Some comments on this piece by @NLENTS.
I quote him in italics and my comments are in bold characters. Presumably, polar bear APOB must be highly optimized for handling the high cholesterol burden. This is a reasonable inference Somehow, Behe draws the opposite conclusion No, not really. What he said in DD is that the mutations in polar bear APOB were likely to be damaging. This is not incompatible with the notion that polar bear APOB must be highly optimized for handling the high cholesterol burden. Donât forget that APOB is multifonctional, and, as a result, you can have damaging mutations affecting a particular function but not the others. In this situation, it is entirely possible that the resulting damaged APOB protein could be better for coping with high cholesterol burden. This is puzzling because he notes that humans and mice with mutations that diminish the function of APOB are more prone to suffer heart disease Agreed, this is kind of puzzling, for, as far as I can tell, it doesnât seem to strengthen his case.
But polar bears do not get cholesterol-driven heart disease, so the logical inference to draw from these data is that polar bear APOB is enhanced , not diminished, by the mutations.
Given the functional complexity of APOB and our lack of knowledge regarding lipid metabolism in polar bear, I donât think this conclusion is warranted.
Thus, the location of the APOB mutations provides more support that enhancement, not diminishment, has occurred. In the case of a multifunctional protein such as APOB, this is untrue.
This program (polyphen-2) can predict whether a given mutation diminishes the function of a protein based on how closely it corresponds to human genetic variation that is known to cause pathology As far as I can tell, this is incorrect, for PolyPhen-2 also relies on structural features to assess the possible diminishing effect of mutations http://genetics.bwh.harvard.edu/pph2/dokuwiki/overview
Okay, but if itâs better at coping with the high cholesterol burden, then it wouldnât be damaged, would it? At this point, we would now have to quibble about what the word damaged means in the context of a multifunctional protein. But considering that the only function being discussed in DD is cholesterol clearance, thatâs real rhetorical gymnastics just to rescue his unfounded claim.
Of course. If there other functions that are relevant to this discussion here, Behe didnât mention them.
Maybe, maybe not. But there is simply NO reason to jump to his conclusions. Itâs murky for sure, but the point is that his position, on balance, is the LESS supported inference and therefore offers no support for his thesis.
I disagree. Notice I didnât say it was definitive, but that it was âmore support.â And I defend that. Functions are often mostly housed in specific domains in proteins. Thatâs why you can often rescue essential functions by providing just small parts of a protein.
Yes, but these are inferred based on the functional/clinical data. The structural inferences (based on the nature of the amino acid change) are applied after the program identifies critical regions using the training it received with the clinical data. @swamidass - isnât that correct?
So from an educatorâs perspective, what do you think is the best vehicle for explaining this to laypeople and undergraduates? I can think of 3 candidates:
Why endangered species need us to facilitate outbreeding
Complex inherited diseases in which the variants have extremely low penetrance, as in my field of inherited cardiomyopathies
This is not true, for the passage on the polar bear APOB example in DD, which comprises only six little sentences, doesnât mention cholesterol clearance at all.
I disagree. Behe has at least the PolyPhen-2 data as well as a very compelling mice study to support his view. His opponents have no experimental data to support the opposite view that the mutations found in polar bear APOB might be constructive at the biochemical level. This is well explained by Behe himself in the piece below.
How can Behe claim that the mutations were not constructive using PolyPhen when PolyPhen does not even have âconstructiveâ (or anything similar) as a possible output?
Using an inaccurate algorithm trained on human sequence to make grand claims about polar bear protein function just isnât going to cut it. Behe needs more data to support the claims he is making.
PolyPhen is a machine learning algorithm that translates information (such as structural inferences) to functional effect (from clinical data). So yes, it does take structural inferences to into account, but only to identify what has no effect vs. what has negative effect. It doesnât have a category for a positive effect, because the clinical data doesnât annotate things that way.
For this reason, it is common (and correct) to conceptually interpret its output as either âpositive or negative effectâ vs. âno effect at all.â
The fact of the matter is that we have no computational way of objectively distinguishing between positive vs. negative effect. A mutation that increases the hardiness of cancer is positive for the cancer, but negative for the patient. All algorithms can really do is predict how likely it was that there was a change in function, and (with the right data) whether or not those changes are likely to benefit the cancer or impact the patient.
Polyphen is not operating at that level though. All it is really doing is predicting if there is a change in function. It is an unequivocal error to construe its predictions as determining the biochemical âdegradationâ of proteins. That is, flat out, not what it is doing.
Itâs surprising that I have to say this again, but he does not âhaveâ the PolyPhen data. As much as he tried to manipulate it to say what he wants it to, it doesnât.
And the mice study isnât evidence for his position, either. The APOB+/- mice have reduced levels of circulating cholesterol. Polar bears have elevated circulating cholesterol. Quoting from the paper, âTotal plasma cholesterol levels were also reduced in the heterozygotes, albeit to a lesser extent ('20%). Because the mouse carries most of its plasma cholesterol on non-apo-B-containing particles(i.e.,HDL), this result was also not unexpected.â To be clear, Iâm not saying that its evidence that APOB is enhanced in polar bears but itâs certainly not evidence for his position, either.
But we havenât made that claim, other than to say that itâs possible. Weâre just claiming that there isnât evidence that itâs diminished.
But the point that is bigger than all others is that none of these variants are fixed in the polar bear population.
And the PolyPhen web page even explicitly states that it is based on human data to be used for human variants. The authors of the paper should not have used it; Behe capitalized on their error to misinform the public.
