Is evolution of proteins impossible?

At Uncommon Descent, “niwrad” has posted a link to a Sequences Probability Calculator. This webserver allows you to set a number of trials (“chemical reactions”) per second, the number of letters per position (20 for amino acids) and a sequence length, and then it calculates how long it will take for you to get exactly that sequence. Each trial assumes that you draw a sequence at random, and success is only when you exactly match the target sequence. This of course takes nearly forever.

So in effect the process is one of random mutation without natural selection present, or random mutation with natural selection that shows no increase in fitness when a sequence partially matches the target. This leads to many thoughts about evolution, such as:

  • Do different species show different sequences for a given protein? Typically they do, so the above scheme implies that they can’t have evolved from common ancestors that had a different protein sequence. They each must have been the result of a separate special creation event.
  • If an experimenter takes a gene from one species and puts it into another, so that the protein sequence is now that of the source species, does it still function? If not, why are people so concerned about making transgenic organisms (they’d all be dead anyway)?
  • If we make a protein sequence by combining part of a sequence from one species and the rest of that protein sequence from another, will that show function in either of the parent species? (Typically yes, it will).

Does a consideration of the experimental evidence show that the SPC fails to take account of the function of nearby sequences?

The author of the Sequences Probability Calculator views evolution as basically impossible. The SPC assumes that any change in a protein makes it unable to function. Each species sits on a high fitness peak with no shoulders. In fact, experimental studies of protein function are usually frustrating, because it is hard to find noticeable difference of function, at least ones big enough to measure in the laboratory.

141 thoughts on “Is evolution of proteins impossible?

  1. In that post Murray introduces what he describes as A Simple Argument for Intelligent Design.  And what is it? It is that designed things have (properties like) “FSCI, dFSCI, Irreducible Complexity, Semiotic System” which can be observed and which cannot result from non-design processes. 

    Well, we’ve heard that before. And all those properties either cannot be defined clearly (dFCSI, Semiotic System) or can be shown, in straightforward models, to come to be in a living system by natural selection (FCSI, Irreducible Complexity).

    So there’s nothing new there. And Murray even admits that

    One might argue that the method by which ID proponents make the differential evaluation between natural and product of ID (FSCI, dFSCI, Irreducible Complexity, Semiotic System) is incorrect or insufficient, but one can hardly argue such a difference doesn’t exist or is not quantifiable in some way, nor can they argue that it makes no difference to the investigation.

     
    Yes. Of course. If you can find property X, which you can show living systems have, and show that this property arises in systems that are designed, and that it is not possible for property X to arise in living systems by natural selection, then you have a powerful argument that these features of living systems are the result of Design.

    But showing that property X cannot come to be in living systems by natural selection is the hard part. All such attempts have been convincingly refuted, and Murray does not admit that.

  2. But showing that property X cannot come to be in living systems by natural selection is the hard part. All such attempts have been convincingly refuted, and Murray does not admit that.

    Symmetry is a regular feature within the atomic/molecular realm. It is no surprise that those underlying templates will produce patterns that appear designed at the macroscopic level.

    “Broken symmetries” are evidence of underlying forces that act on the structures that develop on top of those underlying templates. As structures get more complex, intermolecular interactions become weaker and more susceptible to interactions with the environment in which these structures are immersed.

    Nevertheless, it appears that even macroscopic forces are minimized by macroscopic structures that take on various symmetric shapes. Over time, such forces acting on evolving structures trim these structures into shapes that minimize the energies of interaction with their surroundings.

    The fact that humans can learn to make efficient, symmetric, and highly functional designs found in nature is simply mechanical art imitating nature. Many human designs really are found to have already arisen by natural selection in nature.

    Furthermore, even when humans learn by trial and error, their mechanical arts and products develop symmetries found in nature. It is much easier to push a long, tapered hull through the water than it is to push a square raft.

    In fact, I would go even farther and assert that humans learned very early on, in their interactions with their environments, that behaviors have consequences; hence “moral rules” as well. Atomic forces tell atoms and molecules how to behave; the macroscopic forces of nature tell humans – at least those who will pay attention – how to behave.

