Home » Intelligent Design » Designing Networks of Genes…..

Designing Networks of Genes…..

I just picked up this article at PhysOrg.com. The kinds of things that scientists are up to these days are quite interesting. Here’s a sample:

Researchers design and build networks of genes, splicing them into bacterial genomes to run specific tasks or manufacture desired molecules – a process akin to installing biological computer software. Though the field is rapidly advancing, the gene-based tools available to synthetic biologists remain limited.

I found the allusion to “installing computer software” quite compelling. Will these ‘synthetic biologists’ be the ones to settle for us the question of whether intelligence is present in the genome? This work is in the May 29th issue of Science, for those who have online access.

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36 Responses to Designing Networks of Genes…..

  1. The abstract (from DOI: 10.1126/science.1172005):

    Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.

    Personally, I don’t see how this kind of work would “settle for us the question of whether intelligence is present in the genome”.

  2. I don’t think it will settle that question either. Groups intentionally drawing analogies to software design will wind up with gene networks that look like human software. That is not going to tell us much about natural gene networks.

  3. I doubt it will settle the question. Though as our engineering capabilities continue to advance, it does seem to at the very least demonstrate the power of ‘intelligent design’ in general.

    If some day we’re able to create a universe in a laboratory (a la the proposals of Andrei Linde), would that count as evidence of intelligent design? What about if we were able to create a simulation of a universe?

  4. For the record… gene splicing is the agreed-upon physical mechanism by which the designer works, yes?

  5. To #4, Lenoxus: No, gene-splicing is not the agreed-upon physical mechanism.

    To #1,2, and 3:

    Is it possible, in the face of such outright manipulation of a genome, to deny that the genome contains real-life information?

    Second question: if it contains real-life information, whence did this arise?

    Third question: other than in the genome, where, in nature, do we find this type of information?

  6. From the abstract:

    “Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting.”

    Fourth question: if we can “program” cells using principles of modern computing, then this means that cells are similar in many respects to computers. Should we change Fred Hoyle’s famous remark about evolution to read that the likelihood that humans came about by evolution is as probable as a tornado passing through an electronics store and putting together a computer?

    If we can intelligently manipulate the genome to produce desired ends, like we would a designed instrument such as a computer, then what is the basis for saying that the genome is NOT designed?

    It’s around this kind of thinking that I’m suggesting that synthetic biologists might settle the question for us. That is, if they find more and more intricate ways to manipulate the genome it would seem that at some point the only rational thing to conclude is that the genome has been designed.

  7. Mr PaV,

    1 – I don’t think anyone has ever argued that there is no information in the genome!

    2 – All evolution can say is “From previous genomes, and chance”.

    3 – You need to be clearer about what “type” means.

    4 – It depends on the analogy chosen. If you look at the gene network as a program, the cell is like the OS. But these capabilities are so basic that you could also draw an analogy to chip design. In this case, the cell is more like the silicon substrate.

    If I substitute the word ‘rocks’ for ‘genome’ in your last sentence, you can see that it doesn’t have a lot of force.

  8. Mr. Nakashima,

    If I substitute the word ‘rocks’ for ‘genome’ in your last sentence, you can see that it doesn’t have a lot of force.

    Why would you do this though? If I substituted the turbines on a 747 with bottle rockets it wouldn’t have much force either. What would you be illustrating by doing so, or how is that a counter point to how complex the turbines are?

  9. Nakashima: [7];

    1. If you concede information, are you then comfortable saying that ‘chance’ occurences have brought about this assemblage of information? Where else do we see this in nature?

    2. You’re presuming the presence of a genome. Now, if I ask you whence this genome arose, you might be tempted to retort that this would be no more than switching the debate from Darwinian evolution to origin of life issues. However, bear this in mind, if I thought blind forces could alone could account for the very first genome, then I wouldn’t be quibbling about what it could do later on. To turn things around, you’re assuming that the first genome arose by chance, and then assuming that chance can remold it afterwards. This is like saying, “I believe that humans are capable of jumping over fifty-story buildings,” and then adding, “I believe that humans can jump over five-story buildings.” Once you assume that chance forces or chance occurences can bring about an incredibly large amount of information, then, of course, it’s a very small step, indeed, to assume that chance forces and such have caused additional information.

