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. phoodoo: So each time you quote a computer simulation, that has pre-specified targets, its busllshit.

    Is “don’t die” a target?

  2. phoodoo:
    Rumraket,
    No evolution (according to you all) has no pre-specified targets.So each time you quote a computer simulation, that has pre-specified targets, its busllshit.

    It’s not an accurate reflection of how evolution works in nature, no.

    phoodoo: But you only call the ones bullshit that don’t accomplish the theory you want them too

    No I don’t, you’re just making this up now.

    Depending on how the different simulations work they all have valid criticisms. Some are closer to how evolution actually works than others. Some only simulate a single mechanism, like natural selection. One such example is Dawkins WEASEL, it is simply a selection simulator. It doesn’t work like evolution works in nature.

    phoodoo:but praise the ones that supposedly do support your theory.that’s how stupid the whole science of your simulations is.

    I agree, if I really did what you accuse me of, that would be stupid and hypocritical. Fortunately I am not guilty of your accusation.

    phoodoo:But you of course want it both ways.

    I actually don’t.

    phoodoo:Make a computer simulation that all it does is break copies aimlessly. See if anything worthwhile ever occurs.

    Can you elaborate on this proposed simulation here? What is being copied, how is it broken and why does it even happen? How it is determined what is “worthwhile” in this simulation?

  3. Did the bacteria in Lenski’s experiment “break copies aimlessly”? No, they did not. So why would we expect a simulation that “breaks copies aimlessly” to simulate evolution?

  4. llanitedave: The evolutionary alternative to humans is not “junk DNA”.

    OK that is a small start. Do you think that a string coding for humans is more interesting than say a string coding for Amoebozoa?

    peace

  5. fifthmonarchyman: OK that is a small start. Do you think that a string coding for humans is more interesting than say a string coding for Amoebozoa?

    peace

    Interesting? No.

  6. Rumraket: Did the bacteria in Lenski’s experiment “break copies aimlessly”?

    Did Lenski’s experiment have a predetermined goal/target?

    Peace

  7. Rumraket: Interesting? No.

    Well there you go, as long as there is nothing specific to explain Evolution does a fine job of explaining. You only run into problems if you believe that particular phenomena require an explanation ( ie are interesting)

    peace

  8. fifthmonarchyman: Did Lenski’s experiment have a predetermined goal/target?

    Peace

    No. Multiple (12 actually) lineages evolved independently and they have evolved in different directions. Only one of the 12 lineages has evolved the ability to utilize citrate under aerobic conditions.

  9. fifthmonarchyman: Well there you go, as long as there is nothing specific to explain Evolution does a fine job of explaining. You only run into problems if you believe that particular phenomena require an explanation ( ie are interesting)

    peace

    You have equivocated between interesting and “requiring explanation”. Amoebezoa requires the same level of explanation as Homo Sapiens, in the sense that they both exist and as such we want to explain how they came to exist.

    Evolution explains them both as the product of natural selection, mutation and genetic drift from their ancestors.

  10. fifthmonarchyman: Did Lenski’s experiment have a predetermined goal/target?

    It’s important to distinguish between a target “problem” to be solved, a target “solution” and a target “sequence”.

    The Sanford paper has a target “sequence”, and in WEASEL, all three are the same.

    In AVIDA and the citrate experiments only the “problem” is specified. As in nature, where the “problem” is presented by the environment.

  11. Elizabeth: It’s important to distinguish between a target “problem” to be solved, a target “solution” and a target “sequence”.

    The Sanford paper has a target “sequence”, and in WEASEL, all three are the same.

    In AVIDA and the citrate experiments only the “problem” is specified. As in nature, where the “problem” is presented by the environment.

    That is true, but I think it is important to also explain that in the Lenski experiment, there is no actual picking of the fittest going on. Nobody selects interesting bacteria from the previous day to continue the same experiment onwards. They just grow and reproduce, and what makes it to the next day’s round of incubation is that which manages to outcompete its neighbors.

  12. Rumraket: No. Multiple (12 actually) lineages evolved independently and they have evolved in different directions.

    Are each of the 12 lineages equally interesting? In other words does the ability to utilize citrate under aerobic conditions require an explanation in your view?

    peace

  13. Elizabeth:

    In [….] the citrate experiments only the “problem” is specified.

    I am not a biologist, and may be wrong, but my understanding of Lenski’s experiment was that the only “problem” was survival. There was no expectation at the outset of breeding a strain that could metabolise citrate.

  14. Elizabeth: In AVIDA and the citrate experiments only the “problem” is specified.

    Is the evolution of human level intelligence a problem that needs an explanation?

