Tag: science

The Best They’ve Got II

Yesterday, I posted the first part of my critical review of Jason Rosenhouse’s 2022 book Failures of Mathematical Anti-Evolutionism, published by Cambridge University Press, in which I demonstrated how he badly misrepresented significant elements of the 1966 Wistar Symposium and how he falsely claimed that the biologists there had adequately answered the challenges posed to the Neo-Darwinian Modern Synthesis by the mathematicians.

Rosenhouse also makes three important assertions in a single paragraph on page 124 in Chapter 4: The Legacy of the Wistar Conference, each of which claims that subsequent work has vindicated the biologists and refuted the mathematicians. However, none of them is accompanied by any evidence within the chapter itself.

Assertion 1: “Molecular biology and computer science were both in a very rudimentary state when the conference was held in 1966. Both fields have blossomed spectacularly in the ensuing decades, with results that have not been kind to the perspectives of Eden and Schützenberger. Molecular biologists have learned a lot about the geometrical structure of protein space, and their results make Eden’s simplistic combinatorial calculations look hopelessly naive.”

Rosenhouse provides no citations. He names no studies nor molecular biologists. No results actually described. No quantifications are offered, just a general statement about how subsequent developments “have not been kind”, whatever that is actually supposed to mean. Rosenhouse does not tell the reader what the geometrical structure of protein space actually looks like, whether functional proteins are in fact densely connected by single-step mutations, or what fraction of single-residue changes preserve function in any specific protein family. He simply asserts that the results exist and implies that those results are devastating for the arguments presented by Eden and Schützenberger, then moves on. The reader is expected to take this on faith and, presumably, to wait for all of this to be shown to him in Chapter 6.

This failure to actually support his assertions with any details at all is particularly egregious because either those results exist or they do not. If molecular biologists have demonstrated that functional proteins are densely connected stepping stones in sequence space, that result would have a name, a date, and a journal. Rosenhouse does not provide any of these. The most relevant empirical work, deep mutational scanning studies, actually shows the opposite of what Rosenhouse implies. Single-residue changes to most proteins tend to reduce or destroy function. The fitness landscape is rugged, not smooth. Eden’s 1966 concerns about the rarity of functional proteins in sequence space have been confirmed by subsequent experimental work, not refuted by it.

Assertion 2: “Schützenberger’s arguments about computer simulations have likewise not held up, and computer simulations of the evolutionary process are now commonplace.”

This is a non sequitur disguised as a refutation. The fact that computer simulations of evolution are “commonplace” does not even begin to address Schützenberger’s argument. Schützenberger’s point was not that you cannot simulate selection on a computer. His point was that random typographic changes to a program, changes that are not guided by a fitness function designed by the programmer, do not produce functional programs. The existence of evolutionary algorithms does not refute this, because every evolutionary algorithm ever written has a programmer-designed fitness function that does exactly what Schützenberger said biology lacks: it provides the mapping between typographic changes and functional outcomes. The programmer is the intelligence that Schützenberger said was missing. Dawkins’s WEASEL program is the perfect example: it works because Dawkins specified the target string, the fitness function, and the selection rule. Remove any of these programmer-supplied components and his simulation produces nothing. Rosenhouse does not address this distinction at all. He simply notes that computer simulations exist and treats their existence as a refutation, as if Falcon 3.0 and Spore somehow proved Schützenberger wrong.

Assertion 3: The section heading “The Two Pillars of Mathematical Anti-Evolutionism” and the final section imply that subsequent chapters will deliver the killing blow. The chapter ends by promising that “We will discuss this work in Chapter 6.”

This is the most revealing move. Rosenhouse has spent an entire chapter arguing that the mathematicians at Wistar were wrong and that the biologists successfully answered them. But his own chapter provides no quantitative refutation of any of the three mathematical arguments provided by the biologists at the time or by anyone else since. Eden’s sequence-space calculation stands unchallenged by any number Rosenhouse provides. Ulam’s rate calculation stands unchallenged by any rate Rosenhouse computes. Schützenberger’s formal-language argument stands unchallenged by any mechanism Rosenhouse identifies. After 26 pages of rhetoric, historical misrepresentation, and posturing, the actual mathematical demonstration is deferred to a later chapter the reader has yet to read.