    3. From a mathematical point of view, I suppose there are many things that possess ‘information’. The ‘type’ of information I’m talking about is ‘functional’ information. Genomes bring about actual, productive, and directed changes. Where else do you see this happening in nature?

    4. I disagree. The synthetic code, which must certainly be made of nucleotides, is similar to the silicon substrate. The ‘cell’ is like a computer.

    I’m old enough to remember feeding punch cards into a large computer. The nucleotides are nothing more than those punch cards. So….the cell must act like the computer. And, of course, we all consider computers to be ‘designed’, don’t we?

  10. That is, if they find more and more intricate ways to manipulate rocks it would seem that at some point the only rational thing to conclude is that rocks have been designed.

    So, moving from stacking rocks on top of each other to grinding them up to make cement makes it rational to conclude that the rocks have been designed?

    if increasinglyManipulible(x), then designed(x)

    Mr PaulN,

    If the argument is a 747, genomes vs rocks is a choice of paint job, not a choice of engine. The engine is the validity of the inference from our powers to the nature of a substance.

  11. Mr. Nakashima,

    So, moving from stacking rocks on top of each other to grinding them up to make cement makes it rational to conclude that the rocks have been designed?

    I think the main trouble I’m having with your analogy is equating rocks and genomes to each other as raw materials. If rocks existed in their natural state displaying high amounts of specified complexity such as Mt. Rushmore, then you might have a point. What validates a design inference is the highly complex and specified nature of an array of interdependent physical working processes in it’s natural state, i.e. a laptop. In analyzing the design of a laptop, the origin of the raw materials used are irrelevant, but rather how they came together to create an incredibly complex piece of machinery with specified functionality.

    If the argument is a 747, genomes vs rocks is a choice of paint job, not a choice of engine…

    I think this helps me understand your position a little more. So you see the difference in integrated information and isolated functionality between rocks and genomes in their natural state as merely different paint jobs? I’m not trying to misrepresent your view, just trying to clarify. Please correct me if I’m wrong.

    The engine is the validity of the inference from our powers to the nature of a substance.

    Correct, and this is the inference we make when we not only analyze genomes, but gain knowledge in altering them. I don’t see how this inference can similarly be made when analyzing rocks, as rocks don’t naturally contain anywhere near the specified complexity of genomes.

  12. Sorry, meant to include this first in the previous post:

    That is, if they find more and more intricate ways to manipulate rocks it would seem that at some point the only rational thing to conclude is that rocks have been designed.

    While I ultimately believe that everything in the universe was designed, I still think there’s a wide margin between manipulating rocks vs. manipulating genomes, and the conclusion you can come to in each scenario. There seems to be a sharp disconnect between the inherent specified complexity in genomes vs. the rest of the outside environment, including rocks. This just as well applies to the inherent specified complexity within say, a computer operating system vs. clouds that just happen to form the shape of an I or a U (which is already a rare occurrence in itself if you think about it).

    If manipulating rocks were equivalent to say, manipulating the V8 engine within a new Dodge Challenger, then I could understand your statement. But I think the main case here is the amount of brain power and highly calculated changes required to manipulate something such as the engine of a Dodge Challenger to do something completely different than the complex function of what it is already inherently able to do without hindering the sensitive and orchestrated mechanics.

  13. Also, please bear with me, I’m on of the younger participants on this blog, and I have yet to obtain the vocabulary and verbal finesse that many of you guys have in order to properly flesh out all of my thoughts and refine them to their suitable communicative potential. I get frustrated with myself because of this sometimes…

  14. Mr PaulN,

    Of course, we bear with you! You bear with me so well. I must be of the same age bracket as Mr PaV, because I also used to work feeding cards into a mainframe.

    I have framed Mr PaV’s argument as

    for all x,
    increasingMutabilityByHumans(x)
    implies
    designedByDesigner(x)

    Is it true that you accept the “for all x” part? The argument is just as true for rocks as it is for genomes, but perhaps it is more ‘obvious’ for genomes?

