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ICC 2013: Calling all Darwinists, where is your best population genetics simulation?

While having lunch at ICC 2013 with biologist and genetic engineer Robert Carter and the unnamed evolutionary biologist who got laughed off stage (let us call him Erik), I raised a question which the evolutionary biologist and other Darwinists (including Michael Lynch) have not provided satisfactory answers for, namely, “what is the evolutionary simulation that will resolve problems of speed limits of evolution, cost of substitution, rate of substitution, neutral evolution, Haldane’s dilemma, Muller’s ratchet, Haldane’s ratchet, Kondrashov’s question, mutational meltdown, etc?”

John Sanford, Walter ReMine, John Baumgardner, Wes Brewer, Paul Gibson, Robert Carter, others created Mendel’s Accountant. Erik kept lambasting the program, “did you model recombination, do you model variable population sizes, do you model linkage, synergistic epistasis, truncation selection, heterozygous advantage, etc.” To Erik’s astonishment, Robert Carter said, “yes”. Erik was horrified, since he was so sure there had to have been some flaw in Mendel’s Accountant because Darwinism can’t be false. Erik knew we had him up against the ropes in this discussion. Erik gave the standard Darwinist line, “Haldane was wrong because he used unrealistic parameters.”

I then said to Erik, “Ok, can you tell me what software evolutionary biologists use to answer these questions? What results do you get when you use realistic parameters?” Erik look stunned! :shock: I called his bluff. He said, “I don’t know, but I’m sure it’s out there.” Wish I had a photo of the look on his face. A picture is worth a thousand words. :-)

Walter ReMiine made the same observation. Walter wrote Michael Lynch to ask, and Lynch said there weren’t any. Jody Hey at Rutgers has a simulation, but it doesn’t have the depth of Mendel’s Accountant. Further, Walter got a hold of Hey’s public domain program and discovered an interesting bug (feature).

Hey uses the standard evolutionist trick or renormalizing the fittest individual for every generation. What this means is suppose the children on average are sicker than the parents — in this case, functionally speaking the next generation is less fit than the parents, but using Enron-like accounting, Hey’s program simply renormalizes the notion of “fittest” to the fittest of the sick kids, not the fittest relative to the healthier parents. (I delved into this less-than-honest equivocation in Death of the Fittest.) When ReMine set the default to non-renormalization, the populations went extinct!

So, I’m calling all Darwinists, what is your software and what are your results:

1. What is the speed of substitution through natural selection under realistic parameters. Haldane says 1 trait per 300 generations for human populations. What is your figure? I asked Erik that same question, and he was evasive. So Darwinists, what is your figure? The human genome has 3 giga base pairs, how many of these per generation can be evolved via selection versus drift?

2. If there are N deleterious mutations per individual, how are they purified out of the genome without causing extinction. For 6 deleterious mutations per individual, using the Poisson distribution, I calculate a human female will have to make over 800 kids in addition to truncation selection. So how is genetic deterioration arrested except through the Enron-like accounting trick of renormalization?

3. What is the fixation rate of slightly deleterious mutations?

4. What is the accumulation of harmful mutations that aren’t fixed? I predicted it would be on the order of N for N harmful mutations per individual or some proportion of N (like 0.5 N).

So Darwinists, what is your software, and what are your results? I’d think if evolutionary theory is so scientific, it shouldn’t be the creationists making these simulations, but evolutionary biologists! So what is your software, what are your figures, and what are your parameters. And please don’t cite Nunney, who claims to have solved Haldane’s dilemma but refuses to let his software and assumptions and procedures be scrutinized in the public domain. At least Hey was more forthright, but unfortunately Hey’s software affirmed the results of Mendel’s accountant.

As I’ve said, Mendel’s Accountant affirms what is already well accepted in evolutionary literature, except that it goes a step further and shows where it will lead (not in favor of Darwinism). See: If not Rupe and Sanford, would you rather believe Wiki?.

So the Darwinists keep lambasting Mendel’s Accountant. Fine, where is the Darwinist software and what are the answers to the above questions? Here is your chance to shine, guys.

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85 Responses to ICC 2013: Calling all Darwinists, where is your best population genetics simulation?

  1. I have been waiting so long for some realistic time calculations from neodarwinism! What is going on??

  2. Could you please fix this url: (near the top of the op)

    “unnamed evolutionary biologist who got laughed off stage”

    thanks.

  3. owendw,

    Fixed. Sorry for the trouble. Thanks for the correction.

    Sal

  4. Thanks! Now I can enjoy your challenge to the Darwin party – I can’t wait to see the mathematical evidence that mutation is a creative process . . . but I fear I may not live that long.

  5. Hey uses the standard evolutionist trick or renormalizing the fittest individual for every generation. What this means is suppose the children on average are sicker than the parents.

    Why would the fitness of parents be an issue if the children are not competing with them for resources? They’re dead, they might have been more fit but they cannot exploit this advantage from the grave.

  6. Why would the fitness of parents be an issue if the children are not competing with them for resources? They’re dead, they might have been more fit but they cannot exploit this advantage from the grave.

    So are you admitting it is standard to cover-up genetic deterioration in a population by ignoring the fact the ancestors are healthier than descendants?

    In such case, the notion of fitness relative to functionality is somewhat meaningless.

    So fitness of the parents is an issue if you’re concerned about health and well-being versus reproductive success. If descendants are on average sicker than ancestors, shouldn’t we call evolution “survival of the sickest”?

    Any way, thank you for responding, and if you have answers for the questions posed, feel free to provide them.

  7. Sal, I think it would be best called “survival of the less sick of the sicklings”.

  8. So are you admitting it is standard to cover-up genetic deterioration in a population by ignoring the fact the ancestors are healthier than descendants?