Which is why, in my third and final post on Rosenhouse’s book, we’ll examine whether he delivered on those three promises or not.

DISCUSS ON SG

The Best They’ve Got I

One name that was unfamiliar to me was brought up several times amidst the panoply of purported “criticisms” and “debunkings” of Probability Zero that are presently being flung around by hundreds of evolutionary enthusiasts, very few of whom have actually read the book. That name is Jason Rosenhouse, the author of Failures of Mathematical Anti-Evolutionism, published by Cambridge University Press in 2022.

Anti-scientific misinformation has become a serious problem on many fronts, including vaccinations and climate change. One of these fronts is the persistence of anti-evolutionism, which has recently been given a superficially professional gloss in the form of the intelligent design movement. Far from solely being of interest to researchers in biology, anti-evolutionism must be recognized as part of a broader campaign with a conservative religious and political agenda. Much of the rhetorical effectiveness of anti-evolutionism comes from its reliance on seemingly precise mathematical arguments. This book, the first of its kind to be written by a mathematician, discusses and refutes these arguments. Along the way, it also clarifies common misconceptions about both biology and mathematics. Both lay audiences and professionals will find the book to be accessible and informative.

I read it, of course, in order to see if he had somehow anticipated my own demonstration of the mathematical impossibility of evolution by natural selection, selective sweeps, neutral sweeps, genetic drift, ILS, biased gene conversion, and every other imagined mechanism, but, as it turns out, he hadn’t. Nothing that he addresses in his book has anything whatsoever to do with my own mathematical work on the subject. Rosenhouse’s book has two primary objectives. First and foremost, he was attempting to defuse the anti-evolutionary work of the Intelligent Design community, beginning with Michael Behe and William Dembski. Since I’m not familiar with their work and since their work does not overlap with mine, I’ll leave it to the latter to address Mr. Rosenhouse’s critique.

Rosenhouse’s book is objectively bad. It purports to be a critique of mathematics as used by ID proponents and of my mathematical work in particular. Yet it betrays a lack of comprehension throughout. It makes a virtue of misrepresentation.

I’m not in a position to have an opinion one way or the other. However, what I can say is that Dembke’s summary is consistent with the parts of the book that addressed something I do know, and which concern Rosenhouse’s attempt to mitigate the serious damage to the mathematical credibility of evolutionary theory that resulted from the 1966 Wistar Symposium, which I have read and to which I devoted an entire chapter of PZ. To put it charitably, Rosenhouse systematically misrepresents the entire debate between the mathematicians and the biologists, and falsely claims that the mathematical issues raised by the mathematicians there were successfully addressed by the biologists present.

His account of Wistar is simply not accurate. It is a systematic misrepresentation of the transcript of the Symposium in three different ways: factual errors, strategic omissions, and interpretive falsehoods and distortions. Here is a systematic analysis of Rosenhouse’s description of the symposium:

