The Failures of Mathematical Anti-Evolutionism

You can. But before the fact, you don’t know which event to compute the probability for. Computing the probability of drawing a full house is futile if you then draw a flush instead.

All this talk of before-the-fact vs after-the-fact with poker is a smokescreen to hide that whenever you talk about biological systems instead of card games, you’re computing the probability of something that has already happened - because if it hadn’t happened you wouldn’t know what probability to compute - hence it’s after-the-fact.

Feel free to counter this by computing the before-the-fact probability of evolving something that did not actually evolve. Until then, you’re just bait-and-switching.

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Well, how about here, then? “Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs”

Well, the de novo proteins were on average about 150 amino-acids long. It would be surprising if there was an all-selectable pathway to proteins of this length.

“We analyzed the characteristics of these de novo protein-coding genes. Consistent with previous reports [4], we found that the gene products were smaller, with a median length of 150.5 amino-acids, compared with 416 amino-acids in the human genome, suggesting the difficulty in de novo origination of long ORFs…”

“When chloroquine is no longer used to treat malaria patients in a region, the mutant strain of P. falciparum declines and the original strain makes a comeback, indicating that the mutant is weaker than the original strain in the absence of the toxic chloroquine. [9]” (The Edge of Evolution, pp. 50-51)

“9.Kublin, J. G., Cortese, J. F., Njunju, E. M., Mukadam, R. A., Wirima, J. J., Kazembe, P. N., Djimde, A. A., Kouriba, B., Taylor, T. E., and Plowe, C. V.2003. Reemergence of chloroquine-sensitive Plasmodium falciparum malaria after cessation of chloroquine use in Malawi. J. Infect. Dis. 187:1870–75; Cooper, R. A., Hartwig, C. L., Ferdig, M. T. 2005. Pfcrt is more than the Plasmodium falciparum chloroquine resistance gene: a functional and evolutionary perspective. Acta. Trop. 94:170–80. Drug resistance mutation in pfmdr, the other protein involved in chloroquine resistance, also incurs a fitness cost (Hayward, R., Saliba, K. J.,Kirk, K. 2005. pfmdr1 mutations associated with chloroquine resistance incur a fitness cost in Plasmodium falciparum. Mol. Microbiol. 55:1285–95).”

“In 1993, Malawi became the first African country to replace chloroquine with sulfadoxine-pyrimethamine nationwide in response to high rates of chloroquine-resistant falciparum malaria. To determine whether withdrawal of chloroquine can lead to the reemergence of chloroquine sensitivity, the prevalence of the pfcrt 76T molecular marker for chloroquine-resistant Plasmodium falciparum malaria was retrospectively measured in Blantyre, Malawi. The prevalence of the chloroquine-resistant pfcrt genotype decreased from 85% in 1992 to 13% in 2000. In 2001, chloroquine cleared 100% of 63 asymptomatic P. falciparum infections, no isolates were resistant to chloroquine in vitro, and no infections with the chloroquine-resistant pfcrt genotype were detected.” (from here)

I think this implies both mutations are subject to negative selection.

The rate of chloroquine resistance is about the square of the rate of atovaquone resistance, which requires one mutation. This is what we would expect, if chloroquine resistance requires two independent, singly-non-selectable mutations.

How so? As far as I have read, they say there are two known paths, with two mutations required in each path, for basic resistance.

I’ve posted his argument in these threads, it has to do with considerations of protein shape space. I refer you to Behe’s book, if you want the full argument.

But they won’t last long, if they are singly somewhat deleterious.

My point is that viewed before the fact, the probability of an event can be less than 1, whereas after the fact, it is 1 or 0. So we have to pick one perspective, and stick with it. I choose “before the fact”, because that’s really the probability of interest, in card games, and in biological systems.

IOW “These go up to 11.” And just what does the length of the protein have to do with this?

I will repeat the question one more time: Why can the mutations necessary for these new(ish) proteins not arise one at a time? They don’t have to each be selectable. But even if they did, they would not have to occur simultaneously. Why would they?

Why do you think it implies that? One thing you do not seem to appreciate is that chloroquine would exert a strong selective pressure in favour of resistant strains. Once the drug is withdrawn, this pressure no longer exists and other variants are free to arise. It is not necessary that the resistant strain be subject to negative selection. But that is not the main problem you have here, so I just add that for your edification.

