Category: Intelligent Design Creationism Watch

Rich Lenski takes down Michael Behe and his ID creationism: Part IV

March 7, 2019 • 11:15 am

Rich Lenski, an evolutionary biologist at Michigan State, has put up his fourth (and penultimate) post on his website (Telliamed Revisited) criticizing Michael Behe’s new Intelligent Design book, Darwin Devolves: The New Science About DNA That Challenges Evolution. You can see the post, which is his most thorough yet, by clicking on the website below. (I’ve posted takes on the first three parts here, here, and here.)

It’s a good read and easily comprehensible to the layperson who knows just a tad of biology. What Lenski describes is an experiment on the evolution of viruses in the lab. And that experiment demolishes Behe’s claim that if something looks “irreducibly complex”, it could not have involved natural selection acting on sequentially-occurring mutations, and therefore required the mutagenic intervention of The Great Intelligent Designer. (Behe, a pious Catholic, of course thinks that the Designer is the Christian God, but, to try to make ID look religion-neutral, he has hedged and said that the Designer could be some other “being” like space aliens. Why either gods or aliens would alter evolution by making mutations rather than creating species de novo is clearly beyond our poor powers of comprehension.)

The experiment also contradicts Behe’s contention that evolution almost always relies on adaptive but broken or inactivated genes (natural selection can sometimes favor such genes because they reduce fitness by making proteins that are no longer useful). Behe (who has distorted the evidence for this claim in his polar bear story) likes this view because it implies that evolution eventually stops without the Designer’s intervention, for if adaptive evolution always relies on inactivated genes, then it’s supposed to wind down. (That is not true, even if the vast bulk of evolution rested on “broken genes”, which it does not. And there are many adaptations we know of that involve changes in genes that don’t inactivate them.) At any rate, the viral evolution observed in Lenski’s lab certainly did not involve broken or deactivated genes.

I’ll let you read about the virus experiment yourself; here’s Lenski’s conclusion, and he tells me that there’s one more part to go in his series. Behe should be nursing a bruised tuchas now.

As Nathan Lents, Joshua Swamidass, and I wrote in our book review, “Ultimately, Darwin Devolves fails to challenge modern evolutionary science because, once again, Behe does not fully engage with it. He misrepresents theory and avoids evidence that challenges him.”

If you’ve followed the logic and evidence in the three systems I’ve written about—polar bears adapting to a new diet, bacteria fine-tuning and even evolving new functions as they adapt to laboratory conditions, and viruses evolving a new port of entry into their hosts—you’ll understand why Behe’s arguments against evolution aren’t taken seriously by the vast majority of biologists. As for Behe’s arguments for intelligent design, they rest on his incredulity about what evolution is able to achieve, and they make no testable predictions about how the designer intervenes in the evolutionary process.

Speaking of Lents, he’s written a longer piece in Skeptic Magazine about Behe’s book (click on the screenshot). If you’ve read the pieces by Lents and Lenski that I’ve highlighted on this site (e.g. here), you won’t learn much new, but it’s a good summary of the problems with Behe’s book, and a good place to refer curious readers who want a one-stop review of Behe’s nonsense..

As for Behe’s book, it’s not doing anywhere as well as his first two books, particularly Darwin’s Black Box. Although there are all five-star reviews from the benighted ID crowd, undoubtedly an orchestrated thing, they aren’t enough to get the book above the 2000 mark. Either readers are tired of ID or tired of Behe, but neither he nor the Discovery Institute can be pleased at the lame sales record. Note, though, that the book is #1 in both creationism (which is what it is) and Developmental Biology, which it certainly isn’t:

 

Rich Lenski continues his demolition of Michael Behe’s new book

February 23, 2019 • 1:15 pm

As you probably know from reading this site, ID creationist Michael Behe has a new book coming out this week: Darwin Devolves: The New Science About DNA That Challenges Evolution (note the unclear antecedent, which could be either “New Science” or “DNA”).  Various scientists have weighed in, none of them positively, and there’s been considerable criticism by biologists Nathan Lents, Joshua Swamidass, and Rich Lenski, including a damning review in Science.

Lents continued his criticism on The Human Evolution Blog (see here,  here and here) and Lenski, whom Behe attacked strongly in the book, promised a three-part rebuttal of Behe’s ideas on his own website, Telliamed Revisited, which is now being extended (see here and here for Lenski’s parts 1 and 2).

Yesterday Lenski put up part 3 (screenshot below), which is an expansion of earlier criticism by Lents on whether a gene likely involved in the adaptive evolution of polar bears—a gene concerned with fat metabolism—was really “broken” or “damaged”.

One of Behe’s major theses in the book is that evolution is self-limiting, as, he argues, nearly all adaptations are based on damaged genes, and when a gene is damaged or inactivated, it can accumulate more mutations that eventually render it functionless and unable to revive. Thus, he concludes, evolution by natural selection runs itself into the ground. God An Intelligent Designer then has to step in to make things right.