  15. [14] Nakashima:

    Let’s be more serious. If I use playdough to fashion what looks like a squirrel, indeed, the squirrel is ‘designed’, but is not the repositor of intelligence—just physical forces. Human agency has manipulated this object, and it can be manipulated more and more, but this does not mean that it has any raw powers of its own.

    What you seem to repeatedly miss is that the genome is able to process information, and that the only things that we’re familiar with that can also process information are electronic objects that have been designed in one fashion or another. We didn’t fashion the genome. Who did?

  16. Mr PaV,

    Sorry to ignore your messages while replying to Mr PaulN.

    Yes, the information in the genome arose from physical forces, chance, and history. It was designed by no-one. Our ability to design with the same materials does not lead to a design inference that only intelligent agents can create such structures.

    Between chance and history, I think history has made the greater contribution. It is far more important to have the results of previous trials available than it is to have many trials in parallel.

    ps – I appreciate the humor in saying ‘lets be serious’, and then talking about playdough! :)

  17. [16]

    Our ability to design with the same materials does not lead to a design inference that only intelligent agents can create such structures.

    In the post your responding to I wrote this:

    “. . . the only things that we’re familiar with that can also process information are electronic objects that have been designed in one fashion or another.”

    You’re looking at only half of the argument. Where, other than the genome, do you see ‘information processing’ taking place? Where? You’re presuming that the genome developed by itself through history. That’s an assumption on your part. You have to prove that the genome arose through history. Where’s the proof? In the absence of such proof, we have the other side of the argument: that is, that the only objects whose history we know with surety, and which process information, have been designed by humans. Is this a logical proof? No. But as Stephen Meyer has argued, persuasively, the hypothesis that the genome is designed has more “explanatory power” than that of Darwinian mechanisms.

    I’m glad you have a sense of humor!

  18. Mr PaV,

    A sense of humor is very important to maintaining perspective! Joy is so often accompanied by laughter.

    Do you accept the evidence for common descent over time? I think if Stephen Meyer can write about the Cambrian Explosion he must accept these things are real.

    To your question, where do we see similar information processing, I will have to give two answers. If by information processing, you mean the gene regulatory networks operating in the cell, I would say we can see similar netowrks in ecology, and other eedback systems. If you mean DNA transcription and copying, I would say that we see it more simply in templating (with errors) in crystal growth and other natural systems.

    I’m obviously wary of saying we see similar information processing in modern human computers. That is because I think this is a bad analogy.

    If we go back to your analogy of genome to deck of punch cards, imagine an elaborate system of card readers, sorters, copiers attached eventually to some CNC milling machines. The instructions on the cards, after several steps of sorting, copying, etc direct the milling machines to make parts for more card readers, sorters, copiers, and milling machines!

    I think that is a rough analogy to the processes going on in the cell. But you may notice that we don’t have a CPU anywhere. That is because there isn’t one in the cell. So while analogies to digital information work, analogies to modern computers don’t work.

  19. [18] Mr. Nakashima:

    I believe in “commonality” of descent. This means that structures and functions are shared.

    One, infamous example, given for evolution was by a man named Berra. He said that looking at the change in the style of Chevy Corvettes over the years demonstrated that they were related to one another, and had evolved from one another. I think you’re already familiar with this example from another thread. Well, Corvettes use similar nuts and bolts, steel and fabric, sheet metal and glass, etc, etc. This is “commonality” of descent, but it is not “common descent”: that is, the 1956 Corvette didn’t turn into the 1957 Corvette. Indeed, the more proper way of expressing this would be to talk of ‘commonality’ of DESIGN, rather than talk of ‘commonality’ of descent? That was Berra’s big blunder.

    So, I do believe in the ‘commonality’ of organisms, and I do believe that one species can give rise to a completely different species, but I believe that this change in species, on large scales, can only come about by outside instrumentality, just as to go from a 1956 Corvette to a 1957 Corvette involves outside agency.

    As to your choices of ‘information processing’, in the case of ecology, the analogy fails. Why? Because, if we ask the question, What makes up an ecosystem?, the answer is: organisms, which, as we know, all contain genomes. So we find ourselves back to the genome, don’t we.