Factual Errors

  1. “Only two posed challenges to evolution’s fundamental soundness.”
    Rosenhouse claims only Eden and Schützenberger challenged evolution, and that Ulam “was not challenging the fundamental soundness of the theory.” This is flatly contradicted by the transcript. Ulam explicitly states: “What I am going to do will come to Eden’s conclusions.” He also says, in the discussion, “In contrast to the tone of the discussion I took, personally, I believe that the numbers I took are very optimistic”—meaning he believes the real situation for neo-Darwinism is worse than his model suggests, not that he was merely sketching a neutral mathematical exercise. Rosenhouse’s selective quotation of Ulam’s modest throat-clearing about “schematic thinking” and “a starting point for discussion” is a textbook example of mistaking courtesy for agnosticism. Ulam was just being polite. He was not even remotely neutral on the fundamental soundness of evolution.
  2. “Schützenberger’s presentation is muddled.”
    The transcript appears muddled because it was OCR’d and the scanning was very bad. Schützenberger’s argument is perfectly clear: he introduced three topological spaces, argued that the mapping between the first and second is the unsolved problem, and concluded that “there is a considerable gap in the neo-Darwinian theory of evolution, and we believe that this gap cannot be bridged within the current conception of biology.” Rosenhouse treats the garbled OCR as evidence of confused thinking. This is either dishonest or lazy. He could have checked a physical copy of the proceedings like I did.
  3. The attribution of the “stepping-stone” argument to the biologists.
    Rosenhouse constructs an elaborate analogy involving truffle hogs, river crossings, stepping stones and presents it as though it captures what the biologists actually said at Wistar. It does not. No biologist at the conference presented a stepping-stone model of protein evolution. No biologist calculated the density of functional proteins in the neighborhood of any existing protein. No biologist demonstrated that the local search space is sufficiently dense to support the model. Rosenhouse invented the analogy in 2022 and projected it backward onto a 1966 transcript where it does not appear. This is the classic Fictional Defender move we’ve seen from both the Neo-Darwinists and the Neo-Kantians: constructing a more defensible version of the position than any past figure ever actually articulated, then declaring that this post-facto invented defense answers the challenge to the original’s case.
  4. Ulam’s quote about Eden is misrepresented.
    Rosenhouse quotes Ulam saying that Eden’s comments “refer to a random construction of such molecules and even those of us who are in the majority here, the non-mathematicians, realize that this is not the problem at all.” He uses this to claim Ulam was criticizing Eden. But the transcript shows Ulam was agreeing with Eden’s broader point while noting that the first five minutes of Eden’s talk addressed a preliminary issue that was not the central problem. Ulam immediately goes on to develop his own argument about rates that reaches the same conclusion Eden reached. Rosenhouse presents Ulam as an ally of the biologists. The transcript shows him as an ally of Eden.

Strategic Omissions

  1. Wald’s complete irrelevance is never acknowledged.
    Rosenhouse does not mention that George Wald’s formal presentation on “The Problems of Vicarious Selection” had absolutely nothing to do with the mathematical challenges. Wald talked about luminescent bacteria on deep-sea fish and the mating habits of eels and lampreys. This was one of the “formidable talents” assembled to respond to the mathematicians, and his response was to give a paper on an entirely different subject. Rosenhouse presents the biologists as having answered the challenges effectively. He omits the fact that one of his star witnesses didn’t even show up to the fight.
  2. Lewontin’s admission is buried.
    Rosenhouse quotes Lewontin’s point about enzyme changes as though it settles the matter. He does not mention Lewontin’s admission, under direct questioning from Schützenberger, that he cannot justify the continuity assumption that small genetic changes typically produce small phenotypic changes. The transcript records Lewontin saying, “That is a very good question. I don’t know.” This is the single most important exchange in the entire symposium, because the continuity assumption is what makes hill-climbing selection work. Without it, the entire stepping-stone model that Rosenhouse constructed collapses. He omits it entirely. I, of course, specifically cited it in Probability Zero.
  3. Wald’s observation that supported Eden is omitted.
    Wald stated that he was “hard put to find a single instance” where a single amino acid change in hemoglobin did not “change markedly the properties.” This is relevant to Eden’s argument about the ruggedness of the fitness landscape—if nearly every single-residue change has significant functional consequences, then the space is rugged, not smooth, and local search is unreliable. Rosenhouse omits this because it directly contradicts his stepping-stone narrative.
  4. Crosby’s support for the mathematicians is left out.
    Rosenhouse quotes Crosby’s exasperated comment about “gorgeous unreality” as though it refutes the mathematicians. He does not mention that in the discussion of Eden’s paper, Crosby actually supported Eden’s argument, noting that each intermediate stage “has got to be capable of existing viably” and that frame-shift mutations “decrease enormously the possibility of intermediate stages being viable.” Crosby was frustrated with what he felt were oversimplifications in Ulam’s model; he was not dismissing the mathematical challenge as a whole.
  5. No biologist produced a single calculation.
    This is the single most important omission in the entire chapter. Rosenhouse never acknowledges that not one biologist at the conference produced a single calculation that contradicted the mathematicians’ conclusions, because acknowledging it would destroy his thesis. Eden calculated the size of sequence space. No one calculated a smaller space. Ulam calculated a rate. No one calculated a faster rate. Schützenberger asked for a mechanism. No one demonstrated one. The biologists asserted, objected, analogized, and hand-waved. They did not even attempt to do the math. Rosenhouse’s entire chapter is structured to conceal this fact.

