells sticking together in an amorphous blob as they did under selection for settling, the algae formed predation-resistant, spherical units of four, eight or 16 cells that look almost identical to related species of algae that are naturally multicellular.-"''It's likely that what we've seen in the predation experiments recapitulates some of the early steps of evolution," says Herron.-"Neither Ratcliff's yeast nor Herron's algae has unequivocally crossed the critical threshold to multicellularity, which would require cells to divide labour between them, says Richard Michod of the University of Arizona in Tucson.-"But the experiments are an important step along that road. "They're opening up new avenues for approaching this question," he says."

A giant virus has genes that make histones. Viruses don't have histones. Why?:

https://www.sciencedaily.com/releases/2018/02/180207102751.htm

"In the study, Erives analyzed the genome of a virus family called Marseilleviridae and found it shares a similar set of genes, called core histones, with eukaryotes.

"That places Marseilleviridae, and perhaps its viral relatives, somewhere along eukaryotes' evolutionary journey.

"'We now know that eukaryotes are more closely related to viruses," says Erives, "and the reason is because they share core histones, which are fundamental to eukaryotes."

"Core histones are packagers, like professional gift-wrappers. They're proteins that, in humans, coil DNA in the chromosomes so vital genetic information is compact and protected. Prokaryotes don't have core histones, so somehow, somewhere, eukaryotes picked them up.

"Viruses like Marseilleviridae may have been the source. (An alternative and equally fascinating explanation is that an ancestor of the Marseilleviridae picked up this gene from a proto-eukaryotic organism, an intermediate between prokaryotes and eukaryotes.)

***

"As he analyzed Marseilleviridae's genomes in data provided by the National Institutes of Health, Erives noticed the giant virus family encodes the eukaryotic core histones H2B-H2A and H3-H4. Unlike eukaryotes, however, these Marseilleviridae core histones are primitively fused as dimer proteins.

"'So, when I saw this, it was wild," Erives says. "No one has ever seen a virus with histones."

"Moreover, he realized Marseilleviridae "did not get these genes from any one eukaryotic lineage living, but rather from some ancestor who was proto-eukaryotic -- that is, on its way to becoming a eukaryote. Until now, no 'organism' was known to have core histone genes besides eukaryotic cells," he says.

"The discovery begs a larger question about the role giant viruses have played in the evolution of all life on Earth. Erives likens giant viruses to vines spreading out into the cellular tree of life -- sampling here, borrowing there, and sharing genetic material among the branches of archaea, bacteria, and eukaryotes.

"'Giant viruses have genes that no one has seen before," he says. "They're conserved. They've been using them for something, and for a very long time. Why not use them now to peer into the past?'"

Comment: There is a theory that viruses have helped direct evolution. Is horizontal gene transfer a mechanism here? See this entry from our past:

https://www.agnosticweb.com/index.php?id=20373

DAVID: Here is a study on tilapia sub-species that is an attempt to explain variations:-http://phys.org/news/2014-09-cichlid-fish-genome-story-evolution.html-Involving gene duplications and microRNA activities.-Thank you as always for these fascinating articles. QUOTE: Analysis of the genomes revealed a remarkably high rate of gene duplication across all species. Gene duplication occurs when cellular hardware creates two copies of a gene. These events are an essential source of genetic novelty leading to evolutionary innovation. One copy, freed from selection, could adapt to a new function, or be turned off or even serve as a "spare" if the original gene is damaged. Alternatively, the original function can be divided, giving different roles to each copy of the gene. -Although clearly the cichlid is still a cichlid, and we are talking more of adaptation than innovation here, it's worth noting that evolutionary innovation is already being spoken of as a result of this process.-Here is another quote: Fernald said that scientists recognize that it might not be a single gene making this type of decision, but rather a constellation of genes - or microRNAs or other factors - that, when expressed together, can control a behaviour.-This is the sort of cooperative decision-making that must also be involved in innovation. Even if we restrict ourselves to the behaviour of these fish, there can be little doubt that it argues intelligence, and so once more you are faced with your dilemma. Did your God preprogramme this behaviour 3.7 billion years ago? Did he dabble with the lakes and/or with fishy automatons? Or is there a mechanism within the genome of these organisms which takes its own autonomous decisions in accordance with the needs and opportunities presented by the environment?

dhw: This is the sort of cooperative decision-making that must also be involved in innovation. Even if we restrict ourselves to the behaviour of these fish, there can be little doubt that it argues intelligence, and so once more you are faced with your dilemma. Did your God preprogramme this behaviour 3.7 billion years ago? Did he dabble with the lakes and/or with fishy automatons? Or is there a mechanism within the genome of these organisms which takes its own autonomous decisions in accordance with the needs and opportunities presented by the environment?-There is no doubt evolution proceeds through intelligent information. Our debate for the past months has not solved the problems presented by your question. But we do recognize tht life must be run by a very complex computerized program as represented by DNA and all of its tricks. Frances Crick's declaration that three bases must code for each amino acid, is only the beginning of the story, and we are only a tiny way through the study of how it all works.