Behe is wrong. Indeed, although we have examples of adaptive evolution based on inactivated genes, we also have many that don’t involve “broken genes”, and as long as a reasonable number of mutations involve changes in gene function or regulation, or things like gene duplication, chimeric genes, and so on, Behe’s claim holds no water.

One of the genes that Behe claimed was inactivated during adaptive evolution of polar bears from ancestral brownish bears was ApoB, which regulates the amount of fat in the blood. Behe claimed in his book that the gene’s evolution in polar bears involved many “inactivating” mutations. Lents pointed out that there was no evidence for this; on the contrary, even the authors of the paper analyzing the sequence of that gene found evidence that some of those substitutions were not involved in breaking the gene, but improved its function.

Behe replied, calling Lents an “incompetent reviewer” (without even giving his name!) and presenting some data that, he said, showed that the ApoB substitutions were “possibly damaging” or “probably damaging.

That was a mistake, for, as Lents showed, Behe was duplicitous in his reply, having omitted from his table all the mutations that the authors’ algorithm said were “benign”. Lents is charitable about this, but I can see no explanation except that Behe left out data inimical to his hypothesis. And that seems misleading and deceptive.  As I said, Lents is kinder to Behe than I would have been:

In Behe’s defense, he doesn’t explicitly say that he’s presenting the whole Table. So he isn’t lying exactly. Instead, he says that he is presenting “the relevant information” from the Table. I find this deeply misleading. This whole discussion is about the nature of adaptive mutations in the evolution of species and Behe’s arguments is that most of them are damaging. By presenting only the mutations that are predicted to fit that argument, he is intentionally leaving out evidence that is contrary to his position.

After all, what is the purpose of showing the chart at all? To show that some mutations that drove polar bear evolution are damaging? He didn’t need a chart to make that point and no one would argue with that. I suspect that if the unaltered Table S7 gave the impression that the overwhelming number of adaptive mutations were damaging, Behe would have shown the whole thing.

In reality, Table S7 does not give that impression at all, and so he slices it up with surgical precision so that he can present “the relevant information,” that is, the information that appears to support his position. And, at least when it comes to APOB, even the selectively edited information probably doesn’t support his position either, regardless of what the predictive algorithm says, as I (and the study’s authors!) explain above.

The evolution of polar bears is the opening story of Behe’s book, the example he uses to describe his concept of “devolution.” But if you actually consult the data itself, it tells a very different story than Behe does.

Lenski’s new post (click on screenshot), goes into the polar bear gene in detail, and also explains how scientists determine whether a mutation in a gene is advantageous, benign, or damaging—not an easy matter when all you have is its DNA sequence.

Lenski points out that the algorithm used by the real scientists who did the ApoB study is unable to detect adaptive changes that improve the function of the protein: it is limited to detecting “benign”, “possibly damaging” or “probably damaging” mutations. Not only did Behe leave out the “benign” mutations, but didn’t bother to mention that the algorithm can’t show changed or improved function for any mutations. And I call that duplicitous. Here’s Lenski’s take; the emphases are his.

The program simply cannot detect or suggest that a protein might have some improved activity or altered function.

The authors of the paper recognized these limiting assumptions and their implications for the evolution of polar bears. In fact, they specifically interpreted the APOB mutations as follows (p. 789): “… we find nine fixed missense mutations in the polar bear … Five of the nine cluster within the N-terminal βα1 domain of the APOB gene, although the region comprises only 22% of the protein … 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.” In a news piece about this research, one of the paper’s authors, Rasmus Nielsen, said: “The APOB variant in polar bears must be to do with the transport and storage of cholesterol … Perhaps it makes the process more efficient.” In other words, these mutations may not have damaged the protein at all, but quite possibly improved one of its activities, namely the clearance of cholesterol from the blood of a species that subsists on an extremely high-fat diet.

It appears Behe either overlooked or ignored the authors’ interpretation. Determining whether those authors or Behe are right would require in-depth studies of the biochemical properties of the protein variants, their activities in the polar bear circulatory stream, and their consequences for survival and reproductive success on the bear’s natural diet. That’s a tall order, and we’re unlikely to see such studies because of the technical and logistical challenges. The point is that many proteins, including ApoB, are complex entities that have multiple biochemical activities (ApoB binds multiple lipids), the level and importance of which may depend on both intrinsic (different tissues) and environmental (dietary) contexts. In this example, Behe seems to have been too eager and even determined to describe mutations as damaging a gene, even when the evidence suggests an alternative explanation.

Now this may seem an arcane discussion about protein function, but if you’ve gathered anything from this post, Lenski’s post, and Lents’s posts, it should be that Behe has not been intellectually honest in treating the data in a key example used to make his case that natural selection nearly always relies on broken genes. But what do you expect from a creationist who’s deeply religious and who’s counting on the data to make the case for God?

I’m told that Behe really believes the kind of palaver he uses to make the case for “irreducible complexity” and Intelligent Design. But really, how can you leave out data and distort the conclusions of others, without being conscious of what you’re doing? One might almost conclude that Behe is lying for God.