Falsehoods and Distortions

  1. The Kansas/New Jersey analogy is backwards.
    Rosenhouse argues that Schützenberger’s computer-program analogy fails because computer languages are like Kansas (words widely scattered) while the genetic code is like New Jersey (words densely packed). His evidence is that there are 64 codons and all of them code for something. This is true at the codon level, but it is irrelevant to Schützenberger’s argument, which was about proteins, not codons. Every codon codes for an amino acid or a stop, but that does not mean every protein is functional. The question is not whether every three-letter word in the genetic language means something, but whether every 250-letter sentence is grammatical. The answer is overwhelmingly no. Eden had already shown this: the space of 250-residue proteins is ~10^325, and the number of functional proteins that have ever existed is ~10^52. Rosenhouse attacked a strawman of his own construction, refuted an argument Schützenberger was not making, and claimed to have refuted Schützenberger.
  2. Waddington’s summary is presented as authoritative.
    Rosenhouse quotes Waddington’s summary as “exactly right” and as proof that the biologists won the argument. But Waddington’s summary is a diplomatic statement of the biologists’ position, not a demonstration that the position is correct. Waddington asserts that “the meaningful section” of explored sequence space “is quite large in comparison with all the things that could conceivably be made out of it in single steps.” This is an empirical claim. He provides no data to support it. He provides no calculation. He simply asserts it. Rosenhouse treats this assertion as though it were a proof. It is not. It is the claim that required proving, and no one at Wistar even tried to prove it.
  3. Mayr’s “adjust the figures” quote is reinterpreted in a false context.
    Rosenhouse devotes enormous effort to providing context for Mayr’s statement that “somehow or other by adjusting these figures we will come out all right.” He tries to claim that Mayr was making the sophisticated point that Ulam’s model was too simple to be useful. But the transcript shows Mayr was simply retreating to the argument from existence. “We are comforted by knowing that evolution has occurred” is not a mathematical rebuttal. It is not even a scientific argument. It is a profession of blind faith. Mayr was asserting that the numbers must work out because the conclusion is already known. It was nothing more than an appeal to hope in help that would never arrive.
  4. The “biologists were right” framing is unsupported by the transcript.
    Rosenhouse attempts to paint the picture that the biologists successfully answered the mathematicians at Wistarr. The transcript proves the opposite. The biologists offered qualitative objections (things are more complicated than your model), anecdotal counterexamples (hemoglobin variants survive single changes), conceptual reframings (you’re modeling it wrong), and existential assertions (evolution happened, so the math must work). None of these constitute a quantitative refutation. None of them even began to solve the problems the mathematicians identified. And the mathematicians themselves did not accept the biologists’ responses as adequate, and the closing remarks by the host of the symposium made it clear that he did not believe the biologists’ collective response was adequate or that the situation had been resolved.

In my second post on Failures of Mathematical Anti-Evolutionism later this week, I’ll review whether Jason Rosenhouse provided any evidence of his claim in the book that the Wistar mathematicians’ various anti-evolutionary arguments were successfully refuted during the sixty years since the end of the Symposium or not.

DISCUSS ON SG

Erika Needs Help

Fair enough. She’s going to need all the help that she can get. But I really fail to see what difference it’s going to make, no matter how many butterfly collectors she assembles.