    Are there any other candidate sequences that will yield human level intelligence?

    peace

  15. fifthmonarchyman: Are each of the 12 lineages equally interesting? In other words does the ability to utilize citrate under aerobic conditions require an explanation in your view?
    peace

    They are all equally interesting in the sense that they all equally require an explanation for their individual properties.

  16. Tamara Knight: I am not a biologist, and may be wrong, but my understanding of Lenski’s experiment was that the only “problem” was survival. There was no expectation at the outset of breeding a strain that could metabolise citrate.

    I think she means that there necessarily had to have been a decision about what kind of environment the bacteria were to be grown in. Do we grow them in LB media or something else? Do we grow them at 22 degrees C or 37 or something else? And so on.

  17. Rumraket: I think it is important to also explain that in the Lenski experiment, there is no actual picking of the fittest going on.

    There is pre-picking going on.

    The experiment is designed so that bacteria that are deemed more interesting will survive to reproduce. In this case more interesting equals better at metabolizing citrate

    peace

  18. fifthmonarchyman: Are each of the 12 lineages equally interesting? In other words does the ability to utilize citrate under aerobic conditions require an explanation in your view?

    Equally interesting to whom? An observed increase in fuction in one population allows the underlying mutations to be examined. To the researcher trying to do this, I’m sure this strain was much more interesting. My understanding is that he/she not only explained it, but showed it was repeatable. That is, ancestors of the population that had aquired the function carried a previous neutral mutation, and could once again aquire the new function by way of a second beneficial mutation acting on the pre-existing neutral one.

  19. Rumraket: They are all equally interesting in the sense that they all equally require an explanation for their individual properties.

    Here is where we disagree.

    A lot more “ink” has been spilt discussing the lineage that utilizes citrate under aerobic conditions. That tells me that for most of us that lineage is more interesting.

    I’m not aware of folks spending a lot of time trying to explain the individual proprieties in the other lineages. If they are doing so it’s not been covered in the press AFAIK perhaps this is because the public is not that interested.

    I would be interested to know if there is a complex function that arose that was not actively selected for in the experiment.

    peace

  20. fifthmonarchyman,
    There is pre-picking going on.
    The experiment is designed so that bacteria that are deemed more interesting will survive to reproduce. In this case more interesting equals better at metabolizing citrate

    Except in this case it was not “better at”, it was “able to”. If there is any “picking” involved, by definition in this case it can only have occured after the evolution .

  21. Tamara Knight: Equally interesting to whom?

    That is the question I am asking. I think humans are uniquely interesting. Folks here seem to disagree.

    I want to know what the odds of their arrival are. If you don’t care then you wont find the stuff like Sanford paper to be of much value

    peace

  22. fifthmonarchyman: There is pre-picking going on.

    The experiment is designed so that bacteria that are deemed more interesting will survive to reproduce. In this case more interesting equals better at metabolizing citrate

    This like saying the arctic has been designed to pre-pick for brown bears better at becoming white and hunting for food in the snow and ice.

    In a sense you are basically saying that you expect it to be inevitable that an organism placed in a new environment will adapt and evolve to exploit any niche available therein.
    I don’t belive you meant to imply that, so you either have to modify your statement or accept that this is what you believe.

  23. Tamara Knight: If there is any “picking” involved, by definition in this case it can only have occured after the evolution .

    The decision to target citrate utilization was done before the experiment began. The design of the environment was made with this target in mind.

    As rumracket says “evolution does not work that way”

    peace

  24. Rumraket: In a sense you are basically saying that you expect it to be inevitable that an organism placed in a new environment will adapt and evolve to exploit any niche available therein.

    I would not say it’s inevitable. Limits and complications are possible

    I would however say that life is designed to adapt and evolve to exploit any and every niche available.

    peace

  25. fifthmonarchyman: The decision to target citrate utilizationwas done before the experiment began. The design of the environment was made with this target in mind.

    Technically the bacteria used in the experiment could already utilize citrate, so the experiment was merely run with the kinds of compounds the bacteria were already capable of using.

    The thing that changed during the course of the experiment, is the bacteria evolved such that they could use it when oxygen was present. Normally they only switch to using citrate if there is no oxygen in the environment.

  26. fifthmonarchyman: Is the evolution of human level intelligence a problem that needs an explanation?

    Well, it’s a particularly interesting problem, but no different, in principle, from the the evolution of, say, wrists, or lungs, or wings, or eyes, teeth, or opposable thumbs. They all “need” explanation in the sense that it would be neat to have some idea of the specific likely pathway, but more important is to find the principles that govern the evolution of useful features, such as, wrists, lungs, teeth, intelligence, etc.

