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The fine work of Joe Felsenstein and M. Wilson Sayres

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Joe Felsenstein is an evolutionist that has a unique distinction of having his work favorably cited by creationists and bible scholars (except where he disagrees). For example, religious scholars are using Joe’s work to find descendants of the line of priests from the time of the Bible’s King David. See: Y-Chromosomal Aaron.

Joe is also widely credited with coining the phrase “Muller’s ratchet”, a concept articulated in a paper 40 years ago! He must have written that when he was really young, 1973 was a while back.

The wiki entry on Muller’s ratchet:

In evolutionary genetics, Muller’s ratchet (named after Hermann Joseph Muller, by analogy with a ratchet mechanism) is the process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner.

In other words, Darwinian evolution doesn’t always clean out the bad, real evolution ensures some of the bad becomes permanent!

Muller’s ratchet actually applies in sexually reproducing creatures if the genetic material has regions like the Y-Chromosome where material is passed off only from father to son. (More on that later as it relates to M. Wilson Sayres recent paper). And my best reading of Joe’s paper suggests that creatures with recombinatorial ability are not immune to getting twisted by problems similar to that of Muller’s ratchet, only that they have a better advantageous defense against it in small populations. So a “ratchet” is universal, just not as deadly in species with the ability to exchange genetic material. Whatever we wish to call it, the “ratchet” problem both in asexual and sexually reproducing species remains.

The paper is Evolutionary Advantage of Recombination .The paper is technical and apologies in advance to Joe if what I state mischaracterizes his position, but I will do my best to explain from my lay perspective.

But first, there is the problem of defining the notions of “deleterious” or “fit” mutations. If we define something as harmful or beneficial based only on the criteria of successful reproduction, we run in to some nasty paradoxes which Andreas Wagner, Lewontin, and others saw clearly. A quasi humorous take of this problem was pointed out in my discussion Survival of the sickest, Why we need Disease and a more technical discussion in Dennett’s strange idea is a bad idea for recognizing biological function . Simply stated, sickness and blindness in the Darwinian world can be viewed as “beneficial” and this leads to problems in defining what is actually “fit”, because the notion of “fit” is fluid. Lewontin pointed out in population genetics the notion of “beneficial” becomes so fluid as to become meaningless. Dennett’s strange idea goes into the details of this problem.

Secondly, because a population could be far sicker than its ancestors but still reproductively “fit” in terms of offspring, the problem of malfunction is equivocated away by “compensatory mutations” which enable more reproductive success but not restoration of function. Thus a population of blind cave fish in a dark cave can be viewed as supremely fit over the cave fish that have functioning eyes. The problem of Muller’s ratchet is alleviated through a process of implicit equivocation (I’m not saying it’s deliberate, but a serious oversight).

With those two caveats regarding the notion of “fit”, it is still helpful to see the effect of Muller’s ratchet. The paper delves into the notion of a bad mutation sweeping through a population and then becoming a feature of the entire population, a process we call fixation. When all the members of the population have the defective gene, the mutation is said to be “fixed”. How can selection fail? To understand the reasons selection can fail, see Gambler’s Ruin Is Darwin’s Ruin.

Problematic is that when this condition happens (where all individuals permanently have the bad mutation), the bad mutation by definition it is now the new baseline, and it ceases to be bad, just like blindness in cave fish. As long as we get some compensatory mutation to improve the number of offspring generated, the problem of lost function is equivocated away by the fluid notions of what it means for a population to be fit.

Joe’s paper goes into the problem of Muller’s ratchet instilling dysfunctional features into all members of population, the main point being that sexually reproducing creatures are better able to resist getting twisted by a ratchet than asexually reproducing creatures.

But Muller’s ratchet understates the problem of bad mutations, since the ratchet only deals with mutations that get fixed into every individual in a population, not ones that are in subsets of the population but are still harmful. Muller’s ratchet says some of the bad mutations become permanent, but another problem is that the number of bad mutations keep increasing even if they are not permanent.

Here is a conceptual cartoon of the problem in asexually reproducing genes. The red dots represent mutations, the broken ginger bread men represent serious expression of the bad gene. The broken ginger bread men are eliminated by selection, some of the bad genes are never purged, they accumulate over time. Humans may be subject to thousands of harmful mutations per individual per generation. The cartoon only uses one mutation per individual per generation to drive its point home.:

http://youtu.be/SrIDjvpx7w4

Muller’s ratchet delves into the likelihood the bad mutants will be “fixed” into a population, but that isn’t even the final problem, the problem is purging the bad mutations that aren’t even fixed. Muller’s ratchet guarantees some mutations will become more or less permanent, but with sufficient numbers of mutations per individual per generation, it is evident the deterioration and dysfunction will eventually become the norm even if Muller’s ratchet doesn’t infuse a given bad mutation into every member of the population. Only by allowing sickness to be redefined as “fit” does the problem really go away on paper.

