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. Joe Felsenstein

    Please Steve, enlighten us. How is any of what you say verified by niwrad’s SPC calculator? It does not have natural selection in it, so any effect of natural selection cannot be examined by looking at the results of the SPC.

  2. Steve

    Flint, you are unwittingly conceding the involvement of intelligent processes.  Your selection is the final step, not the only step.

    You want to mumble through the prologue and body of the story and go straight to the epilogue and hope only the epilogue sticks in people’s minds seeing as the preceeding dialogue was ( hopefully) inaudible.

  3. Steve

    I thought that was the point Prof.  NS cannot be included as it is a result, not a process; although it is often mischaracterized as a process.   The process takes place in the genome, not ‘out there’ in the environment somewhere.  

    Lenki’s bacteria is a good case in point.  Exposed to extreme environmental conditions the bacteria takes action.  It commences several attempts at mutations.  It copies itself, sees what happens and keeps mutating until a successful configuration takes place.  

    How does it ‘know’ this?  Well, from what evidence that is being gathered, bacteria in colony act as a single organism.  There is cell to cell comms.  So the colony can monitor and assess its own mutation progress across its ‘composite body’.  

    Take out the intelligent factor as described above, and there is no evolution to speak of as the bacteria colony would experience a quick death; hence the SPC.  

    and yes, I believe this is what Nirwad is getting at.  Evolution has to be an intelligent process or it would fail miserably.

  4. Steve

    Now you are getting it, Prof.

    Life in general is intelligent.  How could it not be?  We can’t just punt the ball to some emergent woo-woo phenomena.  Logic dictates that life in general must possess intelligence or it could not give rise to human intelligence in particular.  And experimental evidence is providing more and more support for the truth of this logical conclusion.

    I fail to see how such a straight forward concept would be so hard to wrap one’s brain around.
     

  5. RichRich Post author

    Steve: ” There is cell to cell comms. So the colony can monitor and assess its own mutation progress across its ‘composite body’.  ”

    Hmmm…

    183631B: Hey, you there?
    322421F: Yeah. ‘sup?
    183631B: Are you getting this citrate thing too?
    322421F: Yeah! it sucks
    183631B: I wish we could metabolize it..
    322421F: Hell yeah. someone should do something.
    183631B: …I WILL! I’m gonna MUTATE
    322421F: WOAH..dude. Awesome!
    183631B: WORD.
    322421F: Frameshift or point mutation? You gonna potentiate?
    183631B: I don’t know. Let’s ask Jesus.

    Something like that?   
     
         

  6. Steve

    Its amazing the projection that goes on in Mike’s head.  There is nothing to ‘expose’.  I freely provided my identity years ago.  

    By the way, there was absolutely no tauting in these posts or any other post at PT.  In fact, it seems Mike is the one doing the taunting (whats that rhetorical tool Mike likes to use- ah yes, turning the tables).  Note the characterization of my job as a ‘peddler’, insinuating that I sell carpets on the streets of Taipei.  Isn’t that something.  Where in fact my company produces technical textiles for the sportswear industry.  what even more sad is that he thinks Taipei is part of China?  Poor Mike.

    But I wouldn’t expect Mike or John to make a true characterization of what really is, just a purposeful mischaracterization to put proponents of ID in the worst possible light.   What else is new?  

    Hey Mike, why not try staying on topic as I have been.  Is that too much too ask? 

  7. Steve

    Im surprised Prof.  Felsenstein.  You of all people seemed to be above wisecracks.

    Note I said life is intelligent.  I didn’t say carrots were intelligent.  One of the bugs that seems to crawl in darwinian evolutionary brains is too consistently think in isolated terms and then string those isolated results and believe you have stumbled upon reality.

    Do you think carrots live in isolation?     So what if intelligence comes in many forms?  Why would you characterize human intelligence as the only form or the only one that counts?

    But more to the point, why not taking a crack at the logic?  If man is embedded in nature, does not that make nature the author of that intelligence?  

    So nature must possess intelligence.  Do you agree or not?

    If so, then nature is the author of all intelligent processes, regardless of whether they exist in humans, e.coli, or carrots.

  8. Steve

    So Rich, why would you wish to characterize what happens in cell comms from a human perspective?  

    It need not be done to understand the basic fact that bacteria do exhibit intelligent processes like cell to cell communication.  It is not a joke but basic really brought to you by none other than scientific exploration.

    Surprise, surprise.

  9. OMTWO

    Steve,

    ” There is cell to cell comms. So the colony can monitor and assess its own mutation progress across its ‘composite body’. ”

     

    Out of interest, why did only some lineages in Lenski’s experiment obtain the ability to use citrate as a food source? If there is “intelligence” present, then it sure seems to like emulating what we’d expect if there was not…

  10. Steve

    By the way, Prof. Felsenstein,

    NS must be ‘impotent’ if it does not include the intelligent activity observed in species.   