Blind fish compared to same species with sight. Fish in caves lose sight and circadian rhythms:-http://www.the-scientist.com//?articles.view/articleNo/41088/title/Cave-dwelling-Fish-Fail-to-Keep-Time/

Spetner's new book describes something I have forgotten. Nylon is new to the world, but there are bacteria that can metabolize nutrients from it after about 20 years from the appearance of nylon. There are at least two species of bacteria that can do it. It involves the development of two enzymes, the same ones in both species. Not new species but new metabolism. IM or did God know nylon was coming? This is I feel an epigenetic IM.

DAVID: Spetner's new book describes something I have forgotten. Nylon is new to the world, but there are bacteria that can metabolize nutrients from it after about 20 years from the appearance of nylon. There are at least two species of bacteria that can do it. It involves the development of two enzymes, the same ones in both species. Not new species but new metabolism. IM or did God know nylon was coming? This is I feel an epigenetic IM.-A clear example of an organism altering parts of itself in order to exploit a change in its environment. As you say, the species remains the same - this is a minor adaptation. But if organisms have the potential to change their own metabolism, the question arises as to how far they can carry the process. No-one has ever observed the formation of a new species, and so all explanations are hypothetical. In this case, however, we know from observation that organisms have a mechanism that enables them to make changes in themselves. We should therefore accept the possibility that in conditions unknown to us that same mechanism might be capable of more fundamental changes.

DAVID: Spetner's new book describes something I have forgotten. Nylon is new to the world, but there are bacteria that can metabolize nutrients from it after about 20 years from the appearance of nylon. -> dhw: A clear example of an organism altering parts of itself in order to exploit a change in its environment. As you say, the species remains the same - this is a minor adaptation. .... We should therefore accept the possibility that in conditions unknown to us that same mechanism might be capable of more fundamental changes.-I certainly agree that epigenetic changes we know about so far suggest that more fundamental changes are possible through an epigenetic IM. But you have missed one point: the two separate bacterial types invented the same two enzymes! This is evidence of my proposed 'patterns' approach to evolution, supported by Tony. And strongly suggests my thought that the IM (epigenetic) is given guidelines to follow from an earlier time in evolution. Enzymes are big bulky molecules, with thousands of amino acids. If it took only 20 years there has to be guidance, immediate or from past instruction/ information.

Tony:I am going to go out on a limb and say that David doesn't like my reasoning for two reasons. A) David is a trained scientist, B) Though a theist, David is not (to my knowledge) a Christian, and prefers his God a little less "human" (and I use the term VERY loosely). Whereas I see God as an individual, powerful though he is, with thoughts and feelings similar in kind with ours, David sees him(it) without any personification.-Tony and I start from two very different points, as he beautifully explains, and we logically reach different conclusions. With my Jewish background, I see a single God-head. I have tried to work backward from the scientific discoveries I've read and interpreted to try and reach reasonable explanations for me. I avoid the Bibles, both of them. Genesis was thought to have six authors and there are four Gospels. What is included in both Bibles was chosen by committies from available material, some writings left out. Bible by committee does not give me innerrancy. > > Tony: This would greatly reduce the amount of time and effort needed to create each species. Humans can mass produce things once we have the right recipe for them, even things that vary slightly from one instance of them to the next. When you "zoom" out far enough, you can see that this mass production is sort of what has happened. Designing the rules that govern things and then setting them in motion takes far less time and energy than hand-crafting each and every particle.-This summary of Tony's computer approach makes sense.

DAVID: True, but my problem with your theory is that you are giving properties to cells that I know they do not have and are not capable of using. > > dhw: You do not know this. You believe it,-Yes I DO know it. I know the function of cells and I know how they operate and I am fully aware of cells capabilities. You are one inventing stuff about cells that cannot exist. I am the one who has exposed you to the cognitive functions of cells. Believe me, it is minimal. I react with incredulity when I see a functioning kidney in action. I don't believe you come close to understanding how complex that it. It simply had to be planned. There is no way it formed bit by bit, following error after error. The Cambrian tells us that. Tony tells you that. My idea of a creative mechanism, if you noted, included the idea that plans are there, ready for the using when indicated. Creation of something new happens when necessary as evolution unfolds. I view your theory as wishful thinking to get around the idea that the genome is a computer program, and the only two choices we know to explain evolution are chance or design. Asking the cells to design themselves into new organs when they have no ability to plan is, in my view, a third way that cannot exist, in any reasonable theory.