  3. n fact, I would go even farther and assert that humans learned very early on, in their interactions with their environments, that behaviors have consequences; hence “moral rules” as well. Atomic forces tell atoms and molecules how to behave; the macroscopic forces of nature tell humans – at least those who will pay attention – how to behave.

     

    Uh, no. If this were true, all species would share the same morality. Clearly this is not so. Indeed, human morality is entirely different from any other, probably unique.

    Moral rules are rules of thumb that tend to facilitate a given social orientation, which in turn arises from the nature of the group — if there is even a group at all. For example, behaviors appropriate to species that give birth seldom are hopelessly inappropriate for species that lay millions of eggs and hope a few survive to adulthood. Behaviors appropriate to isolated hunters which interact only to breed and then very briefly, are hopelessly inappropriate to species that live in cooperative groups.

    We haven’t derived our moral rules from “macroscopic forces of nature”, but rather from trial and error consistent with our nature as a gregarious long-lived slow-breeding, slow-maturing, language-using species.   

  4. Well, obviously a certain level of intelligence is required for “morality” to emerge; but even other social species have established “rules” and hierarchies within their groups.

    Elephant groups have matriarchs with long memories and knowledge of where things are. Killing off older members of social animal groups disrupts their “societies” in rather dramatic ways.

    Many of us who have lived in Hawaii have witnessed “myna bird courts” in which a group of mynas form a circle around a myna on the ground while chattering among themselves as the single myna cowers in the center of the circle. These sometimes end in the death of the myna in the center; and at other times with a good roughing up and being let go.

    We haven’t derived our moral rules from “macroscopic forces of nature”, but rather from trial and error consistent with our nature as a gregarious long-lived slow-breeding, slow-maturing, language-using species.

    Sure; social creatures share their experiences. But those experiences have to come from interactions with the environment (which obviously includes other creatures). People with unrealistic illusions and who live inside their heads all the time don’t fair well unless they are sheltered and protected by a larger society that is capable of supporting them even if when they contribute nothing of value to the larger society.

    The implicit context in talking about humans is that intelligence and social structure have evolved. Other non-social creatures survive by being “wired right” at birth. If not wired right, they go extinct. So even in these cases the “forces of nature” prune the creatures that survive long term.

  5. The point is that different species have different behavioral rules, different imperatives suitable to their lifestyles. Unlike physics and chemistry, there is no universal moral code, no universal rule set. The way cats and dogs (who share a common ancestor not all that far back) have evolved entirely different lifestyles is very different from the rules of molecular bonding, which do not evolve.

  6. That is to be expected; living organisms are more complex. There will be a much greater range of characteristics that survive depending on those characteristics and the niches they find in the environment.

    This is a general rule with complexity. Simpler systems, such as atoms, are more tightly bound. They have fewer “responses” to “stimuli” in their environment than do molecules. Complex molecules have many more properties. Large organic molecules have even more properties that respond to their environment.

    Continuing on up the chain of complexity all the way to living organisms, we should of course expect a larger variety of fits to the environment. We should also expect that such complexes of atoms and molecules, if they exist within a temperature range in which they are not tightly bound, will find nearly every niche that is available.

    The fact that such complexes are sentient simply allows more degrees of freedom for adaption to the environment.

    I suspect it remains to be seen if human intelligence really has the potential to adapt in the long run. Given our effect on our environment, we may simply be outsmarting ourselves. Maybe tough, stupid, and ruthlessly aggressive is better for the long haul. It’s not even clear that self-regulation of our numbers would be “wise” in the long haul. Time will tell. So far, the dinosaurs had a much longer run than humans; and what wiped out the dinosaurs was pretty extreme. It’s doubtful that humans could have survived either; too delicate, and with a brain that needs too much energy.

  7. Your general statement was that the macroscopic forces of nature tell humans how to behave. This is either incorrect or very misleading — or maybe I’m misinterpreting you. The macroscopic forces of nature certainly do NOT tell humans how to behave, if we consider that all species are subject to the same macroscopic forces of nature, and all behave very differently.