GIVE ME YOUR OPINIONS ON VOX DAY’S WORK TO APPEAR IN AN UPCOMING VIDEO:

Hey guys (and Mr. Theodore Beale)

As I compose a video on the work of Creationist/Bad Guy Vox Day (Theodore Beale) I have been paying close attention to his blog. You will be pleased to know he has posted an update to his evolution-defeater: Mittens 3.0 (for real this time).

Additionally this man has been crashing out and obsessively making blog posts responding to Youtube comments (instead of just responding to the comments). For this morning’s post we see this charming line regarding friends of the channel Grayson and Creation Myths:

“It should be amusing to catalog all of the various things this slur is going to get wrong in his desperate attempt to prove that math which has been confirmed by every major AI system and more than 10 math PhDs is “stupid”.”

Setting aside the AI stuff, wow 10 math phds! Now I am only aware of three people with doctorates who have “vetted” Day’s work, and they are all associates of the Discovery Institute, but I thought this might be a fun opportunity.

Many of you are highly credentialed and have atomized various portions of Day’s anti-evolution “model” here and elsewhere. I thought it might be fun to compile a list to act as both a resource for why this clown is wrong and as a fun dig in an upcoming video of mine.

Here’s the activity:

If you have a bachelors, masters, or doctorate and have reviewed any of Day’s work please leave a comment outlining your favorite blunder and your credentials.

It does not have to be limited to Mittens 3.0 because Probability Zero (which contains all prior errors) is still for sale and therefore is a part of the public record until Day issues a formal retraction.

This list will appear in an upcoming video of mine so please keep that in mind before commenting! I’m hoping to have a nice count of “credentialed people who think Day’s math (+ assumptions which go into it) is steaming hot garbage”.

Additional acknowledgements:

  • No Day is not worth any of our time but since his work was broadcast to my audience I have a responsibility to provide a detailed counter.
  • Yes Day is a dweeb

This is fascinating. The more credentials, the merrier, I always say. So. Many. Skulls!

Are you not entertained!

I am, of course, deeply intimidated by this formidable army of credentialed academics being arrayed against me. I feel like Sauron in Mordor, alone and surrounded by implacable foes.

Is this how it always ends for dark lords?

Will there never be a happy ending?

UPDATE: Let them do their thing and take their best shot. Don’t correct them. Don’t argue with them. Don’t engage with them at all. Let’s see what they can do with what they’ve got. After they drop the Team Evolution video, that will be the time to have some fun.

DISCUSS ON SG

They Didn’t Read the Book

A regular here jumped on the grenade for everyone who, like myself, lacked the fortitude to sit through three-and-a-half hours of two people discussing a book that neither of them had bothered to read, and thereby gleaned the following information from the recent video by Dr. Erika and Dr. Hanson.

  • Erika: “Will doesn’t include in his presentation how d is actually calculated, but I suspected it was probably in Vox’s book. So I just texted one of my several friends who are reading through the book right now and sort of yucking it up with me via text messages over it, and I was like, ‘Hey, does anybody have the definition for his selection coefficient d?’ And my friend said that on page 153, in the chapter titled ‘The Overlapping Generations Problem,’ d is defined as the fraction of the population replaced per time unit…”
  • Dr. Hanson: “So because of all of that, I don’t foresee any population geneticist, one, even knowing who Vox is, or two, being like bothering with ever reading a book that’s probably mostly written by AI.”
  • Erika: “That’s just based off of what Will presented to us. Of course, Vox has a book floating around out there. I wonder—I wonder if maybe I should read it and then, like, make fun of it with some of my friends? Like, go through some of the more in-depth claims, or I should say extraneous claims, that exist in that book. That might be fun…”
  • Erika: “There’s no doubt in my mind that Vox is going to respond to this video, and he’s probably going to say something to the tune of, ‘You didn’t answer all of the points that I made in my book. All you did was address Will Duffy’s points.’ And it’s like, yes, that was the priority of this video.”
  • Erika: “It’s also worth noting that in some places he has complained that people who criticize him actually haven’t read his book… So all of those things together put an evil little idea in my head. I was talking to Zach and a couple other of my friends who have relevant formal training in areas in and surrounding this exact topic, and we kind of just thought to ourselves, ‘Man, what if we just did read the book? What if we read it and then got together and critiqued the book as a whole, and we can each bring our favorite parts of the book to this round table together and we can sort of atomize it?’ …You can expect that to come within a couple of weeks, a week maybe, of this video. We’re just going to actually go through Probability Zero, and it’s probably going to take a long time.”

