The DI responds to my now--two-years-old review of ROTGH

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Well, to my surprise, suddenly Casey Luskin at the DI has posted a response to my review of Return of the God Hypothesis, sort of wrapped in a response to someone else’s review.

It’s sort of amusing. It lets you know what kind of a fellow they think I am:

As noted, Puck Mendelssohn (hereafter “PM”) is an Amazon reviewer who frequently posts nasty and uncivil reviews of ID books, full of hateful invective and personal attacks.

That, of course, is not even close to being true. I’m very careful not to make personal attacks. I do attack the substance, however, and with the DI, as everyone knows, there is a routine, consistent, ongoing drumbeat of pure dishonesty. I would fall badly short as a reviewer if I did not point that out, and that means, in the DI’s case, pointing it out a lot. But this is, of course, not hateful invective and it’s not a personal attack. It is a substantive attack, and what annoys the DI is that they know I’m right.

As usual, of course, they distract and confuse. I pointed out in my review that Meyer’s statement that mammals arose abruptly in the fossil record without any evident connection to ancestors could only be the product of incompetence or dishonesty; that’s objectively true. What Luskin does, instead of facing that uncomfortable fact, is shift the topic and say that there was an explosion of mammalian diversity in the Tertiary – a completely different subject.

He then claims that I’ve complained that Meyer didn’t cite Kemp’s excellent book, The Origin and Evolution of Mammals. Again, objectively false: I made no such complaint but did suggest that anyone who’d like to learn about the topic should read that book rather than Meyer’s Hopeless Monster III.

And then he charts some synapsid skulls and says, by gum, these are all kinds of different sizes! Surely they can’t be related to one another (and show what Luskin, showing his ignorance, mis-labels as “reptile to mammal evolution”) if some of 'em are big and some of 'em are small! Of course, the existence of these synapsids is precisely what Meyer has denied, a denial so embarrassing that Luskin is forced to try to obfuscate it. Meyer made no point about skull sizes, and if he had, it would have been almost as embarrassing as the point he did make.

From there it gets sillier, as he tries to defend Meyer’s indefensible reliance upon Axe. Really? Goodness, gracious, isn’t that getting a little bit silly after the rough debunking that that foolishness has received from all quarters? On that: belated thanks to @Mercer, whose assistance in helping me understand the issues was invaluable.

As it happens, my original review is not presently on display at Amazon, due to one of those odd editorial hiccups which happen there from time to time, so I’m attaching a copy of the review.

rotghpuck.pdf (632.0 KB)

At moments like this I always get a chuckle out of the fact that the DI would very much like to have ideas that can drive debate in actual scientific circles; instead, they are busying themselves misleading their devotees about a review written pseudonymously by a retired lawyer who lives just across town and has the misfortune of finding DI books amusing. I’d find a better hobby, if it didn’t tweak them so badly.

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You know how it goes … if the DI didn’t have anything silly to say, they wouldn’t have anything to say at all. :wink:

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Perhaps they mis-heard mother’s old advice that if you don’t have something nice to say, you shouldn’t say anything at all. But, then, they seldom say anything nice, either, as they blunder along trying to make it sound like mainstream science is lying about evolution.

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Stephen Meyer: “It is therefore overwhelmingly more likely than not that a random mutational search would have failed to produce even one new functional (information-rich) DNA sequence capable of coding for one new protein fold in the entire history of life on earth.”

Ahh the good ole bait and switch. Here Meyer is confusing the probability of randomly selecting a protein sequence adopting the beta-lactamase fold and catalyzing beta-lactam hydrolysis, with the probability of selecting a protein sequence able to carry out a fitness-improving function.

We are simply not required to believe that TEM-1 beta-lactamase was produced by de novo evolution from non-coding DNA. Incidentally we know from phylogenetic inference it evolved from DD-peptidases by duplication and divergence, not de novo from randomly picking stuff out of sequence space.

They always get this wrong, knowing it is wrong. @Agauger on this very forum has herself explained that Axe’s experiment is not an estimate of finding any novel functional protein in sequence space. It happened in this post

(My bold)

Ann Gauger: I don’t think you have understood Axe’s paper.That’s the most charitable I can be: you either don’t understand or are mischaracterizing. Your last sentence makes it clear. Axe estimates the prevalence of sequences that adopt a specific functional fold; he doesn’t expect every protein to be a beta lactamase. You must know that.