    At best, we could say that the macroscopic forces of nature provide some fairly broad and loose constraints on behaviors, consistent with survival one way or another. But given the macroscopic forces of nature, one could never hope to derive the behaviors of any unknown species. Or even hope to come close.  Morality emerges from livestyle within an environmental niche, and is not directed by any general forces.

  8. We haven’t derived our moral rules from “macroscopic forces of nature”, but rather from trial and error consistent with our nature as a gregarious long-lived slow-breeding, slow-maturing, language-using species.   

     

    Actually, neither of those options is correct.  Our morality is in many respect analogous to language:  rule-based and useful, rooted in evolution, but expressed in any of a number of arbitrary and capricious ways.  Morality is not so much trial and error learning, as culturally imposed and whimsical for its own sake.

    There probably is some fundamental ethical sense of right and wrong that’s based in human empathy, and which is more-or-less common throughout the human species, but the cultural rules, traditions, and mores that are usually lumped into “morality” have very little to do with knowledge, and more to do with current idiom.

  9. Sorry about trying to be a bit poetic. I should have learned from my attempts at a popularization that I don’t have that ability. I promise not do it again.

    But is a fact that all stimuli any organism experiences are the result of forces. Those arise, for example, from changes in momentum when a photon is captured by a molecule (photons carry momentum) to changes in potential energy as an organism changes its spatial configurations. Eardrums respond to tiny changes in air pressure. Nerves respond to temperature, which is the average kinetic energy per degree of freedom of the molecules striking the nerve. Those momentum transfers result in forces that cause electrons and molecules within the nerves to accelerate. All time rates of change in momentum result in forces.

    There is a fundamental reason why complex organisms are only “aware” of macroscopic forces. If they were small enough to be battered by molecular forces that ripped them apart, they wouldn’t be “aware.” They have to be large enough and complex enough to not only average out the constant molecular bombardment that shows up as the background temperature in which they remain “soft,” they also have to be complex enough to store information and also have enough degrees of freedom to adapt.

    Some of our senses lie at the threshold of sensitivity to individual molecular and photon bombardment; and some people with unimpaired senses can become aware of it under only very tightly controlled circumstances. Astronauts, for example, have experienced flashes of light within their eyes from Cherenkov radiation from particles passing through the vitreous in their eyes.

    In most cases, however, transfers of momentum from photons and molecules are averaged over many molecules. Some people can hear the “hiss” of air molecules bombarding their eardrums if they are placed in a carefully designed quiet room.

    If you have reasonably good sensitivity to pitch, you can hear the extended sound of a musical instrument or orchestra appear to go flat when you yawn. Yawning stretches parts of the inner ear that respond to specific frequencies. This increased tension raises the frequency response of a given mechanical attachment to a given nerve that is associated with a particular frequency, causing that nerve connection to the brain to identify a higher frequency as a lower frequency.

    The more we know about the responses of our nervous system to stimuli, the more we recognize that we respond to forces bombarding us continually. I suppose viruses and amoeba don’t have enough intelligence to care, but they are at the lower limits of being able to average out individual molecular impacts. And none of us living organisms are immune to changes in temperature.

  10. Well, I did put moral rules and morality in quotes; meaning rules for behavior, or how one should behave in a given situation, as learned from experience. It’s my fault for trying to be “poetic.”

    Social animals, especially humans, can often pass the lessons learned from individual experience on to others (well, sometimes anyway). Obviously that experience includes interactions with others. It is also obvious that some experiences can result in lessons learned simultaneously by a number of people experiencing the same phenomenon.

    The advantages of intelligence and culture are that lessons learned from the environment – and that includes other members of the same species – can be transmitted to other members of the species even before those other members encounter those particular situations. One can even learn from other species.

    So, collectively, social animals such as humans can learn more efficiently in many circumstances.

    But this is all getting a bit pedantic; which is what I had intended to avoid by using my apparently not-so-poetic quotes.

  11. Back to the topic with more of William J Murray’s continuing confusion.

    So, again, my question to you is (re-phrasing #23 for brevity): Whether or not we currently have such a method, can the admittedly obvious difference between known ID objects such as battleships and other known, inorganic, presumably natural phenomena in principle be quantified?