Lenski isn’t done with taking Behe to the woodshed yet: as he says, “I initially planned to write three posts, but it will now be more than that, as I delve deeper into several issues.”  Behe’s tuchas is going to be smarting after this!

 

More criticisms of Behe’s new ID book

February 19, 2019 • 2:10 pm

I won’t belabor these two new critiques, as you can read both pieces for yourself, and I’m just keeping you up to date as Behe’s new creationist Intelligent Design book, Darwin Devolves heads to press in a week.

Actually, although IDers frenetically argue that their theory is NOT creationism, it really is a species of creationism, for it posits that God The Intelligent Designer creates new mutations required for important adaptations to evolve, mutations that couldn’t accumulate by natural selection alone. The only difference between Behe and, say, Duane Gish is that whereas Gish thought that God made birds, squirrels, and trees, Behe thinks that God made the mutations required for natural selection to bring about birds, squirrels, and trees.

I wonder whether, at the Discovery Institute, the Christians and Orthodox Jews ever ponder how their God has Himself “devolved” from a majestic de novo creator to a Heavenly Mutagen—a Divine Alpha Particle.  Why did God want to make new forms by tweaking the DNA in undetectable ways rather than just poofing them into existence? Such are the mysteries of biological theology.

Speaking of devolving, Nathan Lents has yet another critique of Behe on The Human Evolution Blog, this time centering on the word “Devolves” in the book’s title. Click on the screenshot:

It’s a short critique involving Lents’s claim that the term “devolve” is a neologism coined by Behe and doesn’t make any sense. He thinks this on three grounds, and I agree with about 2.5 of them. I quote (indented); flush left text is mine:

Misunderstanding #1: Behe seems to think that evolution is the accumulation of  complexity. If so, it’s no wonder that he has such angst about it. The reality is that evolution is aimless, sloppy, and produces clunky solutions as often as it does elegant ones. Our own bodies are filled with glitches and goofs left over from the imprecision of natural selection. This may be deeply unsatisfying to some, but nature cares little about our satisfaction.

This fundamental misunderstanding of the nature of evolution is a serious error, especially for someone who has dedicated his career to critiquing modern evolutionary theory. But it not the only one.

Agreed, since to Behe “devolution” is the loss of a trait or a reduction of complexity, yet sometimes losing a trait or becoming simpler is adaptively useful (fleas, for instance, lost their wings).

Misunderstanding #2: Behe’s notion of “irreducible complexity” demands that natural selection can only work if every single step on an evolutionary path is advantageous. We know that’s not true. Populations of organisms harbor a great deal of genetic diversity generated by gene duplications, neutral mutations (and even slightly deleterious ones), recombination, and even rare but dramatic events like chromosomal duplications or rearrangements, and horizontal gene transfer (which may actually be not as rare as we thought). Evolutionary forces then act on all that diversity in unpredictable ways. In Darwin Devolves, you will not find discussions of any of this. Behe either ignores or quickly dismisses these phenomena, despite the key role they play in the generation of the very complexity that Behe doesn’t think that nature can build.

Agreed. Behe apparently does not discuss alternative pathways for building adaptations that look “irreducibly complex” but in reality involve either straight natural selection, neutral evolution as an intermediate, or even slightly deleterious mutations, as well as important processes like gene duplication.

Misunderstanding #3: Behe frequently speaks as though natural selection (which he often calls Darwinism) is the only evolutionary force. In reality, natural selection is joined by genetic drift, neutral theory, exaptation, gene flow, sexual selection, hybridization, punctuated equilibrium, frequency-dependent selection, and dozens of other forces. Behe constantly repeats his refrain that natural selection cannot account for everything we see in nature. Yeah, we know. And we’ve known that for a very long time.

Well, here I think Lents has made some semantic errors. For instance, neutral theory is really a theory of selectively neutral alleles that evolve largely through genetic drift, so it’s not something separate from drift, and it’s a theory, not an “evolutionary force.” Exaptation, frequency-dependent selection, and sexual selection ARE subsets of natural selection, not something entirely different. Punctuated equilibrium is not known to be responsible for the evolution of any adaptation, at least not in the convoluted form presented by Gould and Eldredge. And Lents leaves out a truly unique evolutionary force: meiotic drive—evolution occurring through differential segregation of alleles at meiosis. Finally, both exaptation and punctuated equilibrium are not “forces” but phenomena.

Behe does err if he indeed neglects genetic drift in the evolution of adaptations, as it’s undoubtedly been important, including in some pathways Behe sees as “irreducibly complex”. But if I were Lents I wouldn’t leave myself open to criticism by saying that “exaptation” and “frequency-dependent selection” are forces different from natural selection.