The idea of Muller’s ratchet inspired creationists to begin investigating the problem of bad mutations. Unfortunately, creationists are not sufficiently recognizing the definitional difficulties that Lewontin realized when trying to define fitness, namely the statistical interpretation of “fit” leads to absurdities such as Survival of the sickest, Why we need Disease.

Regrettably, unlike most of my posts at UD, I don’t feel comfortable in asserting a black and white conclusion that Darwinism is definitely wrong based on Joe Felsenstein’s work (not that he would ever say that either). But Joe, like so many population geneticists (Haldane, Fisher, Crow, Kimura, Nachman, Crowell, Kondrashov, etc.) have a peculiar stature of commanding great admiration from ID proponents and creationists (i.e., Dembski frequently refers to Fisher in favorable terms). The population geneticists have unwittingly inspired creationists with the conviction that life was created.

Finally, I’d like to salute M. Wilson Sayres who reminded me by her published work that the human genome is showing signs of deterioration. This is consistent with findings in different areas of population genetics. See: Sanford’s pro-ID thesis supported by PNAS, read it and weep, literally. I quoted, Michael Lynch in that essay:

Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).

Thus, the preceding observations paint a rather stark picture. At least in highly industrialized societies, the impact of deleterious mutations is accumulating on a time scale that is approximately the same as that for scenarios associated with global warming—perhaps not of great concern over a span of one or two generations, but with very considerable consequences on time scales of tens of generations.

Michael Lynch

M. Wilson Sayres reported publication of her paper here: Gene Survival and Death on the Y-Chromosome. Her work showed that even on the assumption of evolution, there seems to be substantial deterioration in the Y-chromosome.

In contrast, even without evolutionary assumption, Bryan Sykes at Oxford is noting emergence of irreversible dysfunction in the Y-Chromosome in the present day by comparing fathers to sons to grandsons etc. Sykes wrote the book Adam’s Curse: A future without men (a title that should no doubt be welcomed by the Feminist GNUs and Skepchicks). About the book:

Bryan Sykes follows up The Seven Daughters of Eve with the equally challenging and well-written Adam’s Curse. This time, instead of following humanity’s heritage back to the first women, Sykes looks forward to a possible future without men. The seeds of the book’s topics were sown when Sykes met a pre-eminent pharmaceutical company chairman who shared his surname. Using the Y chromosome, which is passed nearly unchanged from father to son, the author found that he shared a distant ancestor with the other Sykes. Along the way, he discovered that the Y chromosome was worth examining more closely. The first third of Adam’s Curse is devoted to a clear and comprehensive lesson about genetics, the second narrates several fascinating stories of tracing ancestry via the Y chromosome, and the last chapters explore the history of male humanity and its future. Some readers will eagerly skim until they reach Chapter 21, where Sykes gets to the heart of the matter–why and how the Y chromosome has created a world where men overwhelmingly own the wealth and power, commit the crimes, and fight the wars. He uses the structural puniness of the Y chromosome to demonstrate that men are as unnecessary biologically as they are dominant socially. Sykes’ provocative and quite personal book is likely to be unpopular among science readers who prefer their biology divorced from sociology, but his points taken in context will be difficult to refute.

Another relevant study is:
Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree.

Dr. Sayres was very kind to respond to my queries at Pandas Thumb. My question was:

Dr. Sayres,

Does your work agree with that of Bryan Sykes at Oxford who asserted that the Y-chromosome is dying quickly. He feels this could lead to extinction in about 100,000 years.

Some have argued that even thought humans reproduce sexually, that Muller’s ratchet applies to Y-chromosomes, and hence it’s unlikely that recovery will happen damaged genes as might be the case where genetic material can be exchanged and mixed from both parents.

Thank you in advance, and congratulations on your publication.

Dr. Sayres responded:

Hi Salvador,

I don’t think that there is clear evidence that the Y will become extinct in 100,000. There are many ways to avoid this. One of which has already occurred on the human sex chromosomes – the addition of a large autosomal segment to both the X and the Y (we call it the X-added or Y-added region). This region is autosomal in marsupials, but sex-linked in eutherian mammals. We have an extra table in the supplement of the paper discussed here that shows that gene loss occurs relatively quickly at first, then seems to slow down. This is consistent with previous work I did looking at substitution rates over evolutionary time in the X/Y-added regions (where we observe that very quickly after recombination is suppressed, the substitution rate increases on the Y, but then it does not continue to increase, at least for the surviving genes).