In his experimental case he used a particular beta lactamase and calculated the proportion of possible sequences with that fold that could carry out that function.

It becomes particularly interesting when we read what she says says next:

He then went on to generalize, making use of 2 studies with similar approaches, namely the use of mutagenesis to determine what proportion of sequences can carry out that fold’s function after mutagenesis.

That fold’s function. But the function of that fold can be carried out by protein with completely dissimilar folds. The function of beta-lactam hydrolysis. The break-down of beta-lactam antibiotics by consumption of water in the reaction. As noted Puck, the function has been selected in catalytic antibodies. It is known to exist in a completely different family of proteins known as metallo beta-lactamases which has an entirely different fold that is unrelated to TEM-1 beta-lactamase.

That means Axe’s experiment LOGICALLY cannot be an estimate of the “proportion of sequences can carry out that fold’s function!”, since that fold’s function exist in other folds. AXE 2004 IS TRASH.

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From EN (my bold):

Thus, Shahsavarian et al. (2017) really did not measure the likelihood of creating a beta-lactamase enzyme from scratch.

A) Neither did Axe. He provided some sort of rough estimate of what Ann Gauger says, the probability of a sequence that BOTH adopts the TEM-1 beta-lactamase fold AND functions as a beta-lactamase.

B) That’s NOT “the likelihood of creating a beta-lactamase enzyme from scratch.” because there are OTHER folds capable of beta-lactam hydrolysis. For forks sake! Can you EVER get this thing right in your propagandamill?

To do so they would have had to measure the difficulty of both creating a stable structure (very hard)

Keefe & Szostak 2001. “Very hard” turns out to be something like 10-11, and that’s actually quite an underestimate of the probability since Keefe & Szostak selects only for ATP binding, rather than any fitness-enhancing function.

They only measured the latter, not both combined. Thus this really did not measure the same difficult task (generating both) that Axe measured.

Nobody believes the beta-lactamase evolved de novo from junk DNA (or something to that effect). We know from phylogenetic inference it evolved DD-peptidases.

Incidentally enzymes are thought to have mostly evolved from simpler substrate binding proteins which are usually much more prevalent in protein sequence space (Keefe & Szostak 2001 again). Once a protein has evolved the capacity for specific binding, the binding site can further evolve into an active site.
A similar evolutionary strategy as is thought to have first produced substrate-binding proteins de-novo and for enzymes to have evolved from these in turn, is usually exploited in directed evolution experiments when new enzymatic functions are sought, for example, in antibodies. A substrate is presented to antibodies for binding, and from the more successful binders are catalysts selected.

My bold again:

Finally, PM cites the evolvability of COVID as evidence that new proteins can evolve. Mutations in the SARS-CoV-2 spike protein are very common — but they always preserve the overall shape and structure of the spike protein. So yes, you can mutate a protein to a limited extent provided that you don’t change its overall shape or structure. Indeed, Meyer and Axe in particular have been very clear in affirming that mutations can modify and even optimize existing protein functions provided they do not alter the structure of the protein fold. They have instead insisted that the mutation/selection mechanism lacks the ability to generate novel protein folds in part because as mutations accumulate they will degrade and destroy the structure of the fold long before a new fold can arise.

I will just answer with this:

Insert all the references on de novo proteins such as artic fish antifreeze proteins, BSC4, tURF13, VPU1 etc. etc.

They live in complete denial.

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I guess now they’ll have to accuse you of “hateful invective and personal attacks,” too. The alternative would be for them to put together a credible and persuasive response to this, but we all know how often that happens where the DI is concerned.

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As a participant in many of those Amazon book review discussion threads, I can confirm from personal observation that Puck’s very detailed reviews were hard-hitting and unrelenting—but never ad hominem or petty. (In other words, they were nothing like a Casey Luskin review.)

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The third review is by “Puck Mendelssohn,” a pseudonym, who describes himself as an atheist, attorney, and small business owner, and whose claim to fame is posting potty-mouthed reviews of ID books on Amazon.