Now you might say that my criticism of this one small part of Lents’s piece is going to make Behe happy, as he’ll crow, “See, Coyne takes issue with Lents’s criticism of my book,” but that’s bullshit. As Steve Gould said in his essay “Evolution as fact and theory” (he’s referring to his colleagues’ attempts to make him stop criticizing traditional evolutionary theory because that would play into the hands of creationists)

But most of all I am saddened by a trend I am just beginning to discern among my colleagues. I sense that some now wish to mute the healthy debate about theory that has brought new life to evolutionary biology. It provides grist for creationist mills, they say, even if only by distortion. Perhaps we should lie low and rally around the flag of strict Darwinism, at least for the moment—a kind of old-time religion on our part.

But we should borrow another metaphor and recognize that we too have to tread a straight and narrow path, surrounded by roads to perdition. For if we ever begin to suppress our search to understand nature, to quench our own intellectual excitement in a misguided effort to present a united front where it does not and should not exist, then we are truly lost.

Make no mistake: I’m on Lents’s side here, but I do criticize the way he categorizes “evolutionary forces.” That, however, should give no succor to Behe. But he’ll take what he can get—he’s a creationist, for crying out loud.

Finally, Rich Lenski, whose work on E. coli was apparently criticized in Behe’s book, has published part two of a three-part critique of Darwin Devolves on his (Lenski’s) website Telliamed Revisited (click on screenshot):

Being a nice guy, Lenski is trying to handle the irascible Behe with kid gloves, claiming that he and Behe agree about at least two things. The first is that Behe “remains upbeat about [Lenski’s] research” Second, that both Lenski and Behe are both interested in and fascinated by evolution. But that tiny speck of agreement is where the comity ends, for then Lenski pulls out his cudgel:

Whether for secular or religious reasons, we humans are deeply interested in where we came from and how we came about. In my own small way, I take pleasure in knowing that my lab’s research helps people get a glimpse of how evolution works.

I’m concerned, though, when these scientific and religious perspectives get intertwined and confused, even when they concern those big, important questions that interest all of us. I get even more concerned when I see what I regard as non-scientific ideas (such as “intelligent agents” introducing “purposeful design” by unstated and untestable means) being used to undermine the admittedly imperfect (and always subject to revision) understanding of evolution that science provides to those who want to learn. And I am most disturbed when these confusions appear to be part of a deliberate “wedge” strategy with ulterior sociopolitical motives. People will undoubtedly have diverse views about whether scientific explanations are adequate and/or satisfying ways to understand the world, but I see danger in trying to undermine scientific methodology and reasoning to advance religious beliefs and political goals.

This is Lenski’s kindly way of saying, “Stop injecting your religion into science, you duplicitous git, because it doesn’t help us make progress.”

Rich Lenski answers ID creationist Michael Behe, dismantles “Behe’s First Rule of Adaptive Evolution”

February 17, 2019 • 10:00 am

Rich Lenski, a well known biologist at Michigan State University and head of the team which has conducted an equally well known long-term evolution experiment in E. coli (they have a generation every twenty minutes or so, and the experiment has run for 30 years), is the subject of a long attack in Michael Behe’s new Intelligent-Design (ID) book, Darwin Devolves.  Apparently Behe argued that Lenski’s work didn’t show real progressive evolution of a meaningful sort, but simply showed that bacteria could adapt to lab conditions by “breaking genes”: deactivating genes through missense or nonsense mutations. As Lenski and coauthors Nathan Lents and Joshua Swamidass showed in a short but damning review of Behe’s book in Science, Behe’s claim about Lenski’s experiment was wrong:

In the grand scheme of evolution, mutations serve only to break structures and degrade functions, Behe argues. He allows that mutation and natural selection can explain species- and genus-level diversification, but only through the degradation of genes. Something else, he insists, is required for meaningful innovation. Here, Behe invokes a “purposeful design” by an “intelligent agent.”

There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function—an expected mode of adaptation to a simple laboratory environment, by the way—while dismissing improved functions and deriding one new one as a “sideshow” (1). (Full disclosure: The findings in question were published by coauthor Richard Lenski.)

As I’ve written before, Behe’s thesis here is meant to show that, without the help of the “Intelligent Designer” (aka God), real progressive evolution is self-limiting, for all it does it create adaptations based on broken or deactivated genes. The accumulation of broken genes eventually makes further evolution impossible: once you have a genome full of broken genes, further progress is limited and so God has to step in to make those mutations that can’t occur naturally. (I’m always amused at the religious IDers diminution of God’s role from de novo creator of all organisms to that of a mutagen: a Divine Carcinogen.)

Behe’s thesis is expressed in his “First Rule of Adaptive Evolution”, which Lenski analyzes (and dismantles) in a post on his website (see link below).

I didn’t know that Lenski even had a website, but there you go. It’s called Telliamed Revisited, and his latest post (click below) is the first of three essays in which he’ll analyze Behe’s book. This is useful, as the three-authored Science critique was only 650 words long—not sufficient to analyze the scientific theses of a 352-page book. Lents has already expanded the criticism of Behe’s book on The Human Evolution Blog and on the AIPT site., but since Lenski and his microbial experiment were the targets of special criticism by Behe, it’s especially appropriate that Lenski himself respond.

