Population Genetics

Population genetics has long been a predictor for evolutionary application in any given population. The premise is simple enough, as it employs an algorithm to quantify and determine how and why adaptations and gene frequency occurs. There is, however, a problem to be dealt with, first addressed by JBS Haldane, a 19th century evolutionary biologist/geneticist. He introduced, mathematically, the maximum possible likelihood of human mutation rates. His studies were the first to calculate the finite number of possible allele frequencies caused by recurring mutations at a gene locus and introduced the idea of a "cost" function to natural selection.While forming his thesis, he came to the revelation that there was a finite limit of possible beneficial mutations that later was coined as "The Haldane Dilemma." There exists a maximum of 1,667 beneficial substitutions over the past ten million years of the lineage that leads to modern man. The argument has been expounded by others who assert that substitutions into the population might be larger than a nucleotide. This includes insertion/deletion or inversion/duplication. Each of these count as a substitution, therefore the argument places a limit on the total number of substitutions. And this limitation has a profound impact on punctuated equilibrium, because this maximum number presents a problem for the pace at which evolution could occur."Several factors could reduce the 1,667 limit significantly. For example, according to Eldredge and Gould's evolutionary theory, punctuated equilibria, species are in statis at least 99% of the time, and Gould claimed punc-eq applies to human evolution. According to Gould (in his last book, The Structure of Evolutionary Theory) genetic change would typically cease during statis. If correct, this factor alone could reduce the Haldane limit by a factor of about 100, to a limit of 17 substitutions. I was the first to bring up this relationship between punc-eq and Haldane's Dilemma." -Walter Remine"I shall investigate the following case mathematically. A population is in equilibrium under selection and mutation. One or more genes are rare because their appearance by mutation is balanced by natural selection. A sudden change occurs in the environment, for example, pollution by smoke, a change of climate, the introduction of a new food source, predator, or pathogen, and above all migration to a new habitat. It will be shown later that the general conclusions are not affected if the change is slow. The species is less adapted to the new environment, and its reproductive capacity is lowered. It is gradually improved as a result of natural selection. But meanwhile, a number of deaths, or their equivalents in lowered fertility, have occurred." -JBS HaldaneWhat kind of effect, if any, does the "Cost theory" or "Haldanes Dilemma" present on population genetics?

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

Did you have a specific grievance with the computation?

ReMine has posted a challenge to question his thesis.Answer the following questions:

To help your discussion, start with the simplest conceivable scenario. The simpler the scenario, the more obvious will be your confusion:

Focus strictly on a single generation. If you can answer the questions for a single generation, then the same logic can be applied over-and-over again, to each and every generation. But if you cannot answer the questions for even one generation, then you have no business going further.

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Then answer those questions again at each step of the following ever-looser assumptions:

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

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What kind of effect, if any, does the "Cost theory" or "Haldanes Dilemma" present on population genetics?

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These issues are mischaracterizations of his argument. The argument is not about the genetic difference between divergent organisms. The figures were first supported by many eminent evolutionists before 1957. He is simply reiterating an argument posed by an evolutionist, Haldane, who candidly offered the theorum in the interest of scoence, not the special interest of evolution. ReMine answers his critics by stating:"If you compare divergent organisms (such as living chimps and living humans) on the basis of genetic or protein sequences, then you are misrepresenting my argument. That makes my argument less direct, more confusing, and most importantly, it grants evolutionists large fudge-factors that operate in their favor. That is why evolutionists typically (near universally) misrepresent my argument in this manner. They are attempting to grant favors to themselves, by misrepresenting my argument.

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Typically they do that by claiming I made an "invalid assumption" that they will "correct." That is falsehood. My argument assumes humans evolved from an ape-like ancestor (as evolutionists allege), and then shows a serious problem with that. Evolutionists cannot legitimately attack that as an "invalid assumption" in need of "correction."

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The public can understand Haldane's Dilemma, and readily sees it as a serious problem. Everything necessary to communicate the problem (the 1,667 limit) was available in 1957 when Haldane published his paper. Yet evolutionists did not communicate it to the public. They still haven't. In this matter they were grossly negligent. This is now a fact of history, and cannot be changed.