    In the case of crystal growth and such, I don’t think there’s any comparison between crystal growth—guided as it is via quantum mechanics—and DNA replication and transcription. But leaving this objection to the one side, what specifically happens in the case of ‘synthetic biology’, and in genomes everywhere, is information processing via coded messaging, that is, via an analogue of language. Computers operate using the laws of quantum mechanics, but these laws are incidental. What is critical is the use of ‘machine language’.

    In your analogy of a ‘milling machine’, you claim that no CPU is involved, yet you state this: “The instructions on the cards, after several steps of sorting, copying, etc direct the milling machines to make parts for more card readers, sorters, copiers, and milling machines!” My question to you is this: How can instructions be ‘read’ without a CPU being present?

    Here’s a related question: what do you mean by instructions? You talk about “punch cards”, well, WHO punches them? What language does he or she use? Be careful, because if you start saying that this ‘milling machine’ punches cards in the same way that the genome mutates, you would still be presuming that the genome functions as an information processor, which is what I claim. You then would simply be claiming that a machine can act like the genome. But, then, I ask the question: where have you seen machines in real life other than those produced by intelligent agents—we humans?

  20. So, I do believe in the ‘commonality’ of organisms, and I do believe that one species can give rise to a completely different species, but I believe that this change in species, on large scales, can only come about by outside instrumentality, just as to go from a 1956 Corvette to a 1957 Corvette involves outside agency.

    Any theories on why the designer specifically chooses to design using the nested hierarchies that are exactly what the branching theory of evolution predicts?

    Why the designer doesn’t choose to design structures de novo (as in the case of the Corvette C5 v. the Corvette C4) rather than merely tinkering with what already there?

    Why there are historical local rather than modern global design optima?

    I know what the answers to these questions will be, and as far as I can see, those answers strip ID of all of its predictive power. ID could actually be a scientific claim–albeit one that I think has been adequately falsified–but it becomes non-testable when everything can merely be explained away by the caprice of the designer.

  21. [20] Tajimas D

    Any theories on why the designer specifically chooses to design using the nested hierarchies that are exactly what the branching theory of evolution predicts?

    If the Designer chooses not to create everything de novo, then you will end up with ‘nested heirarchies’. So, then, the question is no more than why did the Designer not choose to especially created each form of life? I don’t know. Why is the atomic number of hydrogen 1? Can you please answer me that, and, simply restating the definition of what atomic number means just won’t do.

    Why there are historical local rather than modern global design optima?

    Maybe you could put this into English. Are we talking about Corvettes or Ferraris?

  22. Mr PaV,

    We can’t push our punced card analogy too far. Punched cards are analogous to nucleotides. I n discussing the information processing system, they are just a given.

  23. If the Designer chooses not to create everything de novo…

    This is the reply I expected. As I said, by reducing ID to the caprices of the designer, you render it as unfalsifiable as Descartes’ “evil daemon”.

    The question is: How can ID be a workable, testable scientific theory if one can claim that the designer chose to design everything exactly as evolutionary theory predicts? In addition, how can we know from independent evidence–which is required to test your hypothesis–that these are indeed the caprices of the designer?

    Maybe you could put this into English.

    I would have thought that it was rather clear already. Adaptive evolution works by “hill-climbing” in a fitness landscape. Because adaptive evolution can only ever allow us to walk uphill—although drift allows lateral and even some downward walking—ultimately it leads not to the global maximum (the overall ‘most effective design’), but to a local maximum (a ‘good-enough design’).

    In other words, why are many biological features suboptimal? And why should even these suboptimalities be retained in nested hierarchies, when the designer presumably could have chosen to step in and fix them at any time? Again, the answer I expect to hear is “the intellectual limitations of the designer”. I have already discussed what I feel are the flaws of this answer.

  24. How can ID be a workable, testable scientific theory if one can claim that the designer chose to design everything exactly as evolutionary theory predicts?

    evolution doesn’t predict anything..and if you want to prove me wrong, predict the next step in the ‘evolution’ of the swine flu virus. The evolutionist looks at the world through darwinian glasses, and, as dawkins said, it appears designed, but you have to refuse to believe your own lying eyes, and tell yourself ‘it evolved…it evolved’ because evolution HAS to be true.

    as far as a ‘fitness landscape’ you cannot define fitness other than by saying ‘it survives’ so how do you something is fit? it survives..natural selection is nothing more than a tautolgy.