    I’m not asking you if such a method exist, only if one could in principle be developed.

    He wants to set aside biology for the moment; apparently in order to attempt to establish something about identifying design. Presumably, after he has established whatever it is he is trying to establish, he can conclude that biological structures are designed.

    None of the people posting over at UD, including Murray, seem to recognize the vast quantitative difference between the energies of interaction among atoms and molecules and what the corresponding energies of interaction would have to be among steel plates. Nor do they recognize that there are quantum mechanical rules for atoms and molecules but not for steel plates.

    They apparently want to establish that a direct “Look; see it is obvious!” method is philosophically sufficient.

  12. Unfortunately, no one here, especially Elzinga ever gets to the core of the issue.  How is incremental change a satisfactory explanation for life’s development?  

    We constantly here of incremental change’s plausibility; yet never seeing its demonstration.  In the context of this OP, we can see the incremental change formation of proteins is not only implausible but bordering on the impossible.  so incremental change becomes too simplistic a concept to tackle the issue.  Why keep driving with worn tires?

    If it’s an appeal to logic and reason, ID is the better bet.  Information as an independent entity interacting with matter is a more reasonable explanation than incremental change, if not the more parsimonous.  In fact it is more rational, as it dovetails with actual experience.

    Think about it.  Have you ever seen a home that is the result of incremental change; where the chairs were created from a fruit crate, the stove from a minor sink hole that the kitchen happened to wrap itsself around’ where the walls came about as a result of high winds picking up sheets of plywood from a nearby woodshop; where the plumbling came from tracks dug by erosion of the soft sandstone foundation.

    When have we ever seen multiple makeshift solutions simultaneously come together except maybe in the case of a shack in a shanty town? Even then its a mixture of ad hoc solutions yet with a modicum of planning added in.

    In fact, the only experience we have of incremental change is in singular examples of makeshift tools, simple devices, and furniture to solve immediate problems.  

    Are we then to assume that Darwinian evolution can be likened to a shanty town?  but what of the cosmopolitan cities? what caused them?  In contrast to the shanty town, cities are the result of pre-planning in many cases, modular planning over time in other cases, mixed with dashes of ‘shackiness’  (to accomodate the independent, stubborn minded).

    Contrasting the two, a planned city is way more efficient, livable, and desirable than the makeshift shanty town.

    So all of this talk from the likes of the Elzinga’s in this world is useless banter.  They purposefully avoid tackling the elephant in the room, denying an elephant exists.  Problem solved.  

    If that were so, we could all go home.

  13. Sorry, that was mostly off-topic.  The Original Post noted that niwrad’s simulation assumed that evolution of proteins was almost impossible. And complained that this flew in the face of data about variation of proteins within species, differences of proteins in related species, and experimental evidence on moving proteins between species.

    So now Steve says, totally wrongly, that

    In the context of this OP, we can see the incremental change formation of proteins is not only implausible but bordering on the impossible.

    when that is the opposite of what my Original Post said!

    The rest is hazy analogy, not worth following up here (if you want a human design example of multiple makeshift solutions coming together, try the modern automobile). Let’s not follow up on the details of the design analogy stuff. But instead ask Steve how he justifies niwrad’s assumptions, and how he deals with the fact that they conflict massively with experimental data.

     

  14. OMTWO:

    Yet that is not a problem when ID supporters claim that the evolution of proteins *is* impossible.

    So in the discussions here at TSZ with gpuccio, did he ever claim protein evolution was impossible?

    Did you have any particular ID supporter in mind?

  15. Joe Felsenstein:

    I am going to police this discussion to avoid troll-like diversions: they will go to Guano or Sandbox.

    What, specifically, will you consider diversionary?

     

  16. Joe Felsenstein:

    In a sense, what the “essence” of a protein is really is the question.

    Ah. thank you.

    More recent experimental evolution evidence shows that proteins from the same gene that are not identical in sequence can often be moved from one species to another without their function being noticeably changed.

