The Three Musketeers vs D’Artagnan

Every few years the world of the supporters of Intelligent Design becomes ecstatic when the founding father of their thought liberating movement – Dr. Michael Behe – publishes a new book against Darwinism…Due to that, apparently some churches’ records show an increased mass attendance, confessions, donations…etc. It is almost as if one the apostles of Jesus Christ wrote another book of the Bible even though Behe clams his publications are not religious but rather scientific…

But not everyone is celebrating… Does this mean the end of evolution?

The Intelligent Design movement has many powerful enemies who not only represent the opposite to ID, or atheistic (materialism), views of life origins. Some even claim to support intelligent design…of sort, as long as that design also includes evolution…Confused? Wait until the debate gets heated… 😉

So, what’s this book kerfuffle all about, one might ask?

Well, in short: some of most profound world views are colliding…again… as Behe and many of his comrades at the Discovery Institute also had published many books and papers in the past.

The Three Musketeers of neo-Darwinism, or some sort of theistic evolutionary theory, involved in the upcoming debate are represented by:

Dr. Richard Lenski – an experimental scientist who claims to have achieved an equivalency of millions of years of human evolution by growing bacteria in the lab for the last 25 years…

Dr. Nathan Lents – Professor of Biology, John Jay College; Admin, The Human Evolution Blog; Blogger, Psychology Today; Author of “Not So Different” and “Human Errors.”

Dr. S. Joshua Swamidass, MD PhD, a professor at Washington University in Saint Louis, the confessing scientists and a Christian, who some believe became “the devil’s advocate” in order to defeat the enemy of true science (in this case represented by neo-Darwinism or evolution) the intelligent design movement and its founding father Michael Behe…

Today, February 7th at 2 pm, of unknown time zone, “the circus” (as Swamidass described it) of the differing worldviews will have begun; the three musketeers against the lone ranger, Dr. Michael Behe, PhD- Professor of Biological Sciences at Lehigh University in Pennsylvania.

What’s at stake? Some might agree that everything…

The subject of the first stage of “the circus” and the major speck in the eyes of the three musketeers representing evolution is the book by Michal Behe:

Darwin Devolves: The New Science About DNA That Challenges Evolution

This article criticizing Behe’s book and the discussion blog will appear at Science Magazine:
http://science.sciencemag.org/content/363/6427/590

https://blogs.sciencemag.org/books/2019/02/07/darwin-devolves/

It should be entertaining 😉 I hope to be a small part of it… Some of my colleagues promised to join in as well…

Let the hunger games of Evolution vs ID begin!!! 😉

453 thoughts on “The Three Musketeers vs D’Artagnan

  1. J-Mac: It sure appears to be the case to some… but how would you prove it or disprove it?

    Many molecular functions, such as ligand binding, can in principle be tested in the lab. I would pick a somewhat more accessible organism though.

    The main point is that we both understand The First Rule of Adaptive Evolution to be about decreasing molecular function.

    J-Mac: Corneel: Do you agree with Behe that polar bears adapted to a high-cholestrol diet by degrading one or more of the molecular functions of APOB?

    J-Mac: Yes and no…

    Could you specify that a bit? Don’t leave me guessing.

    J-Mac: Your are joking, right???

    C’mon, it makes perfect sense.

    Some pigmentation genes were degraded => Loss of pigmentation in fur (devolution)
    Some pigmentation genes were “upgraded” => Increased pigmentation in skin (evolution).

  2. J-Mac: Your are joking, right??? Or you have been drinking what OMagain has been drinking?

    An alternative response would have been to explain why you thought the proffered explanation was unlikely.

  3. At evolutionnews, Behe provides the following tortured quote from his book:

    In fact, of all the mutations in the 17 genes that were most highly selected, about half were predicted to damage the function of the respective coded proteins. Furthermore, since most altered genes bore several mutations, only 3 to 6 (depending on the method of estimation) out of 17 genes were free of degrading changes. Put differently, 65%-83% of helpful, positively-selected genes are estimated to have suffered at least one damaging mutation.

    He then helpfully provides a list of 25 mutations that are predicted to be either “possibly damaging” or “probably damaging” to support this case.
    He describes this list as

    Below is the relevant information from Liu et al.’s Table S7. Those who can understand the table will see that it supports every actual, undistorted claim I made about the polar bear.

