Mendel’s Accountant again….

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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….”

  2. Allan Miller:
    Frankie,

    .Back to sloganising. Did I say it was? Mayr was an advocate of what you tend to call ‘blind watchmaker evolution’, and was not an advocate of Design. That’s the trouble with bringing experts in – why should one take them as the final word on X, if one regards everything else they said as horseshit?

    Mayr never presents any scientific evidence for evolution. He said that the answers will be coming sometime in the future.

  3. Patrick:
    Frankie,

    We posit the entailments of the design.

    Without constraints, literally anything is possible.That means that literally anything can be calledan “entailment” of an unconstrained designer.That’s a vacuous position.

    ID has said what will falsify the design inference, Patrick. And ID is not about the designer.

  4. Frankie,

    Newton and anyone who understands science.

    And all Scotsmen! So, Newton thought God was pushing the planets around then, absent a means to test that they weren’t? Interesting.

  5. Allan Miller:
    Frankie,

    And all Scotsmen! So, Newton thought God was pushing the planets around then, absent a means to test that they weren’t? Interesting.

    Newton never said that God was pushing the planets around.

  6. Frankie,

    Mayr never presents any scientific evidence for evolution. He said that the answers will be coming sometime in the future.

    So why do you give a shit what he says about it?

  7. Allan Miller:
    Frankie,

    So why do you give a shit what he says about it?

    He is an expert. His word means more than yours. Geez just accept the fact that your understanding of evolution is different from the experts.

  8. Frankie,

    Newton never said that God was pushing the planets around.

    But you said that, supposedly on from his authority, blind and undirected was ‘at the bottom’. If you invoke gravity as not blind and undirected, why not selection?

  9. Allan Miller:
    Frankie,

    But you said that, supposedly on from his authority, blind and undirected was ‘at the bottom’. If you invoke gravity as not blind and undirected, why not selection?

    Blind and undirected are at the bottom of all scientists’ list of causes. And gravity is evidence for ID. And I say that natural selection is blind and undirected. It cannot be modeled.

  10. Frankie,

    He is an expert. His word means more than yours. Geez just accept the fact that your understanding of evolution is different from the experts.

    Which experts, and on which particular aspects? You are being very vague.

  11. Frankie,

    Blind and undirected are at the bottom of all scientists’ list of causes.

    So you think scientists prefer non-ID causes least of all? I think you are talking through your backside.

    And gravity is evidence for ID.

    No it isn’t! Is this your stupid explanatory filter again?

    And I say that natural selection is blind and undirected. It cannot be modeled.

    So you think Mendel’s Accountant is not a valid model of evolution?

  12. Frankie: And I say that natural selection is blind and undirected.

    Toaster repair men don’t generally get listened to on that topic, do they? So what you have to say is frankly irrelevant, ‘Frankie’.

  14. Zachriel: The “targets” are the hypotheses that are being tested by the experiment. It’s typical in an experiment to have control variables, which, in this case, includes the environment.

    fifthmonarchyman: correct and the hypothesis was?

    We’ve provided that information more than once.

    Zachriel: With regards to rates of evolution, the question was whether evolution will stop after the organism reaches an adaptive maximum. It turns out that evolution continues, generally slowing down; but, as with the case of citrate utilization, sometimes that equilibrium is punctuated by a burst of evolution.

    With regards to repeatability, it’s a long-standing question as to whether evolution inevitably tends towards certain solutions, or whether it is contingent on previous pathways. The experiment shows that evolution is, at least some of the time, contingent.

    Zachriel: With regards to the rate of evolution, one hypothesis is that, in a stable environment, adaptation will reach a local maximum, and then stop. A contrary hypothesis is that adaptation will continue at a slower rate, punctuated with periods of more rapid evolution. The latter was observed.

    With regards to repeatability, one hypothesis is that given the same situation, evolution will follow the same pathway. A contrary hypothesis is that evolution may follow different paths. The latter was observed.