    IMO

    Are there any other candidate sequences that will yield human level intelligence?

    Not sure what you mean by “other”. I specifically think we should NOT be looking for “candidate sequences”.

  27. fifthmonarchyman: There is pre-picking going on.
    The experiment is designed so that bacteria that are deemed more interesting will survive to reproduce. In this case more interesting equals better at metabolizing citrate

    This is utter bullshit. The experiment was designed to monitor change. There was no expectation that citrate metabolism would evolve within the expected span of the experiment. Nor has the experiment been discontinued as a result of achieving a goal.

    The only expectation was drift.

  28. fifthmonarchyman: I would however say that life is designed to adapt and evolve to exploit any and every niche available.

    Well, it doesn’t do that. You are painting bulls eyes after the arrow has landed.

    When a population must adapt in order to survive, the most likely outcome is extinction.

  29. When a population must adapt in order to survive, the most likely outcome is extinction.

    Well said — ergo extinction is the more natural course of real evolution, not the emergence of complexity to deal with. Elimination of Species according to Natural Expectation.

  30. Mung: Great. So you’re only 5-6 years out of date. Where is the latest source code?

    Here’s the website. We had emailed the author in 2009, but never received a response. The current version still has the bug.
    http://mendelsaccount.sourceforge.net/

    Simple tests show that the program doesn’t comport with biological observations. The question we had was why it didn’t work.

    Working fitness is the result of random effects on adaptive fitness. However, the divide by zero-to-one function largely erases any signal from adaptive fitness. Nor is it a tunable parameter. This single line means that adaptive fitness is of negligible effect, which renders the entire program non-functional and meaningless. The claimed genetic meltdown is an artifact of bad programming.

    In order to replicate Mendel’s Accountant’s exciting achievement of overthrowing a century of evolutionary science, we created an alternative program, Gregor’s Bookkeeper (unpublished), which uses a tunable noise parameter to represent random effects, gamma distribution of beneficial to deleterious mutations, roulette wheel mating, dominant and recessive alleles, as well as drift in fecundity, population size, and mutation rate.
    http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?act=ST;f=14;t=6034;st=150#entry147439

  31. stcordova: Well said — ergo extinction is the more natural course of real evolution, not the emergence of complexity to deal with. Elimination of Species according to Natural Expectation.

    And that is what we observe. Most species go extinct. However, robustness to change is itself a “heritable” characteristic at the level of the population – so as time goes on, we’d expect lineages with heritable characteristics that promote adaptive evolution to preferentially survive.

    So capacity to evolve adaptively is itself subject to selective evolution.

  32. Zachriel: We had emailed the author in 2009, but never received a response. The current version still has the bug.

    That’s worth a letter to the journal, I would have thought.

  33. stcordova: Well said — ergo extinction is the more natural course of real evolution, not the emergence of complexity to deal with. Elimination of Species according to Natural Expectation.

    Yes, which is why many more species have gone extinct, than could ever simultaneously exist, in the process of evolving that complexity.

    In a sense you could say the complexity of extant life has been paid for in the deaths of countless species.

    Except the thing about “more natural”, less likely or more complicated outcomes are not “less natural”.

  34. I don’t see anything actually wrong with the paper, except for the repeated claims that it is “biologically realistic”

    That’s why I suggested evolutionists create their own models based on first principles of population genetics and give their waiting time figures.

    Mendel’s Accountant does confirm classic results like those of Kimura for fixation rate and time of fixation. No one has explored, to my knowledge the waiting time for evolution of coordinated structures. I don’t think other models will give materially different results since Mendel is based on standard population genetics.

    Fixation rate of nearly neutrals: Mendel’s Accountant agrees with mainstream

    Time to fixation: Mendel’s accountant agrees with mainstream

    Genetic Entropy: some agreement, some disagreement

    Waiting Time: TBD, not studied by mainstream

    I believe some change (aka mutation) must be non-random with respect to evolving coordinated function. Darwinian Selection can’t select toward non-existent coordinated traits.

    Biological systems have a round about way of doing things like a Rube Goldberg machine. There is lots of pointless metabolic extravagance like the Peacock’s tail being part of the reproductive ritual.

    Darwinian selection didn’t explain such extravagance of Peacock’s tails in Darwin’s day, it doesn’t today.

  35. stcordova: That’s why I suggested evolutionists create their own models based on first principles of population genetics

    The problem there is that population genetics isn’t built on “first principles”. That’s the problem as I see it with MA. The equations of population genetics are clever simplifications of much more complex processes that result from far more fundamental principles i.e. the principle of heritable variance and biased survival.