    In other words, why are many biological features suboptimal?

    who are you to judge what is optimal? I find this line of reasoning fascinating from evolutionists. did it ever cross your mind that the Designer did NOT want you to be optimal? (whatever optimal is)

    oh and as far as ‘stepping in and fixing things’ given whats going on in the world, that could happen at any time…

  25. tsmith,

    evolution doesn’t predict anything..and if you want to prove me wrong, predict the next step in the ‘evolution’ of the swine flu virus.

    Good point. It always baffles me when Darwinists bring up this “prediction” stuff, when it’s clear ToE makes no such predictions of its own. Darwinists can’t even explain why chimps stopped evolving, even after the fact.

  26. [22] Mr. Nakashima,

    I disagree. Punched cards are not analagous to nucleotides. Punched cards use machine language, and are ‘punched’ by intelligent agents. Punched cards are analogous to genomes, which contain functional information, and which, therefore, have all the hallmarks of intelligent design, just as punched cards do. You can’t presume that material forces alone brought about the genome, and then use the functionality of the genome to demonstrate that nature can, indeed, contain functional information. This is circular reasoning.

  27. Mr PaV,

    The nucleotides are nothing more than those punch cards.

    These are your words in post 9. I
    have tried to apply them in what I thought was the most straightforward way.

  28. [23] Tajimas D,

    I don’t want to waste a lot of time responding to your post. Here’s why. You aren’t demonstrating sufficient self-criticism when it comes to the positions you maintain.

    Here are just two simple demonstrations of this:

    (1) Nested heirarchies is something that nature demonstrates; it’s not something that “evolution predicts”. Have you no sense of the history of Darwin’s thought? His theory was a way of explaining ‘nested heirarchies’ without invoking special creation. Darwin uses that as a starting point, and simply states that his theory is consistent with what we see in nature. Have you ever heard of Carol Linneaus? He preceded Darwin by about 50 to 75 years, and his system of classification as well.

    Secondly, Michael Denton, in his book Evolution: A Theory in Crisis, uses the then (1976) recent discoveries of molecular biology to show that the expected “nested heirarchies” aren’t found at the molecular level—in defiance of Darwinian predictions. Why don’t you read books that question your way of thinking? I do. I have yet to find any arguments by Darwinians that even begin to be compelling. But I read the stuff—unless they get downright silly, as does Dawkin’s The Blind Wathcmaker.

    (2) Have you any concpetion at all of what you’re talking about when you speak of “local landscapes” and “global landscapes”? Do you have any idea whatsoever of how steep these supposed “landscapes” are? When dealing with a simple protein, the slope of the landscape, differentiating between “functional” and “non-functional” configurations, verges on the infinite. Is there some way you would like to propose to ‘scale’ such a ‘slope’?

    If you want to talk about ‘fitness landscapes’ and such, you should understand that it’s simply a mathematical way of describing something that defies the understanding of anyone. What I mean is that there are ways in which genomes react to many outside factors that result in very different phenotypes; but, all this is, is a way of mathematically describing how reproduction and environmental stimuli can result in phenotypic changes. You can mathematically ‘simulate’ weather conditions and weather forecasts; and they can be quite accurate over short periods of time, but that doesn’t mean you know, or understand what is happenning. It’s simply a simulation. Isn’t that, in fact, how these kinds of “landscapes” are generated, through computer-generated mathematics? All these ‘fitness landscapes’ demonstrate is that the genome is not written in stone. But, go ahead, explain how, using ‘fitness landscapes’, you can have one species turn into another species at the level of higher taxa. I await. If you do a good job, then you can publish it, because I haven’t read one account of this that doesn’t come across more than mere ‘hand-waving’.

  29. Tajimas D,

    I don’t want to waste a lot of time responding to your post. Here’s why. You aren’t demonstrating sufficient self-criticism when it comes to the positions you maintain.

    But at least he maintains a position. Or did he change his position about nucleotides being punch cards recently.

  30. (1) Nested heirarchies is something that nature demonstrates; it’s not something that “evolution predicts”.

    This is simply untrue. I’m quite sensitive to postdictions being passed off as predictions (something that is common among evolutionary psychologists), but you’re wrong here.

