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

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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! 😯 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.

Comments
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?Phinehas
September 16, 2013
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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.Elizabeth B Liddle
September 14, 2013
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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?Phinehas
September 13, 2013
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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. :(Phinehas
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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?Phinehas
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.Chesterton
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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"send" - "second" - sorry!Elizabeth B Liddle
September 13, 2013
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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".Elizabeth B Liddle
September 13, 2013
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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...Phinehas
September 13, 2013
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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 allelesChesterton
September 13, 2013
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It ain't darwinian if the selection or the production is artificial. That's just a fact.Joe
September 13, 2013
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Mayr is right. But the Darwinian part works equally well if the production of genetic variation is artificial, as in GM crops.Elizabeth B Liddle
September 13, 2013
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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.
Joe
September 13, 2013
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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?Joe
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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)Joe
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.Chesterton
September 13, 2013
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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.Joe
September 13, 2013
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HT a friend through e-mail
The friend gave me permission to identify him, it was JoeCoder. Salscordova
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.Chesterton
September 13, 2013
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What is it with you guys and teleology?
What is it with you and materialism?cantor
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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Ooops - Except that has nothing to do with Darwinain evolution- you are equivocating again.Joe
September 13, 2013
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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.Joe
September 13, 2013
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