Interesting. I was pretty confident that Erika hadn’t read the book, but I was under the impression that Dr. Hanson had read the 2nd edition, specifically, on the basis of some of his comments. Believe it or not, I have no problem whatsoever with evolutionists attempting to critique Probability Zero or The Frozen Gene without bothering to read them first. It’s their credibility and their careers on the line, not mine. And they certainly make my job as the author significantly easier, because I have neither the reason nor the responsibility to respond to any critique by anyone who hasn’t read the book he is purporting to critique and isn’t even addressing the relevant details.

So that’s my initial response to their 210 minutes of not discussing my book: they didn’t read it and they didn’t discuss it, they simply discussed what they imagined it must be. Although perhaps someone should warn Erika what happened to the last female critic who thought that reading through one of my books and critiquing it would be fun.

But talking about the book without reading it is absolutely fine, so long as that’s made clear, which both of them obviously did. I have never paid attention to their videos before and they have yet to give me any reason to start doing so. I might as reasonably respond by talking about The Refutation of Kant and providing proof of the amphiboly in das Ding an sich, as that’s another of my books they also haven’t read. Or, for that matter, the Amorran formations in A Throne of Bones.

This isn’t to say that their video is worthless. To the contrary, it gives us a very clear picture of the current state of the field’s mainstream understanding of itself as well as how it is unprepared to defend this particular front. Now, perhaps this evolutionary round table Erika is assembling will do better. It certainly should do better on the basis of actually having a target at which to shoot. And when I respond, I will respond in detail to every material criticism of my mathematical disproof of evolution by any, all, and every mechanism, including natural selection, raised in both of the videos. While I am aware that Erika and Dr. Hanson spent some time discussing me on a personal level, I didn’t even bother reading that part of the transcript.

I’ve been getting attacked personally for 25 years now. I don’t care. I’m a former Wax Trax! recording artist and my own fans and Vile Faceless Minions refer to me as Supreme Dark Lord. So I think the mainstream narrative of me being a Very Bad Man has been sufficiently established that we can all just take it as given and get on with the substantive discussion. I mean, what part of “downright evil” is hard to understand?

  • “Vox Day is one sick puppy.” —Dr. P.Z. Myers, PhD
  • “Vox Day is a fascist mega-dickbag and less a human being than one long sequence of junk DNA.” —Dr. Phil Sandifer, PhD
  • “I consider Vox Day one step, either direction, from certifiable.” —Mike Resnick, science fiction author, 38-time Hugo Award nominee
  • “I think I have made my disgust with Vox Day and his Rabid Puppies clear.” —George R. R. Martin, fantasy author, 19-time Hugo Award nominee
  • “Vox Day rises all the way to ‘downright evil’. ” —Patrick Nielsen Hayden, Manager of Science Fiction, Tor Books, 15-time Hugo Award nominee
  • “Vox Day is a real bigoted shithole of a human being.” —John Scalzi, three-time SFWA President and science fiction author, 9-time Hugo nominee
  • “Vox Day and his followers made it impossible for me to remain silent, keep calm, and carry on.” —Connie Willis, science fiction author, 24-time Hugo Award nominee
  • “The real burning question is, ‘what will Vox Day attack next?’” —Charles Stross, science fiction author, 15-time Hugo Award nominee

Well, at least we have the answer to Charles Stross’s question, as St. Darwin is truly dead. And thanks to one of my readers, we can even add to the collection:

  • “Vox Day is one of the worst people I have covered in this channel. He is unambiguously a raging racist, giga-misogynist and clinical narcissist (no hyperbole).”—Erika Whatever her name is, Youtuber and armchair psychiatrist

My only thought is that she never covered Richard Dawkins, Stephen Gould, Steven Pinker, Ed Boyden, Marc Hauser, Martin Nowak, David Sloan Wilson, George Church, or any of the other big-name evolutionists who used to hang out with Jeffrey Epstein? Well, I suppose she did say only “one of the worst”. I’ll just have to do better.