    I will say that you’re absolutely CORRECT in stating the historical context, however, it can easily be demonstrated from _first principles_ that continuously subdividing populations result in nested hierarchies of characteristics. That’s an intrinsic feature of any branching pattern where there is some retention of parental characteristics. There’s independent evidence on the matter that tells us that if life evolved as Darwin suggested, we should expect a branching pattern.

    There is precisely ZERO reason to expect such a pattern from design, and there’s no independent evidence that could suggest that the designer prefers such a branching pattern.

    Secondly, Michael Denton, in his book Evolution: A Theory in Crisis, uses the then (1976) recent discoveries of molecular biology to show that the expected “nested heirarchies” aren’t found at the molecular level—in defiance of Darwinian predictions.

    Denton was wrong, and if I’m not mistaken, in Nature’s Destiny he refuted the very point that you just quoted and admitted as much. In suggesting the continuity of molecular evolution he gives as an illustrative example (http://www.talkorigins.org/faqs/comdesc/camp.html):

    In the case of primate DNA, for example, all the sequences in the hemoglobin gene cluster in man, chimp, gorilla, gibbon, etc., can be interconverted via single base change steps to form a perfect evolutionary tree relating the higher primates together in a system that looks as natural as could be imagined. There is not the slightest indication of any discontinuity.

    Next:

    When dealing with a simple protein, the slope of the landscape, differentiating between “functional” and “non-functional” configurations, verges on the infinite. Is there some way you would like to propose to ’scale’ such a ’slope’?

    Not true. First, the numerous “leaky mutations” provide gentle gradation toward fitness peaks. Second, many different amino acid sequences are capable of having similar structure and doing the same job. Third, there’s exaptation. Fourth, each gene that is has evolved by selection is already rather well adapted to its environment and can therefore be found on or around a peak.

    But, go ahead, explain how, using ‘fitness landscapes’, you can have one species turn into another species at the level of higher taxa.

    Explain how species turn into other species at the level of higher taxa (such as genus, family, etc.)? Sorry, your question doesn’t make sense.

  31. This is simply untrue. I’m quite sensitive to postdictions being passed off as predictions (something that is common among evolutionary psychologists), but you’re wrong here.

    You’ve missed the point. I talked about Linneaus. The Linneans system of classification IS a nested heirarchy. That’s why there are phyla, classes, orders, etc. This predates Darwin. Darwin argued that according to his theory, these nested heirarchies might simply be the result of natural selection. His is an argument for conformity between existing classification and the theory he proposes; it’s not a prediction.

    As to whether Darwinian theory ‘supposes’ this, while having life designed does not need to ‘suppose’ this, what does that matter one way or the other? Darwinism is an explanation, not a prediction. Design is an explanation, not a prediction.

    As to Denton, and your Talk.Origin citation, they are guilty of quote-mining. Denton presupposes ‘microevolution’ in Nature’s Destiny—a book I’ve read. Have you?—but this is no surprise: he plainly says he believes in microevolution in Theory in Crisis. The whole theme of ND has very little, to almost nothing, to do with evolution. His arguments in TofC are still valid. Why not read it? Or are you afraid?

    Next, as to fitness functions of proteins, there are studies out there, and numbers published. I’m speaking about actual research, not just hand-waving. Look up the studies. Look at the numbers. And then think about what they’re telling you.

    As to the species question, I was simply trying to avoid the distinction between macro and micro evolution because I was rather sure you would go off on a tangent about it.

    We know there is a certain level of plasticity between related species, but is there a limit to this plasticity? Darwin basically says ‘no.’ Darwinists basically say ‘no’. What does nature say about it? Yes. When you read Darwinists trying to explain how one species gives rise to another, it’s no more than a ‘just-so’ story. That’s why I suggest you actually explain it. You’ll win a Nobel Prize for sure. So, please, go ahead and explain it.

  32. You’ve missed the point. I talked about Linneaus. The Linneans system of classification IS a nested heirarchy.

    Yes. And Darwin used that when he derived the theory of natural selection. I agreed with all that.