    Yet Giuseppe Sermonti in Why Is A Fly Not A Horse wrote:

    Proteins transferred from one kingdom to another through biological smuggling did, indeed, form in their new environment, but they often failed to function. The amino acids making up the proteins duly placed themselves in the proper sequence, but they failed to take up the spatial configuration necessary to make the proteins as active as they were in the donor species.

    To be completely honest, I wish there were one or more citations to support this claim, but alas, they are not provided.

  17. Alan Miller:

    The essence of a protein is that it is a polymer comprised of amino acids.

    I think it’s possible to construct polymers comprised of amino acids that are not in fact proteins. Do you disagree?

    Did I miss something in your definition?

  18. Allan Miller:

    But ultimately, over ‘deep time’, the commonality degrades, and it becomes harder to tell.

    Is this your explanation for the lack of continuity between protein superfamilies? Did you raise this in the discussion with gpuccio?

  19. Mike Elzinga:

    All this is summarize by a concept that ID/creationists have continually sneered at; namely that the Earth is an open system. They have never understood what that really means.

    lol

    If that’s not OT for this thread, what is?

  20. Flint:

    I guess I should expect to dissolve any minute.

    Submerge yourself in the proper medium, and yes, you should.

  21. What Alan Miller said is true, and it’s completely irrelevant if some amino-acid polymers would not be classed as proteins.

    All proteins ARE at least polymers of amino-acids, even if they are decorated with other chemical moieties (glycoproteins. lipoproteins, etc.)

    So was there a point to your comment? – because it doesn’t look that way. 

  22. The thermodynamics-and-evolution stuff is OT for this thread. So is the essence-of-a-protein stuff. The exception to that is the issue of which parts of a protein can change and still have it do the same job.

    The Sandbox, or the previous threads that cover thermodynamics, will be enjoyable places to discuss those. 

  23. As the Original Post here argues, niwrad in effect argued that protein evolution was impossible. Unless you take niwrad’s SPC program to not apply to protein evolution after the Origin Of Life. niward wasn’t clear about that.

  24. My explanation for the lack of continuity between protein superfamilities is this: that is how superfamilies are defined. You declare a new one when you can’t find evidence of continuity.

    In any case the argument of the OP in this thread is not whether superfamilies could or could not be connected in evolution. niwrad’s argument was, in effect, that the protein sequence in a single species could not be altered. niwrad’s superfamilies were one sequence in one species.  This is way more restrictive than Michael Behe’s argument.

  25. Sermonti is in disagreement with “niwrad”. Because by putting it that way, Sermonti is (quietly) acknowledging that proteins transferred within a kingdom often do work.  niwrad’s calculator implies that they don’t. Whether proteins work in different kingdoms is a good topic for some other thread or for the Sandbox.

  26. As I asked the last time you drove by here: Which definition of “information” are you using?  How exactly does it “interact” with chemistry?

  27. Mung:

    Did I miss something in your definition?

    I take on board Joe F’s termination of the ‘essence-of-a-protein’ discussion, but would note that Mung did miss something: the entire rest of the paragraph. I went on to describe peptide bonding between chained acids, which is the ‘essence’ of a peptide, which is the essence of a protein. Polymerisation through side-chain bonding (the only alternative) is not the class of molecule under discussion, and not a class of molecule I am aware of existing in biology.

    One source of confusion is, I think, that when Joe says “can proteins evolve?”, he means can they change sequence from one to another by genetic amendment. Whereas people (eg Mung) may have in mind the evolution of protein as a whole class of biological molecule: proteins vs Protein. This discussion is on the former. See (eg) one of the many ‘semiotic’ threads for discussion of the latter. 

  28. Alan is correct, the issue of “evolution of protein as a whole class of biological molecule” is interesting but not the topic. The issue was whether there was some valid argument that the sequence of a protein in one species and the sequence of the same protein in another could have evolved from a common ancestor. Does niwrad’s argument address that? Does it have any validity?

  29. The issue of “evolution of protein as a whole class of biological molecule” is interesting but not the topic. The issue was whether there was some valid argument that the sequence of a protein in one species and the sequence of the same protein in another could have evolved from a common ancestor. Does niwrad’s argument address that? Does it have any validity?