    I don’t understand why such a result would be strange or contradictory. In vivo species go extinct all the time, it would be a mistake to presume that evolution has a goal of always making each species more fit, and each generation more fit than the previous. A species can be very fit, but if outcompeted by other species, the children will become less fit without any mutation. Individuals in an climate or chemical environment that is too challenging will be less fit than their parents.

    Are you using “sicker” and “healthier” as synonyms for less and more fit, or do they mean different things?

    So fitness of the parents is an issue if you’re concerned about health and well-being versus reproductive success.

    I don’t think health and wellbeing, apart from reproductive success, is relevant to a discussion of evolution. Evolution will make the sickest, dumbest creatures possible if that’s what’s necessary to maximize fecundity and population.

  9. I don’t think health and wellbeing, apart from reproductive success, is relevant to a discussion of evolution. Evolution will make the sickest, dumbest creatures possible if that’s what’s necessary to maximize fecundity and population.

    Ironically, I agree with you on that point. Thank you for your response.

  10. Or to put the last sentence in proper terms: In a certain environment, if sick, dumb creatures are the most fecund and successful, that’s what you’ll get.

  11. Ironically, I agree with you on that point.

    I don’t see the problem then… why is it wrong to renormalize fitness with successive generations?

  12. I don’t see the problem then… why is it wrong to renormalize fitness with successive generations?

    Thanks for asking such a good question. Many evolutionary biologists don’t see it as a problem, and are dismayed that engineers find it to be a problem. There is something of a cultural conflict between the two disciplines. It is no surprise many of the critics of evolutionary theory are engineers.

    There are two separate discussions:

    1. reproductive success
    2. evolution of design

    Evolution of design is foremost in the minds of those at UD.

    If evolution of novel design are reproductively disfavored, then this is a problem for Dawkins hypothesis that design is the result of evolution. If existing designs are not sufficiently maintained because of mutational accumulation, then evolution is not a good explanation for the appearance of complex designs in nature.

    The population genetic arguments are relevant to determining if evolutionary mechanisms can created integrated complexity.

    If selection can only fix 1 trait every 300 generations, then it become hard to believe the increase in complexity in humans from the chimp-human ancestor was due to selection (only 1000 changes, perhaps at the nucleotide level could fixate through selection)

    One could invoke neutral evolution, neutral drift and mutation, but then that’s just claiming luck creates the designs in nature. Former engineers like myself find this hard to believe on theoretical grounds.

    PS
    A not-so-nice description of this conflict between engineers and evolutionary biologists is here:
    http://rationalwiki.org/wiki/Salem_Hypothesis

    I don’t agree with the characterization, but the Salem Hypothesis probably has a grain of truth to it as seen in this present discussion. What I see as a problem is not a problem to you. And that is one source of our disagreements.

  13. Why would the fitness of parents be an issue if the children are not competing with them for resources?

    why is it wrong to renormalize fitness with successive generations?

    Perhaps because it does not accurately model the real world, where they are not competing solely among themselves?

  14. sigaba,

    More to a specific example of Haldane’s dilemma. If there are numerous orphan genes, then how did they evolve. Haldane’s dilemma creates a serious problem for the evolution of the individual nucleotides (along with codon bias) via natural selection. Say an orphan might has 1000 nucleotides, and if there are a thousand orphans in one mammalian genome, this may constitute a sufficient gap to question selection as the mechanism of creating those orphans.

    These are questions that are worth exploring, I’m not so sure that proposed evolutionary mechanisms are adequate, in fact, it looks problematic enough that I find ID more believable.

  15. Case in point of reproductive success in the presence of genetic deterioration.

    Humans are more populous now than ever, but it is believed on average we are sicker genetically speaking:

    Myopia
    Diabetes
    Asthma
    Emotional disorders
    Reduced intelligence

    The list goes on. As Fodor complained, the definitions of what it means to be selected for or reproductively successful are to vague to form a coherent theory…

    Are we more or less fit than in the past given we’ve figured out how to make more humans…

  16. Humans are more populous now than ever, but it is believed on average we are sicker genetically speaking

    What is your basis for describing these traits as deleterious?

    I find that your assignment of certain genetic traits and good and bad has a distasteful eugenic flavor, which I am certain you do not intend but I think is a consequence of this kind of argument.

    Are we more or less fit than in the past given we’ve figured out how to make more humans…

    By definition, if we’ve figured out how to make more, we’re more fit in the evobio sense. We might be fat, ugly and dumb, but as long as the gametes are meeting up the system continues to work. We only have to be smarter or better sighted than the next man, after all, no other animal can offer realistic competition with even a relatively nearsighted, dullard human.

    I’ll stay away from your quantitative analysis because I don’t have the background to follow it.

  17. I think moving the argument to be around why renormalizing is or isn’t the correct thing to do is bypassing the fact that the accumulation of deleterious mutations in the population is therefore occurring and has the consequence of the population trending sicker. This is not onward and upward evolution, it’s devolution. Such a process would not build up an immune system where there as none – as one example.

  18. JGuy, evolution doesn’t go “onwards and upwards” at all. Most lineages go extinct. Ours probably will as well.

    And it is true that mutations are accumulating in the human population that would make us sicker if we lived in a world in which we didn’t have ways to make us well.

    In other words, currently we live in a fairly benign environment in which mutations can accumulate that would kill us in a harsher one.

    However, we are still doing pretty well. And if a global plague wipes out 99% of us and life as we know it, mutations that are neutral in the current environment will suddenly become deleterious, and become rapidly rarer.

  19. I think moving the argument to be around why renormalizing is or isn’t the correct thing to do is bypassing the fact that the accumulation of deleterious mutations in the population is therefore occurring and has the consequence of the population trending sicker.

    Well, it’s an important point on methodology, I pointed out that it was a deviation from nature on a point and the defense was that “engineers see things differently from scientists.”