    The point I’m making is that (in the case of Darwin’s theory) it can be demonstrated from first principles that this is exactly what we should expect, which gives us independent evidence and allows us to make testable hypotheses based on the theory. Using the theory of special creation (as per Linnaeus), there is absolutely no a priori reason to expect such a hierarchy, and the “theory” makes no falsifiable claims.

    Compare the two approaches.

    Mine:

    All of this evidence points to John being the murderer. Now, assuming that John is the murderer, it follows as a demonstrable mathematical truth that we would have all of this evidence, as well as A, B, and C. These hypotheses are testable, and have been confirmed. (Although other alternatives could also lead to the same pattern, the only alternative thus far suggested is that it the crime was committed by a trickster daemon whose existence has not yet been demonstrated.) Therefore, John is guilty.

    Yours:

    All of the evidence points to the daemon being the murderer. For instance, I have this gun with John’s fingerprints on it. Assuming that the daemon wiped his own fingerprints off and put John’s fingerprints on, this is exactly what I should expect. In addition, the daemon had the motive to kill, as demonstrated by the fact that the victim is dead. Incidentally, this is all also evidence that the daemon exists. Therefore, the daemon is guilty.

    Next claim:

    As to Denton, and your Talk.Origin citation, they are guilty of quote-mining. Denton presupposes ‘microevolution’ in Nature’s Destiny—a book I’ve read. Have you?—but this is no surprise: he plainly says he believes in microevolution in Theory in Crisis. The whole theme of ND has very little, to almost nothing, to do with evolution. His arguments in TofC are still valid.

    I thought it was rather well-known that Denton has recanted. He no longer promotes ID and is no longer affiliated with the DI. Nature’s Destiny promotes completely naturalistic evolution provided for by God’s fine-tuning of the universe, no?

    Next, as to fitness functions of proteins, there are studies out there, and numbers published. I’m speaking about actual research, not just hand-waving. Look up the studies. Look at the numbers. And then think about what they’re telling you.

    Have you been getting your data from Kirk Durston instead of an honest scientist? Do you believe it when someone like Janet Folger says there is a 10^62 chance of a protein forming?

    Simple example: if you align human myoglobin, haemoglobin-alpha and haemoglobin-beta, you’ll find that the sequences are only 18% identical at the AA level. Yet they have extremely similar 3D structures and perform similar tasks. Why? Gentle gradation up fitness slopes. Even the highly conserved H21 His in hemoglobin is not absolutely required for function, as demonstrated by foetal gamma chains.

    We know there is a certain level of plasticity between related species, but is there a limit to this plasticity? Darwin basically says ‘no.’ Darwinists basically say ‘no’.

    Absolutely incorrect. Limits to ‘plasticity’ are key to evolutionary theory. Without them, evolution would be no more than a random walk that would never get complexity off the ground. Cladistics would be impossible because sibling taxa would have nothing in common and there would be no nested hierarchies.

    However, ID and creationism make a very powerful claim on this front, namely that “you can’t get there from here”. That may or may not be true (although I’ve seen no evidence that it is true). Unfortunately, it’s also unfalsifiable, because in order to falsify it, we’d have to determine every single evolutionary path, including ones for which we no longer have any data.

  33. [27] Mr. Nakashima,

    When saying in [9] that the nucleotides are like the punched cards used in old-time main-frame computers, what was left unstated—but what was yet consistent within the analogy I was using—was that there was a particular arrangement of those nucleotides. These arrangements are, roughly speaking, equivalent to genomes. The analogy has two parts: (a) punched cards are ‘punched’ using the language called ‘machine language’, and the computer, which ‘reads’ the ‘machine language’ is able to carry out functions, and (b) nucleotides are arranged according to a ‘coded language’ (and, as these arrangements exist in the cell, we call them genomes), and, the cell is able to ‘read’ this ‘coded language’ and carry out functions. That’s the analogy.

    The dilemna you have to solve is how, by chance, can a ‘language’ come into existence. How do you propose to do that?

    [29] sparc,

    Why do I get the impression that you’re a troll from Panda’s Thumb? Is it because of your sarcasm? Probably. Be more substantive….or else.

  34. [32] Tajimas D,

    I’m growing very impatient with this exchange since it’s going nowhere.

