Mendel’s Accountant again….

Journal club time: paper by Sanford et al: The Waiting Time Problem in a Model Hominin Population.  I’ve pasted the abstract below.

Have at it guys 🙂

Background

Functional information is normally communicated using specific, context-dependent strings of symbolic characters. This is true within the human realm (texts and computer programs), and also within the biological realm (nucleic acids and proteins). In biology, strings of nucleotides encode much of the information within living cells. How do such information-bearing nucleotide strings arise and become established?

Methods

This paper uses comprehensive numerical simulation to understand what types of nucleotide strings can realistically be established via the mutation/selection process, given a reasonable timeframe. The program Mendel’s Accountant realistically simulates the mutation/selection process, and was modified so that a starting string of nucleotides could be specified, and a corresponding target string of nucleotides could be specified. We simulated a classic pre-human hominin population of at least 10,000 individuals, with a generation time of 20 years, and with very strong selection (50 % selective elimination). Random point mutations were generated within the starting string. Whenever an instance of the target string arose, all individuals carrying the target string were assigned a specified reproductive advantage. When natural selection had successfully amplified an instance of the target string to the point of fixation, the experiment was halted, and the waiting time statistics were tabulated. Using this methodology we tested the effect of mutation rate, string length, fitness benefit, and population size on waiting time to fixation.

Results

Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive.

Conclusion

We show that the waiting time problem is a significant constraint on the macroevolution of the classic hominin population. Routine establishment of specific beneficial strings of two or more nucleotides becomes very problematic.

844 thoughts on “Mendel’s Accountant again….

  1. If we can elucidate all of the mechanical processes that go into making a car and allowing it to run, does that mean that mother nature can produce one?

  2. GlenDavidson: Follow the evidence.

    It’s better to explain much than to explain nothing (saying that evolutionary theory doesn’t exist means nothing, btw).That’s why ID is ignored by science.

    Glen Davidson

    Well there isn’t a scientific theory of evolution and your position can only explain disease and deformities.

    Congratulations

  3. newton: Without knowing the method of death how does one determine whether a crime has been committed ,Frankie?

    They can do so without a body. Go figure.

  4. Frankie:
    If we can elucidate all of the mechanical chemical processes that go into making a car cell and allowing it to run, does that mean that mother nature we can produce design one?

  5. petrushka: Show me that living things can be designed, or you are just spewing bullshit.

    Seeing all that you do is spew bullshit yours is very meaningless statement I can show you the evidence that living organisms are intelligently designed. But you would just ignore it or choke on it, again.

  6. petrushka:
    Frankie, show me it is possible to design a protein without trial and error.

    Tell me why that is a requirement. ID is OK with directed evolution. You are just an equivocating bullshit spewer so you can’t understand that simple point. 😛

  7. Frankie: Tell me why that is a requirement. ID is OK with directed evolution. You are just an equivocating bullshit spewer so you can’t understand that simple point.

    Show us that biological design is possible.

  8. petrushka: And you know it was designed how?

    Recall that yuo are not anti evolution.

    It meets the criteria and you don’t have anything that can explain it. All you can do is whine about ID all the while remaining ignorant as to what ID says.

    Recall that you are an equivocator…

  9. Again, petrushka, if you don’t like the design inference all you have to do is step up and demonstrate undirected processes can produce what we say was designed. Absent that all you have is whining.

  10. This is really very simple. We know that that megalithic structures can be built using ancient technology because we have taken the trouble to find the original tools and to replicate and test low tech methods. So we know it’s possible.

    So such replication exists for protein codes or for regulatory networks. When a pharmaceutical company designs a drug they set up a massive artificial evolution system and screen millions of candidates.

  11. petrushka:
    This is really very simple. We know that that megalithic structures can be built using ancient technology because we have taken the trouble to find the original tools and to replicate and test low tech methods. So we know it’s possible.

    And yet there are many such structures that we don’t know how they did it.

    So such replication exists for protein codes or for regulatory networks. When a pharmaceutical company designs a drug they set up a massive artificial evolution system and screen millions of candidates.

    More gibberish- so what? ID is OK with artificial evolution.

    What was your comment addressing, petrushka? Please be specific.

  12. One other thing overlooked by Behe. In any reasonably sized population, every possible point mutation will occur and be tested in a very few generations. Any change that might be artificially introduced would be superfluous.

  13. petrushka:
    One other thing overlooked by Behe. In any reasonably sized population, every possible point mutation will occur and be tested in a very few generations. Any change that might be artificially introduced would be superfluous.

    LoL! Please present the evidence to support your claim about Behe. Also support you claim about artificially induced mutations being superfluous.

  14. Frankie: LoL! Please present the evidence to support your claim about Behe. Also support you claim about artificially induced mutations being superfluous.

    Evidence:

    No matter what the exact value of the human mutation rate, every single possible point mutation will happen in just a few generations somewhere among the seven billion or so people on Earth.

    Reported by Larry Moran.
    http://sandwalk.blogspot.com/2015/10/human-mutation-rates.html?m=1#comment-form

    Reference:

    Shendure, J., and Akey, J.M. (2015) The origins, determinants, and consequences of human mutations. Science, 349:1478-1483. [doi: 10.1126/science.aaa9119]

    This is simple math. The principle was observed by Lenski in his long term evolution experiment.