DAVID: True, but my problem with your theory is that you are giving properties to cells that I know they do not have and are not capable of using. dhw: You do not know this. You believe it.-DAVID: Yes I DO know it. I know the function of cells and I know how they operate and I am fully aware of cells capabilities. You are one inventing stuff about cells that cannot exist. My idea of a creative mechanism, if you noted, included the idea that plans are there, ready for the using when indicated. Creation of something new happens when necessary as evolution unfolds. I view your theory as wishful thinking to get around the idea that the genome is a computer program, and the only two choices we know to explain evolution are chance or design. Asking the cells to design themselves into new organs when they have no ability to plan is, in my view, a third way that cannot exist, in any reasonable theory.-I have indeed noted the fact that according to your reasonable theory (which bothered you on 20 August but stopped bothering you when you decided to call preprogramming an inventive mechanism, in a volte face that involved distorting the meaning of inventive), your God installed a programme in the first living cells that passed down plans for every single innovation and natural wonder that evolution has produced for the last 3.7 billion years. And this programme also allows for every single variation in environmental conditions. You are confident that this programme will be found in the genomic computer, where your God has hidden it. You dismiss the idea of your God inventing - and hiding - a mechanism that can do its own inventing (a bit like the mechanism he invented for humans, and other animals). I wonder how one can tell the difference between cells that have organized themselves by cooperation and cells that have followed a given plan. It's like ants, which for all the world seem to be thinking as they plan their homes and their strategies and their responses to changing environments. But you know they are not thinking. They are obeying a programme God prepared for them 3.7 billion years ago. You also prefer this to your God dabbling, although your fellow theist Tony prefers the dabbling theory for separate species because, unlike you, he doesn't believe in progressive evolution through innovation. All three hypotheses exclude chance. I hope this is a fair summary!

dhw:Firstly, I don't think you should use inventive of a mechanism that invents nothing and merely carries out pre-planned instructions. Preplanning and preprogramming are far clearer.-Fair enough. I said I was thinking out loud. I should probably have used the term "creative mechanism" with the implication taht it carries background plans in it. > > dhw: Therefore there are gaps in our knowledge, and your theory depends just as much as mine on speculation as to what lies in those gaps.-True, but my problem with your theory is that you are giving properties to cells taht I know they do not have and are not capable of using. See my comment about your 'thinking' cells below.- > dhw: But other forms of life, including plants and bacteria, do their own thinking, and if they didn't, they wouldn't survive. -You are equating the ability to react with "thought".We find only minimal reflective thinking in other manmmals and now you want to put it into amoeba? > > DAVID: It is very apparent to me (and Tony) that speciation requires the input of new information in the genome. Either the information is already there, ready to be tapped when required by environmental changes, or there is directed input. I favor the former. > > dhw: This is your preprogramming versus your dabbling. ..... Of course we shall never find those first computers,-You have sidestepped the issue of is the genome really a computer or not. Tony and I say it is. It is programmed. It required information to be in the code of the program. You have said roughly, your theory can't work if the genome is a computer.-> DAVID: As I see it, your theory requires itty-bitty, which has never been in the fossil record. Remember, I started as an agnostic. There are reasons why I am a theist, and this is a major one. > > My theory does not require itty-bitty. -Yes, it does. Tony explains it well today.-> dhw; Your two theories (preprogramming and dabbling) seem to me to depend on our finding something a few million degrees beyond what is now known. Remember, I started as a theist, and then an atheist. There are reasons why I am an agnostic, and this is a major one. -And I am not an agnostic because the genome requires information for a quaternary digital code, far beyond human invention, among other thoughts you have seen of mine.

I've presented horizontal gene transfer in bacteria as a basic life evolution pattern obviously present at the single-cell level. Now more evidence is appearing for gene transfer working from single cell to eukaryotes:-http://newsbeat.washington.edu/story/animals-steal-defenses-bacteria-" When we started digging into genome databases, we were surprised to find that toxin genes we thought were present only in bacteria were also in several animals, explained co-author Matt Daugherty, a postdoctoral fellow in the Malik lab. We immediately started wondering why they were there. "Their analyses revealed that these genes had jumped from bacteria into animals. These genes had become permanently incorporated into the genomes of these animals through a process known as horizontal gene transfer. While such transfer events are common between microbes, very few genes have been reported to jump from bacteria to more complex organisms."