    I’ve read the manual on MENDEL, and I have some questions which I don’t really see answers for.

    * It creates mutations and assigns them a beneficial or harmful value — is this a scalar score? Is it dependent on some environmental factor — positive or for some individuals but harmful or neutral for other individuals (like the alleles for sickle cell, skin melanin, or lactose intolerance)?

    * When you select the number of children a mother has, is that the number of live births, the number of reproducing offspring, or the number of fertilization events? Are costs associated with births? How is miscarriage modeled?

    * Is competition between individuals in a population modeled, for food, mates? How is competition with other populations in an environment modeled?

    * Is kin selection or sexual selection modeled?

    * If you use a carrying capacity population model, how are changes to carrying capacity modeled? Carrying capacity depends on food sources, which are subject to adaptations.

    My impression is that you couldn’t really model an animal like a chimpanzee with a program like this. Certain adaptations, in particular bipedalism, toolmaking and hierarchical social structure, can have radical nonlinear effects on fitness.

  20. There are many software packages for simulating different aspects of population genetics, but usually do something interesting you have to code your own simulation, or, even, explore the properties of a mathematical model.

    For the cost of substituion (“haldane’s dilmea”) we can use this approach to establish there is only a “cost” in when selections is imposed form outside (e.g. predation, or a changing climate) not for intra-specific competition. It seems odd, to me at least, to call this a cost of substitution, not a genetic load forced on a population due to its environment. Anyway, you can calculate the “speed” limit imposed on natural selection in those cases, with the cost spread across multiple loci, and see how all the parameters influence it. In that specific case there is a cost, but it’s not nearly as harsh as Haldane suggested.

    I had to laugh at your calling Michael Lynch a “Darwinist” – I don’ think he’d take to kindly to that

  21. If there are numerous orphan genes, then how did they evolve. Haldane’s dilemma creates a serious problem for the evolution of the individual nucleotides (along with codon bias) via natural selection.

    Why? Each true orphan is one is one substitution, and would arise by soft selection (or no selection, come to that). I don’t think Haldane’s dilemma is relevant to this question at all

  22. Lizzie:

    JGuy, evolution doesn’t go “onwards and upwards” at all.

    It does in Darwin’s only diagram in his book “On the Origin of Species…”.

    Just sayin’

  23. I guess another question would be, where is Intelligent Design’s best population genetics simulation?

    We have Mendel’s Accountant, which is purported to be an accurate model of the neo-Darwinian/modern evolutionary synthesis, and it report that the model doesn’t match the natural history. So where is the ID model that does match the natural history?

  24. It does in Darwin’s only diagram in his book “On the Origin of Species…”.

    If that’s as good as you’ve got this thread is over…

  25. It does in Darwin’s only diagram in his book “On the Origin of Species…”

    If that’s as good as you’ve got this thread is over

    Yeah – it’s also, and it hardly matters, not true. The branches go up the page, but there is no sense of progress in either the figure or the explanatory text. (Darwin is talking about divergent selection as a diversifying force)

  26. Oh OK, so metazoans are NOT onwards and upwards of prokaryotes. :roll:

    Let’s see, according to Darwin living organisms started very simple and has definitely progressed to more complex organisms, including organisms that can classify all organisms.

    BTW sigaba, how are those magnetic stripes hovering over the ocean floor?

  27. Joe, the basis of your argument is the direction a diagram was drawn on a piece of paper. You lose. Just stop.

  28. AVS, the basis for my argument was laid out in comment 26. The drawing represents exactly what I said. You lose. So shut up.

  29. Oh OK, so metazoans are NOT onwards and upwards of prokaryotes.

    I don’t know, how are you going to measure that? In any case, it doesn’t follow from the fact that one lineage progressed over time that evolution is a progressive process.

    If evolution was a random walk with respect to “progress” some lineages would go “upwards” others wouldn’t.

  30. You:
    It does in Darwin’s only diagram in his book “On the Origin of Species…”.
    Just sayin’

    My interpretation:
    Because he drew the diagram in the upwards directions, he was therefore showing that evolution has a direction “upwards and onwards.”

    Did I misinterpret or are you really that dumb?

  31. AVS, wd400, Lizzie and sigaba-

    I F#@ked up- Just the tree of life NOT Darwin’s diagram in “On the Origin of Species…”. I forgot that was just a generic diagram depicting ancestor-descendent relationships.

    So my apologies.

    According to the tree of life organisms have gone onwards and upwards. And yes I understand that is NOT a requirement and it just happened that way on this planet.

  32. Oh OK, so metazoans are NOT onwards and upwards of prokaryotes.

    In terms of their breadth of adaptations they’re far superior. No metazoan can live in boiling water, nor can count their population in the 10^30s *(there are 3.9 * 10^23 in your gut alone). It’s all a question of suitability for a particular purpose; they’ll far outlive us on Earth, that’s for certain.

    I’m not sure it does any good to quote back at me stuff I talk to UB about — that guy’s so far off in Gödel-Escher-Bach-land that I can hardly make heads or tails of what I’m trying to say out of context, let alone him.

    AVS, the basis for my argument was laid out in comment 26. The drawing represents exactly what I said. You lose. So shut up.

    There were, like, real points being made about 10 comments ago :(

  33. Oh OK, so metazoans are NOT onwards and upwards of prokaryotes.

    I don’t know, how are you going to measure that?

    Number of parts. Or do you think that it is OK for the unguided OoL to start with say, metazoans? And if you don’t think that is OK, why?

  34. sigaba:

    In terms of their breadth of adaptations they’re far superior.

    Sometimes simple is better. Unguided evolution likes simple.

  35. Sometimes simple is better. Unguided evolution likes simple.

    When is complicated better? It might be better if you phrased this as “sometimes simple is all that’s possible,” that way you make your point and avoid speculating on the designer’s purpose.