  15. petrushka: Evidence:

    Reported by Larry Moran.
    http://sandwalk.blogspot.com/2015/10/human-mutation-rates.html?m=1#comment-form

    Reference:

    Shendure, J., and Akey, J.M. (2015) The origins, determinants, and consequences of human mutations. Science, 349:1478-1483. [doi: 10.1126/science.aaa9119]

    This is simple math. The principle was observed by Lenski in his long term evolution experiment.

    OK so you cannot support your claim about Behe. Typical

    And Moran doesn’t know if mutations are accidents, errors and mistakes. Whoopsie

  16. Frankie: Yes, we know that you are desperate. CSI isn’t the only tool for design detection.

    So ,Frankie, if we show a missing body could happen by natural processes does that falsify design?

  17. newton: So ,Frankie, if we show a missing body could happen by natural processes does that falsify design?

    Only if someone said that body was missing due to foul play.

  18. Logically if we don’t know if mutations are accidents, errors or mistakes we don’t know if they are deliberate either.

    So ID gains no support there.

  19. Logically if we can say that living organisms were intelligently designed then we can safely say the bulk of subsequent genetic change was directed.

    See also “Not By Chance” Spetner, 1997

    One nice example is Lenski’s E. coli- one of which took an existing gene- the only gene that produced a protein that transports citrate- and put it under control of an existing promoter which allowed the gene to be expressed in the presence of O2.

  20. The

    OMagain:
    Logically if we don’t know if mutations are accidents, errors or mistakes we don’t know if they are deliberate either.
    So ID gains no support there.

    It doesn’t matter. All the lotto numbers get played. Intervention or front loading would be superfluous.

  21. petrushka:
    TheIt doesn’t matter. All the lotto numbers get played. Intervention or front loading would be superfluous.

    Only if undirected processes can produce the lotto

  22. petrushka: All the lotto numbers get played. Intervention or front loading would be superfluous.

    Yes, it’s a point I’ve never seen an IDist grasp. If all permutations are iterated through then front-loading adds nothing that would not already be present. If all permutations are iterated through then “programmed responses to environmental cues” adds nothing that would not already be present.

    And as we saw with Lenski, there were no pre-programmed responses unless “mutate randomly” is such a response.

  23. The word “undirected” suffers from weasel-passive problems IMO.

    Do IDists mean “not directed by anyone”? Because there are plenty of directional processes that aren’t directed BY anyone, but by some kind of attractor – gravity, low energy state, a magnet, etc.

    I suggest that evolution IS “directed” in the sense that that populations flow towards low-energy minima – configurations in which you get most offspring bang for your least energy buck.

  24. Frankie: Only if undirected processes can produce the lotto

    So you are conceding that once replicators exist, and replication is imperfect, evolution is inevitable.

  25. Elizabeth:
    The word “undirected” suffers from weasel-passive problems IMO.

    Do IDists mean “not directed by anyone”?Because there are plenty of directional processes that aren’t directed BY anyone, but by some kind of attractor – gravity, low energy state, a magnet, etc.

    I suggest that evolution IS “directed” in the sense that that populations flow towardslow-energy minima – configurations in which you get most offspring bang for your least energy buck.

    Undirected as in accidental/ happenstance. And your version of directed has nothing to do with that. ID means directed as in planned, not accidental, intentional.

  26. petrushka: So you are conceding that once replicators exist, and replication is imperfect, evolution is inevitable.

    Your continued equivocation is annoying. The self-sustained replication of RNAs did not produce any evolution beyond the ability to reproduce faster. And that was intelligent designed- the ability to reproduce.

    Organism evolve by design. Undirected evolution, ie happenstance mutations, is impotent and cannot be modeled.

  27. OMagain: Yes, it’s a point I’ve never seen an IDist grasp. If all permutations are iterated through then front-loading adds nothing that would not already be present. If all permutations are iterated through then “programmed responses to environmental cues” adds nothing that would not already be present.

    And as we saw with Lenski, there were no pre-programmed responses unless “mutate randomly” is such a response.

    Great, when someone can actually model your view of evolution you will have something.

  28. Frankie: Only if someone said that body was missing due to foul play.

    You said if natural processes could create the effect ,design was falsified and that design could be determined without knowing how( foul play). Is design falsified by your own standard or not?

  29. newton: You said if natural processes could create the effect ,design was falsified and that design could be determined without knowing how( foul play). Is design falsified by your own standard or not?

    It is a case by case thing. Grow up.

  30. Frankie: It is a case by case thing. Grow up.

    No Frankie, your test for falsification has been falsified. You cannot prove something is not designed because natural processes can create the pattern.

    ID, at least by your test, is unfalsiable. Now if you have a who,how or why it may be a different story, but you don’t have those things.

  31. newton: No Frankie, your test for falsification has been falsified. You cannot prove something is not designed because natural processes can create the pattern.

    ID, at least by your test, is unfalsiable. Now if you have a who,how or why it may be a different story, but you don’t have those things.

    ID is both testable and falsifiable. We have said exactly how to do so. Your ignorance is not an argument let alone a refutation.

  32. Obviously “newton” is ignorant of Isaac Newton’s four rules of scientific investigation, Occam’s Razor and parsimony.

  33. Frankie: ID is both testable and falsifiable. We have said exactly how to do so. Your ignorance is not an argument let alone a refutation.

    Sticking your fingers in your ears is not a persuasive rebuttal

  34. Frankie:
    Obviously “newton” is ignorant of Isaac Newton’s four rules of scientific investigation, Occam’s Razor and parsimony.

    He is familiar with basic logic. No air quotes necessary, ” Frankie”

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