You really need to explain why you think these traits require simultaneous mutations.

Yes. If you insist it requires simultaneous mutations, please quote where this is said in the paper. Please, no more Nigel Tufnel. Give us the quote.

No, you really haven’t. You just think you have. “These go to eleven” is not an argument, sorry.

Again, support this assertion. And how deleterious is “somewhat”? Have you heard of nearly neutral theory?

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No, your claim is about protein-protein binding sites. You’re very bad at inferring content from titles and abstracts.

You’re terminally confused.

The intermittent selection, even if all patients took chloroquine, is the reason why fixation of mutant HAPLOTYPES is so rare, not mutational requirements.

And that’s overall. It just as easily could be that some of the alleles that confer chloroquine resistance have decreased fitness in the intermediate hosts irrespective of chloroquine.

[quote=“lee_merrill, post:80, topic:15042”]

The rate of chloroquine resistance is not merely a function of mutation, but of intermittent selection, recombination, epistasis, etc. Behe’s “calculation” ignores all of these important factors.

You did not read carefully. There are two MAIN paths. You are misrepresenting the bit of the paper you quoted.

[quote=“lee_merrill, post:80, topic:15042”]

No, it does not, as there is nothing that sophisticated in Behe’s book. You’ve been bamboozled. Again, high-affinity, specific binding is evolved from random variation in your immune system in only 2 weeks.

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I’ve restored part of my post that was omitted by @lee_merrill when he responded:

So you’re not going to calculate any before-the-fact probabilities of anything other than what you know evolved. All your biological system calculations are done after-the-fact, and your claims otherwise are untrue. You are bait-and-switching.

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If Behe is basing his probabilities on what evolution does then he is picking after the fact.

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Yes, that is another problem with Behe’s argument that we have not discussed at length here. This chart is from the paper entirely on which Behe based his 10-20 number1, and lists the conditions that must be met before a chloroquine resistant strain is detected in human beings:

image

Behe ignores points 2-8 and pretends the frequency is accounted for entirely by factor 1. That, by itself, ought to be sufficient to sink his argument if he had one. But the other point that is easily missed is that Behe does not even have an argument. He just has a series of unrelated points, each of which is true to varying degrees, and then he magically conjures a conclusion from them. Try map out his argument and see if you disagree. In fact, I might do that myself…

1JCI - Antimalarial drug resistance

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The longer the protein, the more unlikely it is to have an all-selectable pathway to it.

They don’t have to occur simultaneously, but if one or more of the mutations required, is non-selectable (which would seem likely, since most mutations are actually deleterious), then multiple mutations would need to occur basically simultaneously.

It’s a deduction, first a minimum of two mutations is required: “A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity.” Then, based on the rate of occurrence of chloroquine resistance (1 in 10^20) versus atovaquone resistance (1 in 10^12) we can deduce that chloroquine resistance requires two simultaneous mutations.

Deleterious mutations are selected against, why do I need to support this assertion? And chloroquine resistance mutations disappear in a few years, which would seem to imply that these mutations are not just neutral.

WHY???

Human proteins are littered with neutral mutations that have accumulated over hundreds of millions of years. The two papers @Rumraket has linked to show how there are multiple pathways that utilize neutral mutations, so they are plentiful. Also, there are many human proteins that have known mutations to almost all non-lethal positions in the protein within the current population.

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You all are misunderstanding me, I’m saying that when you are evaluating a probability, you have to pick before-the-fact or after-the fact, regardless of whether the event has actually occurred. All the interesting probabilities are deduced by viewing the event before-the-fact, so everyone will generally focus there.

I was assuming that it is not uncommon for proteins to bind to other proteins.

I’m not sure why you emphasize haplotypes, here? And Behe’s point is that the mutant appears to be weaker, that’s a pretty plain point.

Again, Behe is not calculating, he is observing what evolution does.

“Multiple mutational pathways led to saturable CQ transport via PfCRT, but these could be separated into two main lineages.” (Summers et al.) It sounds like “separated” implies total division into two lineages.

So how do you calculate the number of possible combinations of two mutations, one neutral and one beneficial, that can result in a selectable function in a given genome?

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Proteins do not need an all selectable pathway, though. Why do you keep saying they do?