DAVID: I've presented horizontal gene transfer in bacteria as a basic life evolution pattern obviously present at the single-cell level. Now more evidence is appearing for gene transfer working from single cell to eukaryotes:-http://newsbeat.washington.edu/story/animals-steal-defenses-bacteria- When we started digging into genome databases, we were surprised to find that toxin genes we thought were present only in bacteria were also in several animals, explained co-author Matt Daugherty, a postdoctoral fellow in the Malik lab. We immediately started wondering why they were there.-"Their analyses revealed that these genes had jumped from bacteria into animals. These genes had become permanently incorporated into the genomes of these animals through a process known as horizontal gene transfer. While such transfer events are common between microbes, very few genes have been reported to jump from bacteria to more complex organisms."-Thank you for this illustration of how, by extension, an autonomous inventive mechanism might work. I'm reminded of an article you recommended earlier on this thread by Stephen L. Talbott. He points out, for instance, that organisms are masterful participants in, and revisers of, their own genomes; that the organism responds intelligently, and in accord with its own purposes, to whatever it encounters in its environment, including the environment of its own body; that there is a cooperative fusion of distinct microorganisms, a process requiring an almost unimaginable degree of intricate coordination among previously independent life processes; and he quotes Barbara McClintock's 1983 Nobel address, in which she called for more research into the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged, to which he adds that subsequent research has shown how far-seeing she was.

dhw: I'm reminded of an article you recommended earlier on this thread by Stephen L. Talbott. He points out, for instance, that organisms are masterful participants in, and revisers of, their own genomes; -Talbott's conclusions need to be reviewed:- "it is startling to realize that the entire brief for demoting human beings, and organisms in general, to meaningless scraps of molecular machinery  a demotion that fuels the long-running science-religion wars and that, as shocking revelation, supposedly stands on a par with Copernicus's heliocentric proposal  rests on the vague conjunction of two scarcely creditable concepts: the randomness of mutations and the fitness of organisms. And, strangely, this shocking revelation has been sold to us in the context of a descriptive biological literature that, from the molecular level on up, remains almost nothing but a documentation of the meaningfully organized, goal-directed stories of living creatures.-"Here, then, is what the advocates of evolutionary mindlessness and meaninglessness would have us overlook. We must overlook, first of all, the fact that organisms are masterful participants in, and revisers of, their own genomes, taking a leading position in the most intricate, subtle, and intentional genomic dance one could possibly imagine. And then we must overlook the way the organism responds intelligently, and in accord with its own purposes, to whatever it encounters in its environment, including the environment of its own body, and including what we may prefer to view as accidents. Then, too, we are asked to ignore not only the living, reproducing creatures whose intensely directed lives provide the only basis we have ever known for the dynamic processes of evolution, but also all the meaning of the larger environment in which these creatures participate  an environment compounded of all the infinitely complex ecological interactions that play out in significant balances, imbalances, competition, cooperation, symbioses, and all the rest, yielding the marvelously varied and interwoven living communities we find in savannah and rainforest, desert and meadow, stream and ocean, mountain and valley. And then, finally, we must be sure to pay no heed to the fact that the fitness, against which we have assumed our notion of randomness could be defined, is one of the most obscure, ill-formed concepts in all of science."-"This something random looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a Randomness of the gaps, demanding an extraordinarily blind faith. At the very least, we have a right to ask, Can you be a little more explicit here? A faith that fills the ever-shrinking gaps in our knowledge of the organism with a potent meaninglessness capable of transforming everything else into an illusion is a faith that could benefit from some minimal grounding. Otherwise, we can hardly avoid suspecting that the importance of randomness in the minds of the faithful is due to its being the only presumed scrap of a weapon in a compulsive struggle to deny all the obvious meaning of our lives."-http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness-He is crying for a recognition of purpose.