It is true that Muller’s ratchet applies to the Y chromosomes, but recent work I’m doing now (submitting a revised version in the next few weeks) shows that purifying selection, and specifically background selection, because nearly all of the content on the Y is linked, is quite strong on the human Y chromosome, acting to retain the little content it has left.

But, if we (humans) did “lose” the Y chromosome, we would still survive. The sex-determining region would likely jump to an autosomal chromosome, and the whole wonderful process would start all over again. Or, maybe some other mechanism we haven’t yet anticipated.

Best, Melissa

The issues raised do not have closure, and it is evident there are pointed disagreements on evolution, especially on the efficacy of “purifying selection”. Creationists argue purifying selection will never be sufficient (the cartoon above tries to display in simplest terms why purifying selection must logically fail).

The research and discussions will just have to keep moving forward, and hopefully more clarity will emerge in due time. I’ll just have to leave it at that for now.

Many kind regards to Dr. Felsenstein and Dr. Sayres for their willingness to dialogue.

Comments
Is Nick still pretending that he can educate James Tour? What a laugh.Mung
May 31, 2013
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Nick Matzke:
Ask Joe Felsenstein, he’ll tell you the same thing. Better yet, read his book, “Inferring Phylogenies”. I read it for my qualifying exam. Why should I take you seriously when you have basic misunderstandings that would get you failed in phylogenetics 101?
OMG! That must be one of "the golden books of knowledge" I've been asking you to reveal to us ignorant "creationists." I can buy this book and learn all about the truth of your alleged field of "macro-evolutionary theory?" But it's a bit dated, isn't it?Mung
May 31, 2013
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Eric, UPB, thanks mates! lack of response from nick noted. Yes, the search for truth never ends. I'd just love to know what the "truth" was that Nick discovered in his "macro-evolutionary" studies and why he is so unwilling to share it with the rest of us? I guess I am just naturally skeptical of those who claim to know truth but are not willing to share it or how they arrived at it. Sounds cultish, yes?Mung
May 31, 2013
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As difficult as Kimura's math is, for high mutation rates, a lot of issues become pretty much moot. For example, in the case of U=5.6, does it really matter that one has moderate selective advantage over his peers through "synergistic epistasis" or that the worst individual is guaranteed to die via "synergistic epistasis". From JoeCoder's calculation above, if only one individual lived out of 806, a random chance of survival is 0.12%. If the eugenically clean individual is 5 times better than the sick individual to survive, his chance of survival is only in the ball park of .60% (approximately). So let's be generous and say he has a 1% chance of survival, that's not very good. The next generation will thus have a 99% chance of being defective, and that is on the generous assumption that human females can give birth to 806 children! I have friends who have genetic mutations that are slightly deleterious (allergies, myopia, etc.) who have children, and sadly some very fine healthy people who died early due to car accidents, etc. If mutation rates are high enough relative to birth rates, it really doesn't matter how advantaged one individual may be over another if the selective advantage is moderate. The discussion has helped justify extending the cartoon model of asexually reproducing species to sexually reproducing species in principle. In other words, it was quite legitimate to be putting red dots (mutations) in all the gingerbread kids. One can't run away from the concept conveyed by the cartoon because it is now backed up with the math. Dawkins weasel has now been defeated by ReMine's gingerbread kids. :-) PS If someone wants to volunteer to redo the cartoon (to make it a little more entertaining) that would be great. Hint hint!scordova
May 30, 2013
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lol @ ba77JoeCoder
May 30, 2013
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sure would make Frisbee in the park a blast! :)bornagain77
May 30, 2013
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Okie Dokie scordova, now that you are getting the math of evolution down pat, can you finally give me a ballpark prediction on a burning question I have that Mr. Matzke refused to give me an answer for. Please tell me, using all the power of artificial selection, approximately how many generations it will take me to get a bird-dog. I mean a real bird-dog that flies not one that hunts birds! :)bornagain77
May 30, 2013
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Sorry, I should've made it clear in the beginning this was before selection. Or to put it another way, assumes omniscient artificial selection.JoeCoder
May 30, 2013
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It now totally makes sense that Kimura used the Poissan distribution. This is a beautiful illustration:
The classic Poisson example is the data set of von Bortkiewicz (1898), for the chance of a Prussian cavalryman being killed by the kick of a horse. Ten army corps were observed over 20 years, giving a total of 200 observations of one corps for a one year period. The period or module of observation is thus one year. The total deaths from horse kicks were 122, and the average number of deaths per year per corps was thus 122/200 = 0.61. This is a rate of less than 1. It is also obvious that it is meaningless to ask how many times per year a cavalryman was not killed by the kick of a horse. In any given year, we expect to observe, well, not exactly 0.61 deaths in one corps (that is not possible; deaths occur in modules of 1), but sometimes none, sometimes one, occasionally two, perhaps once in a while three, and (we might intuitively expect) very rarely any more. Here, then, is the classic Poisson situation: a rare event, whose average rate is small, with observations made over many small intervals of time. Let us see if our formula gives a close fit for the actual Prussian data, where r = 0.61 is the average number expected per year for the whole sample, and the successive terms of the Poisson formula are the successive probabilities. Remember that our formula for each term in the distribution is: p(k) = r*k / (k!)(e*r)(5) We may start by asking, given r = 0.61, what is the probability of no deaths by horse kick in a given year (module of observation)? For k = 0, we get by substitution p(0) = (0.61)*0 / (0!)(e*0.61) = 1 / (1)(1.8404) = 0.5434 Given that probability, then over the 200 years observed we should expect to find a total of 108.68 = 109 years with zero deaths. It turns out that 109 is exactly the number of years in which the Prussian data recorded no deaths from horse kicks. The match between expected and actual values is not merely good, it is perfect. http://www.umass.edu/wsp/statistics/lessons/poisson/#classic
scordova
May 30, 2013
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JoeCoder WHOA! Look at equation 1.4 in Kimura's paper. Thanks a million!!!!
Under free recombination between mutant genes, i may be distributed with a Poisson distribution, fi = e^-lambda lambda^i/i! where lambda is the average number of mutant genes per individual before selection
It's the same formula in Kimura's paper, just different symbols!scordova
May 30, 2013
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But I'm impressed scordova that you derived it on your own. I have a minor in math but I barely remember anything about the Poisson distribution. I wasn't sure which one it was.JoeCoder
May 30, 2013
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I believe the formula dates back to a 1966 paper by Kimura. That's what Nachman & Crowell 2000 cite for it (last paragraph). But I haven't made an attempt to follow the math within Kimura's paper.JoeCoder
May 30, 2013
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computerist @80: Good point.Eric Anderson
May 30, 2013
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regarding this
1-e^-U
I said
The formula only says how many offspring are needed to create a eugenically fit kid, it doesn’t say much about the survival of that kid.
based on intuition, not any formal derivation. I looked on the net and I saw something looking like that in Luria and Delbruck's work, and then that led me to the Poisson distribution, so it looks like that paper is merely using the Poisson distribution http://en.wikipedia.org/wiki/Poisson_distribution I used a k-parameter of zero (for zero mutants), and then substituting the mutation rate as the lambda-parameter. So let k = 0 lamda = mutation rate = u That is: percent of population with no mutation = P(k,lambda) = P(0,u) = (U^0)(e^-U)/0! = e^-U Hence the number of mutated individuals is
1-e^-U
http://www.umass.edu/wsp/statistics/lessons/poisson/#classicscordova
May 30, 2013
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@JoeCoder, RM's = random mutationscomputerist
May 30, 2013
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@computerist, what are RM's?JoeCoder
May 30, 2013
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The Darwinian process is simply too volatile (ie: it can quickly lose even a "well adapted" state, never mind a state which hasn't yet "adapted" or formed). Take RM's which is indiscriminate; that is it doesn't "care" about the current state of the system. The environment in turn acts as another indiscriminate factor with respect to the current state of the system. We find that internal bottom-up (RM) and external top-down (environment) dynamics are acting against the possible net increase in FCSI. CharlieD, perhaps you would like to explain how the Darwinian mechanism gets around this?computerist
May 30, 2013
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I wish we wouldn't mock those that disagree with us, even when they start it. Let's be bigger than that. Besides it wastes space that could be used for fruitful dialog.JoeCoder
May 30, 2013
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'I want to be like you, Nick. I want to become an expert in Macro-Evolutionary Theory. I want to be able to debate Emeritus Professors and set them straight about their misunderstandings.' Nick is still sulking because the God he doesn't believe in, isn't as nice as, ihvho, He should be. In fact, he thinks He's downright nasty.Axel
May 30, 2013
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Yes, it assumes strong/artificial selection. Under realistic parameters a rate of 1.0 is probably still too high. Sorry for the confusion.JoeCoder
May 30, 2013
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CharlieD wrote: In fact I sat in on a seminar today about the genomic convergence of the thylacine and dog
I would really like more information on this if you can link me. I'm not trying to troll or debate you on this, but am genuinely interested in the wold/thylacine convergence. This is the first time I had ever heard anything about genomic convergence.JoeCoder
May 30, 2013
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But it has to be higher than an average of 1 for it to be a problem, since the average means that in large families some will have 2 or 3 and others will have 0. To calculate how much is too high, see the 1-e^-U equation in my post @63.