  36. WD400,

    There are many software packages for simulating different aspects of population genetics, but usually do something interesting you have to code your own simulation, or, even, explore the properties of a mathematical model.

    Thank you for the response, but specific names or projects or papers would be helpful. For Haldane’s dilemma, Nunney’s secret program, Ewens program come to mind. For mutational meltdown, Jody Hey’s.

    Sigaba,

    I’ve read the manual on MENDEL, and I have some questions which I don’t really see answers for.

    By MENDEL I presume you mean Mendel’s accountant. I respect you have questions, but maybe we could just bypass this if you can suggest a program that evolutionists have developed and what answers they’ve come up with such as the rate of substitution via natural selection.

    So feel free to name a specific simulation that gives numbers.

    Why? Each true orphan is one is one substitution, and would arise by soft selection (or no selection, come to that). I don’t think Haldane’s dilemma is relevant to this question at all

    No it’s not, unless you invoke A new mechanism of evolution — POOF.

    To that end, I’ve not yet seen answers to:

    1. substitution rate via natural selection under realistic parameters

    2. solution to the harmful accumulation rate order N for a mutation rate of N except through renormalization

    These are basic questions that should have answers if people like Dawkins are claiming that selection can create the designs of life. Even if one is not an ID proponent, answers to Haldane’s dilemma would indicate whether most evolution proceeds neutrally or via selection. I’ve publicly sided with the neutralists…

  37. sigaba:

    When is complicated better?

    When simple isn’t sufficient.

  38. Ok, how about a concrete example. WD400 proposes lactose persistence trait will overtake the human population. How long will that take before every human on the planet is lactose persistent?

    Sal

  39. I respect you have questions, but maybe we could just bypass this if you can suggest a program that evolutionists have developed and what answers they’ve come up with such as the rate of substitution via natural selection.

    I’m not sure anyone’s conceded that a computer model can usefully model this, I haven’t, my whole point is that the real system has too many unknowns an nonlinearities. Computer modeling is incredible technology in physics and problems with small numbers of known parameters, but outside of that it’s pretty mixed. We can barely model the price of a Treasury Bond on a daily basis, despite decades of work on the part of our best mathematicians, and now you propose to dispose of the entire evolutionary synthesis because the computer model doesn’t square with 100,000 years of natural history?

    It’s a clichéd point but this isn’t evidence of design, it’s just evidence against the present evolutionary model, if we grant (arguendo) that the Mendel model exhaustively simulates the modern evolutionary synthesis (which I don’t).

    You could address this by naming a specific ID simulation that is more accurate. Mendel’s Accountant is your software running with your parameters, I think the burden is on you to provide the counterexample.

  40. selection.

    I’m not sure anyone’s conceded that a computer model can usefully model this, I haven’t,

    You do not have to model every complexity, model the most ideal case with generous assumptions, and if the most ideal case fails why should the more complex less-than-ideal case succeed? Example, assume all deleterious mutations are purged, what is the necessary reproduction rate needed to sustain purifying selection. I provided the mainstream number based on the Poisson distribution in :

    http://www.uncommondescent.com.....e-fittest/

    Mendel’s accountant affirms this, and this is already known.

    Assume we have slightly deleterious mutations, how many go to fixation. Mendel’s Accountant yields the mainstream number predicted by Kimura.

    Assume realistic parameters for human evolution. Mendel’s Accountant yields the number predicted by Haldane.

    If one feels it cannot be modeled, I respect that, but lets be honest, that isn’t exactly reassuring that one has found an evolutionary mechanism in operation today that can be extrapolated to the past.

    I said before, if we look at the present day and recent past, Mendel’s Accountant seems fairly accurate– i.e. humans are getting sicker even though they are more reproductively successful.

  41. If one feels it cannot be modeled, I respect that, but lets be honest, that isn’t exactly reassuring that one has found an evolutionary mechanism in operation today that can be extrapolated to the past.

    Replace “evolutionary mechanism” with “Intelligent Design mechanism” and the statement is just as true, and we are at an impasse.

    I don’t really buy the idea that a scientific proposition has to be modeled with a computer in order for it to be valid or persuasive; that would imply that we had no reliable scientific theories until the Manhattan Project.

    humans are getting sicker even though they are more reproductively successful

    I’m kinda coming to the conclusion that your concept of “sicker” is unscientific, that you’ve got some ideal human somewhere and deviations therefrom are “sick.” You can’t define “sick” in objective terms for the purposes of this inquiry.

  42. Liz:

    …evolution doesn’t go “onwards and upwards” at all.

    So, if we start calling it “devolution” instead, no one would have any heartburn over that? I’m OK discussing the Theory of Devolution if everyone else is. Any objectors?

  43. I’m OK discussing the Theory of Devolution if everyone else is.

    What is it with you guys and teleology?

  44. With the manhattan project we had a working example which is better than a computer simulation. With evolutionary biology you have neither working examples nor simulations, and the equations and theories that evolution does have (from population genetics) don’t actually support Darwinian evolution as the main mechanism of evolution.

    Evolutionary theory would be more believable if we saw new proteins evolving, we don’t, instead we see them disappearing from the biosphere.

    If you want to go from computer models to hard data, such as observed extinction rates and genetic deterioration, then I’m not so sure that helps evolutionary theory.

    I’m kinda coming to the conclusion that your concept of “sicker” is unscientific, that you’ve got some ideal human somewhere and deviations therefrom are “sick.”

    Say what? That was the conclusion of Michael Lynch, Bryan Sykes, and the Darwinists Eugenecists — or are you saying we’re getting healthier with each generation on average. Here are some notions of more sickness:

    Diabetes
    Asthma
    Allergies
    Obesity
    Emotional Disorders
    Autism

    If you say I’m unscientific, you may as well claim that for most of the medical profession that recognizes these as defects.