  30. Is this your explanation for the lack of continuity between protein superfamilies?

    No, it is simply a possible ‘natural’ cause of that discontinuity. One that should be borne in mind before gp’s ‘necessity mechanisms’ can be ruled out. As an illustration, if a sequence of N bases is substituted linearly, once per time t, then after a period Nt one would have only about 37% of the original sequence. After 2Nt you halve that, and so on. Eventually, the similarities are too few to be statistically distinguishable from random pairs.

  31. At post number 11, niwrad makes this assertion:

    Most biopolymers must have specific sequence of symbols to work. So their generation by random evolution has unavoidably something to do with the probability of generating those specific sequences of symbols by chance. There are other aspects of biopolymers that are more difficult to simulate (e.g. their tridimensional shape). Instead, to compute the probability of the mere symbolic sequence is easier because is a combinatorial problem and is what this tool tries to do somehow.

    If a particular “sequence of symbols” doesn’t “work,” it isn’t incorporated in any living organism; or it might just be a different “organism.” Of course, there is also the issue of what is meant by the sequence “working.” If it doesn’t do something you expected, or if it does something you didn’t expect, does that mean it is verschlecht?

    To say that this “Sequence Probability Calculator” is a “tool” because you define the issue as a “combinatorial problem” that is easier to calculate is really no different than saying it is an addition problem because addition is easier to do. Why does niwred look at the problem this way?

    Take the negative logarithm of the probability calculation and call it “information.” What does that tell us?

    Simulating the chemical reactions leading to various kinds of molecules is a far more involved process of computer programming and the use of super computers with parallel processing than niwrad apparently realizes. Research in these areas follows many different paths, only one of which involves computer modeling.

    Also, on WJM’s thread at number 83, Murray makes this comment:

    LT: I appreciate your candor, but I’m not interested in demonstrating the obvious. If we cannot agree that a battleship obviously requires ID in its explanation, we have no common grounds upon which to build a meaningful dialogue, much less debate, about ID.

    If I am recalling correctly, there is now a “semiotic theory of ID” by UB that is supposed to explain proteins better than physics and chemistry. Murray’s thread appears to be hung up at trying to articulate whether or not there is a way in principle to quantify the “obvious difference” between ID and non-ID; in this case with a battleship.

    The same set of misconceptions are operating here as are operating in the thread by niwrad. Chemistry, physics, biology, and natural selection are all ignored in the building up of evolving structures; and the problem of the formation of things like proteins is recast as a simple combinatorial problem. How likely is it that we will find a battleship in the rubble of an avalanche?

    Ask the wrong questions, and you get the wrong answers most of the time.

    We are left with a bunch of woo-woo assertions about “semiotics” and “information” doing the job of making “impossible” assemblies; but we never see any recognition of the fact that we have taken these assemblies apart and know a great deal about the chemistry, the physics, and the natural processes behind their existence.

    One might expect that an impartial observer trying to decide who is making sense would seek to learn more about the physics, chemistry, and biology as well as the “semiotics” and “information.” As near as I can judge, we can get all kinds of material on the science, going all the way back to high school; but no matter how hard we try, we can’t get an explanation of “semiotics” and “information” nailed down.

    Yet proteins still exist.

  32. Mike, how is your comment responsive to the issues raised in the Original Post?  I came within inches of sending this one to the Sandbox. You are responding to a lot of assertions made by UD advocates — which do not deal with the topic of this thread.

  33. Joe:

    Apparently I don’t understand what you were attempting to do with your references to the conversations taking place over at UD. My only interest in them has been for what they can teach us about basic misunderstandings and misrepresentations of science. I have no problem with the studies of proteins or anything else. Puzzles are research questions to be addressed. If we don’t know something, we study it. We don’t throw up our hands and assert it’s impossible, therefore design.

    I don’t see a problem with different sequences; changes in “function” occur at all levels of complexity. Those changes could be quantum jumps or they could lie on a sort of continuum. Whether or not they perform some “function” depends on the environment in which they end up and what one means by some “function” in that environment.