First, Lenski summarizes Behe’s “First Rule” (my emphasis below):

Behe’s latest book is centered around what he calls “The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring.” As he wrote in an immediate, dismissive response to our review: “The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population.”

Then Lenski makes a simple point which appears to show that Behe is being intellectually dishonest. (He’s already been intellectually dishonest by implying that nearly all adaptive mutations are known to degrade or break genes, as we have many counterexamples.) Here’s what he says, referring to the sentence I’ve put in bold above (the bold below is Lenski’s):

Behe’s next sentence then asserts the power of the “de-evolutionary” process of gene degradation. This is an unjustifiable extrapolation, yet it is central to Behe’s latest book. (It’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.) Yes, natural selection sometimes increases the frequency of broken and degraded genes in populations. But when it comes to the power of natural selection, what is most frequent versus most important can be very different things. What is most important in evolution, and in many other contexts, depends on timescales and the cumulative magnitude of effects. As a familiar example, some rhinoviruses are the most frequent source of viral infections in our lives (hence the expression “common cold”), but infections by HIV or Ebola, while less common, are far more consequential.

. . . In the same vein, even if many more mutations destroy functions than produce new functions, the latter category has been far more consequential in the history of life. That is because a new function may enable a lineage to colonize a new habitat or realm, setting off what evolutionary biologists call an “adaptive radiation” that massively increases not only the numbers of organisms but, over time, the diversity of species and even higher taxa.

. . . 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.

This isn’t rocket science. If Behe’s thesis is that broken genes present a big problem for continuing adaptive evolution, then one has to accept the thesis that nearly all broken or degraded genes are those genes involved in adaptation. And yes, some inactivated genes are involved in adaptations. But we also know of many adaptations based on non-broken genes, including those with changed functions as well as duplicated genes, cobbled-together genes, horizontally transferred genes, and so on. If, as I’ve said, only 50% of all adaptations involve these sorts of genes as opposed to “broken” genes, the natural selection will not lead to the stalling of evolution so important to Behe. Further, if a higher proportion of “changed function/new function mutations” are involved in major adaptations that are associated with the rise of new taxa, then the broken or blunted genes become even less important.

As Lenski notes, the frequency of mutations that degrade rather than change the function of genes does not tell us the frequency of degraded genes that are involved in adaptation, and the frequency of degraded genes that are involved in adaptation does not tell us the frequency of degraded genes involved in adaptations that are associated with new biological diversity. Behe surely realizes this, as he’s not stupid, but chooses not to make that point. Lenski had to make it for him.

Lenski is being quite kind when he says “it’s not the sort of error I would expect from anyone who is deeply engaged in an earnest effort to understand evolutionary science and present it to the public.” I would go farther and say “this is the sort of error that I would expect from a neo-creationist who’s trying to distort the empirical data in order to delude the public into thinking that there are severe problems with modern evolutionary theory.”

Behe is notoriously thin-skinned, and will undoubtedly go after Lenski at the intelligent-design Evolution News site, which, understandably, does not allow any comments. Behe’s ID buddies will also pitch in and help him out, as they’ve already been doing, for they want this book to sell well and create the widespread scientific acceptance of ID that the Wedge Document said would occur by 2018. LOL on that!

ID has not been widely accepted in science: it’s been scorned, laughed at, and deemed by the courts as religion and not science. If it were scientifically accepted, you’d get a better panoply of people endorsing the book than these four people who constitute the entirety of the editorial reviews on the Amazon page of Darwin Devolves:

Axe and Minnich are both associated with the ID-creationist Discovery Institute, and so are already in bed with Intelligent Design. Carlson is a member of the Christian Faculty Forum, has testified publicly about his deep faith, and thus shows that virtually all proponents of ID are religious. He’s also a Fellow of the Id-ish International Society for Complexity, Information, and Design; other fellows include William Lane Craig, Alvin Plantinga, and the whole Discovery Institute crew (Nelson, Behe, Dembski, and so on). Leisola is also an ID advocate and has written a book about his transformation from advocate of naturalism to worshiper of the Great Designer.  Leisola’s  Finnish Wikipedia page notes (translated by Google):

Leisola is a creationist . He believes that the world is only a few thousand years old and sees the flood of water as a historic global flood. [18]

Leisola has delivered several books in Finnish, whose authors adopt a pseudo-scientific [19] concept of ” intelligent design ” and make claims against the scientific theory of evolution . In 1981, he delivered AE Wilder-Smith’s Natural Sciences Not Known for Evolution (WSOY, 144 p.). Leisola founded the Datakirjatpublishing company in 2000 because Finnish publishers refused to publish his translation of the book ” Evolution – critical analysis ” by Siegfried Scherer and Reinhard Junker . [20] Dictionaries published The first edition of the Evolutionary-Critical Analysis book in 2000. [21]  The dictionaries have since published other pseudo-scientific and evolutionary works:

  • William A. Dembski, 2002, Intelligent Plan Idea , Data Books, 256 s.

  • Marwin Lubenow, 2005, Myth of Monkeys – Controversy over Timing of Fossils , Data Books, 380s .