No, not if they are neutral. Which, contrary to your claim there, most of them are. Your problem is you just swallow everything Behe tells you, and he is usually wrong about what he says.

Major logic fail. Even if the Summers paper didn’t actually tell you why CR arises infrequently as it does, your reasoning would still be invalid. There are any number of reasons that a particular trait might arise infrequently besides a requirement for simultaneous mutations. But as it happens, the paper actually tells you why the resistant strain is less frequent than might be expected. Note the bolded sentence:

Mutations in the chloroquine resistance transporter (PfCRT) are the primary determinant of chloroquine (CQ) resistance in the malaria parasite Plasmodium falciparum . A number of distinct PfCRT haplotypes, containing between 4 and 10 mutations, have given rise to CQ resistance in different parts of the world. Here we present a detailed molecular analysis of the number of mutations (and the order of addition) required to confer CQ transport activity upon the PfCRT as well as a kinetic characterization of diverse forms of PfCRT. We measured the ability of more than 100 variants of PfCRT to transport CQ when expressed at the surface of Xenopus laevis oocytes. Multiple mutational pathways led to saturable CQ transport via PfCRT, but these could be separated into two main lineages. Moreover, the attainment of full activity followed a rigid process in which mutations had to be added in a specific order to avoid reductions in CQ transport activity. A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. The finding that diverse PfCRT variants are all limited in their capacity to transport CQ suggests that resistance could be overcome by reoptimizing the CQ dosage.

Got it? The mutations had to be added in a specific order, but were still added one at a time. The astonishing thing is that it says right there that Behe is wrong, yet he and his gullible sycophants actually thought this paper vindicated him! I find that very strange, and very sad. Don’t you?

Jeez, you really don’t read very carefully. Go look at what I actually asked, then see if you can come up with an answer.

"In a few YEARS??!!! " And you honestly think drift alone is not capable of removing a variant that is not subject to selection either way in an organism that reproduces as rapidly as C. falciparum in a matter of a “few YEARS?”

This is the problem: You really have no understanding of the bare basics of this subject, so you are vulnerable to Behe’s underhanded efforts to bamboozle you with his BS because he is saying something you want to be true. I actually feel sorry for you, because then you come onto a forum like this and embarrass yourself.

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Sorry, I should have said “deleterious” instead of “non-selectable”.

No, Behe observes what evolution did, this includes all the factors. But the following statement, specifically for chloroquine resistance, seems clear: " Resistance to chloroquine in P. falciparum has arisen spontaneously less than ten times in the past fifty years (14). This suggests that the per-parasite probability of developing resistance de novo is on the order of 1 in 1020 parasite multiplications."

  • Chloroquine resistance occurs in about 1 in 10^20 organisms, requiring two singly-deleterious mutations
  • We’ll call a CCC a chloroquine-complexity cluster, an event requiring two singly-deleterious mutations.
  • A double-CCC (an event requiring two CCCs) is beyond the edge of evolution.
  • Based on considerations from shape space, a new protein-protein binding site would need several singly-deleterious mutations, or a CCC.
  • So two such binding sites would be a double-CCC, beyond the edge of evolution.

No, your non sequitur does not become true by your repeating it. Behe ignores all but one and misrepresents himself as in agreement with White.

There’s noting about simultaneous mutations in there. What is clear is the list in the same paper that Behe ignores.

BTW, Faizal asked you to map out Behe’s argument, not just reiterate his assertions.

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He has made zero observations. He has used textual misattributions to claim that it’s all about mutation.

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Another “These go to 11.” If he took all the factors into account, then how does what he concludes about chloroquine resistant apply to every other trait in every other organism, where completelhy different factors are at play?

Objectively wrong, as you should know by now. Why are you repeating a falsehood?

Sure, call it whatever you want. Call it “Rumplestiltskin” if that’s what you want to do."

OK, sure. Lots of things are beyond the “edge of evolution.” No one expects the malaria bug to evolve the ability to do differential calculus while playing the banjo.

Codswallop. How does this follow from what preceded it, even if what preceded was true (which it isn’t)?

More codswallop.

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To be fair, I actually think @lee_merrill did map out Behe’s “argument”, such as it is.

It really does seem to be a series of assertions, most of them outright contradicted by empirical evidence, with no logical connection from one to the next.

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