    The difficulties in studying complex structures such a proteins lie in that complexity; and in one’s preconceptions about what constitutes function. As I understand it, gene splicing has become a rather routine procedure. Splicing parts of complex molecules into other complex molecules is likely to produce a wide variety of behaviors; some of which are little different from others, and others of which are dramatically different. So what is the big issue here? Research is complicated; so what’s new? We slog through it and gradually build up the picture of what is going on.

    The misconceptions of the ID/creationists are of interest only because they seek to interfere politically with the educations of others; otherwise, they are simply excruciatingly boring repetitions that have been going on for decades now.

    In the light of their political activity, understanding those misconceptions – and their abandonment of already established knowledge – is something useful to know even though they apparently have no intention of correcting their misunderstandings and misrepresentations.

  34. Joe:

    Evolution among superfamilies is Off Topic. Take it elsewhere.

    Well, you’re the boss, but I would consider the gradual disappearance of the signal of relatedness to be relevant. 

    niwrad says this:

    For example, about proteins and biopolymers, it doesn’t include the deterministic effect of amino acids forcing other amino acids to come with them, which could make the sequence more probable. Besides it doesn’t deal with all the specialized cases where functional issues somehow dominate the sequence structure.

    Among those ‘functional issues’ discarded appears to be the rather vital one of inheritance. Superfamilies, and identical sequences in close relatives, are at the extremes of a potential continuum. When we have two sequences, they have between them two pieces of information for comparative analysis: their similarities and their differences. The similarities provide a context, an alignment, for the differences. And any series of imperfect replication would be expected to start as fully-similar and end as fully-different.

    His model would be a relevant one if we found no commonality between proteins among similar modern species. That is, without even the degrading element of time, every protein sequence must (on the face of it) be a result of a random shake of the dice. He wouldn’t then be arguing that no protein can change, but that the differences between species are too great to be accounted for by a known random process.

    But that is not the case. Sequence commonality diminishes but gradually, alongside other measures of relatedness. So though people try and push back, ultimately to the lack of commonality displayed between different protein modules in the same species or across kingdoms, they dismiss the additional element of time. The wider you spread your net, the deeper in time you push, and the more signal degradation there is.

    So ultimately, I think niwrad is imagining an ancient family tree with just one bud, and applying his SPC to that. It has (in his mind’s eye) a complex interactive protein system, and although he might concede that those proteins may subsequently evolve, he asserts that that primordial system is already beyond some probabilistic bound.

    Whereas there is a real possibility that, were we able to follow sequences back through history, the relationships among presently dissimilar sequence would gradually start to reassert themselves, emerging from the signal-degraded modern world and converging upon original ancestry. One cannot easily prove conclusively (to a Creationist’s satisfaction) that that is how history would rewind, but there are strong mechanistic reasons to suppose that such an ‘arrow of convergence’ would be a reality, extrapolated from the directionality of the proteins we can access, and analysis of inheritance processes.

  35. Alan Miller:

    So ultimately, I think niwrad is imagining an ancient family tree with just one bud, and applying his SPC to that. It has (in his mind’s eye) a complex interactive protein system, and although he might concede that those proteins may subsequently evolve, he asserts that that primordial system is already beyond some probabilistic bound.

    So I think you are concluding that niwrad was not arguing that species could not arise in evolution, but rather that some primordial system could not evolve in the first place. In other words, the SPC only applies to the Origin Of Life and not to more recent evolution. niward did say, in subsequent comments on the SPC, that the situation niwrad was thinking of was the OOL. But it was left unclear whether it was also intended to model evolution after the OOL.

  36. Again, the origin of the universe, of life, and of all species happened as a single atomic event in creationist doctrine. It’s apparently very difficult theologically for them to consider these things in isolation.

  37. … unless the creationist involved only is claiming that major groups were created and that after that there was evolution.

    But in any case, niwrad’s simulation is supposed to be of evolution, not creation. It is supposed to show how impossible the assertions of evolutionary biologists are. The question is, is it intended to show what must have happened in a naturalistic theory of the OOL? And/or, is it supposed to describe what an evolutionary biologist would be assuming about the process that results in a protein in one species? niwrad has left that unclear.

  38. Prof.,

    What I think Nimrad’s SPC does show is that evolutionary biology’s assertions that organisms ‘stumble’ (are not in any way in control) upon correct sequences , regardless of how they are acquired is false.