Despite being a recently diagnosed clinical narcissist, I don’t need their attention. I never sent out a single press release for the book. I’ve done zero book signings and no public events. There was no book launch party. You can even see from my publication history that I almost entirely stopped paying attention to evolution from February to September. So whether they engage or not makes very little difference to me. If and when they do, I’ll address the critiques and any mistakes they identify. If they don’t, then the work stands as it is until someone can come along and actually show that it doesn’t.

DISCUSS ON SG

PZ on PZ

Hey, the old wannabe Fifth Horseman of the New Atheism is back! They’re mostly dead now and he’s been irrelevant for at least a decade, but apparently if there is one thing that is going to wake him up and get that weary old ticker thumping again, it’s the unholy marriage of William Dembski and myself. Which is really a terribly dramatic way to describe an interview, but whatever.

Vox has an undergraduate degree in economics and East Asian studies from Bucknell University, a small private liberal arts college. He does not have a science degree, and by his own admission he did not exactly apply himself to his studies….Any student who tells me that their achievement was developing an intuitive grasp of a subject is bullshitting me. Then he confirms it: Vox Day was a slacker who learned nothing in college.

He wishes he dropped out after his first semester, he seldom went to class, and didn’t bother reading the textbook — and he probably thinks that means he must have been a genius, rather than a lazy goof. It doesn’t speak well of Bucknell or his professors that they decided to get rid of him by putting him in a program of independent studies, rather than flunking him. I sorta sympathize with them. You get attached to your students and want to help them succeed, so you coach them through and design a limited curriculum that matches their abilities to allow them to finish the program. I guess we’re doing the students no favor if that just means their ego is stoked.

So if he has no background in or comprehension of biology, how did he write MITTENS? He explains it all: Apparently the proper way to use AI is to hammer its outputs through multiple iterations until it tells you the answer you want to hear.

He really does think he has disproven all of evolution all by himself, with a paper that contains all of 11 citations (a number I’d find unacceptable in an undergrad student paper that was much more narrow in its scope). Even worse, 7 of those citations are to the LTEE, and contradict his conclusions, and 2 are to ape genome sequencing papers whose authors would be surprised to learn how their work is being distorted. At least he has 2 that reinforce his argument, sorta, but they’re both also written by Vox Day.

So this is an argument made by an unqualified buffoon who churned it out of a battery of AIs, written with negligible knowledge of the scientific literature, and rubber-stamped by a couple of biased dorks from the Discovery Institute.

I’m definitely archiving this, because I very much want to have PZ on the record stating that I did everything by myself, with only a battery of AIs and an unacceptable number citations in an undergrad student paper. It’s going to be really fun to know that he is struggling to accept the reality that the man he has sincerely believed to be “an unqualified buffoon” has always been a world-class genius of historic levels, far more significant in the course of human intellectual development than sweet St. Darwin himself, who somehow managed to cripple Man’s correct understanding of his own origins for 167 years and counting.

Science was born free and everywhere it is in chains. I can’t do much about physics or sociology, but at least I can set the geneticists and biologists free.

The thing that I am finding so terribly amusing about all of this is that these scientific charlatans are so uncurious and so prone to posturing and resting on their credentials that it literally never occurs to them that I am nothing like them. It never occurs to them that maybe my professors weren’t stroking my ego, or making sure a lazy goof got his degree, but rather, catering to a student they regarded as “a brilliant fuckup”. Which is a direct quote from my favorite professor, by the way.

It never occurs to them to wonder why I wish I had dropped out of college. Jensen Huang knows. More than anyone, he’s the primary beneficiary of my return to university. But if you don’t understand why, that’s another story for another day.