    Curious readers might wonder what Table S7 actually carries, and what Behe deemed “the relevant information” to provide his readership.
    Here goes:
    Table S7 lists 48 identified mutations in the 17 genes. It uses two different algorithms to estimate whether the mutations are “benign”, “possibly damaging”, or “probably damaging”.
    Using the more pessimistic Div algorithm, 23 mutations are benign, 25 possibly/probably damaging. All but 3 genes carry one or more ‘damaging’ mutations.
    Using the more optimistic Var algorithm, 32 mutations are benign, 16 possibly/probably damaging. All but 6 genes carry one or more ‘damaging’ mutations.
    [That’s where Behe’s “3 to 6, (depending on the method of estimation)” caveat comes from]
    What does Behe provide his readers as “the relevant information” from Table S7 that will support every claim he made about the polar bear?
    He uses the more pessimistic algorithm, Div, and he carefully omits all 23 benign mutations!
    That is dishonest; the benign mutations are key to the statements he quotes.
    In separate news, “damaging” does not mean, in Table S7, what he needs it to mean for his argument. That error may merely be wishful thinking.

  4. DNA_Jock:
    That is dishonest; the benign mutations are key to the statements he quotes.
    In separate news, “damaging” doesnot mean, in Table S7, what he needs it to mean for his argument. That error may merely be wishful thinking.

    Even worse for Behe, as pointed out over on PS:
    “In this context, the software program just outputs “damaging” if it is likely to be a function changing mutation. As a quirk of this program, it calls both increases and decreases in function “damaging.” It appears that Behe misunderstood how this program works. We expect many beneficial mutations to be called “damaging” by this software, but this does not mean that they are likely to degrade or destroy the function of the protein when applied to data like this.”

    This COMPLETELY undermines Behe’s reliance on the “damaging”/”benign” score output by this software for his case.

  5. You have to hand it to Swamidass, Lents and Lenski. Provoking such an intemperate and dishonest response from Behe! Well done! 😂

  6. Alan Fox: You have to hand it to Swamidass, Lents and Lenski. Provoking such an intemperate and dishonest response from Behe! Well done!

    Looking at the table above and comparing it to the table he actually posted, well, hard to see a way out of that.

    EDIT: That nobody forced him to publish! He did not have to even respond. And these are the people J-Mac, Mung et al have hitched their wagon to!

  7. Rumraket: Mung donates to the DI? HAahahaha

    Yeah. I know, Rum, I know.
    Remember we’re talking about Mr I-believe-in-common-descent-but-I-don’t-even-know-why

  8. Behe has responded to his book review with a longer, more detail rebuttal:

    Train Wreck of a Review: A Response to Lenski et al. in Science

    https://evolutionnews.org/2019/02/train-wreck-of-a-review-a-response-to-lenski-et-al-in-science/

    I find one thing very strange. Behe ignores Lents and almost doesn’t mention Swamidass unless he has to…

    Lents, I can understand because of his embarrassment with the Human Errors, which I exposed…Swamidass’ hypocrisy has probably become an issue with his claims that he wants to “help” Behe and then he builds strawmen against him to do so… It must be the new, peaceful way of “Christianity”… or something…

  9. Can the team of experts here either confirm or refute by what mechanism the polar bears’ hair follicles cells do not produce pigment, unlike their brown ancestors?

    Also, can the same team of experts here either confirm or refute the notion of the ApoB protein that either protects the development cardiovascular diseases in mammals or not and by what mechanism?
    I bet my change in my pocket today, (my kids took some for pizza) that nobody will be able to come up with scientific evidence regarding the Eskimos mechanism of their “evolutionary” adaptation to the same diet the polar bear must have gone through… It was just as high in fat as the polar bears’….

  10. The only problem I have with this is, why would anyone, in the right frame of mind, celebrate that there is a slight possibility that God/ID doesn’t exist? Are they murderers? Are they responsible for the mishandling of the garbage disposal? Are they weird because they see the world differently than the great majority?

  11. Corneel: Some pigmentation genes were “upgraded” => Increased pigmentation in skin (evolution).

    Really?
    What if you are wrong?
    You will become a ……right? 😉

  12. Corneel: Many molecular functions, such as ligand binding, can in principle be tested in the lab. I would pick a somewhat more accessible organism though.

    The main point is that we both understand The First Rule of Adaptive Evolution to be about decreasing molecular function.

    What organism (s)? Be more specific!

  13. Corneel: J-Mac: Corneel: Do you agree with Behe that polar bears adapted to a high-cholestrol diet by degrading one or more of the molecular functions of APOB?