    Population genetics (Joe will tell me if I am wrong) allow us to substitute the chaos of evolutionary process with relatively orderly and well-behaved equations that work very well under certain specified assumptions.

    AVIDA, in contrast to MA, doesn’t use population genetics parameters to simulate evolution – it actually runs evolutionary processes to produce populations that adapt to thrive within the environment provided.

  36. Tamara Knight: I am not a biologist, and may be wrong, but my understanding of Lenski’s experiment was that the only “problem” was survival. There was no expectation at the outset of breeding a strain that could metabolise citrate.

    thanks to you and rumraket for making this clear.

    I should have said something like: only the problem was provided – a problem WAS provided, in the form of a citrate substrate.

    And one strain managed to solved the problem of how to utilise that substrate.

  37. Cordova, what you are aking for can’t be done. Instead of searching for something specific, evolution is just searcjing for “whatever works”. So if we are to estimate the average waiting time for “anything that works while requiring X number of mutations” we need to have an idea about how frequent “things that work” are in the immediate phenotypical space to our starting point. But “things that work” work contingently on environment, so now we need extremely detailed knowledge of the environment too. And so we are suddenly where we can’t just do population genetics, we need to simulate a physical world to make the kinds of estimates you want. And we just don’t have that kind of technology yet.

  38. stcordova: Genetic Entropy: some agreement, some disagreement

    Mendel’s Accountant does not properly model even simple cases of natural selection. This is because the working fitness function is broken.

  39. Zachriel,

    Thanks for the code snippets. It’s worth looking into, but I think the latest incarnation is written in Python and some of the FORTRAN has been superceded.

  40. Rumraket: And so we are suddenly where we can’t just do population genetics, we need to simulate a physical world to make the kinds of estimates you want. And we just don’t have that kind of technology yet.

    Exactly. But we CAN do proof-of-concept studies, such as AVIDA, which show that functions that require interacting components, non-selected components, and even components which, alone, are markedly deleterious, nonetheless evolve given relatively few “rewards” for simpler functions. And also show that any one function can come about by a large number of different sequences.

  41. stcordova: Thanks for the code snippets. It’s worth looking into, but I think the latest incarnation is written in Python and some of the FORTRAN has been superceded.

    The recent Sanford et al. paper links to http://sourceforge.net/projects/mendelsaccount/, which indicates that the program is written in Fortran, Perl, and JavaScript. The download still includes the Fortran source code, with the bug. Perhaps it’s no longer being used. If so, do you have the actual working source code?

    If the bug was removed at some point, that should have been documented somewhere, and the original results thrown out. Even someone with a rudimentary knowledge of arithmetic can see why the division severely dilutes the signal from natural selection, meaning the program doesn’t even properly model simple cases that are easily observed in nature.

  42. And we just don’t have that kind of technology yet.

    We have the technology, it’s called the real world in real time!

    Lenski showed new digestive function can evolve, but it took a bacterial population with thousands of generations and abundant offspring. New function evolved at a glacial pace, and why expect, for homonins with smaller reproductive excesses and more time between generations (20 years vs. 20 minutes for E. Coli) to have short waiting times.

    In the real world you have abundant extinction in the present day. Functioning architectures are lost faster than they are created in the biosphere.

    You’ll complain, “that’s because of man’s industrialization”. So what? That’s what is real. Darwinian theory relies on evolution of Rube Goldberg complexity by environments that are never directly observed, only postulated.

    The more specific (specified) an environment has to be to facilitate the evolution of Rube Goldberg complexity, the more improbable and far from natural expectation it will be as a matter of principle.

    If complexity naturally arises, it should not have many qualifiers in the evolution of that complexity, much like heat going from a hot body to a cold body is the more phenomenon (vs. the reverse where air conditioners exist).

    One does not need a lot of qualifiers to argue heat is more inclined to flow from a hot body to a cold one, and that to do this you need some specific mechanism like an air conditioner.

    In like manner if Darwinian selection evolves Rube Goldberg complexity whereby tasks like making babies is done in a increasing roundabout manner as we go up the ladder from prokaryotes to humans, it should happen in environments that don’t need to have lots of qualifiers and specification.

    The fact that extinction is happening rapidly today and evolutionists complain man is accelerating the cause for destruction of complexity today is an example of adding qualifiers. If anything, man is ADDING to the selection pressure on other species, not detracting from it. And look what is happening.