    Only when included in intelligent activity does NS become part of a process.  On its own, it is a statistic; nothing more.

    I am beginning to suspect that the phrase ‘natural selection ‘acting’ on random mutation (variation) is evolutionary scientists’ way of tiptoeing around the obvious fact that it is the genome that contains the process, not NS/RM(V).
     

  11. OMTWO

    Steve,
    Out of interest what version of ID do you support? 

    Or, in other words, how does your version of ID explain the evolution of proteins?

    Designer intervention? If so, how often?
    Rules of physics? So, no intervention after big bang then?

    etc etc.

    You complain that people are not making true characterizations of what ID actually is so I’m asking straight out – what is “ID” to you? Until that’s know it can hardly be misrepresented can it?

    So, Steve, how does ID explain he origin of proteins? What evidence do you have that explicitly supports that claim?    

  12. Joe Felsenstein

    Steve wrote:

    Im surprised Prof.  Felsenstein.  You of all people seemed to be above wisecracks.

    It’s called a reductio ad absurdum. The idea that the carrot plant is intelligent and picks and chooses its mutants is absurd.

    Note I said life is intelligent.  I didn’t say carrots were intelligent.
     One of the bugs that seems to crawl in darwinian evolutionary brains is too consistently think in isolated terms and then string those isolated results and believe you have stumbled upon reality.

    Do you think carrots live in isolation?     So what if intelligence comes in many forms?  Why would you characterize human intelligence as the only form or the only one that counts?

    But more to the point, why not taking a crack at the logic?  If man is embedded in nature, does not that make nature the author of that intelligence?

    So nature must possess intelligence.  Do you agree or not?

    If so, then nature is the author of all intelligent processes, regardless of whether they exist in humans, e.coli, or carrots.

    It does not follow. Intelligence in humans arises by natural processes, and is seen (at least in part) in our near relatives. It does not follow that carrot plants are intelligent, or that mudslides are intelligent.

    It does not follow that mutational processes are intelligent. OMTWO made the cogent point that an intelligent process of mutation would not vary widely from lineage to lineage. In fact this very issue was addressed early in the history of bacterial genetics. Were mutants arising randomly, or were those genetic changes the result of “instruction”. The experiments of Luria and Delbrück nailed that one (it was randomness, not instruction) and they won a Nobel Prize for that.

    [Steve:] NS must be ‘impotent’ if it does not include the intelligent activity observed in species.   Only when included in intelligent activity does NS become part of a process.  On its own, it is a statistic; nothing more.

    I am beginning to suspect that the phrase ‘natural selection ‘acting’ on random mutation (variation) is evolutionary scientists’ way of tiptoeing around the obvious fact that it is the genome that contains the process, not NS/RM(V).

    This is semantic game-playing. Different genotypes have different probabilities of survival and reproduction, The resulting process is called natural selection.

    I’ve just this week been teaching my graduate course in theoretical population genetics. I’ve been giving them the equations for change of gene frequencies under natural selection. Apparently Steve wouldn’t want me to teach that, because natural selection is just a result, not a process.

    This is frequently heard from pro-ID commenters whenever we try to explain natural selection. We’re lectured on how it doesn’t really exist.

    By the same logic: Brownian motion isn’t a process (it’s just the movements and collisions of individual molecules). Landslides aren’t processes (just rocks moving). Flow of heat shouldn’t be discussed. … and so on.

    But scientists unapologetically discuss them, and it is helpful to do that. And raising this semantic objection isn’t helpful to understanding what is going on.

  13. Joe Felsenstein

    Steve wrote:

    Im surprised Prof.  Felsenstein.  You of all people seemed to be above wisecracks.

    It’s called a reductio ad absurdum. The idea that the carrot plant is intelligent and picks and chooses its mutants is absurd.

    Note I said life is intelligent.  I didn’t say carrots were intelligent.
     One of the bugs that seems to crawl in darwinian evolutionary brains is too consistently think in isolated terms and then string those isolated results and believe you have stumbled upon reality.

    Do you think carrots live in isolation?     So what if intelligence comes in many forms?  Why would you characterize human intelligence as the only form or the only one that counts?

    But more to the point, why not taking a crack at the logic?  If man is embedded in nature, does not that make nature the author of that intelligence?

    So nature must possess intelligence.  Do you agree or not?

    If so, then nature is the author of all intelligent processes, regardless of whether they exist in humans, e.coli, or carrots.

    It does not follow. Intelligence in humans arises by natural processes, and is seen (at least in part) in our near relatives. It does not follow that carrot plants are intelligent, or that mudslides are intelligent.