    Lenski: The first set of questions, about the dynamics of adaptation, had clear expectations that were testable in a fairly standard hypothesis-driven framework. For example, I was pretty sure we would see the rate of fitness improvement decelerate over time, and it has; and I was also pretty sure we’d see a quasi-step-like dynamic to the early fitness increases, and we did. Nonetheless, these analyses have yielded surprises as well, including evidence that fitness can increase indefinitely, and essentially without limit, even in a constant environment.

  15. OMagain: Toaster repair men don’t generally get listened to on that topic, do they? So what you have to say is frankly irrelevant, ‘Frankie’.

    Well Dawkins says that NS is blind. Others say it is mindless and doesn’t have any foresight. The experts agree with what I said. OTOH you are still an ignorant loser.

  17. Frankie: Well Dawkins says that NS is blind.

    Funny how you listen to what Dawkins has to say only sometimes.

    Frankie: The experts agree with what I said.

    Well, why don’t you say something and then put what the “experts” have to say next to that and show how your statement is supported?

    Frankie: OTOH you are still an ignorant loser.

    so ronery

  18. OMagain: Funny how you listen to what Dawkins has to say only sometimes.

    Well, why don’t you say something and then put what the “experts” have to say next to that and show how your statement is supported?

    so ronery

    I listen to what is actually supported. And I have done exactly what you requested. Again your ignorance is not a refutation.

  19. Frankie: Experts on evolution- you are being obtuse.

    Evolution is a vast topic. Funny how you never want to talk about specifics Joe.

    For instance, your claim is that evolution does not provide a nested hierarchy. Your “support” for that is someone saying that evolution does not produce “clean” breaks and you’ve expanded that into evolution does not created nested hierarchies.

    That is not support. If the “experts” agree with you that evolution does not created nested hierarchies then simply quote someone directly saying that.

    If you can’t, well, you lose.

  20. OMagain: Evolution is a vast topic. Funny how you never want to talk about specifics Joe.

    For instance, your claim is that evolution does not provide a nested hierarchy. Your “support” for that is someone saying that evolution does not produce “clean” breaks and you’ve expanded that into evolution does not created nested hierarchies.

    That is not support. If the “experts” agree with you that evolution does not created nested hierarchies then simply quote someone directly saying that.

    If you can’t, well, you lose.

    You don’t have any specifics to discuss. And I have supported my claim about nested hierarchies and evolution- TRANSITIONAL FORMS.

  21. Zachriel: With regards to rates of evolution, the question was whether evolution* will stop after the organism reaches an adaptive maximum.

    * Adaptive evolution.

  22. Frankie: ID has said what will falsify the design inference, Patrick. And ID is not about the designer.

    What are the entailments of design that are not dependent on the ability of the designer?

  23. Frankie: And I have done exactly what you requested

    No, you have not.

    Frankie: Read it and weep:

    The goals of scientists like Linnaeus and Cuvier- to organize the chaos of life’s diversity- are much easier to achieve if each species has a Platonic essence that distinguishes it from all others, in the same way that the absence of legs and eyelids is essential to snakes and distinguishes it from other reptiles. In this Platonic worldview, the task of naturalists is to find the essence of each species. Actually, that understates the case: In an essentialist world, the essence really is the species. Contrast this with an ever-changing evolving world, where species incessantly spew forth new species that can blend with each other. The snake Eupodophis from the late Cretaceous period, which had rudimentary legs, and the glass lizard, which is alive today and lacks legs, are just two of many witnesses to the blurry boundaries of species. Evolution’s messy world is anathema to the clear, pristine order essentialism craves. It is thus no accident that Plato and his essentialism became the “great antihero of evolutionism,” as the twentieth century zoologist Ernst Mayr called it.- Andreas Wagner, “Arrival of the Fittest”, pages 9-10

    I see nothing in there that supports your claim. Perhaps you could point to it?

    It might be the case that in your opinion blurry boundaries disallow nested hierarchies, but as discussed your opinion is not all that relevant.

    But if all those people agree with you, funny how you can’t actually find a single quote where they actually say what you claim they are saying. Not for a single one of them.

    How very strange!