 

These are hardly the brand of endorsements you want if you’re trying to divorce ID from creationism and make it part of mainstream science.

Scientists scrutinize just two examples in Behe’s new book; find them deeply misleading

February 13, 2019 • 9:15 am

Here’s a post by biologists Nathan Lents and Arthur Hunt (Hunt’s name isn’t under the title), examining just two cases touted by Michael Behe as showing “de-evolution” in Behe’s new ID book Darwin Devolves: The New Science about DNA That Challenges Evolution. The cases involve the loss of fur pigment and changes in fat metabolism in polar bears, whose ancestors were like brown bears eating a brown-bear diet (omnivorous) and having brown or blackish coats. When darker bears encountered cold climates, their fur evolved white coloration. Polars bears also had a much fattier diet, and so their fat-processing genes evolved as well. How did this happen? As it turns out, Behe presents the story wrongly—probably deliberately.

According to these and other reviewers, Behe’s Big Claim in the book is that since nearly all adaptations are based on “broken genes”—genes that are inactivated, either by acquiring a missense or nonsense mutation, or an amino acid substitution that makes the gene product inactive—evolution by natural selection simply involves the accumulation of one broken gene after another. In that way, says Behe, evolution is “self limiting”, since when an adaptation is based on inactive genes, it can’t be reversed (“dead genes” tend to acquire more mutations that render them even deader). In other words, by accumulating successively broken genes, evolution works its way into a corner from which it can’t extricate itself by further evolution (broken genes are hard to un-break).

Behe claims that this is true for the polar bear: that the genes that turned the ancestral coat white and changed the fat metabolism were broken genes. But when you examine the paper supposedly supporting Behe’s claim, you find, argue Lents and Hunt, that about half of them don’t seem to have any damaging mutations, and that perhaps “none of the 17 most positively selected genes in polar bears are ‘damaged’.”

In fact, we can even grant Behe a figure of 50% of genes involved in adaptation being broken, and it still doesn’t matter. For if just half of genes involved in new adaptations do new or different things and are not damaged, then his thesis doesn’t work: evolution doesn’t grind to a halt. And, as I’ve said, there are lots of genetic changes that don’t involve broken genes, including duplications, mutations that affect gene regulation, and so on.

Finally, Lents and Hunt look at one gene, APOB, that’s involved in fat metabolism and has apparently changed by selection in polar bears (you can judge the past working of selection by looking at the relative number of amino acid substitutions in a protein compared to what you’d expect if there were no selection). In Darwin Devolves, Behe claims that researchers detected multiple mutations in the polar bear’s APOB gene and concluded that the new mutations were “very likely to be damaging—that is, likely to degrade or destroy the function of the protein that the gene codes for.” (That’s a quote from Behe’s book.)

But that’s not true. It’s not what the researchers concluded. Lents and Hunt looked up the 2014 Cell paper on the population genomics of polar bears, and found that the authors actually say this (Lents’s and Hunt’s emphases):

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 ba1 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.

Missense mutations are mutations that change the amino acid coded for by the mutated triplet of codons; these amino acid changes do not necessarily “break” or “inactive” a protein. And in the case of APOB they apparently don’t: they likely help the protein clear cholesterol from the blood. (The clustering in a functional region is already a clue that they aren’t random “breakage” mutations.) Or, as Lents and Hunt say,

Clearly, the authors do not expect the polar bear APOB to be “broken.” Rather, a bare majority of the amino acid changes are in the most important region for the clearing of cholesterol from the blood. In other words, these mutations likely enhance the function of apoB, at least when it comes to surviving on a diet high in saturated fats.

It is also worth noting that apoB does much more than clear fatty acids from the blood. It is a very large protein that has many biochemical activities and is a central player for lipid and cholesterol transport. Even if “damaging” mutations might be beneficial in one context, they could very well be harmful or lethal in another. Moreover, mice that lack apoB are not viable.

. . . To recap: 1.) There is no evidence for Behe’s claim that APOB is degraded or diminished in polar bears and everything we know about the protein from other mammals suggests the opposite. And 2.) Behe’s claim that the most common adaptive changes in polar bears are those that degrade or destroy proteins is not supported, and the evidence suggests otherwise. Those are just the errors that we found in his first example.

And yet Behe makes this bold claim:

It seems, then, that the magnificent Ursus maritimus has adjusted to its harsh environment mainly by degrading genes its ancestors already possessed. Despite its impressive abilities, rather than evolving, it has adapted predominantly by devolving. What that portends for our conception of evolution is the principal topic of this book.

Which lay reader would contest that, not having read the technical literature?

You can read your post for the data on other proteins, but Behe is clearly counting on his readers, who aren’t scientists, to take him at his word and not dig up an arcane paper on population genetics in a technical journal.

Behe always likes to argue that if an evolutionist makes one error or misrepresentation in a presentation, then the author’s whole presentation is cast into doubt—along with evolutionary theory itself. Well, what’s good for the goose is good for the panderer. Behe’s “evolution-nearly-always-works-by-breaking-genes” claim is not supported by this example, and we know of many other examples that don’t support it, either.

