Uncommon Descent Serving The Intelligent Design Community

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

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

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
It does in Darwin’s only diagram in his book “On the Origin of Species…”
If that’s as good as you’ve got this thread is over
Yeah - it's also, and it hardly matters, not true. The branches go up the page, but there is no sense of progress in either the figure or the explanatory text. (Darwin is talking about divergent selection as a diversifying force)wd400
September 12, 2013
September
09
Sep
12
12
2013
04:38 PM
4
04
38
PM
PDT
It does in Darwin’s only diagram in his book “On the Origin of Species…”.
If that's as good as you've got this thread is over...sigaba
September 12, 2013
September
09
Sep
12
12
2013
04:20 PM
4
04
20
PM
PDT
I guess another question would be, where is Intelligent Design's best population genetics simulation? We have Mendel's Accountant, which is purported to be an accurate model of the neo-Darwinian/modern evolutionary synthesis, and it report that the model doesn't match the natural history. So where is the ID model that does match the natural history?sigaba
September 12, 2013
September
09
Sep
12
12
2013
04:19 PM
4
04
19
PM
PDT
Lizzie:
JGuy, evolution doesn’t go “onwards and upwards” at all.
It does in Darwin's only diagram in his book "On the Origin of Species...". Just sayin'Joe
September 12, 2013
September
09
Sep
12
12
2013
04:17 PM
4
04
17
PM
PDT
If there are numerous orphan genes, then how did they evolve. Haldane’s dilemma creates a serious problem for the evolution of the individual nucleotides (along with codon bias) via natural selection. Why? Each true orphan is one is one substitution, and would arise by soft selection (or no selection, come to that). I don't think Haldane's dilemma is relevant to this question at allwd400
September 12, 2013
September
09
Sep
12
12
2013
03:57 PM
3
03
57
PM
PDT
There are many software packages for simulating different aspects of population genetics, but usually do something interesting you have to code your own simulation, or, even, explore the properties of a mathematical model. For the cost of substituion ("haldane's dilmea") we can use this approach to establish there is only a "cost" in when selections is imposed form outside (e.g. predation, or a changing climate) not for intra-specific competition. It seems odd, to me at least, to call this a cost of substitution, not a genetic load forced on a population due to its environment. Anyway, you can calculate the "speed" limit imposed on natural selection in those cases, with the cost spread across multiple loci, and see how all the parameters influence it. In that specific case there is a cost, but it's not nearly as harsh as Haldane suggested. I had to laugh at your calling Michael Lynch a "Darwinist" - I don' think he'd take to kindly to thatwd400
September 12, 2013
September
09
Sep
12
12
2013
03:54 PM
3
03
54
PM
PDT
I think moving the argument to be around why renormalizing is or isn’t the correct thing to do is bypassing the fact that the accumulation of deleterious mutations in the population is therefore occurring and has the consequence of the population trending sicker.
Well, it's an important point on methodology, I pointed out that it was a deviation from nature on a point and the defense was that "engineers see things differently from scientists." I've read the manual on MENDEL, and I have some questions which I don't really see answers for. * It creates mutations and assigns them a beneficial or harmful value -- is this a scalar score? Is it dependent on some environmental factor -- positive or for some individuals but harmful or neutral for other individuals (like the alleles for sickle cell, skin melanin, or lactose intolerance)? * When you select the number of children a mother has, is that the number of live births, the number of reproducing offspring, or the number of fertilization events? Are costs associated with births? How is miscarriage modeled? * Is competition between individuals in a population modeled, for food, mates? How is competition with other populations in an environment modeled? * Is kin selection or sexual selection modeled? * If you use a carrying capacity population model, how are changes to carrying capacity modeled? Carrying capacity depends on food sources, which are subject to adaptations. My impression is that you couldn't really model an animal like a chimpanzee with a program like this. Certain adaptations, in particular bipedalism, toolmaking and hierarchical social structure, can have radical nonlinear effects on fitness.sigaba
September 12, 2013
September
09
Sep
12
12
2013
03:32 PM
3
03
32
PM
PDT
JGuy, evolution doesn't go "onwards and upwards" at all. Most lineages go extinct. Ours probably will as well. And it is true that mutations are accumulating in the human population that would make us sicker if we lived in a world in which we didn't have ways to make us well. In other words, currently we live in a fairly benign environment in which mutations can accumulate that would kill us in a harsher one. However, we are still doing pretty well. And if a global plague wipes out 99% of us and life as we know it, mutations that are neutral in the current environment will suddenly become deleterious, and become rapidly rarer.Elizabeth B Liddle
September 12, 2013
September
09
Sep
12
12
2013
03:12 PM
3
03
12
PM
PDT
I think moving the argument to be around why renormalizing is or isn't the correct thing to do is bypassing the fact that the accumulation of deleterious mutations in the population is therefore occurring and has the consequence of the population trending sicker. This is not onward and upward evolution, it's devolution. Such a process would not build up an immune system where there as none - as one example.JGuy
September 12, 2013
September
09
Sep
12
12
2013
01:48 PM
1
01
48
PM
PDT
Humans are more populous now than ever, but it is believed on average we are sicker genetically speaking
What is your basis for describing these traits as deleterious? I find that your assignment of certain genetic traits and good and bad has a distasteful eugenic flavor, which I am certain you do not intend but I think is a consequence of this kind of argument.