dhw: I'm reminded of an article you recommended earlier on this thread by Stephen L. Talbott. He points out, for instance, that organisms are masterful participants in, and revisers of, their own genomes... DAVID: Talbott's conclusions need to be reviewed:-QUOTE: "it is startling to realize that the entire brief for demoting human beings, and organisms in general, to meaningless scraps of molecular machinery  a demotion that fuels the long-running science-religion wars and that, as shocking revelation, supposedly stands on a par with Copernicus's heliocentric proposal  rests on the vague conjunction of two scarcely creditable concepts: the randomness of mutations and the fitness of organisms... etc.-Do by all means let us review Talbott's conclusions, but let us bear in mind that our subject is whether or not evolution is driven by an autonomous inventive mechanism within the cell (to be more precise, within the genome). You and I have long since, and ad nauseam, dismissed the theory of random mutations. Fitness is a different subject which we needn't dwell on here as I'm sure we both agree with Talbott. The rest of this conclusion is summed up by your own comment: He is crying for a recognition of purpose. Yes he is, but his purpose has absolutely nothing in common with yours, which I will sum up as being that God preprogrammed every innovation and complex lifestyle 3.7 billion years ago in order to create and provide for human beings, and the brain in the genome is capable of nothing more than minor adaptations. You have conveniently overlooked a number of Talbott's statements, as well as those I quoted yesterday concerning the intelligence, cooperation and control exercised by microorganisms (cells). Here are some more extracts from the essay you recommended so highly: Quote: "Overlooking all this, we are supposed to see  somewhere  blind, mindless, random, purposeless automatisms at the ultimate explanatory root of all genetic variation leading to evolutionary change."-Perhaps you would like to take this as meaning that automatisms are governed by God's purpose and so are not random, but Talbott says that current research endorses McClintock's views concerning the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a thoughtful' manner when challenged. They are therefore NOT automatons in his opinion, and they do not merely implement God's programmes. If you still think Talbott's arguments support yours, please read again this passage, which we discussed last time we dealt with his essay: QUOTE: Although the word has its legitimate uses, you will not find me speaking of design, simply because  as I've made abundantly clear in previous articles  organisms cannot be understood as having been designed, machine-like, whether by an engineer-God or a Blind Watchmaker elevated to god-like status. If organisms participate in a higher life, it is a participation that works from within  at a deep level the ancients recognized as that of the logos informing all things. It is a sharing of the springs of life and being, not a mere receptivity to some sort of external mechanical tinkering modeled anthropocentrically on human engineering.-He goes much further than I would by actually rejecting the God hypothesis, but in the context even you can hardly avoid linking a participation that works from within to an autonomous inventive mechanism (as opposed to a mechanical automaton obeying God's instructions). It in fact ties in neatly with panpsychism, but that is another subject: we are dealing with the mechanisms that drive evolution, and not with their origin. Here is another passage that contradicts your own view just as emphatically as it contradicts Dawkins and Dennett:-QUOTE: Where, then, do we find dumb, lifeless mechanisms blindly engendering new life forms? Where do we see anything other than the elaborate, interwoven, overwhelmingly meaningful activity of living beings, playing out at every level, from the molecular to the ecological?-Margulis, McClintock, Shapiro, Albrecht-Buehler also tell you that cells are living, sentient, cognitive, intelligent beings. Talbott clearly agrees and is proposing that these qualities have combined at all levels to deliberately drive evolution onwards by producing new life forms. Of course there is a purpose behind their deliberate actions - and we can see the fulfilment of that purpose when organisms survive and flourish.

I'm not going to quote your comments. I went back and looked at the entire essay. There are quotes that fit both sides of our issues. The essay reads like Nagel's Mind and Cosmos. Nagel doesn't understand where consciousness came from and wants a 'third way' theory so as not to have to espouse Theism. Talbott's essay is the same sort of philosophic ruminating. He starts with Dawkins and Dennett and poo-poos both of them for a form of mechanistic reductionism that doesn't define what we see in life. In so doing he raised many points that fit my thinking and many points that fit your thinking. Both he an Nagel walk a thought tightrope so as not to fall on either side of the debate. They both remind me of your thinking. To me it is cut and dried that there must be a God. I see only chance or design, as alternatives. I see only design as possible. It is interesting that I found Talbott through the Uncommon Descent website, which is the main ID website. They have reacted like I have. I can see why.

DAVID: I'm not going to quote your comments. I went back and looked at the entire essay. There are quotes that fit both sides of our issues. The essay reads like Nagel's Mind and Cosmos. Nagel doesn't understand where consciousness came from and wants a 'third way' theory so as not to have to espouse Theism. Talbott's essay is the same sort of philosophic ruminating. He starts with Dawkins and Dennett and poo-poos both of them for a form of mechanistic reductionism that doesn't define what we see in life. In so doing he raised many points that fit my thinking and many points that fit your thinking. Both he an Nagel walk a thought tightrope so as not to fall on either side of the debate. They both remind me of your thinking. To me it is cut and dried that there must be a God. I see only chance or design, as alternatives. I see only design as possible. It is interesting that I found Talbott through the Uncommon Descent website, which is the main ID website. They have reacted like I have. I can see why.-But our subject is NOT chance v. design. I began my post by asking you to bear in mind that our subject is whether or not evolution is driven by an autonomous inventive mechanism within the cell... and over and over again I have emphasized that the IM does not preclude design. Of course Talbott's attack on randomness can be used to support theism and design (though in his case not theistic design), and my own IM hypothesis also supports design (though different from yours) and can be viewed theistically. I have drawn your attention to passages in which Talbott quite explicitly puts the case for the autonomous intelligence of the cell, which he links to the creation of new life forms. You, by contrast, maintain that the cell is an automaton, and although you have conceded that the genome may contain an inventive mechanism, you insist that it can't invent anything (it's only capable of minor adaptations). Your own hypothesis is that from the very beginning God preprogrammed all the innovations and complex lifestyles that have punctuated evolution from bacteria to humans. THAT is our subject. So please find me a reference in Talbott that supports your preprogramming hypothesis as opposed to my intelligent mechanism hypothesis. Bet you can't. See also my post under Evidence for pattern development; mulling, and mull some more.