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For many decades already, evolutionary literature claimed Haldane's Dilemma was "solved." But that would require evolutionists to solve all the crucial components of the problem ” including the number of substitutions needed to create all the human adaptations. Evolutionists have scarcely begun to do that. Haldane's Dilemma was never solved." 1. Haldane used principles, and models of genetics and selection, that remain exceptionally predominant today in evolutionary genetics textbooks.2. In addition, Haldane used assumptions that favor evolution. When you 'break' such an assumption, not only do you not solve Haldane's Dilemma, you make the problem worse.3. Some of Haldane's assumptions were used (as still commonly done today) in order to simplify the math and generalize the results. You cannot solve Haldane's Dilemma by breaking one of these particular assumptions, since that merely complicates the problem without solving it. There is always a cost of substitution, no matter what model is used. Evolutionists must identify a model that actually solves Haldane's Dilemma, while remaining plausible on other grounds. They have not done that.As for the specious plea that genetics has developed more since the 1950's, one first has to consider that the backbone of genetics have not changed, such as Mendelian genetics. Its a simple, but elegant model that has straightfoward questions that have languished as far as being solved. ReMine lists some of the objections made by TalkOrigins and offers explanations for them.Haldane's Old Model: Haldane used a multiplicative-fitness model. (Moreover, for the parameters he used, it also approximates an additive-fitness model.) Both of those fitness models are still predominantly used today. Everything in "Haldane's model" is current with today's practice of evolutionary genetics (including Haldane's uses of fitness, fitness models, selection, alleles, genes, dominance, and Mendelian segregation). So if evolutionists throw-out "Haldane's model" they must also throw-out the modern textbooks on evolutionary genetics.Small selection coefficients? - Haldane assumed selection coefficients approaching zero. This gives the absolute minimum total-cost of substitution in each case. If you break Haldane's assumption, and invoke higher selection coefficients, then the cost increases, resulting in fewer substitutions, and Haldane's Dilemma worsens.The environmental-change scenario? - Haldane assumed substitutions begin in a peculiar way, via an environmental-change scenario. The scenario operates as follows. Neutral and slightly harmful mutations (though almost always eliminated outright) sometimes drift upwards in frequency, to arrive at moderate frequencies. Then, when the environment changes, one of these neutral or slightly harmful mutations is converted (it is alleged) into a beneficial mutation. This elevated starting frequency is where Haldane begins to tally the total-cost of the substitution. By giving the substitution a free head-start to an elevated frequency, it lowers the total cost of substitution. This cost-reduction is the only impact of the environmental-change scenario that Haldane allowed into his calculations. If you break Haldane's assumption, then it raises the total-cost of substitution, and worsens Haldane's Dilemma.Constant population size? - Haldane assumed the population size remains constant throughout a given substitution (though he allowed large varieties of population size, each for a different substitution). That was done partly for mathematical simplification (in the era before computers were readily available to readers). When evolutionists break this assumption, they do not "solve" Haldane's Dilemma. They merely obscure it further. There is always a cost of substitution; it is unavoidable. It is not enough to merely object to Haldane's simplification. Evolutionists must actually s-o-l-v-e Haldane's Dilemma.Infinite population size? - Evolutionists sometimes claim Haldane assumed an unrealistic "infinite population size." That is untrue. If Haldane had done that, then the total-cost of substitution would always be infinite - when Haldane calculated its average value is 30. So Haldane obviously did not use an infinite population size. Rather, Haldane used something at the other end of the spectrum. To see it, take a haploid species, and suppose there are two independent alleles, A and B (at independently segregating loci), each with a frequency of one per thousand. By random mating, the genotype AB (containing both alleles, A and B) would have a frequency of one per million. But if the population size is only one thousand individuals, then in a given generation, genotype AB cannot actually exist at a frequency of one in a million. Instead, either that genotype exists as a whole individual, or it does not exist - it either has a frequency of one per thousand, or zero. There is no 'in-between' when dealing with individuals that are quantized into whole-bodies. This difficulty is handled by Haldane, and by virtually all textbooks today, in the same way - by using non-quantized individuals. To greatly simplify the math, and to generalize the results, they allow a genotype to exist at its expected frequency (without having to quantize the genotype into, say, 1000 whole-bodies). Put simply, Haldane assumed non-quantized individuals, not infinite population size. If evolutionists want to throw-out that simplifying assumption, then they would have to throw-out virtually all of today's evolutionary genetics textbooks. And it still would not solve Haldane's Dilemma. How does he misstate Gould? The period of stasis is important to the pace of evolution. He is saying that, (actually, Haldane is saying, he is simply agreeing), that there is a finite number of possible mutations, whether by insertions, deleterious, or otherwise. He is also asking that the genetic load, genetic death, and selective pressures be examined and answered with any measure of credibility.