    It does not follow that mutational processes are intelligent. OMTWO made the cogent point that an intelligent process of mutation would not vary widely from lineage to lineage. In fact this very issue was addressed early in the history of bacterial genetics. Were mutants arising randomly, or were those genetic changes the result of “instruction”. The experiments of Luria and Delbrück nailed that one (it was randomness, not instruction) and they won a Nobel Prize for that.

    [Steve:] NS must be ‘impotent’ if it does not include the intelligent activity observed in species.   Only when included in intelligent activity does NS become part of a process.  On its own, it is a statistic; nothing more.

    I am beginning to suspect that the phrase ‘natural selection ‘acting’ on random mutation (variation) is evolutionary scientists’ way of tiptoeing around the obvious fact that it is the genome that contains the process, not NS/RM(V).

    This is semantic game-playing. Different genotypes have different probabilities of survival and reproduction, The resulting process is called natural selection.

    I’ve just this week been teaching my graduate course in theoretical population genetics. I’ve been giving them the equations for change of gene frequencies under natural selection. Apparently Steve wouldn’t want me to teach that, because natural selection is just a result, not a process.

    This is frequently heard from pro-ID commenters whenever we try to explain natural selection. We’re lectured on how it doesn’t really exist.

    By the same logic: Brownian motion isn’t a process (it’s just the movements and collistions of individual molecules). Landslides aren’t processes (just rocks moving). Flow of heat shouldn’t be discussed. … and so on.

    But scientists unapologetically discuss them, and it is helpful to do that. And raising this semantic objection isn’t helpful to understanding what is going on.

  14. Steve

    I support a front loading position.  I support the original definition of evolution as ‘an unfolding of pre-existing rudiments’.  I support the notion that life is succumbing to the effects of the environment and is degrading from an original optimum design; in contrast to the darwinian evolutionary take that the genome is a mess as a result of unguided processes.

    I think we can predict that some time in the future we should be able to detect something like quantum templates that act as command and control of the development of lifeforms. In fact, if im not mistaken we are going in the direction of understanding light as instrumental in genomic activity.  so it wont be all that long before we make the jump to the intelligent properties of light.

    I will not doubt be accused of promoting woo.  But what is future scientific discovery except woo in our current thinking.  Just imagine Aquinas talking about the possibility of storing information in DNA back in 1200.  Would have no doubt been accused of talking to imaginary friends and been branded some sort of devil.

    But here’s some more woo for you.  Consider force and information as intelligent entities; force interacting with information, creating matter/life.

    Sure you don’t have to go there to do lab work/specific points of research.  But if you want to truly understand life at its core/foundation, you (pl) won’t be able to avoid IMO paying a visit to this notion.

     

  15. DNA_Jock

    Steve is also indulging in the related, popular sleight-of-hand: viewing RM in isolation, and NS in isolation. And desperately trying to hide the fact that they act iteratively.

    Only when [performed iteratively] does NS become part of a process.  On its own, it is a statistic; nothing more.

    ftfy

  16. OMTWO

    How are you able to have access to this “future scientific thinking” then? 

    Should Aquinas have talked about DNA in 1200 nobody would have understood him. He would have had to teach them many other things before getting to DNA. 

    Yet I can perfectly well understand your “future science”.

    I know what light is. I know what genomic activity is. 

    What’s missing in your reply is the reasons why you believe this “future scientific thinking” is anything other then pure fantasy.

    For example, what leads you to believe that light has “intelligent properties”. What experiment could you design that would illustrate these properties? If none, then on what basis do you make this claim? What is explained by this? 

    Same for your “quantum templates”. What do they explain? What is the current explanation for what you claim they explain? Why is your idea better? How?  How do you know about them if nobody else does? Where did you hear about them? 

    I’m afraid I can’t accuse you of promoting “Woo”. What you are selling does not even rise to that level. At least with your typical wooMeister they attempt to link their blah to reality in some way (the quantum aura, psi etc).

    I don’t see even a tenuous thread linking “quantum templates” to anything in biology. I’m happy to be enlightened however. So, more detail? 

  17. OMTWO

    Given the ratio of extinctions:extant this “intelligent activity” Steve claims is acting sure ain’t doing so well. 

  18. Joe Felsenstein

    I’m as guilty as anyone of allowing this discussion to wander off topic. Earlier it was Steve telling us that niwrad’s SPC simulation showed (something-or-other) about protein evolution. When asked what he thought was happening, he took us off into cosmic intelligence. (Steve, yes, if we saw future science ahead of its time, it might well look like “woo” to us. But most woo is just woo, and not future science.)

    But let’s shift back to protein evolution and the SPC simulation.  I realize we may have exhausted that topic.