    Observations do not agree with theory (of Darwinian selection). We have the models in the real world. Computer simulations like AVIDA are decoupled from the real world because it is only in specific, and therefore improbable environments, that complexity arises via a selection scenario.

    I don’t mean to be belligerent since you guys are more civil than what I’m accustomed to in other forums, but that’s why I don’t accept Darwinian evolution.

    If I weren’t a creationist, I’d go with something like non-random mutation (some evolutionary 3rd way) or multiverse anthropic cosmological principles — at least those will work in principle.

  43. stcordova: In the real world you have abundant extinction in the present day. Functioning architectures are lost faster than they are created in the biosphere.

    What do you mean by this?

    stcordova: One does not need a lot of qualifiers to argue heat is more inclined to flow from a hot body to a cold one, and that to do this you need some specific mechanism like an air conditioner.

    The analogy does not work. Evolution does not violate the 2nd Law.

    stcordova: Observations do not agree with theory (of Darwinian selection). We have the models in the real world. Computer simulations like AVIDA are decoupled from the real world because it is only in specific, and therefore improbable environments, that complexity arises via a selection scenario.

    Why do you say this? What evidence supports this claim?

    stcordova: I don’t mean to be belligerent since you guys are more civil than what I’m accustomed to in other forums, but that’s why I don’t accept Darwinian evolution.

    But you haven’t given a reason!

  44. Functioning architectures are lost faster than they are created in the biosphere.

    Functioning architecture AKA species

    I elaborated here:
    http://www.uncommondescent.com/darwinism/the-price-of-cherry-picking-for-addicted-gamblers-and-believers-in-darwinism/

    Skip past the part about addicted gamblers, and you’ll see the tally of new species created by natural selection versus the number of species eliminated by natural selection via direct observation in the field.

    Regarding the number of species being evolved by Natural Selection in the present day:

    Wins: 0
    Losses: thousands
    Net: -thousands

  45. stcordova: Regarding the number of species being evolved by Natural Selection in the present day:
    Wins: 0
    Losses: thousands
    Net: -thousands

    Mass extinctions have occurred in the past, for various reasons.

    What is your evidence that new species are not arising? Show your work.

  46. stcordova: Lenski showed new digestive function can evolve, but it took a bacterial population with thousands of generations and abundant offspring.

    The genus Homo has been around for about the same number of generations. Not all that much change in biology.

    stcordova: In the real world you have abundant extinction in the present day.Functioning architectures are lost faster than they are created in the biosphere.

    Sure, there’s an ebb and a flow in terms of overall complexity. Earth may be experiencing a mass extinction. Humans depend on their natural environment, so it’s a concern for humans. Not so much for bacteria.

    stcordova: Darwinian theory relies on evolution of Rube Goldberg complexity by environments that are never directly observed, only postulated.

    Actually, we have a great deal of evidence concerning ancient ecosystems.

    stcordova: If anything, man is ADDING to the selection pressure on other species, not detracting from it.

    And when selection pressures are too great, many organisms will go extinct. No biggie — unless you are affected by the extinction event, of course. It’s an opportunity for the survivors! Cockroaches unite!!

  47. stcordova: Functioning architecture AKA species

    I elaborated here:
    http://www.uncommondescent.com/darwinism/the-price-of-cherry-picking-for-addicted-gamblers-and-believers-in-darwinism/

    Skip past the part about addicted gamblers, and you’ll see the tally of new species created by natural selection versus the number of species eliminated by natural selection via direct observation in the field.

    Regarding the number of species being evolved by Natural Selection in the present day:

    Why are you counting “number of species”? Speciation isn’t really a consequence of natural selection. It can occur purely through drift. Considered longitudinally species isn’t even a binary construct.

  48. What is your evidence that new species are not arising? Show your work.

    The problem is I couldn’t find any reports of new species except maybe the Grant’s on the Galopagos Island claiming a new “species” emerged.

    Two creatures unwilling or unable to mate even if descended from a common ancestor, seems a little unworkable as a definition of species.

    How about significant taxonomically restricted genes or morphologies as a means of defining species?

    If you disagree with my general point the number of species on Earth today is declining, then I think you’re in the minority.

    Mass extinctions have occurred in the past, for various reasons.

    And the number of phyla got reduced as are result, didn’t it? 🙂

    Elimination of Phyla by Means of Natural Selection or the Preservation of Favored Phyla in the Struggle for Existence.

  49. stcordova: I don’t mean to be belligerent since you guys are more civil than what I’m accustomed to in other forums, but that’s why I don’t accept Darwinian evolution.

    I also don’t accept your version of Darwinian evolution.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.