But why is Behe trying to make a scientific case against evolution in a “trade book” rather than in the scientific literature? Well, you know why: scientists don’t buy his claims. He thus tries to change accepted science not by appealing to scientists, but by appealing to the scientifically uneducated public.  Now that may make creationists or those who doubt evolution feel better, but it’s not going to make intelligent design theory into “the dominant perspective in science” that was one of the 20-year goals of 1998’s infamous Wedge Document.

For a longer review by Lents, which tells you a bit more about Behe’s ideas in the book, click on this piece published at AIPT.com:

 

The Discovery Institute’s “Scientific Dissent from Darwinism” not so scientific

February 11, 2019 • 11:15 am

The Discovery Institute (DI) likes to make its case for Intelligent Design simply by getting people to sign a petition, the “Scientific Dissent from Darwinism“, which reads thusly:

Signatories of the Scientific Dissent From Darwinism must either hold a Ph.D. in a scientific field such as biology, chemistry, mathematics, engineering, computer science, or one of the other natural sciences; or they must hold an M.D. and serve as a professor of medicine. Signatories must also agree with the following statement:

“We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

You can see the signatories here; according to The College Fix article below, and a blurb by the Discovery Institute, they now number 1,043. The fact that the signers exceeded 1000 is cause for great celebration in Seattle.

Although there’s not, as far as I know, a list of scientists who accept “Darwinism” (I’d call it “modern evolutionary theory”), it would of course be much longer.  But scientific truth isn’t determined by lists of names, even of people who hold Ph.Ds (see below for their “qualifications”). It’s determined by the published work of scientists and whether it’s accepted by the scientific community. And using that criterion, ID has failed miserably.

It’s sad that The College Fix, a right-wing website that often has decent though slanted articles on the shenanigans of woke students at universities, has chosen the anti-evolution hill to die on. Of course the author of this article (click on screenshot) goes to Liberty University, where you have to sign on to creationism as a student and teacher.

The Right apparently hasn’t realized yet that they don’t gain intellectual credibility by espousing creationism or attacking established truths in evolutionary biology.

At any rate, The Sensuous Curmudgeon isn’t impressed. In a post about the list a week ago, they note this about “Project Steve“, which is the National Center for Science Education’s lighthearted but real list of scientists named Steve who have a Ph.D. and support evolution. The NCSE of course doesn’t use lists to support the truth of evolution; this is just a list to mock the Discovery Institute’s list.  Here’s what the 1400 Steves signed:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.

And the Sensuous Curmudgeon’s comment on the DI’s crowing about the 1000+ signers of their anti-Darwin list:

The Discoveroids have a new post about it at their creationist blog: Skepticism About Darwinian Evolution Grows as 1,000+ Scientists Share Their Doubts. Here are some excerpts, with bold font added by us for emphasis, and occasional Curmudgeonly interjections that look [like this]:

Over 1,000 doctoral scientists from around the world have signed a statement publicly expressing their skepticism about the contemporary theory of Darwinian evolution. [Gasp!] The statement, located online at dissentfromdarwin.org, reads: “We are skeptical of claims for the ability of random mutation and natural selection to account for the complexity of life. Careful examination of the evidence for Darwinian theory should be encouraged.”

We always contrast that with “Project Steve,” a splendid enterprise of our friends at the National Center for Science Education (NCSE). It has its own page at their website, and it’s their response to the Discoveroids’ list. The last time we wrote about it was over two years ago: ‘Project Steve’ Now Has 1,400 Steves. They say: “About 1% of the United States population possesses such a first name, so each signatory represents about 100 potential signatories.”

. . . We don’t know how many Steves are on NCSE’s list now, but only ten Steves are statistically equal to all the 1,000 signatures on the Discoveroids’ list. If the Discoveroids limited their list to only “Steves,” they’d have about 10 names. Also, The Discoveroids are far less selective than NCSE in choosing their signatories. The Discoveroids’ list includes a significant number of MDs, dentists, engineers, meteorologists, industrial hygiene specialists, nutritionists, philosophers, political “scientists,” sociologists, and such. On the other hand, everyone on NCSE’s list of Steves has a PhD, and a majority of them are in a biological field.

The Curmudgeon concludes:

So where are we? Well, the Discoveroids finally got their list up to 1,000 names, so that’s something. It’s difficult to come up with a figure for the actual number of scientists in the world, because that term (like the Discoveroids’ list) can include social scientists, political scientists, etc. For the US alone, the American Association for the Advancement of Science has over 120,000 members, so the Discoveroids still have a lot of work to do.

But you’re probably asking yourself, “Well, who are those Ph.D.s who signed the DI’s statement?” Fortunately, DonExodus2 examined the list 11 years ago when there were about 100 signers, and you won’t be impressed by those who put their name to the document. (The videomaker contacted most of the people who signed the document.) Have a listen:

It’s pathetic that the DI spends its time getting signatures on the petition when it should be getting empirical evidence for its theory. After all, in 1998 the Wedge Document said that its 20-year goal was to see ID as the dominant paradigm in science. It’s 2019 now, and that hasn’t happened. And so the Discoveroids engage in ludicrous activities like this.