    J-Mac: Yes and no…

    Could you specify that a bit? Don’t leave me guessing.

    I can’t at this point. Sorry… My last OP was going to address it but I was told to wait until Behe’s book is officially published… I’m eager to address it. Believe me! 😉

  14. J-Mac: The only problem I have with this is, why would anyone, in the right frame of mind, celebrate that there is a slight possibility that God/ID doesn’t exist? Are they murderers? Are they responsible for the mishandling of the garbage disposal? Are they weird because they see the world differently than the great majority?

  15. Rumraket:

    What are you doing up at this hour? Are you disturbed by the football under-the-table-scandal?
    It should have never happed in an idealistic, atheistic country like yours…

  16. OMagain: And these are the people J-Mac, Mung et al have hitched their wagon to!

    I have not hitched my wagon to the idea of “devolution.”

  17. Here is another interesting review of Behe’s book:

    “…Asteroid impacts aren’t common either, but the dinosaurs (among other groups) sure felt the impact of one at the end of the Cretaceous. (There remains some debate about the cause of that mass extinction event, but whatever the cause its consequences were huge.) Luckily for us, though, some early mammals survived. Evolution often leads to dead ends, sometimes as a consequence of exogenous events like asteroids, and other times because adaptations that are useful under a narrow set of conditions (such as those caused by mutations that break or degrade genes) prove vulnerable over time to even subtle changes in the environment. It has been estimated that more than 99% of all species that have ever existed are now extinct. Yet here we are, on a planet that is home to millions of diverse species whose genomes record the history of life.

    Summing up, Behe is right that mutations that break or blunt a gene can be adaptive. And he’s right that, when such mutations are adaptive, they are easy to come by. But Behe is wrong when he implies these facts present a problem for evolutionary biology, because his thesis confuses frequencies over the short run with lasting impacts over the long haul of evolution.”

    Can anybody spot contradictions?

    https://telliamedrevisited.wordpress.com/2019/02/15/does-behes-first-rule-really-show-that-evolutionary-biology-has-a-big-problem/

  18. ” We predict that all these protein-coding changes, possibly aided by regulatory mutations or interactions with other genes, dramatically suppress melanin production and transport, causing the lack of pigment in polar bear fur.Variation in expression of the other color-associated gene, AIM1 (absent in melanoma 1), has been associated with tumor suppression in human melanoma (Trent et al., 1990), a malignant tumor of melanocytes that affects melanin pigment production.

    https://www.cell.com/cell/fulltext/S0092-8674(14)00488-7

    I would like to hear some comments about the three musketeers’ “honesty” about the “white bear” evolution 😂

  19. J-Mac: I would like to hear some comments about the three musketeers’ “honesty” about the “white bear” evolution

    Do you have something to say? Why not say it? Do you expect people to read paragraphs and paragraphs of text that you did not write and infer your meaning?

    You bolded some text. So?

    You appear to be sniggering at something that you believe you’ve now been proved right about, or have shown that somebody else is wrong. Think how enjoyable it would be to put all that together into a single comment and add links and show how you were right all along!

  20. J-Mac: I would like to hear some comments about the three musketeers’ “honesty” about the “white bear” evolution

    And lets say, for example, that there are differing opinions about why polar bears are white. Some say white pigment, some say no pigment at all. Some say Jesus does it.

    You can only make a claim regarding “honesty” when you can demonstrate that someone is acting in bad faith. You’ve not actually done that, as far as I can tell given the quality of your writing. You can’t point out two groups with different scientifically supported options and say one is dishonest. It’s just the data has not allowed that particular question to be resolved one way or the other (yet).

    Note that none of those competing explanations are God/ID related. You continue to proffer nothing except misunderstandings of “Darwin”. And yet you think that you can somehow elevate your vacuous position by finding dishonestly in the actual reality based community.

    Whereas, for a counter example, “Behe-Table-gate” is demonstrably dishonest behaviour. And there you should be focusing your ire if “honestly” is a thing for you.

    Remember what I said about projection earlier? You have seen for yourself now the dishonest tactics of the ID/God brigade. How could you not have? And even if you don’t want to admit it, you are now projecting that onto everything and everyone else.

    How’s that working out for you? Convinced many people about “the quantum” yet?

