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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
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.Elizabeth B Liddle
September 13, 2013
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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/8610134scordova
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.Elizabeth B Liddle
September 13, 2013
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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.sigaba
September 12, 2013
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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-mailscordova
September 12, 2013
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Oh I get it. Are we really going to dig through the Golden Oldies?sigaba
September 12, 2013
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Without the ability to equivocate on words like “evolution” and “fit” and “selection” the Darwinist house of cards crumbles.
I don't follow...sigaba
September 12, 2013
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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.Phinehas
September 12, 2013
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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.sigaba
September 12, 2013
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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."sigaba
September 12, 2013
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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.scordova
September 12, 2013
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I’m OK discussing the Theory of Devolution if everyone else is.
What is it with you guys and teleology?sigaba
September 12, 2013
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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?Phinehas
September 12, 2013
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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.sigaba
September 12, 2013
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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 : https://uncommondescent.com/darwinism/darwins-delusion-vs-death-of-the-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.scordova
September 12, 2013
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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.sigaba
September 12, 2013
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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? Salscordova
September 12, 2013
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sigaba:
When is complicated better?
When simple isn't sufficient.Joe
September 12, 2013
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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...scordova
September 12, 2013
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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.sigaba
September 12, 2013
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sigaba:
In terms of their breadth of adaptations they’re far superior.
Sometimes simple is better. Unguided evolution likes simple.Joe
September 12, 2013
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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?Joe
September 12, 2013
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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 :(sigaba
September 12, 2013
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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.Joe
September 12, 2013
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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?AVS
September 12, 2013
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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.wd400
September 12, 2013
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AVS, the basis for my argument was laid out in comment 26. The drawing represents exactly what I said. You lose. So shut up.Joe
September 12, 2013
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Joe, the basis of your argument is the direction a diagram was drawn on a piece of paper. You lose. Just stop.AVS
September 12, 2013
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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?Joe
September 12, 2013
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