# Bill's math class

Can you explain how someone who is considering the separate creation model, rather than common ancestry, determines that “97% identical” indicates “preserved.” Or, for that matter, how one determines degree of “preservation” at all? As always, specific mathematical demonstrations are expected.

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OK. The lack of punctuation in the post I was responding to got me confused. I think I see now.

Bill why is your treatment of this subject so pathetically superficial? Can you show SOME sign of comprehending that the rate of divergence depends on multiple other factors? Such as:
a) Mutation rate
b) Generation time
c) Time since divergence
d) Level of constraint on sequence(which itself has many contributing factors)
e) population size

Each of those contributes to the rate of divergence.

Mammalian generation times are much longer(months, years, decades) than bacteria(hours, days), which slows the rate of sequence divergence, comparatively.

However, mammalian mutation rates are much higher than bacteria (2-3-4 orders of magnitude differences), which increases the rate of sequence divergence.

However, many mammals are much more closely related in time (some within 60-80 million years, for example) than are many different species of bacteria(some are separated by billions of years of evolution), which means they had less time to accumulate change.

However, mammalian population sizes are tiny compared to bacteria, which reduces the magnitude of effect of purifying selection, which allows (among other things) transposable element activity to inflate genome sizes, which also allows many genes to exist in multiple copies, which further relaxes the strength of selection on individual genes. Etc. etc. etc.

You can’t just say that some gene is “not conserved” and another is “97% identical” and then think you’ve made some sort of point.
You have to compare the numbers you get to the expected level of divergence under neutrality. That means you have to multiply the mutation rate/generation by the number of generations since the species you compare shared a common ancestor.
That means you have to find out when your bacterial species diverged. And you have to find their mutation rates, and their generation times. So then with the expected degree of divergence under neutrality you can then compare it to the observed degree of divergence, and for basically any functional gene you will discover the observed divergence is lower than the expected divergence* given neutrality(there is SOME constraint on anything that has any degree of function). And it always comes in degrees. Different genes, different levels of constraint.

Then you need to do all the same stuff for your mammalian species to see if how much the gene has diverged and compare it to the expected amount of divergence under neutrality (that you have to calculate and show your work).

Then and only then can you start to talk about whether one gene is more conserved in bacteria, than some other completely different gene is conserved in mammals. In degree.

That’s what doing your work means. Doing ALL that and SHOWING IT. You write out the math you do, what numbers you use and why. And THEN with these results that you have SHOWN HOW YOU ARRIVED AT, do you get to make some sort of point with it.

And that’s before we even begin to talk about the response to Behe by Lynch, and Behe’s inept response to it in turn. Which you’ve never shown any sign of understanding.

*Except of course if the gene has been under positive selection for a significant amount of time. Then it will have diverged faster than expected under neutrality.

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The point I was making is that proteins have different sequence constraints which is your
point C.

The rest of your points are simply part of both models.

This is based on mutations being neutral and many vertebrate proteins are constrained as you agree.

KA/KS ratios are a simple way to measure constraint. In the case of beta lactamase the ratio is relatively high as the AA sequence identify is only 25% among 3 different bacteria. A low KA/KS ratio signifies a high level of constraint.

Behe’s model was closer to reality than Lynch’s. You are confirming based on the above that there is varying functional constraint to gene coding proteins. This is not considered in Lynch’s model. The model needs to handle the worst case to validate common ancestry vs a new design. Behe’s model is a more robust test as it considers constrained proteins.

Yet he does, and for Bill, the inclusion of a number counts as highly sophisticated math.

Point C:

OK, Bill. If you say so.

That you wrote that sentence after one that you quoted from @Rumraket would seem to indicate you intended it as a response to what @Rumraket wrote.

The mind boggles.

Please show how you determined this. As usual, specific mathematical calculations are expected.

IOW, Behe’s model shows that highly constrained proteins are unlikely to evolve new functions over a realistic timeine. Am I understanding you correctly?

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Once again I am exerting effort solely for a goal that may be possible to achieve: to get you to start spelling “than” correctly. Are you able and/or willing to try this?