    Did Darwin say, “Oh, if I’m right about things then we should find that this gives rise to this, and this thing here to that thing there, etc, etc, and, reflecting on all this, it should look like a nested heirarchy.” The nested heirarchy already existed. It exists in nature. So you’re predilection to Darwinian theory means that Darwin’s theory predicts nature just the way we see it. Well, guess what, nature happened to precede Darwin by 600 million years. This is no prediction. His theory fits the facts—and no more.

    Now, if I told you that there was a scientist whose theory predicted A, B, and C. And that, with time, A, B, and C all were proved wrong, would you say the theory had been disproved? Fair-minded people would say ‘yes’. What do you say?

    Now Darwin predicted that (A) the fossil record PRIOR to the Cambrian would be just as full of fossils and the rocks since the Camrian. WRONG. Darwin predicted that (B) countless intermediate forms would be found in the fossil record once it was fully excavated. WRONG. Darwin predicted that (C) the notion of sterility between species was really only an illusion, and that if we fully investigated, we would find that fertile hybrids would be the norm. WRONG.

    Sorry, but three strikes and your ‘out’. But not to card carrying, Origins thumping, true believers. Oh, no. He had it all right.

    Darwin’s certainty that ‘sterility’ was a kind of illusion is precisely what I meant about an unlimited plasticity; that is, that there is no limit whatsoever to viable hybrids. But, of course, today’s version of what a species is relies on this limit as a central concept.

    As to Nature’s Destiny, here’s a quote:

    “The avian lung brings us very close to answering Darwin’s challenge: ‘If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.’”

    The books subtitle is:

    “How the Laws of Biology reveal Purpose in the Universe.”

    Now, tell me, does that sound like he’s recanting?

    You wrote:

    Simple example: if you align human myoglobin, haemoglobin-alpha and haemoglobin-beta, you’ll find that the sequences are only 18% identical at the AA level. Yet they have extremely similar 3D structures and perform similar tasks. Why? Gentle gradation up fitness slopes.

    I’m afraid your logic is a bit inverted here. Yes, they have similar 3D structures, and yes, the perform similar functions, which points out that the 18% of a.a. that they share in common are just in the right places. Thus, given that the configuration space for such proteins is so huge, this means that the ‘steps’ you like to envision are not gradual at all, but are huge in their improbability. Now, if the proteins were only 5% different, then the configuration space of all possible functional proteins would be much smaller, and then you might talk of ‘gradual’ steps. So it’s the fact that they’re only 18% similar that makes it improbable that they could shift from one type protein to another—which is just the opposite of what you are thinking.

    I’ve responded this time, but will not respond the next time unless you make better points.

  35. Mr PaV,

    Yes, as I understood your original analogy, each card might be punched with G or T or A or C. And the deck of cards was the DNA sequence. The way I understood the analogy, the cards are read by the reader, the copier, the sorter. My point was that you only need simple mechanical devices like this in an analogy of the cell, you don’t ever need a CPU.

    I don’t think you can address questions such as “where did the language come from?” within the limits of this analogy.

  36. [35] Mr. Nakashima,

    I don’t mean this to be silly, but if the cards simply represented G or T, etc, then it really wouldn’t matter if all of the cards were simply ‘blank cards’ having four different colors. To a CPU, the color would be meaningless, only the location of the punches would carry meaning. IOW, it’s the relative positioning of the nucleotides that holds any functional information the genome might contain. At the strictly nucleotide level, everything is almost indistinguishable, and becomes like white noise.

    I once looked at a 3′x4′ photo of Steve McQueen hanging in an artist’s apartment. At least, that’s what I thought I was looking at. But it turns out that it was actually a rendering of Steve McQueen, based on a photograph, that was made by the artist using a Bic pen!!

    Now, at a distance of 8-10′, you would swear it was a photo. At three feet, you’re not too sure. When you come up close, you begin to see just dots. With a magnifying glass, you would see dots separated by a fair amount of space. The ‘information’ contained in that rendering is based on the relative distance of the dots to one another, and to the relative distance of observer to drawing. But, undoubtedly, the information is there. It’s very easy to say that all we ‘see’ in the cell are chains of amino acids, or chains of G’s, and C’s and T’s ….

    We might have to just simply disagree on this.

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