  24. newton: designer

    “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”- Dr Behe

  25. Frankie: OM is too stupid to grasp what that means.

    What does it mean Joe? Why don’t you try explaining it in your own words?
    Or we could just ask Wagner:

    “We do know, however, that we all come from a single common ancestor. This is not the same as saying that life originated only once. Given the powers of self-organization, I would not be surprised if life arose many times, in hydrothermal vents, in warm ponds, or who knows where else. Among a multitude of faint lights that flickered on and off throughout the earliest history of the planet, some held steady, while others shone more and more brightly. But only one of them became bright enough to spawn all of today’s life. This is not a matter of opinion.”

    A single common ancestor, therefore a nested hierarchy.

  26. OMagain: What does it mean Joe? Why don’t you try explaining it in your own words?
    Or we could just ask Wagner:

    A single common ancestor, therefore a nested hierarchy.

    Umm a single common ancestor does not make it a nested hierarchy. You are either very ignorant or very dishonest.

    AGAIN Linnaean taxonomy is the observed nested hierarchy wrt biology. It has NOTHING to do with descent with modification. The same goes for the US Army- nested hierarchy without branching descent.

  27. Frankie: You are a moron. Of course that quote supports my claim. You have to be very ignorant not to understand that.

    I guess I must be very ignorant then. Why not explain how that quote supports your claim? As if the “Arrival of the Fittest” says evolution is too messy to produce a nested hierarchy you should be able to provide a quote saying that! Rather then what you did produce, which does not even use the phrase ‘nested hierarchies’!

  28. Frankie: I never said nor implied that scientists prefer non-ID causes least of all. Walter Bradly has made the case for gravity being evidence for ID. And what type of evolution are you talking about?

    Do you mean Walter Bradley of the Discovery Institute?

  29. OMagain: I guess I must be very ignorant then. Why not explain how that quote supports your claim? As if the “Arrival of the Fittest” says evolution is too messy to produce a nested hierarchy you should be able to provide a quote saying that! Rather then what you did produce, which does not even use the phrase ‘nested hierarchies’!

    I did provide the quote- you choked on it, as usual.

    TRANSITIONAL FORMS- they belong to more than one set. That violates a nested hierarchy.

  31. Frankie: Umm a single common ancestor does not make it a nested hierarchy.

    Oh? X (the first life) has two descendants, X1 and X2. Is that a nested hierarchy?

    OMagain: AGAIN Linnaean taxonomy is the observed nested hierarchy wrt biology.

    What’s that got to do with if a nested hierarchy is possible or not?

    Frankie: It has NOTHING to do with descent with modification.

    Yes, and that’s why it’s clear to all that you won that $10,000!

  32. Evolution’s messy world is anathema to the clear, pristine order essentialism craves.

    Nested hierarchies require clear and pristine order. And Linnaean taxonomy is the observed nested hierarchy.

  33. X (the first life) has two descendants, X1 and X2. Is that a nested hierarchy?

    Based on what? A family tree is not a nested hierarchy. Ancestor-descendent relationships do not form nested hierarchy.

  34. Frankie,

    Which experts, and on which particular aspects? You are being very vague.

    Experts on evolution- you are being obtuse.

    No, I’m simply asking you to support your claim. You asserted that the view of ‘experts on evolution’ diverges from mine, without any supporting evidence whatsoever.

  35. Frankie,

    ID has said what will falsify the design inference, Patrick.

    What would that be, exactly?

    And ID is not about the designer.

    Intelligent design creationism is all about the designer — it’s just that proponents don’t want to talk about that because it interferes with the goal of injecting sectarian beliefs in public school science classes.

  36. OMagain,

    Funny how you never want to talk about specifics Joe.

    Outing is specifically against the site rules.

    Suggesting that another participant is as willfully ignorant, vulgar, and lacking in common courtesy as one of TSZ’s former commenters is also rude enough to constitute a rule violation.

  37. Frankie: Nested hierarchies require clear and pristine order.

    I’m still awaiting a quote from any one of the people that you say agree with you actually agreeing with you.