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

*delete* double postEdited by nemesis_juggernaut, : No reason given.

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

Again, this isn't ReMine's baby, its Haldane's. The figures were first compiled and tabulated in the 1950's be a host of evolutionists seeking to better understand population genetics. ReMine is just sort of rediscovering the issue and wondering why something this profound was overlooked. For evolution to occur, it requires the substitution of new beneficial mutation into the population to create new biological adaptations that survive the ax of natural selection. The number itself derives from Haldane's calculation that organisms with low reproduction rates, such as humans, (reproducing 0-8) offspring in a parents lifetime) could substitute a new beneficial mutation no more frequently than 1:300 generations. Now, if you really think about, this is completely true and its very straightforward.The best place to start this with a trial error is the human/simian lineage because its relatively easy to quantify. The ancestry between ans apelike ancestor begins around 10 million years ago, which is often offered as the most reasonably generous to give as much leeway as possible, without completely undermining the integrity of the experiment. Mathematically, this is already presenting a problem for possible beneficial mutations. The problem is further compounded when considering that the human adaptations in question are alleged to have evolved mostly within the last two million years. But at the end of the day, no low reproducing lineage could substitute more than 1667 beneficial mutations. That's extremely low. So low as to make all the alleged changes impossible. Well, that's a good question. According to evolutionary geneticists, each of those substitutions is typically represented as one nucleotide, not thousands of nucleotide differences. This is because a change in nucleotides, even in a small amount, can prove fatal to an organism. We all know that DNA has to be in precise order to function properly. Even if we take a small fraction of the 1,667 figure, it becomes less likely to have occured. The odds of having as much as 84 nucleotide change is an astronomical figure that greatly exceeds 10⁵⁰, which is mathematically representative of "absolute zero."If you evidence that such a high number of mutations can occur, benefically, in any organism and still live to pass that on, I'd love to hear about it. You also have to factor in genetic death or genetic load as a substitution cost for every good mutation. You'll see that you'll start to get into the negatives rather quickly at the rate necessary for evolution to have occured efficiently. ReMine goes over this, because you aren't the only one to offer gene clusters as a possible solution, such as pleiotropy or really anything considered polygenous. He states that this is grossly oversimplified to grant the impossible the possibility. Even under terrific circumstances where each gene acts independently of other genes, the figure is still too low."Evolutionists must accept what nature doles out - and we can observe what nature doles out. The issue is fundamentally empirical and observable, not one of telling stories about regulatory genes... when Haldane calculated the total cost of a substitution (=30), he assumed selection coefficients approaching zero, which gives the absolute lowest possible total cost of substitution. The figure rises for higher selection coefficients, and rises especially rapidly when selection coefficients get above one-tenth (s>0.1). Therefore, if evolutionary scenarios invoke high selection coefficients (such as mutations for antibiotic resistance or pesticide resistance), then the total cost of substitution gets quite high - and the number of substitutions (previously at 1,667) goes to a much lower limit.

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In summary, whatever the blend of substitutions, (a) they must correspond to what we observe in nature, and (b) they must meet the cost constraints, (higher selection coefficients will lower the plausible number of substitutions)." -Walter ReMine