dhw: Your own hypothesis is that from the very beginning God preprogrammed all the innovations and complex lifestyles that have punctuated evolution from bacteria to humans. THAT is our subject. So please find me a reference in Talbott that supports your preprogramming hypothesis as opposed to my intelligent mechanism hypothesis. Bet you can't. See also my post under Evidence for pattern development; mulling, and mull some more.-I've said that I am not going to quote Talbott. His writing is verbose, but some of his opinionated quotes fall in line with my thinking and some with yours. He discusses beautifully the problems with the atheistic approach to Darwinism and he ascribes an inventive mechanism to evolved organisms, but it is a nebulous description. They seem to do it be he can't describe how. And that is because none of us know how it is done, or the limits in capability to do the job. Our debate is over the degree of modification. You thinks it is lots, and I think it is much more limited. I'm afraid we have to agree to disagree. There is no doubt epigenetic changes play a role in furthering evolution, but that is as far as Shapiro, the champion of epigenetics, can go. We are forced to wait for further research to clear up the issue if it can. To be precise: an epigenetic IM exists, its limits for invention are unknown.

dhw: Your own hypothesis is that from the very beginning God preprogrammed all the innovations and complex lifestyles that have punctuated evolution from bacteria to humans. THAT is our subject. So please find me a reference in Talbott that supports your preprogramming hypothesis as opposed to my intelligent mechanism hypothesis. Bet you can't. See also my post under Evidence for pattern development; mulling, and mull some more.-DAVID: I've said that I am not going to quote Talbott. His writing is verbose, but some of his opinionated quotes fall in line with my thinking and some with yours. He discusses beautifully the problems with the atheistic approach to Darwinism and he ascribes an inventive mechanism to evolved organisms, but it is a nebulous description. They seem to do it be he can't describe how. And that is because none of us know how it is done, or the limits in capability to do the job. Our debate is over the degree of modification. You thinks it is lots, and I think it is much more limited. I'm afraid we have to agree to disagree. There is no doubt epigenetic changes play a role in furthering evolution, but that is as far as Shapiro, the champion of epigenetics, can go. We are forced to wait for further research to clear up the issue if it can. To be precise: an epigenetic IM exists, its limits for invention are unknown.-I am almost happy with this response, in contrast to your response on the mulling thread! My plea to you all along has been for open-mindedness. Initially, you totally dismissed the concept of the intelligent cell, but you now recognize that there may well be an inventive mechanism within its genome. The great question is the degree of its autonomy. I do not think it IS lots; I think it MAY BE lots. If you put your cowboy six-shooter to my head, I will certainly opt for lots rather than your all-inclusive preprogramming of all innovations and complex lifestyles 3.7 billion years ago, but that is not the point. The limits for invention are unknown, so how can you as a scientist champion one theistic hypothesis and reject the other (remember, I have allowed for your God designing the IM), believing that your dilemma has been solved when this directly relevant and enormously important area of research remains so incomplete?

dhw: The great question is the degree of its autonomy. I do not think it IS lots; I think it MAY BE lots. If you put your cowboy six-shooter to my head, I will certainly opt for lots rather than your all-inclusive preprogramming of all innovations and complex lifestyles 3.7 billion years ago, but that is not the point. The limits for invention are unknown, so how can you as a scientist champion one theistic hypothesis and reject the other (remember, I have allowed for your God designing the IM), believing that your dilemma has been solved when this directly relevant and enormously important area of research remains so incomplete?-My response is simple as previously stated. How do you know the limits of God's ability to program in the beginning? I don't. Early life was complex to begin with. My dabbling problem has to do exactly with my estimate of his powers. Could He do it all from the first or did He have to dabble? With our discussion of an IM as a definite possibility and the Tony's step-wise pattern programming, I am of the opinion that God more than likely did it from the beginning with rare intervention, thereafter. If He was extremely purposeful evolution might have been more direct than it was to arrive at us. Therefore, that any intervention was minimal seems reasonable to me..