  45. That was the conclusion of Michael Lynch, Bryan Sykes, and the Darwinists Eugenecists.

    Lynch’s paper is interesting:

    Because most complex traits in humans have very high heritabilities, the concern then is that unique aspects of human culture, religion, and other social interactions with well intentioned short-term benefits will eventually lead to the long-term genetic deterioration of the human gene pool.

    Human culture is artificial selection, not natural selection. We’re destroying our own genome, nature isn’t doing it for us. He later states that in pre-industrial societies, mutation loads are far lower.

    If you say I’m unscientific, you may as well claim that for most of the medical profession that recognizes these as defects.

    “You can’t define ‘sick’ in objective terms for the purposes of this inquiry.”

  46. I guess the point is that once human beings starting verbalizing and making tools, you can’t really use them as a model species for natural selection anymore.

    Are there examples of genomic deterioration in other animals? Are these results controlled for anthropogenic changes to the environment? I think these would be the next questions.

  47. sigaba:

    P: I’m OK discussing the Theory of Devolution if everyone else is.

    S: What is it with you guys and teleology?

    What is it with you guys and equivocation? Without the ability to equivocate on words like “evolution” and “fit” and “selection” the Darwinist house of cards crumbles.

  48. Without the ability to equivocate on words like “evolution” and “fit” and “selection” the Darwinist house of cards crumbles.

    I don’t follow…

  49. Oh I get it. Are we really going to dig through the Golden Oldies?

  50. I should point out something. With respect to the accumulation of harmful mutations at a rate of N, there are some considerations with the binomial distribution and sexually reproducing species.

    If a mom has 10,000 harmful traits and dad also has 10,000 harmful traits, according to the binomial distribution if they had 5 kids, one will have 9,994 bad mutations. If we have truncation selection, then yes, an equilibrium point where a constantly bad population is maintained that doesn’t get worse, but then we have to assume truncation selection!

    So then the question is, what happens if we have less than truncation selection. We have two means to answer the question:

    1. computer simulations
    2. real populations

    James Crow was perhaps the first big name to assert the equilibrium point, but we don’t know where that point is except to say the absolute limit is the entire genome! I got a good laugh when Walter ReMine told me that’s the clear equilibrium limit.

    In any case, it is an open question for sexually reproducing species, but it seems pretty inevitable that deterioration is inevitable for asexually reproducing species. These are testable assertions.

    HT a friend through e-mail

  51. In any case, it is an open question for sexually reproducing species, but it seems pretty inevitable that deterioration is inevitable for asexually reproducing species.

    I got one guy telling me unguided evolution likes simple unicellular organisms, I got the other guy telling me they’re all impossible!

    Oh well, thank you, this has been an interesting conversation.

  52. Phinehas:

    So, if we start calling it “devolution” instead, no one would have any heartburn over that? I’m OK discussing the Theory of Devolution if everyone else is. Any objectors?

    Yes. Evolution doesn’t mean “downwards” either (not that “devolution” means it either). Adaptive evolution biology is simply a process of optimisation to an environment. A benign environment will tend to render most variants largely neutral. A harsh environment will render most deleterious. A changed environment will change some variants from neutral to beneficial, and some from neutral to deleterious.

    We live in a fairly benign environment so most variants are neutral. But by no means all, and those of us who have an early fertility peak (me for instance) are at risk of leaving no offspring because we live in an environment that tends to cause us to postpone our childbearing till later.

    So I can make a very firm Darwinian prediction about the human lineage: the female fertility window will move steadily later in the lifespan.

  53. Scordova:

    bacteria show no signs of “deterioriating” even though they they reproduce extremely rapidly, and have been doing so for billions of years.

    Of course the overwhelming majority of bacterial lineages go extinct. It doesn’t leave us short of bacteria.

  54. Scordova:

    bacteria show no signs of “deterioriating” even though they they reproduce extremely rapidly, and have been doing so for billions of years.

    There seems to be widespread reductive evolution in microbial genomes.
    http://www4.lu.se/o.o.i.s/30369

    And here is a proposed example of Muller’s ratchet:
    http://www.ncbi.nlm.nih.gov/pubmed/8610134

  55. I completely agree that Muller’s ratchet will tend to operate in “small asexual populations”.

    As a result, the vast majority of bacterial lineages die out.

    Yet we still have bacteria, because the tiny minority that escape the load do just fine – better than fine, because no bacterial population remains “tiny” for long.

    In other words, asexually reproducing organisms persist because they reproduce so abundantly. In contrast, sexually reproducing organisms persist despite not reproducing so abundantly, because sexual reproduction avoids the problem of Muller’s ratchet.

  56. Lizzie:

    So I can make a very firm Darwinian prediction about the human lineage: the female fertility window will move steadily later in the lifespan.

    Except that has nothing to do with farwinain evolution- you are equivocating again.

  57. Ooops -

    Except that has nothing to do with Darwinain evolution- you are equivocating again.

  58. Yes, it does, Joe. I base my prediction on the principle that variants that promote reproduction in the current environment will become more prevalent. That is the basic principle of Darwinian evolution. Now that women have the ability to control their own fertility, and the incentive to postpone child-bearing, those women whose genetics mean they are more fertile later will leave more of their genetic material in the population than those that don’t.

    So the mean peak will move later.

  59. What is it with you guys and teleology?

    What is it with you and materialism?

  60. Now that women have the ability to control their own fertility, and the incentive to postpone child-bearing, those women whose genetics mean they are more fertile later will leave more of their genetic material in the population than those that don’t.

    This would be darwinian evolution if the moving of the peak is due to new genes that make that change irreversible, if not it is just variation on the proportion of genes in the same population.

  61. It’s Darwinian evolution either way, Chesterton. Darwin did not specify where the variation came from.

    But you raise an important point, which I will address.