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

You haven't addressed in what way either of then are wrong. You made a couple of points on what you thought he meant. I even posted ReMine's answer to his critics. Some of which were your objections. But you haven't addressed it, and simply saying, "he's wrong, he's all wrong," does nothing to offer your argument. Likewise, RAZD simply saying, "the math is wrong, its all wrong," doesn't explain how or why. If its wrong, I want to be shown why. If anyone can take ReMine's challenge or demonstrate why its wrong, I and ReMine would certainly concede. Right, Haldane peer reviewed it, and no one could answer the question. It simply faded into obscurity until years later. The point ReMine is making is that it wasn't solved then, and it hasn't been solved now. If there was really a simple solution to overcome the dilemma, why hasn't anything of rigor been offered? Heck, even Maynard-Smith, a very prominent evolutionist, admitted that it really did present a large challenge to the prevailing wisdom. Calling Mendelian genetics the staple of high school genetics is like saying that Newtonian law is the staple of high school law of gravitation. That's reducing its importance to the field to mere child's play. First of all, DNA was already known long before Crick and Watson. This is a bit of a misnomer here. DNA was first discovered in the late 1800's by Friedrich Miescher. Aside from which, Darwin and Wallace and the rest of the gang all knew there were heritable traits before DNA. It didn't take a genius to figure out that animals produce like animals, or that little Timmy bore a striking resemblance to his father.Now, by the time the double-helix was co-discovered in 1953, Haldane published his peer review a whole four years after. Yes, that's in its infancy, but then again, this is all pointless. The backbone, the rules of inheritance, were known long before with Mendelian genetics. DNA is simply a pathway or a mechanism that explains why inheritance does what it does. I never said we haven't learned anything beyond 1957. I said we haven't learned so extraordinary since the 1957 that would pose a legitimate challenge to Haldane's Dilemma. But if you are so certain, you can start by taking the challenge.

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How does he misstate Gould?

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I offered a solution. You haven't offer a rebuttal. Where did I, Haldane, or ReMine say anything about an 'infinite' number of mutations? I said that there is a 'finite' number of possible mutations-- meaning there is a specific limit. Of course it is. That's the thrust of the argument. Of course Haldane knew it. That's why he wrote a paper on it. It sought for someone to reconcile the implications this had. What??? Name me one organism that has a high number of beneficial mutations as the result of point mutations. You know what they offer as examples of beneficial mutations? Yeast, bacteria, and viruses-- all prokaryotes where a single mutation is bound to something good. Big deal. We are talking about a much more complex organism, namely, humans. So, what about eukaryotes? Would the deletion of a single nucleotide lead to a frameshift mutation? Would the 1,667 figure change dramatically if 3 nucleotides changing simultaneously, yet beneifically, offer any real solution? No, it would still be too slow to allow for human evolution. Aside from which, it wouldn't act beneficially because the entire sequence following the mutation would translate into a chain of garbled amino acid sequences. Afterall, this is what we normally expect of mutations. Evolutionists just cling to the hope that so many mutations would have been beneficial, even though finding any such evidence is scant.Edited by nemesis_juggernaut, : No reason given.

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers

Why is this 'obvious?' Lets look at the only known cases of speciation as presented by TalkOrigins. Most of their instances are all in the plant kingdom. Of the few in the animal kingdom, they're all flies-- simple on the molecular level. Now, I'm not even going to go into how many different ways I object to the Drosophila, rather, lets assume they are all legitimate cases of speciation due to beneficial mutations? Of their beneficial mutations, they to cite Sickle Cell Anemia, as if the trade-off between SCA and malaria is really worth mentioning. Beneficial mutations aren't obvious. They are so rare as to be absurd to hang the theory upon them, or to account for all of life's diversity is hinged on their success. And the cases of speciation are so sparse, so as to render evolution as an unwitnessed event that bases its beliefs on inferences rather than empiricism-- which, consequently, is the exact same charge they have against ID.Here's the point of Haldane's Dilemma. Even if a beneficial mutation survived, for it to become fixed in a population, the organisms not carrying it must be eliminated because it will just become swamped in the gene pool. This is the 'cost of substitution.' Most mutations that occur in the average human do not have any affect on our progeny. I think we'd all agree that the most frequent type of mutation is a single nucleotide substitution, that pretty much will go away when we die-- meaning it poses no kind of affect in any evolutionary sense. For a mutation to make a significant impact on an organism and their morphology, is for a mutation to occur during the production of haploid production. An accident in replication anywhere else in the body will only affect the specific cell where the injury occurred. We have these kinds of mutations all the time in our body, but it doesn't go anywhere. They die with us. So, really, mentioning that we have so many mutations already is inconsequential. Edited by nemesis_juggernaut, : Having problems formatting properly

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Faith is not a pathetic sentiment, but robust, vigorous confidence built on the fact that God is holy love. You cannot see Him just now, you cannot fully understand what He's doing, but you know that you know Him." -Oswald Chambers