    It is clear from experimental evidence that organisms are active in the gene trading and protein ‘building’ biz.  They are not ‘throwing out their gold teeth to see how they roll’ as Steely Dan might put it, except in cases of extreme stress, where the learning curve pressure is steep.

    In fact, as more evidence pours in, it becomes clearer that organisms are really ‘utilizing’ their tools, not standing by as unguided processes commandeer the steering wheel.  Granted, it is may be easy to confuse an organism’s loss of control of its own genome with unguided processes.  

    But since the whole Darwinian evolutionary idea of unguided processes is steadily being eroded by incoming evidence, the better bet is loss of control, which lends credence to concepts ID puts forth; i.e. pre-existing tools and templates, etc.

    Nimrad’s SPC is one of many ‘spatulas’ and ‘chisels’ being used to reshape the definition of evolution back into its original form, that of  ‘a rolling out’, not that of  ‘a building up’.

     
     

  39. Nirwad makes this disclaimer:

    “Disclaimer: this is a mathematical tool dealing with processes considered purely random. It doesn’t pretend to simulate the physical, chemical, biological, functional constraints specific of the processes.”

    Furthermore, that elementary, high school level physics/chemistry calculation remains. If kilogram masses had the same charge-to-mass ratios as, say, protons, then electron volt energies of interactions at separations on the order of nanometers scale up to energies of interaction on the order of 1010 megatons of TNT for kilogram-sized masses with separations on the order of meters. One can also make further order-of-magnitude estimates that get comparable results.

    Nirwad acknowledged that his “calculator” is essentially a tornado-in-a-junkyard calculator.

    Do you really believe any of the calculations done with this “calculator” – or any of the calculations done by that kairosfocus poster over at UD – have anything to do with any kind of reality regarding atoms and molecules and what kinds of assemblies they make?

    What is your conception of how complex molecules are formed?

  40. I note with amusement two mutations: “nimrad” and “nirwad”.  Nimrad is not Nimrod, but is “Darmin” spelled backwards (you know, Charles Darmin, the
    biologist).  Nirwad is the name “Dawrin” spelled backwards. (You know, Charles Dawrin, the biologist). 

    It beats me how Steve can say that what niwrad’s SPC calculations “show is that evolutionary biology’s assertions that organisms ‘stumble’ (are not in any way in control) upon correct sequences , regardless of how they are acquired is false.”   

    If Steve thinks that evolutionary biology’s theories are that each species reaches its sequences by pure random mutation, with no natural selection and with no evolution from closely similar sequences, then Steve does not know anything about those theories. 

  41. Mike Elzinga: “What is your conception of how complex molecules are formed?”

    It has never been a question of how complex molecules are formed but how they are able to ‘interact’.   How do we explain DNA error correction and DNA repair from a purely physics and chemistry POV?  

    To suggest incremental change as a satisfactory explanation is tantamount to an argument from credulity. 

  42. Unless we allow for selection. Selection! What’s that!

    The fact that error correction is nearly optimal (both better and worse correction produce bad results under careful modeling) must be pure coincidence. Surely selection couldn’t possibly have led to such a bizarre result, right? 

  43. But wait a minute Prof. Felsenstein, the mutation you observed is short-lived and will not end up being fixed in the colony of english words.  It gets ‘recognized’ as ‘defective’ and gets eliminated.  But if the defect is minor, still readable, it’s ‘allowed’ to stay on.  Note how it takes intelligence to recognize that a mutation is acceptable or not.  Discussing mutations as simply having a survival ‘advantage’ is doing an end run around the clear observation of intelligent activity; yes, even in such humble organisms as bacteria.  

    And no, I didn’t say species reach sequences by pure random mutation.  What I am saying is that organisms are clearly aware of what is taking place in their genomes. Declaring NS acting on RM a sufficient explanation is not an honest assessment of what is actually taking place in life.

    I think Nirwad’s SPC clearly demonstrates the impotence of NS acting on RM devoid of the intelligent screening processes species clearly use when dealing with mutations. 

     

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