    Firstly, one definition of evolution is “change in allele frequency over time”. Both drift and Darwinian selection can produce such a change. In this case I predict a specific change in allele frequency via Darwinian mechanisms.

    Secondly, assuming that by “new genes” you mean “new alleles” (new genes are extremely rare), new alleles are being generated all the time. You almost certainly have some alleles that represent gene variants that were possessed by neither of your parents. So both drift and adaptive (Darwinian) evolution is happening all the time, as the frequency of both old and new alleles changes.

    Thirdly, most phenotypic traits are the result of many many genes, and thus of many many alleles. How tall you are depends not on what pair of alleles of a single gene you inherited from your parents, but on whole cocktail of genes of each of which you have two versions.

    So a woman’s fertility window probably (almost certainly) depends on a whole cocktail of genes, many of which will have many polymorphisms in the population, and those polymorphisms are constantly being added to, and changing in frequency. Some of them will tend to push the fertility window one way, some another.

    This means that as time goes on, and women postpone childbearing, those women who happen to have a set of alleles that promote a later fertility window will leave more of those alleles in the population. Those alleles may include brand new ones, fairly new ones, and ones that have been around for ages.

    So I suggest that your distinction is not in practice a distinction. As long as there is a constant drip-feed of new alleles into the population (and there is) each of small effect (so they are neither catastrophic nor wildly beneficial, alone), which most are, as the environment (including the availability of contraception) will tend to result in those that promote a particular trait will become more common, and any new ones that promote that trait will also become more common.

    This is why we breeders manage to breed tiny dogs, for example, something that would be impossible of new alleles of genes that contribute to size weren’t continually appearing in the dog population. They do nothing for average size of dogs in the wild population, but they do a lot for dogs in an environment where being small increases your chances of leaving puppies, so they become more prevalent there.

  62. HT a friend through e-mail

    The friend gave me permission to identify him, it was JoeCoder.

    Sal

  63. Except that has nothing to do with Darwinain evolution- you are equivocating again.

    Lizzie:

    Yes, it does, Joe. I base my prediction on the principle that variants that promote reproduction in the current environment will become more prevalent.

    Lizzie, Darwin required that the changes by random, ie chance events.

    That is the basic principle of Darwinian evolution.

    Not according to Mayr and others.

    Firstly, one definition of evolution is “change in allele frequency over time”.

    Yes and more than darwinian evolution can cause that.

    IOW you are just equivocating because A) you do NOT understand what Darwin said and B) you do not understand that directed evolution can cause allele frequency to change.

  64. Secondly, assuming that by “new genes” you mean “new alleles” (new genes are extremely rare)

    Do you mean that there new genes between us and a chimp?

    You almost certainly have some alleles that represent gene variants that were possessed by neither of your parents. So both drift and adaptive (Darwinian) evolution is happening all the time, as the frequency of both old and new alleles changes.

    How then chimp are humans genoma are 90% identical?

    So I suggest that your distinction is not in practice a distinction. As long as there is a constant drip-feed of new alleles into the population (and there is) each of small effect (so they are neither catastrophic nor wildly beneficial, alone), which most are, as the environment (including the availability of contraception) will tend to result in those that promote a particular trait will become more common, and any new ones that promote that trait will also become more common.

    This is why we breeders manage to breed tiny dogs, for example, something that would be impossible of new alleles of genes that contribute to size weren’t continually appearing in the dog population. They do nothing for average size of dogs in the wild population, but they do a lot for dogs in an environment where being small increases your chances of leaving puppies, so they become more prevalent there.

    This is the reason I said your prdiction is not based on the ToE intended as the all the life comes frm a LUCA by RM+NS. Your prediction is based on Evolution intended as variation of the allele composition of a population over time, that I think nobody denies is a scientific fact.

  65. There seem to be there are a few de novo genes between us and the last common ancestor of us and chimps. I seem to recall about 60, so about .03% of genes. But it’s important to distinguish between new alleles of existing genes and new genes.

    This is the reason I said your prdiction is not based on the ToE intended as the all the life comes frm a LUCA by RM+NS. Your prediction is based on Evolution intended as variation of the allele composition of a population over time, that I think nobody denies is a scientific fact.

    Well, you were doubting whether the female fertility window could be anything other than the rearrangement of existing alleles. Almost certainly it will be, because new alleles are being made all the time.

    And if new alleles are being made all the time, there isn’t an “edge” to how far a population can move in order to adapt to a new niche. It’s not limited by the existing allele pool. That’s why, as I said, we have tiny dogs, way tinier than any dog in the wild ancestral population. New alleles have appeared, and been selected, by breeders, to produce tiny dogs. The breeders didn’t make the alleles, they just arrived, as alleles do.

    All life doesn’t come from a “LUCA”. The LUCA was not the earliest life, and its ancestors obviously didn’t come from it. But if you mean that all life today came from a common ancestor, yes, indeed, that is a very well-supported model.

    And as the sexual reproduction process can produce new alleles very frequently, and new genes occasionally, and as these are constantly being fed into the genetic pool of a population, there’s no reason to think that the process of adaptive evolution and drift that we observe in real time couldn’t simply be a small video-shot of a process that has been going on for millions of years, taking us from, say, vertebrate fish to vertebrate air-breathing mammals, just as it can, in a very short time, take us, as I predict, from animals whose female fertility drops off sharply after 30, to animals whose female fertility stays high for considerably longer.

    Too late for me, although I did finally manage to pop one out.

  66. Lizzie:

    But if you mean that all life today came from a common ancestor, yes, indeed, that is a very well-supported model.

    Suported with what? Please be specific. (I bet I can support a common design with the same type of support you choose for universal common descent)

  67. Joe: Lizzie, Darwin required that the changes by random, ie chance events.

    No, he didn’t. He required that natural selection acted on heritable variation. He didn’t know where the variation came from. At one time he favored Lamarck’s idea, which is not random. In any case, it doesn’t matter what he “required”. The essence of Darwinian evolution is heritable variation in reproductive success. It works whether the variants are genetically engineered or accidental.