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Disregarding that it’s point D, if that was your point then it is of no value in this discussion since nobody here denies that. You also chose to make that point with a bad example, since you were comparing the divergence of different proteins in different species with radically different evolutionary rates and times to their common ancestry. For neither protein have you shown how much (or even if) it deviates from the expected degree of divergence.

No, it isn’t based on mutations being neutral. The rate at which mutations occur, is higher in mammals by several orders of magnitude, compared to bacteria.

Yes. But you didn’t do that. It’s simple, but you didn’t do it. You still haven’t done it.

Do it. Show your work.

That’s not a Ka/Ks ratio. It’s a percentage identity. You don’t get a Ka/Ks ratio by just comparing the sequence identity of a bunch of proteins. Wake up *

Show your work. What evidence is there to support Behe’s parameters over those of Lynch’s, are you going to cite a bunch of papers in support of a statement, that says the diametrically opposite of what the papers are saying, like Behe did?

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In his response to Lynch, Behe wrote the following:

In his Editorial (this issue), Professor Hermodson reports that comments sent to him assume a consensus, “Thus, intermediate states must also be assumed to be selected.” Some significant previous work does not make this assumption (Kimura 1985; Ohta 1989), but our paper supports such a consensus. This is a strong requirement—that not only the end products, but steps along the way to a multi-residue function, must be either selected or at least neutral. Michael Lynch makes a similar assumption. Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch’s model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state” (Lynch 2005, this issue). All of his objections to our work stem from this difference.

Here is what Hermodson actually wrote:

The various letters and manuscripts were reviewed as a package by the editors and by outside experts. Some points made by the various commentators include:

• Selection acts continuously, and cumulative effects, rather than a single strongly adaptive change, are the basis of evolution under a Darwinian model. Thus, intermediate states must also be assumed to be selected.

Bill can perhaps be forgiven for misunderstanding this. Behe’s response was probably intended to deceive people more clever than Bill.

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Lynch’s model is based on equally substitutable amino acids.

If we follow the logic everyone agrees Lynch’s model is wrong (assumes equal substitutability of AA"s) so I agree we are done here.

I think it is reasonable that @Meerkat_SK5 can use Behe’s model as a tool to help segment common design and common descent to generate his proposed model.

Look at that complete failure to even attempt to address a single thing you were asked.

In this entire thread. Or any other threads.

At some point you’re just going to need to admit that you can’t back up a single thing you’ve ever said.

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They often are for many sites in many known proteins(see this post: Human Evolution Discussion with Ahmed - #131 by Rumraket). In contrast Behe assumes they’re all deleterious without exception.

So do you have any evidence Behe’s assumption is realistic for any known protein?

No, we aren’t done here Bill. Where’s your evidence?

I think you’re flailing wildly to get out of this one.

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Why start now?

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Here are Behe’s assumptions re substitutability…

An estimate of ρ can be inferred from studies of the tolerance of proteins to amino acid substitution. Although there is variation among different positions in a protein sequence, with surface residues in general being more tolerant of substitution than buried residues, it can be calculated that on average a given position will tolerate about six different amino acid residues and still maintain function (Reidhaar-Olson and Sauer 1988, 1990; Bowie and Sauer 1989; Lim and Sauer 1989; Bowie et al. 1990; Rennell et al. 1991; Axe et al. 1996; Huang et al. 1996; Sauer et al. 1996; Suckow et al. 1996)

Which means… Behe’s assumption is garbage.

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YOU were asked if YOU have any evidence, so quoting Behe, who frequently grossly misreprents the evidence, is an admission that you have none.

Why not be more forthcoming?

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Huh, so Behe, in the same paper, said two completely different things while referencing the exact same set of sources. That… 100% confirms that he was lying in the bit Bill quoted in the other thread. Once again, Bill accidentally provides the best arguments against his own claims.

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We could be charitable and consider the possibility that Behe is just as confused as Bill is in understanding the articles he cites. Did he really think that, in the editorial, Hermodson was citing a scholarly consensus that novel proteins must evolve thru intermediary steps that are each, individually, subject to positive selection. rather than what Hermodson (it seems to me) was actually stating: The commentators had agreed with Lynch’s criticism that Behe’s model does not accurately model Darwinian mechanisms?

It is possible, sure. But it hardly speaks to Behe’s favour that our options are limited to professional incompetence or rank dishonesty.

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