dhw: The great question is the degree of its autonomy. [...] The limits for invention are unknown, so how can you as a scientist champion one theistic hypothesis and reject the other, [...] believing that your dilemma has been solved when this directly relevant and enormously important area of research remains so incomplete?-DAVID: My response is simple as previously stated. How do you know the limits of God's ability to program in the beginning? I don't. Early life was complex to begin with. My dabbling problem has to do exactly with my estimate of his powers. -Not only do we not know the limits of God's powers, but also we do not know the limits of the IM, we do not know the reason why God (if he exists) created life in the first place - though we have both offered the hypothesis that he was bored - and we do not know how evolution was able to advance from single cell to the vast array of animals that include ourselves. Out of this great area of non-knowledge you extrapolate the conclusion that the inventive mechanism can't invent anything, that God's intention from the very beginning was to create humans, and that he preprogrammed every innovation from bacteria to humans from the start, right down to the monarch butterfly's itinerary (though it's not clear what that has to do with humans). I don't find this simple at all.-DAVID: Could He do it all from the first or did He have to dabble? With our discussion of an IM as a definite possibility and the Tony's step-wise pattern programming, I am of the opinion that God more than likely did it from the beginning with rare intervention, thereafter. If He was extremely purposeful evolution might have been more direct than it was to arrive at us. Therefore, that any intervention was minimal seems reasonable to me.-Extremely purposeful is a lovely expression. What does it mean? If God had really, really, really wanted to, he could have created humans more directly, but he only sort of wanted to? So maybe bits of the bush weren't planned? Maybe the IM sometimes did its own thing instead of obeying instructions? Careful - that means autonomy. Rare intervention and any intervention was minimal is a subtle step away from your statement (under DILEMMAS, 22 November at 01:16): I'm accepting the idea that God doesn't have to dabble. So now we have some dabbling after all. How minimal is minimal? Making a human brain, perhaps, since you insist that we are different in kind? Would that be minimal? The problem of environmental change remains unresolved - preprogrammed or left to chance? A suitable environment is not exactly irrelevant to the existence of humans, is it? (See more on the mulling thread.) No, I see nothing simple about your response. Simplistic might be a better term.

A marine microorganism appears to have changed its metabolic machinery to reduce stress by removing some enzymes. Enzymes are enormous molecules and take lots of energy to produce:

https://www.sciencedaily.com/releases/2016/11/161115150109.htm

"Researchers from David Karl's laboratory at the University of Hawai'i at Mānoa (UHM) and from Professor Jens Nielsen's laboratory at Chalmers University of Technology in Göteborg, Sweden, developed a computer model which takes into account hundreds of genes, chemical reactions, and compounds required for the survival of Prochlorococcus, the most abundant photosynthetic microbe on the planet. They found that Prochlorococcus has made extensive alterations to its metabolism as a way to reduce its dependence on phosphorus, an element that is essential and often growth-limiting in the ocean.

***

"Microbes are known to employ three basic strategies to compete for limiting elemental resources: cell quotas may be adjusted, stressed cells may synthesize molecules to make more efficient use of available resources, and cells may access alternatives or more costly sources of the nutrient.

"In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan Prochlorococcus thrives by adopting all three strategies and a fourth, previously unknown strategy.

"'By generating the first detailed model of metabolism for an ecologically important marine microbe, we found that Prochlorococcus has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, thus relieving intracellular demands"

***

"Prochlorococcus has an extremely minimal genome. If it were to lose the function of any one metabolic gene, its survival would be nearly a coin toss. To their surprise, Casey and co-authors discovered that the world's most abundant microbe has performed, through a process called "genome streamlining" -- the concerted loss of frivolous genes over evolutionary time -- a comprehensive re-design of the core metabolic pathways in response to the persistent limitation of phosphorus.

"'The dramatic and widespread change in the metabolic network is really a shock," said Casey. "However, we're seeing that these changes provide a substantial growth advantage for this ubiquitous microbe in phosphorus-limited regions of the ocean, so it seems that where there's a will there's a way."

***

"'We're interested in the underlying principles guiding metabolism and physiology in marine microbes, and that is going to require a deep understanding of not only the 1-dimensional genetic code, but also the 4-dimensional product it codes for," said Casey. "So we're looking to a systems-level approach to incorporate a great variety of physiological and 'omics studies all in one computational structure, with the hope that we can start to learn from the design and interactions of these complex systems.'"

Comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

I don’t quite know what went wrong yesterday, but for some reason, my replies did not get posted!

QUOTE: 'The dramatic and widespread change in the metabolic network is really a shock," said Casey. "However, we're seeing that these changes provide a substantial growth advantage for this ubiquitous microbe in phosphorus-limited regions of the ocean, so it seems that where there's a will there's a way."