Scientists damn Behe’s new book; he responds lamely

February 9, 2019 • 11:30 am

As I’ve mentioned before, Michael Behe has a new creationist (i.e., Intelligent Design) book coming out soon: Darwin Devolves: The New Science about DNA that Challenges Evolution. While its official release date is February 26, three scientists have written an extremely critical review of the book in the journal Science (click on the screenshot below). One of them, Rich Lenski, did the famous lab-evolution experiments in bacteria that Behe discusses (and apparently tries to rebut) in his book. I won’t reiterate what Lents et al. say, as you can read their review below. The title tells the tale.

Behe, like all ID advocates, has a very thin skin. Although his books have sold decently in America because we have so many creationists seeking confirmation of what they like to believe, the response of scientists to Intelligent Design—and Behe’s books—has been pretty similar to the opinion of Judge Jones in the Kitzmiller ID case: this isn’t science but disguised religion.

So not two days passed before Behe responded on the Discovery Institute Evolution News site, crowing in triumph. Click on the screenshot below.

Woo-hoo!???

Behe promises a fuller response to Lents et al., but all his crowing is apparently about the reviewers having not responded to the “central argument of [Behe’s] book”—the “First Rule of Adaptive Evolution”. As Behe says:

In a few days I will offer a detailed rebuttal. But the overwhelmingly important point to notice right up front is that the reviewers (Lenski plus Josh Swamidass over at Peaceful Science and John Jay College biologist Nathan Lents) have absolutely no response to the very central argument of the book. The argument that I summarized as an epigraph on the first page of the book so no one could miss it. The one that I included in the title of a 2010 Quarterly Review of Biology article upon which the book is based. The one for which I chose the most in-your-face moniker that I could think of (consistent with the professional literature) to goad a response: The First Rule of Adaptive Evolution: Break or blunt any gene whose loss would increase the number of offspring. The rule summarizes the fact that the overwhelming tendency of random mutation is to degrade genes, and that very often is helpful. Thus natural selection itself acts as a powerful de-volutionary force, increasing helpful broken and degraded genes in the population.

And they had no response! That’s because there is in fact nothing that can alleviate that fatal flaw in Darwinism. Much more to come soon.

In a separate post on Evolution News, IDer David Klinghoffer simply echoes Behe’s point, and helpfully adds that perhaps Science should have chosen reviewers that could have addressed Behe’s main point.

Unfortunately, Behe appears to have missed the fact that the reviewers did address Behe’s main point—at least twice.  What is that point? It’s apparently the contention that evolution nearly always relies on inactivated genes during nonadaptive evolution, as such genes can be useful (not making a product can increase your fitness if that product is superfluous or injurious in a new environment). On top of that, mutations that “break” or degrade genes are more common than genes that affect or alter gene function. Put these together and you get Behe’s Rule, but the rule itself is broken.

The problem with Behe’s Rule is that yes, random mutation most often degrades genes, and broken genes can be adaptive, but natural selection doesn’t just choose any gene; it chooses ones that increase fitness. And we have many examples of non-broken genes that increase fitness. These include the arising of duplicated genes and then the divergence of those genes to perform new functions on top of old ones—a very common mode of adaptation in nature that has created many useful “gene families.”

And Lents et al. know this. I’ve put in bold Lents et al.’s referral, in their review, to adaptation involving non-broken genes:

Behe argues. He allows that mutation and natural selection can explain species- and genus-level diversification, but only through the degradation of genes. Something else, he insists, is required for meaningful innovation. Here, Behe invokes a “purposeful design” by an “intelligent agent.”

There are indeed many examples of loss-of-function mutations that are advantageous, but Behe is selective in his examples. He dedicates the better part of chapter 7 to discussing a 65,000-generation Escherichia coli experiment, emphasizing the many mutations that arose that degraded function—an expected mode of adaptation to a simple laboratory environment, by the way—while dismissing improved functions and deriding one new one as a “sideshow” (1). (Full disclosure: The findings in question were published by coauthor Richard Lenski.)

. . . Behe is skeptical that gene duplication followed by random mutation and selection can contribute to evolutionary innovation. Yet there is overwhelming evidence that this underlies trichromatic vision in primates (8), olfaction in mammals (9), and developmental innovations in all metazoans through the diversification of HOX genes (10). And in 2012, Andersson et al. showed that new functions can rapidly evolve in a suitable environment (11). Behe acknowledges none of these studies, declaring an absence of evidence for the role of duplications in innovation.

I won’t list the many examples of adaptations based on non-broken genes, which involve far more than duplications (such examples can involve simple amino acid substitutions), but more about that later. In the meantime, the thin-skinned Behe is crowing like a rooster, failing to notice that behind that irascible old rooster is a farmer with an axe and a hunger for chicken stew.