Are we more or less fit than in the past given we’ve figured out how to make more humans…
By definition, if we've figured out how to make more, we're more fit in the evobio sense. We might be fat, ugly and dumb, but as long as the gametes are meeting up the system continues to work. We only have to be smarter or better sighted than the next man, after all, no other animal can offer realistic competition with even a relatively nearsighted, dullard human. I'll stay away from your quantitative analysis because I don't have the background to follow it.sigaba
September 12, 2013
September
09
Sep
12
12
2013
01:34 PM
1
01
34
PM
PDT
Case in point of reproductive success in the presence of genetic deterioration. Humans are more populous now than ever, but it is believed on average we are sicker genetically speaking: Myopia Diabetes Asthma Emotional disorders Reduced intelligence The list goes on. As Fodor complained, the definitions of what it means to be selected for or reproductively successful are to vague to form a coherent theory... Are we more or less fit than in the past given we've figured out how to make more humans...scordova
September 12, 2013
September
09
Sep
12
12
2013
01:05 PM
1
01
05
PM
PDT
sigaba, More to a specific example of Haldane's dilemma. If there are numerous orphan genes, then how did they evolve. Haldane's dilemma creates a serious problem for the evolution of the individual nucleotides (along with codon bias) via natural selection. Say an orphan might has 1000 nucleotides, and if there are a thousand orphans in one mammalian genome, this may constitute a sufficient gap to question selection as the mechanism of creating those orphans. These are questions that are worth exploring, I'm not so sure that proposed evolutionary mechanisms are adequate, in fact, it looks problematic enough that I find ID more believable.scordova
September 12, 2013
September
09
Sep
12
12
2013
01:01 PM
1
01
01
PM
PDT
Why would the fitness of parents be an issue if the children are not competing with them for resources? why is it wrong to renormalize fitness with successive generations?
Perhaps because it does not accurately model the real world, where they are not competing solely among themselves?cantor
September 12, 2013
September
09
Sep
12
12
2013
12:53 PM
12
12
53
PM
PDT
I don’t see the problem then… why is it wrong to renormalize fitness with successive generations?
Thanks for asking such a good question. Many evolutionary biologists don't see it as a problem, and are dismayed that engineers find it to be a problem. There is something of a cultural conflict between the two disciplines. It is no surprise many of the critics of evolutionary theory are engineers. There are two separate discussions: 1. reproductive success 2. evolution of design Evolution of design is foremost in the minds of those at UD. If evolution of novel design are reproductively disfavored, then this is a problem for Dawkins hypothesis that design is the result of evolution. If existing designs are not sufficiently maintained because of mutational accumulation, then evolution is not a good explanation for the appearance of complex designs in nature. The population genetic arguments are relevant to determining if evolutionary mechanisms can created integrated complexity. If selection can only fix 1 trait every 300 generations, then it become hard to believe the increase in complexity in humans from the chimp-human ancestor was due to selection (only 1000 changes, perhaps at the nucleotide level could fixate through selection) One could invoke neutral evolution, neutral drift and mutation, but then that's just claiming luck creates the designs in nature. Former engineers like myself find this hard to believe on theoretical grounds. PS A not-so-nice description of this conflict between engineers and evolutionary biologists is here: http://rationalwiki.org/wiki/Salem_Hypothesis I don't agree with the characterization, but the Salem Hypothesis probably has a grain of truth to it as seen in this present discussion. What I see as a problem is not a problem to you. And that is one source of our disagreements.scordova
September 12, 2013
September
09
Sep
12
12
2013
12:37 PM
12
12
37
PM
PDT
Ironically, I agree with you on that point.
