Brian Miller: Co-option and Irreducible Complexity

It was sarcasm. Joshua believes it, therefore it cannot be bad, is simply absurd.

Why not call the site Peaceful Creationism, more in keeping with what it is really about?


My apologies… I totally missed your sarcasm font.

My reference to Joshua’s work is not because I am defending the principle of “If Joshua believes it, it cannot be bad”.
No. That would be silly.

I reference Joshua’s work because, unlike you apparently, I am here to ADVANCE Joshua’s work. While a great many of our colleagues here seem more intent on hijacking the discussion machinery (dedicated to the question of how much Special Creationism and Evolution can co-exist in the Biblical scenarios) - - so they can discuss Evolution-without-God, or Scientific-Proof-of-Design, or a whole host of other topics that do not advance the work of this site, but actually further entrench the polarized discussions we have all participated in for the last 2, 5, 10 or 50 years!

Calling it Peaceful Creationism is not really the point, wouldn’t you agree? If we advance both Special Creation AND Evolutionary processes as methods of creation used by God, using the term “Creationism” would either be deceptive or off-point. This site is just as much about including scientific evidence in Biblical discussion as discussing miraculous creation as part of understanding the emergence of humanity into the historic (i.e., written) epochs!

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Sounds like Peaceful Creationism would be much more appropriate. The site is less about getting Creationists to peacefully accept science and more about getting scientists to peacefully accept creationism.

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Your instincts for public relations could use a little remedial work …

I am not worried about what Scientists say … they already accept the
reality of the evidence for Human evolution. I am much more worried
about Creationists, who in the aggregate are running wild through the
Electorate, sending poorly prepared men and women into Congress and
the Courts.

So… if you were having problems with American Indians, would you
write a book called “Precious American Cavalry Battles”? Or would you
write a book called “America’s Misguided Wars Against Indigenous

Peaceful Science is intended to be a LESS bellicose version of the
scientific community regarding religious interpretations of human

Speaking of which, you could probably benefit from re-read a few
chapters of this kind of thinking.

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The proteins used in the injectisome (aka T3SS) mentioned by Berg are different from those used in the flagellum, but they play synonymous roles. And, the injectisome appeared later in history than the flagellum.

A literature search seems to reveal that the flagellar proteins play no other role in the cell, so selection could not help preserve them until a minimal set arrived.

The conflict is in assumptions. The first difference between an ID analysis of the evidence and materialist scientists’ analysis is that the latter assumes that homologous proteins in different taxa evolved from a common ancestor through undirected processes. As a consequence, they compare the differences between different proteins or between the same protein in different taxa where the differences in sequences could be dramatic. They then assume that one protein could be gradually transformed into the other. We would not make that assumption since the two different proteins or the two versions of the same protein could represent separate isolated islands in sequence space. Instead, we focus on research which directly studies the limits of change or the actual rarity of functional sequences.

Another assumption of materialists is that observing any change generated by an evolutionary process, or at least an evolution-like process (e.g. abzyme research), justifies the claim that evolution could drive any change of any level of complexity. This logic closely matches that of creationists who study how the flood waters from the Mount St. Hellen explosion generated layering patterns in sedimentary deposits. They argue that the capacity of a violent flood to produce those geological patterns justifies the belief that a massive flood could produce all geological patterns. I mention this comparison not to demean either group but to point out similarities in thinking which could foster healthier dialogue between them.

The experiments I cited which study accumulating mutations resemble evolutionary narratives running in reverse. The structural and sequence differences between flagellar proteins and their hypothetical closest common ancestors are so great that the evolution of the former involves a far different protein sequence entering the vast sea of nonfunctional sequences and then finding some island of functional sequences corresponding to some flagellar protein. The first encounter would be with a barely functional protein surrounded by non-functional neighbors. Then, natural selection could assist in refining the protein, so a sequence would move toward a more optimized performance. This process is vastly more challenging than simply modifying the function of an already existing protein.

The cited experiments demonstrate that the negative impact of mutations and the percentage of harmful mutations increase with the number of accumulated mutations. Note that I am not focusing on what the authors imagine could be true but on what their hard data demonstrates to be true.

The authors discuss how compensatory mutations and buffering effects (e.g. chaperones) could increase the threshold before accumulating mutations destabilize the protein. For instance, the negative effect of one mutation could be undone to some extent by the following one, so the sequence might change significantly more than average with a less negative effect. However, such series of mutations maintaining significant fitness would represent a very narrow corridor in sequence space as judged by the dominance of harmful mutations over compensatory ones.