  38. Patrick: Outing is specifically against the site rules.

    To be fair, Lizzie has also called him that. His schtick and vocabulary are so limited he basically auto-outs.

  40. Patrick: Suggesting that another participant is as willfully ignorant, vulgar, and lacking in common courtesy as one of TSZ’s former commenters is also rude enough to constitute a rule violation.

    I see what you did there.

  41. Richardthughes,

    To be fair, Lizzie has also called him that. His schtick and vocabulary are so limited he basically auto-outs.

    I’ve really gotta work on my delivery.

  43. hotshoe_,

    I see what you did there.

    And you say you don’t have a sense of humor!

    Then again, my wife isn’t convinced I do.

  44. Frankie,

    It doesn’t invalidate the results. The results just do not show that Behe’s IC can evolve.

    Elizabeth has refuted that claim several times. If she doesn’t join in soon, I’ll dig up one of her comments on this topic.

    The Evolving Complex Features thread discussed this very topic. In this comment Lizzie addressed Behe’s IC claims:

    Therefore EQU is IC by both the definitions Behe has offered: if you remove any part it breaks (definition one: IC feature); the only paths to it involve many neutral, and even deleterious, steps (definition two – IC pathways). And yet it evolves.

    There’s more in that thread.

  45. Frankie: You have reading comprehension issues. And no one can demonstrate the mutations in Lenski’s E coli were accidents/ errors/ mistakes.

    That’s what the 12 independent lineages demonstrate. None of them are the same, despite having been grown in the same environment side by side and founded by the same bacterium. So even if it’s “natural genetic engineering”, it’s random. Aka “accidents/errors/mistakes”.

    Some times it helps if you actually know something about the experiment and the results of it. Joe, there were 12 lineages grown side by side, each in their own flask, passed every day to a new one with the same medium, at the same temperature, at the same time, for over 60.000 generations so far. They were founded by same bacterium over 20 years ago. None of those lineages are genetically identical today. The distribution and types of mutations that have accumulated in them are independent. Basically they pass every test for randomness you can think of. It’s random.

  46. I think one reason for the Lenski hate is that ID/Creationists see many of their classic go-to “arguments” destroyed in a single experement.

    Genetic entropy? Seems not or we’d have noticed in 60.000 gens.
    In built responses to environmental cues? Seems not, the environment is static yet none of those lineages are genetically identical. And one one got the citrate bonus prize.

    And so on. These are core ideas for some of the lower-caste ID teamsters as the mathy stuff is over their pay grade, and so these are cherished ideas above all others.

    So, the hate and anger.

    I mean, did you see the Conservapedia attempt on Lenski’s integrity?

    http://scienceblogs.com/pharyngula/2008/06/24/lenski-gives-conservapdia-a-le/

    It was a classic. If you can’t dispute the data then it’s all a fraud by the hegemony of the Darwinian academia!

  47. OMagain: I think one reason for the Lenski hate is that ID/Creationists see many of their classic go-to “arguments” destroyed in a single experement.

    Yep. The experiment that destroyed genetic entropy, irreducible complexity, natural genetic engineering, and various preconfiguration theories, as Pasteur destroyed spontaneous generation.

  49. It is illustrative of the desperation some exhibit. On the one hand, people dismiss as trivial the notion that ‘microevolution’ happens. Yet here we have some of that, in 12 flasks in a lab, that they would chop their legs off rather than accept at face value.

    Likewise (to nod towards the OP) much verbiage has been directed towards the invalidity of GAs/EAs as models of evolution. Till one is used to attempt undermine ‘Darwinism’. Then, they’re triffic!

    I recall BA77 attempting the reverse gambit – ‘we’ like GAs, so here’s one whose results we must accept unquestioningly … accept one, you must accept them all. Hee hee.

  50. Under what metric of species applicable to bacteria, is the evolution in Lenski’s experiment an example of microevolution? I wonder whether any actual tests have been done to try to see if something has changed that would normally be considered “macroevolutionary” change for prokaryotes?

    Sorry for opening this can of worms, but the bacterial speciation question is important here I think?

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