But that assumes strong selection, no? The formula only says how many offspring are needed to create a eugenically fit kid, it doesn't say much about the survival of that kid. Here the problem of gambler's ruin asserts itself, even with advantage, there is no guarantee the eugenically fit kid will live, and especially since we are talking slightly deleterious mutations. Random events can take the fit kid out of the population. This is especially true if we have 99 defective kids and 1 fit kid in a slightly selective advantage. Since this is a slightly selective scenario, it would be fair to say, his chances of survival are around 1%. The more mutations and the weaker they are, the stronger the problem of gambler's ruin becomes. That's how I see it. Is my reasoning incorrect? Thanks in advance.scordova
May 30, 2013
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scordova and Joecoder thanks for the links and correction. scordova, I don't know if you've heard this interview with Walter ReMine yet, but I saw it this morning and set it aside, due to the tremendous respect I've seen for his work on UD, so as to listen to this evening. Interview (with) electrical engineer and information expert Walter ReMine to identify the specific illusions offered by evolutionists when they claim to have established ancestors and evolutionary lineage. ReMine's classic book, The Biotic Message, makes a significant contribution to the anti-evolution literature. http://kgov.com/Walter-ReMinebornagain77
May 30, 2013
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The easiest way to understand some of the problems is the cartoon I provided above. One of John Sanford's associates that co-authored that paper and software presented at the conference, Walter ReMine, helped me to synthesize the conceptual basis of the cartoon. It shows how natural selection, or any sort of selection will ultimately fail for sufficiently high mutation rates. Again, the cartoon is here. It is only 2-minutes long. http://youtu.be/SrIDjvpx7w4 The cartoon approximates the problem of mutation but many of the details simplified out. The math that JoeCoder provided deals with sexually reproducing species, but for even moderately bad mutation rates of 5.6 per individual per generation, the cartoon model is a good approximation.scordova
May 30, 2013
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it has to be higher than an average of 1 for it to be a problem
Assuming artificial selection at least, which isn't realistic.JoeCoder
May 30, 2013
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@BA77 I disagree with your video at 4:28. In the third generation, some will have 4 and some will have 2. Some may even revert back 1 due to shuffling of alleles. They say "one mutation per person per generation would doom the human race". But it has to be higher than an average of 1 for it to be a problem, since the average means that in large families some will have 2 or 3 and others will have 0. To calculate how much is too high, see the 1-e^-U equation in my post @63.JoeCoder
May 30, 2013
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JLAfan2001, this video may make it easier for you to understand (it made the issue clearer for me): Human evolution or extinction - discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video http://www.youtube.com/watch?v=aC_NyFZG7pMbornagain77
May 30, 2013
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It's a bad thing because evolution destroys faster than it creates and this will eventually lead to the extinction of higher animals including us. Bad mutations arrive faster than selection can remove them. Common descent isn't possible unless a creator continually intervenes to fix things up. So it invalidates an "unbroken natural law" view of evolution, but not common descent with intervention as some ID'ers believe. To throw in a source here as evidence that I'm not just blowing smoke: This is from geneticist and atheist to creationist convert John Sanford, whose invention of the gene gun led to the production of most of the world's GM food:
Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern. ... Intensified natural selection only marginally slows the accumulation of deleterious mutations.", Using computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load, Intl. Conf. Computational Science, 2007
Mendel's Accountant, the free/open source program they wrote for the simulation, is peer reviewed and used/cited by other geneticists. You can try it yourself and reproduce their results.JoeCoder
May 30, 2013
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JoeCoder@63 UUHHH, in layman's terms is that a good thing or a bad thing? Are you saying common descent isn't possible using those numbers?JLAfan2001
May 30, 2013
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Or 806 offspring required to maintain constant population size.
Assuming strong selection, so I presume a human mom will actually have to have make more than 806 kids if selection is weak because this presumes the eugencally clean individual will be selected rather that genetically damaged individual who goes around making lots of babies. If supposing random chance (like natural accidents or predators or Jodi Arias) happen to wipe out 805 of the kids, the eugenically clean individual has a less than 99% chance of surviving. Every human mom will have to be an Octo mom times a hundred and then some. And again, we are still making generous assumptions of strong selection of 100% efficacy which isn't really seen in nature. Thanks for your input and constructive criticism. You're more versant at this than any one at UD! Thanks for posting.scordova
May 30, 2013
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