In general, compensatory mutations and buffering increase the threshold for stability by only a limited amount. After a certain number of mutations, the limit is reached, and the protein quickly loses function with most new mutations. After about 10 mutations in B-lactamase and HisA, the majority of the following mutations are lethal. After several more mutations, nearly every subsequent mutation is lethal. These results are from actual bacteria, so they take into account any buffering effects. The authors argue that the destabilizing trend is a general property of proteins.

As a consequence, the rarity of proteins in the region around any functional sequence is so great that no functional protein could ever be found. For instance, the B-lactamase studies indicate that after about 5 non-synonymous mutations, around 1 in 3 amino acids could be tolerated at each site, so the rarity is almost identical to Doug Axe’s results. The HisA results are even worse. After around 10% of the sequences change for either protein, all functionality, based on their numerical fitting, is permanently lost. These regions are completely devoid of functional sequences. As a consequence, most of sequence space is so sparsely populated with functional sequences that no search could ever find any protein in the entire history of the earth.


Where are the experiments demonstrating that these specific proteins would have to cross a “vast sea of nonfunctional sequences”? That seems to be made up.

I can show you genes that are 40% different and still have the same function.

How were they measuring function? How could they detect a change in function if it occurred?

Doug Axe only looked at beta-lactamase activity. There are many more substrates than beta-lactams. Also, Axe only looked at a few sites within the protein.

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What do you believe this would demonstrate? Are you proposing that the two genes are somehow historically related?

Others are claiming that even a small number of changes will do away with function. This is shown to be false by the myriad of proteins that differ by 40% or more but still have the same function.


Originally you said it was two genes, now you say it is two proteins. Which is it? Perhaps it would help if you posted the actual genes or proteins that you are talking about and how you arrived at the figure of 40% difference.

And even if two proteins have differences in amino acid sequence yet perform the same function it still doesn’t follow that if you take each individual protein and modify it that it will still continue to function as it did before. Someone would actually have to do those experiments. That is, after all, what Brian is talking about. Actual experiments with actual proteins.

So you really haven’t answered Brian’s point at all. You’re making an assumption that has not been demonstrated.

He did. Scroll up

And here:


If multiple proteins can perform the same function (which they clearly can) that increases the amount of “targets” that evolution can hit. So finding a function in search space isnt as improbable as it’s made out to be.

Biologists please feel free to critique my comment and increase my understanding. Molecular bio is not my strength.

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But that does not follow either. There is no change in the quantity of targets that exist by virtue of the fact that two proteins perform the same function than by virtue of the fact that two proteins perform two different functions.

I just don’t see how that is the case. I’m a former quarterback so I’ll explain it this way. I’m at practice throwing at targets. There is only one. I hit it from 20 yards maybe 6-7 out of then times. Then a second target is added near the first. I’d say my chances of hitting a target have gone up. I could be aiming at one but make a slightly bad throw and hit the other. There’s more than one way to achieve the “goal”

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Here is the comparison between human and C. elegans cytochrome c. Identity is 58/99, or 59% similarity at the amino acid level.

            GD EKGKKIF  +C QCH V    + KTGP L+G+ GR++GQ  G+ Y+AANKNKG++W 

              TL +YL +PKKYIPGTKM+F G+KK +ERADLI +++

You could try out Homologene if you like. Type in the name of a gene, click on the gene in the search results, and then click on “show pairwise alignement scores” on the next page.


Apparently, you still haven’t learned what the Sharpshooter Fallacy is.


I should clarify by saying that no series of random mutations could find a protein of comparable size and complexity as most of the flagellar proteins if the search started from a significantly different protein in sequence and structure.

I suspect you missed my point. There is more than one way to achieve the goal regardless of whether the second target has the same “function” as the first. The fact that two proteins have the same function is irrelevant. Do you understand what I am saying?

How is that apparent, and how is it that it is not T.j_Runyon who is engaging in the fallacy?

I could agree that if we increase the number of targets that we might improve our chances of hitting one of them (that’s debatable), but what does the fact that the two proteins have the same function have to do with it? Any function would do.

You all are focused on the fact that two proteins have the same function and I say that they have the same function is irrelevant. Why not address that with something of substance.