PolyPhen-2 is an automatic tool for prediction of possible impact of an amino acid substitution on the structure and function of a human protein. This prediction is based on a number of features comprising the sequence, phylogenetic and structural information characterizing the substitution.
I think this is incorrect. Take a mutation within the active site of an enzyme. Donât you think we can predict whether it will have a negative effect on the enzyme activity?
Now, regarding the issue of whether some of the mutations found in polar bear APOB lead to loss of molecular function, why not using VIPUR, a method specifically designed for this purpose? Do you think it may help resolve the issue? If yes, maybe someone here with the required skills/tools could perform the analysis.
I know that it is correct and that you are wrong, from the evidence.
Absolutely not!!!
Gil, weâve literally done this to two different myosins. The most radical side-chain difference possible without changing charge, changing a residue that basically touches the ATP substrate in the active site of an enormously complex enzyme. More than one substitution tested worked, BTW.
Do you ever address any of the many points on which your assumptions are shown to be dead wrong? Do you not realize that you are inadvertently and repeatedly testing the predictions of your ID hypothesis (which you often misrepresent as facts, although you were more modest on this one) and falsifying it?
This tool was published 5 years ago and seems not to be widely used. (I havenât checked Scopus but citation in PubMed Central has been sparse.) Looking at the citations in PMC, I see two very recent publications about similar tools. If someone wanted to do the âanalysisâ of this data set, they would have multiple up-to-date peer-reviewed tools at their disposal. Links below, starting with the final peer-reviewed version of the VIPUR paper. See also this previous discussion of the tools (in 2019) and their effectiveness.
Can you even determine if a ânegative effectâ means increasing or decreasing the enzymes activity? I canât. There isnât enough information to tell.
So one approach that Behe could have done is use changes in the predictions of structural stability as a proxy for âdegradationâ. This is closer to what he means by devolution, and the predictors for protein stability have become reasonably good so as to answer important questions (in aggregate at least).
For example, we could ask, for a random mutation, how likely it is to increase or decrease protein stability. We could ask the same about adaptive mutations.
I havenât done the experiment, but I expect that:
the adaptive mutations would either be the same distribution as the random mutations, or maybe slightly skewed.
Random mutations in mammalian proteins would be almost as likely to increase stability as they are to decrease stability. If Iâm wrong here, I still donât think that increasing protein stability would be a vanishingly unlikely event.
We would see differences in these distributions between mammals and bacteria, possibly with bacterial proteins more optimized for stability and therefore more likely to be destabilized by a mutation.
So those are some hypothesis to test that could be tested with computational predictions. These are far closer to testing Beheâs devolution theory than Polyphen too.
I am not a biologist, but as an intelligent systems guy I think about dynamic and structural forces all the time. So I wonder whether decreasing stability should be characterized as âdegradation,â or whether it is simply one of the axes in a trade-off such that it might be helpful in some situations and harmful in others.
Analogizing from household tools, I find that I need some that are stable (a hammer), some that are very flexible (a plumbing snake), and some that are in-between (a socket wrench). If it is also the case that proteins of various stability can be helpful in various processes (and this is a big if, Iâm not a biologist so I am asking a question), why would a decrease in stability necessarily be characterized as a degradation?
True, but a key component of Beheâs definition of degradation is that it is âbiochemicalâ and often points the opposite direction from âfunction.â He also does address protein stability as something very unlikely to evolve, vis a vis Doug Axe.
So the discussion of âharmfulâ or not misses the point. Behe is arguing that the beneficial mutations are biochemically degrading, because the vast majority of mutations are biochemically degrading. So we need a definition of biochemical degradation that is independent of beneficial/harmful.
Protein stability fits that bill more precisely than anything Behe has committed too, but frankly he never tractably defines biochemical degradation in the first place!
Okay, but if my household tools were slowly evolving, I would think that a trend toward greater stability in my plumbing snake would result in a degradation of its capability.
So Iâm putting the question to the biological utility of âdecreasing stabilityâ == âdegradation.â And if the definition is not helpful for a broad analysis, why should anyone commend the definition to Behe?
Again, I am not a biologist, so I am asking this question so I can learn.
Thanks,
Chris
EDIT: It seems to me that if the best answer is that there is no universally applicable definition of protein degradation, then that should be the response to Behe. âYou cannot make a universal definition protein degradation because the desirable attributes of a protein vary from context to contextâ would make a powerful counterpoint to Beheâs analysisâif itâs true. Which I as a non-biologist do not know.
You are right that stability is not by itself good or bad re âfunction.â If by âstabilityâ we mean âlength of time the protein hangs aroundâ then this is clearly not strictly related to function: in fact, some proteins are rapidly degraded as part of their role in a signaling system. (The classic example here is the ubiquitous Wnt signaling system, in which one key protein is constantly made and then rapidly destroyed. Its âstabilityâ is normally low, and this is a feature not a bug.) Some proteins (especially aggregates) become toxic by being hyperstable.
This, BTW, is why the term âdegradationâ is so confusing (perhaps intentionally so). In a lab studying or using biochemistry, degradation is a pretty specific term that refers to an active process inside cells. Whole fascinating systems are devoted to the destruction of proteins and other cell components, and this is called degradation, indeed often targeted degradation. Cf. the ubiquitin system, in which proteins are âtagged for degradation.â Now walk down the hall of the biology building and listen to some evolutionary biologists or systems biologists chatting. They will talk about âdegradationâ in the way you seem to use it: degraded performance, maybe degraded fitness, etc. In our particular conversation here, this has significant implications for keeping the conversation coherent and even intelligible.