David's comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount? Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.

David's comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

dhw: There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection?

I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless. Survival is not dog eat dog, but is the environment friendly enough for survival, the 'bad luck' theory? Is nature balanced or not?

dhw: Or the same old random mutations plus gradualism that you and I have long since agreed to discount? Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.

I think God gave unicellular organisms the ability to edit their DNA for adaptations to changes in environment, but not to the degree of actual speciation, in agreement with what Shapiro presents.

dhw: There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?

DAVID: I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless.

So which part of Darwin’s thesis is not supported by genetic modification?

dhw: Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.
DAVID: I think God gave unicellular organisms the ability to edit their DNA for adaptations to changes in environment, but not to the degree of actual speciation, in agreement with what Shapiro presents.

Yes, if Shapiro subscribed to the theistic version, he might say God gave cells the INTELLIGENCE to edit their DNA. (Remember, he believes in cellular intelligence.) We do not know whether that intelligence extends so far as to create the multicellular innovations that cause speciation. That is why it is a hypothesis.

DAVID: I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless.

dhw:So which part of Darwin’s thesis is not supported by genetic modification?

Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

DHW: So which part of Darwin’s thesis is not supported by genetic modification?

DAVID: Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

So...once more...which part of Darwin’s thesis is not supported by genetic modification?

DAVID’S comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

DHW: So which part of Darwin’s thesis is not supported by genetic modification?

DAVID: Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

dhw: So...once more...which part of Darwin’s thesis is not supported by genetic modification?

Darwin proposed itty bitty changes like breeders used. That was his thesis! No more. What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification

DAVID’S comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.
DHW: So which part of Darwin’s thesis is not supported by genetic modification?

DAVID: Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

dhw: So...once more...which part of Darwin’s thesis is not supported by genetic modification?
DAVID: Darwin proposed itty bitty changes like breeders used. That was his thesis! No more.

In my original post I asked what part of his thesis you were talking about: “Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?” So you are indeed back to flogging the dead horse of gradualism.

DAVID: What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification.

So Darwin’s thesis of common descent in fact IS supported by genetic modification. But how it happened is still up for grabs, though you and I agree that however it happened, it would not have been random or gradual. Shake hands on this one?

dhw: In my original post I asked what part of his thesis you were talking about: “Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?” So you are indeed back to flogging the dead horse of gradualism.

DAVID: What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification.

dhw:So Darwin’s thesis of common descent in fact IS supported by genetic modification. But how it happened is still up for grabs, though you and I agree that however it happened, it would not have been random or gradual. Shake hands on this one?

No gradualism and we do shake hands on evolution by common descent as Darwin's only real contribution.

Salmonella prove Shapiro's point:

https://phys.org/news/2021-01-salmonella-metabolite-reprogram-krebs-survival.html

"A team of researchers affiliated with several institutions in Israel has discovered the means by which salmonella bacteria use a metabolite to reprogram the Krebs cycle to promote their own survival. In their paper published in the journal Science, the group describes their study of the reaction of salmonella to the presence of succinate and what it revealed about the role succinate might play in bacterial infections in general.

***

"When bacteria enter the body, the immune system carries out a response aimed at killing them to prevent harm. Part of that response involves the activation of macrophages—phagocytic cells that attack and kill pathogens. Prior research has shown that they also produce chemicals that set off an inflammatory response to slow the spread of the pathogen. In this new effort, the researchers took a closer look at that process to better understand why this inflammatory response does not always occur during an infection.

"The researchers chose the bacteria salmonella as a pathogen because it is well understood. Their work involved watching what happened when salmonella entered the macrophages that were intent on killing it. They discovered that once inside the cell, the bacteria made their way to the parts involved in the Krebs cycle—the series of reactions inside certain cells that result in generation of cell energy during aerobic respiration.

"The researchers discovered that the bacteria reprogramed the Krebs cycle to make it behave in ways that enhanced its own chances of survival (such as increasing oxygen in intestinal epithelial cells, making it easier for the bacteria to replicate.) The researchers also discovered via RNA sequencing of both the macrophages and the bacteria that the bacteria activated this process when it sensed the presence of succinate, one of the metabolites produced by the macrophage to instigate an inflammatory response. The researchers suggest that other pathogens also likely sense the presence of succinate and use it to initiate their own survival mechanisms."

Comment: In this case the salmonella reprogram the Krebs cycle by altering DNA in the invaded cells!!! Not their own DNA, which Shapiro studied, but to me editing is editing..

Now a paper describes gene transfer to all branches of life:-http://www.the-scientist.com//?articles.view/articleNo/41555/title/Gene-Jumped-to-All-Three-Domains-of-Life/

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