  21. Since nobody seems to be able to see the “honesty” of the musketeers regarding the “white bear” evolution of “pigment”, let’s focus on the ApoB protein a bit…
    I hope that this discussion will help some of the evolutionary experts here to prepare for the OP we are planning to do once Behe’s book Darwin Devolves is officially published…
    Here is the controversial quote from the Cell Magazine:

    “Due to a lack of appropriate functional studies of polar bears, we were unable to directly identify causal variants. Nevertheless, we assessed the impact of polar bear—specific substitutions on human proteins for top-20 genes under positive selection by computational predictions: a large proportion (ca. 50%) of mutations were predicted to be functionally damaging (Figures 4C and 4D, Table S7). Substantial work has been done on the functional significance of APOB mutations in other mammals. In humans and mice, genetic APOB variants associated with increased levels of apoB are also associated with unusually high plasma concentrations of cholesterol and LDL, which in turn contribute to hypercholesterolemia and heart disease in humans (Benn, 2009, Hegele, 2009). In contrast with brown bear, which has no fixed APOB mutations compared to the giant panda genome, we find nine fixed missense mutations in the polar bear (Figure 5A). Five of the nine cluster within the N-terminal βα1 domain of the APOB gene, although the region comprises only 22% of the protein (binomial test p value = 0.029). This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.

    Let’s see if our team of experts here can identify the key features of the this quote and based on what evidence the authors arrive at the conclusion or the interpretation of the data…

    BTW: For those who are “under the influence”: No, Jesus doesn’t protect the arterial walls of polar bears from the bad, bad cholesterol 😉

    I hope I don’t get in trouble for giving out too many hint about the upcoming OP…🤔

  22. DNA_Jock:
    It’s the contrast with the brown bear that is informative, J-Mac.

    What contrast? Devolutionary contrast?
    Otherwise what’s the fast evolution all about since the the two bears diverged? Nothing? 😉

  23. J-Mac: a large proportion (ca. 50%) of mutations were predicted to be functionally damaging (Figures 4C and 4D, Table S7).

    As pointed out over on PS:
    “In this context, the software program just outputs “damaging” if it is likely to be a function changing mutation. As a quirk of this program, it calls both increases and decreases in function “damaging.” It appears that Behe misunderstood how this program works. We expect many beneficial mutations to be called “damaging” by this software, but this does not mean that they are likely to degrade or destroy the function of the protein when applied to data like this.”

    Also, see picture:

  24. J-Mac: What contrast? Devolutionary contrast?

    So Behe compiles a list of “damaging” mutations to show that the polar bears “devolved”, but the majority of the actual mutations aren’t predicted to be damaging, and Behe mysteriously didn’t include these mutations in his analysis.

    To make matters worse, it is entirely possible that many of the mutations Behe thinks are damaging, are actually function-improving instead, because the computer program used to predict the effect of the mutation simply outputs “damaging” for any mutation that is predicted to affect the function of the protein even, if that mutation actually improves function.

    Is it sinking in yet? Are you starting to grasp the essential details?

  25. Rumraket: As pointed out over on PS:
    “In this context, the software program just outputs “damaging” if it is likely to be a function changing mutation. As a quirk of this program, it calls both increases and decreases in function “damaging.” It appears that Behe misunderstood how this program works. We expect many beneficial mutations to be called “damaging” by this software, but this does not mean that they are likely to degrade or destroy the function of the protein when applied to data like this.”

    Also, see picture:

    Really? Application of data???
    We’ll see about that…😉

    At least you are an honest Darwinist who is willing to concede that Swamidass and Lents were either dishonest, or didn’t do their homework, on the polar bear lack of pigment in the hair follicle cells due to the damaging mutations, right?
    You are not looking for confirmation bias, but rather, honestly follow the argument wherever it may lead, right?

  26. J-Mac,
    You asked biologists to “identify the key features of the [sic] this quote”
    I was pointing you to the sentence that begins “In contrast with brown bear,” You do not seem to have grasped its significance.

    “Is there any other point to which you would wish to draw my attention?”
    “To the curious incident of the dog in the night-time.”

  27. DNA_Jock: “Is there any other point to which you would wish to draw my attention?”

    Yup! I highlighted it but you and Rum omitted it…

    “This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.“

    Do you need some leading questions or you will manage?