I don't see the problem then... why is it wrong to renormalize fitness with successive generations?sigaba
September 12, 2013
September
09
Sep
12
12
2013
12:25 PM
12
12
25
PM
PDT
Or to put the last sentence in proper terms: In a certain environment, if sick, dumb creatures are the most fecund and successful, that's what you'll get.sigaba
September 12, 2013
September
09
Sep
12
12
2013
12:21 PM
12
12
21
PM
PDT
I don’t think health and wellbeing, apart from reproductive success, is relevant to a discussion of evolution. Evolution will make the sickest, dumbest creatures possible if that’s what’s necessary to maximize fecundity and population.
Ironically, I agree with you on that point. Thank you for your response.scordova
September 12, 2013
September
09
Sep
12
12
2013
12:21 PM
12
12
21
PM
PDT
So are you admitting it is standard to cover-up genetic deterioration in a population by ignoring the fact the ancestors are healthier than descendants?
I don't understand why such a result would be strange or contradictory. In vivo species go extinct all the time, it would be a mistake to presume that evolution has a goal of always making each species more fit, and each generation more fit than the previous. A species can be very fit, but if outcompeted by other species, the children will become less fit without any mutation. Individuals in an climate or chemical environment that is too challenging will be less fit than their parents. Are you using "sicker" and "healthier" as synonyms for less and more fit, or do they mean different things?
So fitness of the parents is an issue if you’re concerned about health and well-being versus reproductive success.
I don't think health and wellbeing, apart from reproductive success, is relevant to a discussion of evolution. Evolution will make the sickest, dumbest creatures possible if that's what's necessary to maximize fecundity and population.sigaba
September 12, 2013
September
09
Sep
12
12
2013
12:19 PM
12
12
19
PM
PDT
Sal, I think it would be best called "survival of the less sick of the sicklings".JGuy
September 12, 2013
September
09
Sep
12
12
2013
12:09 PM
12
12
09
PM
PDT
Why would the fitness of parents be an issue if the children are not competing with them for resources? They’re dead, they might have been more fit but they cannot exploit this advantage from the grave.
So are you admitting it is standard to cover-up genetic deterioration in a population by ignoring the fact the ancestors are healthier than descendants? In such case, the notion of fitness relative to functionality is somewhat meaningless. So fitness of the parents is an issue if you're concerned about health and well-being versus reproductive success. If descendants are on average sicker than ancestors, shouldn't we call evolution "survival of the sickest"? Any way, thank you for responding, and if you have answers for the questions posed, feel free to provide them.scordova
September 12, 2013
September
09
Sep
12
12
2013
12:07 PM
12
12
07
PM
PDT
Hey uses the standard evolutionist trick or renormalizing the fittest individual for every generation. What this means is suppose the children on average are sicker than the parents.
Why would the fitness of parents be an issue if the children are not competing with them for resources? They're dead, they might have been more fit but they cannot exploit this advantage from the grave.sigaba
September 12, 2013
September
09
Sep
12
12
2013
11:49 AM
11
11
49
AM
PDT
Thanks! Now I can enjoy your challenge to the Darwin party - I can't wait to see the mathematical evidence that mutation is a creative process . . . but I fear I may not live that long.owendw
September 12, 2013
September
09
Sep
12
12
2013
11:37 AM
11
11
37
AM
PDT
owendw, Fixed. Sorry for the trouble. Thanks for the correction. Salscordova
September 12, 2013
September
09
Sep
12
12
2013
11:25 AM
11
11
25
AM
PDT
Could you please fix this url: (near the top of the op) "unnamed evolutionary biologist who got laughed off stage" thanks.owendw
September 12, 2013
September
09
Sep
12
12
2013
11:13 AM
11
11
13
AM
PDT
I have been waiting so long for some realistic time calculations from neodarwinism! What is going on??Ian Thompson
September 12, 2013
September
09
Sep
12
12
2013
11:03 AM
11
11
03
AM
PDT
1 2 3

Leave a Reply