    Joe: IOW you are just equivocating because A) you do NOT understand what Darwin said and B) you do not understand that directed evolution can cause allele frequency to change.

    I’m less concerned about what Darwin said than in whether heritable variance in reproductive success results in adaptation and it does. We call it “Darwinian evolution”. and, as it happens, it’s what he proposed.

    And of course directed evolution can cause allele frequency to change. Farmers have been doing it for centuries.

  68. Lizzie, Darwin required that the changes by random, ie chance events.

    Lizzie:

    No, he didn’t.

    Yes, he did. He proposed design without a designer.

    And again I have Mayr and other evolutionary biologists to back me up- what do you have besides you?

  69. Ernst Mayr in “What Evolution Is”:

    The first step in selection, the production of genetic variation, is almost exclusively a chance phenomenon except that the nature of the changes at a given locus is strongly constrained. Chance also plays an important role even at the second step, the process of elimination of less fit individuals. Chance may be particularly important in the haphazard survival during periods of mass extinction.

  70. Mayr is right.

    But the Darwinian part works equally well if the production of genetic variation is artificial, as in GM crops.

  71. It ain’t darwinian if the selection or the production is artificial. That’s just a fact.

  72. So Elizabeth you start with

    So I can make a very firm Darwinian prediction about the human lineage: the female fertility window will move steadily later in the lifespan.

    Then you admit that

    Well, you were doubting whether the female fertility window could be anything other than the rearrangement of existing alleles. Almost certainly it will be, because new alleles are being made all the time.

    And to keep alive your “darwinian prediction” say

    there’s no reason to think that the process of adaptive evolution and drift that we observe in real time couldn’t simply be a small video-shot of a process that has been going on for millions of years, taking us from, say, vertebrate fish to vertebrate air-breathing mammals, just as it can, in a very short time, take us, as I predict, from animals whose female fertility drops off sharply after 30, to animals whose female fertility stays high for considerably longer.

    That is the darwinistic ToE, the extrapolation of alleles frequency variation over time as mechanism for the original of species. But your prediction do not come from this extrapolation it come from the observation of frequency variation of alleles

  73. Liz:

    P: So, if we start calling it “devolution” instead, no one would have any heartburn over that? I’m OK discussing the Theory of Devolution if everyone else is. Any objectors?

    L: Yes. Evolution doesn’t mean “downwards” either (not that “devolution” means it either). Adaptive evolution biology is simply a process of optimisation to an environment. A benign environment will tend to render most variants largely neutral. A harsh environment will render most deleterious. A changed environment will change some variants from neutral to beneficial, and some from neutral to deleterious.

    In the minds of most, to “evolve” means to move upward and onward. Perhaps this is the result of how the Tree of Life is typically drawn. Perhaps it is due to popular analogies like “Climbing Mount Improbable.” (Can anyone think of a book on evolution that speaks in terms of “Descending into The Improbable Valley” instead?) Perhaps it is because folks are told that evolution solves the bacteria to man dilemma, and most see that dilemma as very much one of upward-ness, and not just onward-ness. Evolution doesn’t present itself in popular literature as random oscillations of which man is simply a point on the biggest hump. If natural “selection” has no upward component to it, what is it exactly that it can accomplish that can save man from being the product of merely random forces?

    Again, the equivocation is rampant and essential to the survival of the Darwinist. On the one hand, evolution is always couched in terms that paint a clear directional arrow from “lower” to “higher” life forms. But if you try to pin down the science, suddenly any upward implications are denied. We are told that nature “selects,” but when you pin down the science, Darwinists seem confused that folks are thinking in terms of teleology.

    If there is no “upward” component to evolution, then how can it help explain the “upward” progress from bacteria to man?

    Darwinists will suddenly have difficulty understanding what I mean by “higher” life forms or man being in any sense “upward” from bacteria in 3…2…1…

  74. Well, a small nitpick – the theory of evolution does not say that humans evolved from bacteria. But let’s say you meant some kind of primitive one-celled organism no longer extant.

    The theory of evolution accounts for both ancient one-celled organism to modern one-celled organism and ancient once-celled organism to modern multi-celled organism.

    And while multicellular organisms are more complex than single-celled organisms, there isn’t any clear metric to say whether a tiktaalik is more, or less, complex than a human being, or, indeed than a modern fish.

    So the ladder is a poor metaphor. The reason hill-climbing comes into it is that Darwinian evolution is an optimising process. It doesn’t promote complexity per se, indeed, it often simplifies, as complexity is expensive, metabolically, but it does promote optimal probability of breeding successfully in the current environment.

    Your send paragraph is deeply unfair, although I am not accusing you of being deliberately so. I am increasingly aware that the vast majority of those who think there is a problem with “Darwinism” mistake the nature of the claims of evolutionary biology.

    There is no equivocation here, merely a great deal of miscommunication. When a “Darwinist” (me, for instance) tries to clarify, I will often be told I am “equivocating”. The opposite is the case. I am trying to be extremely precise, so as to make sure that no equivocation is possible.

    This is fundamental science, hence the concept of the “operational definition”.

  75. “send” – “second” – sorry!

  76. Chesterton:

    That is the darwinistic ToE, the extrapolation of alleles frequency variation over time as mechanism for the original of species. But your prediction do not come from this extrapolation it come from the observation of frequency variation of alleles

    You seem to be missing the part where I say that new alleles are being generated all the time, and new genes too, though far less frequently! If that is the case, and the evidence is that it is, then what is the problem with the extrapolation?

    Unless you are talking specifically about speciation events – when a population splits into two non-interbreeding, or minimally inter-breeding sub-populations and evolves independently down different lineages.