  28. Oh shit.
    I am sorry if the Sherlock Holmes dialog went over your head.
    You posed an indirect question —

    Let’s see if our team of experts here can identify the key features of the this quote and based on what evidence the authors arrive at the conclusion or the interpretation of the data…

    I answered; twice, actually, since you didn’t pick up on it the first time. My answer: the sentence that begins “In contrast with brown bear,”.
    And in order to gently guide you in the right direction, I offered up the first half of a rather famous exchange, to wit:

    Gregory (Scotland Yard detective, no relation): “Is there any other point to which you would wish to draw my attention?”
    Holmes: “To the curious incident of the dog in the night-time.”
    Gregory: “The dog did nothing in the night-time.”
    Holmes: “That was the curious incident”

    Sherlock’s point was that the dog’s curious inactivity was what enabled him to solve the case.
    I should know better than to offer anything subtle.
    The brown bear did nothing (well its APOB gene did nothing) since the split with the common ancestor. The polar bear fixed nine mutations. That is telling you something; can you figure out what?

    I realize that you attach some great import to the sentence you highlighted. You will have to explain this great import.

  29. DNA_Jock: That is telling you something; can you figure out what?

    That polar bears are immune to evolution?

    DNA_Jock: It’s the contrast with the brown bear that is informative, J-Mac.

    How informative is it if he does not accept common descent?

    #channelingbillcole

  30. DNA_Jock: “In contrast with brown bear,” You do not seem to have grasped its significance.

    “Is there any other point to which you would wish to draw my attention?”

    Can you point out the CONTRAST between brown bear and the polar bear regarding the pigment related mutations?
    You, just like Rum, are not looking for the confirmation bias but rather follow the argument wherever it may lead, right?
    So you are willing to concede that Swamidass and Lents have been dishonest about it or at least hadn’t done their homework, right?

  31. DNA_Jock: I should know better than to offer anything subtle.
    The brown bear did nothing (well its APOB gene did nothing) since the split with the common ancestor. The polar bear fixed nine mutations. That is telling you something; can you figure out what?

    How was the effect of those 9 fixed mutations in brown bear measured or determined, Dr. Watson?

    ETA: I will answer it for you:

    “This domain encodes the surface region and contains the majority of functional domains for lipid transport. We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood.“

    Because mutations were predprominently in the lipid transport was ASSUMED that adaptive changes in ApoB must be positive to clear the killer cholesterol out of blood…
    Assumed because there is no direct evidence that’s what happened…

  32. No, J-Mac, I am not (yet) willing to make any such concession. You have provided me with no reason whatsoever to arrive at such a view.
    We were discussing APOB, but I understand if you are eager to change the subject.

  33. J-Mac: At least you are an honest Darwinist who is willing to concede that Swamidass and Lents were either dishonest, or didn’t do their homework, on the polar bear lack of pigment in the hair follicle cells due to the damaging mutations, right?

    Please explain to me what you think the “lack of pigment in the hair fallicle cells due to damaging mutations” problem in Swamidass and Lents response is.

    What is it you think they have done which is “dishonest” or “didn’t do their homework” about?

    J-Mac: You are not looking for confirmation bias, but rather, honestly follow the argument wherever it may lead, right?

    Yes. Are you?

  34. Rumraket: So Behe compiles a list of “damaging” mutations to show that the polar bears “devolved”…

    Where does Behe claim that polar bears are “devolved”?

  35. Mung: How informative is it if he does not accept common descent?

    LOL
    But J-Mac’s pathetic question asked about the author’s (i.e. Liu et al) thought processes.
    Of course, pace Bill Cole, there’s an argument to be made that the data are highly informative even if you don’t accept common descent: the data are informing you that you are wrong. Every single DNA sequence comparison (that reveals any mismatches) is informing you that you are wrong.
    😀

  36. Rumraket: …and Behe mysteriously didn’t include these mutations in his analysis.

    At this point I don’t believe anything his critics say. I don’t blame you for that though. What analysis by Behe are you referring to? Because I have no more reason to believe you’ve read the book than you have to believe that I have read the book.

  37. DNA_Jock: Every single DNA sequence comparison (that reveals any mismatches) is informing you that you are wrong.

    But you ave failed to explain the FI in those sequences!

    😉

  38. J-Mac: How was the effect of those 9 fixed mutations in brown bear measured or determined, Dr. Watson?

    Yikes, J-Mac, “those 9 fixed mutations” do NOT EXIST in the brown bear.
    THAT is the curious behaviour of the bear in the night: no fixed changes in the APOB gene.
    I think that you don’t understand the meaning of the word “fixed”.

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