  19. Patrick

    I, for one, would be interested in a thread devoted to Steve’s personal ID theory.  In particular, I would like to see his precise definitions for terms like “information” and “front loading”, as well as the details of his proposed experiments that would serve to support or disprove his theory.
     

  20. Mike Elzinga

    There is no “projection” going on; just reporting of your repetitive behaviors on every blog discussion thread on which you appear.

    In every case – including this very thread – people demonstrate repeatedly that you don’t have even the understanding of science what one would expect of a middle school student.

    In fact, on this very thread, you were challenged to respond to a simple calculation that high school chemistry/physics students can do. The implications of the calculation apparently had no meaning whatsoever for you.

    Yet you sneer at science and wallow in woo; making snarky remarks about things for which you obviously have no understanding whatsoever.

    People who do those kinds of things routinely on every site they appear are not doing this out of innocence and sincerity. It’s called taunting. The fact that this has to be explained to you is further evidence of your immaturity. It is every bit as stupid as those disturbed street gangsters who throw insults at kids heading home from school with books under their arms, and who attempt to bully them and beat them up.

    This is the image that others have of your shenanigans on discussion sites such as Panda’s Thumb, Carl Zimmer’s site, and on this site. However you choose to inflate your credentials as a fabric peddler, you come across as an immature teenage bully on the internet. Nobody doubts that you are trying to derail threads by directing all attention to yourself.

    All you are accomplishing is just inviting much smarter people than you to play games with you, mock your indulgence in woo-woo, and laugh at your inability to learn even middle school science. You ask for it; so live with it. You can’t beat up the smart kids any more.

  21. Mung

    I, for one, would be interested in a thread devoted to Patrick’s personal ID theory. Or shall we just ignore his posts as the product of non-intelligent non-design.

  22. Mung

    Joe:

    It’s called a reductio ad absurdum. The idea that the carrot plant is intelligent and picks and chooses its mutants is absurd.

    Equally absurd is the notion that humans are intelligent and pick and choose their mutants.

     

  23. Mung

    Joe:

    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.

    It appears that you are asserting that the essence of a protein is that it has parts, and that those parts can change, but that you are then excluding that from discussion.

     

  24. Mung

    Mike Elzinga:

    In real physical/chemical processes – including those kinds of processes suspected to be involved in the origins of life – complicated mixtures of atoms and molecules are brought together in a heat bath of sufficient energy that unlikely reactions can occur.

    How much energy is required to bring about unlikely reactions?

  25. Joe Felsenstein

    I have little idea what Mung’s comment means. What is relevant for this discussion are facts about proteins that affect whether they can evolve, whether mutations in them lead to sequences that still function. Other issues of “essence” can be discussed elsewhere.

  26. Mung

    Joe Felsenstein:

    I have little idea what Mung’s comment means.

    The meaning of my comment is as follows:

    You refuse to define what a protein <b>is</b>.

    You cannot state the facts about proteins that affect whether they can evolve. You cannot ask whether the evolution of proteins impossible.

    What is relevant for this discussion are facts about proteins that affect whether they can evolve, whether mutations in them lead to sequences that still function. Other issues of “essence” can be discussed elsewhere.

    How do you propose to discus whether proteins can evolve of you cannot define what a protein is?

  27. Joe Felsenstein

    I utterly refuse to get into a discussion of essences. If Mung has some argument that proteins can’t evolve, let’s hear it.  (Or is Mung just asking questions and never answering any?)

  28. damitall2

    My word! All those enzymes, antibodies, albumins, globulins that I use every day of my working life aren’t “real”?

    They certainly act as if they’re real, having an actual physical existence, quantifiable, and capable of being used with reliably predictable results. 

  29. OMTWO

    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? 

  30. rhampton7

    I assume you recognize that there is a real difference between cats and dogs. Other than using the term ‘species’, how else would you describe the distinction? Why?

  31. Mung

    Proud of yourself Joe?

    Why not advocate to get me banned?

    A whopping two comments?

    And they deserved to be sandboxed because?

     

  32. Mung

    Joe F:

    I utterly refuse to get into a discussion of essences.

    Joe says he won’t get into a discussion of ‘what’ it “is” that evolves, while claiming that the ‘it’ that evolves does so by an identifiable mechanism.

     

  33. OMTWO

    Lots of questions there Mung. 

    Here’s a more interesting question:

    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? 

    Any comment? 

  34. Joe Felsenstein

    No, no, OMTWO. Mung just asks random questions, Mung never answers cogent ones.

    And when some of Mung’s comments get moved to Sandbox by me because, as I said at the time, they were irrelevant to that thread, Mung asks why they deserve to be Sandboxed. (Um, because they were irrelevant). 

    It is important to realize that, sadly, Mung does not engage with the relevant stuff.

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