My oh my, I had no idea that Amazon even allowed your potty-mouthed profanity and vulgar language to be posted on their reviews. Words like rank dishon**ty and incomp**ent would make a sailor blush.

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We could be more generous and say that Axe 2004 was wrong, even wrong-headed (the experiments were not designed to support the claim he made, and the interpretation, then and now, was extravagant compared to the data) in 2004. Being wrong is not malpractice in science. It’s part of growing up.

But for two decades, he and his propaganda support team have been claiming that he showed that “proteins are rare and isolated” in that paper. This is wild malpractice. He didn’t show that in 2004 – at best, he provided some evidence in favor of a particular and extreme estimate of protein function rarity. (His paper is occasionally cited today by real scientists, only to show that such estimates span scores of orders of magnitude.) Much worse, though, his paper was one in a constellation, which has grown dramatically in sophistication. Even if that 2004 paper weren’t as weak as it was even then, it would be just one step in our understanding. A step that we now know to be wrong. So, the malpractice is not an over-interpreted set of weak experiments in 2004. It’s the misrepresentation of the paper’s importance, every year since then.

Oh BTW here’s a great 2022 review article, coauthored by Joe Thornton, that could almost have been written to humiliate a former scientist who claims that proteins are impossibly isolated in protein space:

https://doi.org/10.1002/pro.4449

Abstract:

Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.

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Yeah, that “potty-mouthed” reference puzzles me a bit. While one might legitimately call some of these people “big poopyheads,” that’s not really my style. I’m sure it has been said, but not by me, in or out of the potty.

But one of the things the DI relies very heavily upon is the supposition that nobody will actually read the source materials. That is one reason they get away with so much quote-mining, and also a reason that they don’t feel obligated to frame their responses to criticism in such a way as to address the actual substance of the criticism.

So I say that mammals didn’t just poof magically out of the ground like Meyer implies they did, and the retort is, “yeah, well, after the dinosaurs went away they sure did have a huge adaptive radiation. So there.” These people are like performance artists who specialize in the non sequitur.

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Wow. I didn’t realize it will be this year TEM-1 beta-lactamase will celebrate twenty years of not paying rent.

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Maybe the DI should stop making claims Axe 2004 can’t support. Is that too much to ask?

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Agreed. While the experimental approach did have some flaws—such as the use of a deliberately engineered-to-be-extra-temperature-sensitive variant of the enzyme, and he didn’t measure enzymatic activity but simply screened for the emergence of colonies on agar plates containing the MIC of antibiotic (which I would be happy to explain again to anyone why is a problem)—the biggest problem isn’t so much the paper and experiment it details, as it is the extrapolations made by various Discovery Institute authors and writers in their blog posts, articles, and pop-sci apologetics books.

They are constantly selling this idea—by citing Axe 2004 and other studies of a similar nature—that getting new functional proteins to evolve is a big unfathomable improbability, but none of these references are able to support that extrapolation. The experiments are simply not designed in a way that probes the question of how rare are functional proteins in general?. And that is the real question that matters when we are considering whether evolution could have produced any new functional proteins in the history of life.

They keep getting this wrong, year after year, decade after decade.

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That sure brings back memories. I used to have a novelty bumper sticker on my car that read:

TEM-1 β-lactamase is the most common plasmid-encoded β-lactamase in Gram-negative bacteria and is a model class A enzyme.

They used to sell them at the old Stuckey’s interstate highway rest stops right next to the pecan rolls.

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Which is why I always find it a bit bizarre when people suggest that I shouldn’t call them liars. Obviously they know it’s wrong and they choose to keep repeating it anyway, because they also know that their primary audience is profoundly scientifically illiterate. Any pretense that there can truly be a productive dialogue with the proponents of this garbage is doomed to failure.

I loved that bumper sticker! I had that right next to my Robert Crumb “Keep on Truckin’” sticker.

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Been there. Done that. Got the tee shirt from back in the day.

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I had one of these …

TEM2
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I still have the ubiquitous tourist trap gift shop souvenir version:

TEM-1-tshirt

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That, as they say in northern Michigan, is SOO funny!

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And for those who enjoy these comedy piles-on, don’t miss the new Netflix series: Patton Oswalt’s Peaceful Science After Dark.

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