    But again, the differentiation of the lineages is more change-in-allele frequency over time, with the occasional input of a new gene, or the silencing of an old one.

  77. Joe: It ain’t darwinian if the selection or the production is artificial. That’s just a fact.

    It’s your idiosyncratic definition, Joe, not a fact.

    And it’s irrelevant. Heritable variation in reproductive success results in adaptation of a population to the current environment.

    If you don’t want to call that “darwinian” don’t, it doesn’t make it any less true.

  78. If that is the case, and the evidence is that it is, then what is the problem with the extrapolation?

    The point, if you want understand it, is that your prediction is based on frequency allele variation, not in darwinism that it is an extrapolation of the frequency allele variation.

    But again, the differentiation of the lineages is more change-in-allele frequency over time, with the occasional input of a new gene, or the silencing of an old one.

    This is all assumed, we do not have evidence that differentiation is more frequency allele variation and we do not know how could ocuur the occasional inpuy of a new gene.
    Also if that were true, your prediction is not(necessary) based on that.

  79. Yes, my prediction is based on the principle that there is a pool of variance in the population, constantly being replenished by new alleles, some of which will favour late fertility, and those will become more prevalent, including brand new ones, ones that haven’t even appeared yet. That is straight forward Darwinian evolution.

    I don’t understand the second part. We have lots of evidence that new alleles are constantly being generated, and lots of evidence that traits are polygeneic. And that’s what I base my prediction on.

    And we also know a fair bit about how new genes emerge, although that obviously is much less common.

  80. Liz:

    Miscommunication will suffice as a more charitable descriptor for the problem. Clarification is certainly worth pursuing.

    My sense is that the average layperson sees Darwinian evolution as a proposed solution to the LUCA to human dilemma and that, for them, this dilemma is more about an increase in complexity than an increase in diversity; more about an upward climb than a lateral spread; more about the rise of more highly advanced and coordinated systems than about ad hoc differential reproduction; and more about raw creative power than random oscillations.

    Whether Darwinists actively promote the belief that their theory addresses the perceived dilemma or merely allow it to persist may be an open question, but from where I’m standing, the kind of evolution being presented here addresses issues most folks don’t have, remains silent on the issues most folks do have, and does little to correct the perception that what hasn’t been addressed actually has. What does Darwinian evolution have on offer to explain the unbelievably improbable advancement from the first self-replicator to a human being? Surely it is this advancement that defies understanding and begs for an explanation, is it not? Surely it is the progress up that cries out for understanding, is it not?

    Darwinian evolution is an optimising process.

    Even the word “optimize” implies that something is becoming better and not merely different. Most folks will simply adopt it into the upward advancement narrative they believe evolution offers. I understand this kind of “optimize” to be more analogous to liquid resin expanding to fill a cast. Environmental niches form the outlines and life expands obligingly to fill it. But, for me, this merely pushes the dilemma back a step. For me, this is like claiming that a garden gnome wasn’t designed. It may have the appearance of design, but it’s obviously only hardened liquid resin reacting according to liquid dynamics, chemistry and physics. OK. Now where did the apparent design in the cast come from?

  81. Optimize does mean “better” but in a very precise sense in this context; better able to reproduce successfully in the current environment.

    If that means being smarter, cool. If it means not having to waste metabolic resources on eyes that you don’t need, also cool.

    I actually quite like your garden gnome analogy – populations do sort of “flow” into environmental niches and adapt to them. But we don’t have to invoke a designer for the mould – it’s the environment itself, and the resources and threats that it offers.

  82. I actually quite like your garden gnome analogy – populations do sort of “flow” into environmental niches and adapt to them. But we don’t have to invoke a designer for the mould – it’s the environment itself, and the resources and threats that it offers.

    Right. And we don’t have to invoke a designer for the garden gnome mould either – we can suppose it emerged, or whatever. Design? What design?

    We see design, but nothing in evolution that would indicate it has the creative power to bring about the kind of advancement we see in living things, and nothing but random oscillation in the environment, yet humans emerged? It just boggles my mind that a smart person like you could find intellectual satisfaction in that kind of non-answer. :(

  83. Liz:

    Said another way, if life merely expands to take the shape of the environment, and life looks designed, then the shape of the environment looks designed as well. What mechanism explains the apparent design of the environment such that it can produce life that has apparent design? Or is it just random perturbations all the way down? Given enough time, random perturbations might harden into a garden gnome mould as well, I suppose.

    But here’s what bugs me: Why spend time talking about evolution and its rather mundane resin-like properties instead of the real elephant in the room–the surprisingly creative and exceptionally fortuitous shaping power of the environment? After all, which requires more explanation? The resin? Or the mould that appears to be shaped like a garden gnome?

  84. Phinehas: in this case, I’d say, the resin.

    The shaping process is much more interesting than the shape, which is just what’s there.

    To pursue your analogy: it’s a resin that beautifully arranges itself on a rocky planet in such a manner as to use the resources of that planet to sustain itself.

    The resin is the cool part.

  85. Liz:

    Sure, the resin is cool. It just isn’t very helpful in explaining away the apparent design of the garden gnome.

    You can talk about the wonderful properties of the resin all you want, but when someone sees the garden gnome mould sitting there, they are going to have a tendency to nod politely at your enthusiastic endorsement of resin and its properties, point to the mould, and raise their eyebrows. They will do this because they understand intuitively that the real explanation of the origin of the garden gnome–the one that defies the sufficiency of physics and chemistry alone and raises the biggest question marks in the mind of the observer–has merely been shifted to the origin of the mould.

    Isn’t it obvious that explaining the resin’s properties is a comparatively trivial part in explaining the garden gnome’s existence so long as the mould remains unexplained? And isn’t this especially so when one begs off even attempting to explain the origin of the resin?

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