And most of all, it never occurs to them that anyone might use AI creatively in a productive manner, one that observably augments human intelligence and makes things possible that were not previously possible. I’m not, of course, referring to the disproof of evolution by natural selection, since that was a piece of cake so obvious that I cannot believe anyone with half a brain capable of performing long division is still seriously trying to defend it. I never needed any AI assistance or augmentation for that.

Being the first man in history to solve the Agrippan Trilemma and other little puzzles like the Hard Problem of Consciousness, to say nothing of refuting Kant’s critique of pure reason, on the other hand, definitely required a bit of an artificial boost.

Anyhow, I just want PZ to remember every little thing he ever said about me in this regard as the horror gradually dawns in him as more and more people start actually doing the relevant math and confirming it for themselves. Because I won’t. I don’t think about him at all. I genuinely thought Pharyngula shut down years ago.

And here’s the more important thing for him to contemplate. If he was wrong about me, well, that’s going to sting a little. But it’s not really that big a deal in the cosmic scheme of things. But if he was wrong about Jesus Christ, on the other hand, that’s a much more serious problem. So if the former turns out to be true, however unlikely, maybe take another, closer, look at the latter.

UPDATE: Oh, Sweet St. Kimura, PZ doesn’t know the difference between a mutation and a fixation.

  • COMMENTER: Bill Dumbski [sic] is a nobody, full of himself. Every person born has about 100 mutations that neither of their parents had. But being willfully ignorant does have its advantages.
  • PZ: No, no — according to Vox, we are born with at most 1 mutation, and it’s going to be shared with the entire population, eventually. Don’t you know math?

DISCUSS ON SG

Better than a PhD

If you spend the next four minutes watching the video at the link, you will know more about the actual state of evolutionary science than pretty much every single evolutionary biologist and population geneticist on the planet, regardless of how many years they have spent obtaining their credentials and working in the field. You will definitely know more factual information about the subject than Richard Dawkins, Sam Harris, and the earthly remains of Daniel Dennett combined.

I’m neither exaggerating nor joking. That’s how dreadful the state of the science is. Erika and her pet population geneticists would learn more from that four minutes of video than everything they have learned in however many years of graduate education. Besides, this is about their level. They’re certainly not going to read the book, let alone the relevant papers.

Please don’t forget to pick up your complimentary PhD in Evolutionary Biology on the way out.

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Someone Has a Sense of Humor

That, or I really need to place more blind trust in my mathematical intuition. Thus spake Red Team Grok: The ~1,580–1,590 generations per fixation (pooled, strict whole-population definition) is the appropriate figure for “normal” LTEE populations. That is the rate observed in populations that still have intact DNA-repair systems.

The all-population rate of ~132 generations per fixation is real, but it is dominated by the seven hypermutator populations. Those populations have broken mismatch repair (or oxidative-damage repair), are accumulating mutations at ~100× the ancestral rate, show the genomic decay documented by Couce et al., and in several cases exhibit intervals of net loss of high-frequency alleles. They are not healthy, steady-state evolving populations; they are populations that have traded genome maintenance for short-term mutational supply. Calling their throughput “the fastest experimental rate ever measured” without strong qualification is therefore misleading if the intended comparison is to ordinary evolutionary processes.

This is why the source papers (and your own earlier summaries) routinely separated or excluded the hypermutators when stating a representative rate. The corrected data do not change that logic; they simply make the separation cleaner.

Recommended reporting:

  • Primary: Non-mutator pooled rate ≈ 1,587 generations per whole-population fixation (5 populations, 189 fixations).
    Secondary / completeness: When hypermutators are included, the overall rate falls to ~132 generations per fixation (12 populations, 5,496 fixations). This figure is driven by populations with defective DNA repair and should not be treated as a general benchmark for intact systems.
  • That framing is accurate, consistent with prior literature practice, and avoids inflating the apparent speed of ordinary fixation by averaging in genomic-cancer lineages.

The data tables and the analysis are both available at Zenodo: Fixation in the LTEE: Whole-Population Fixation Counts at 500-Generation Resolution

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Repent, Richard

Richard Dawkins put his faith in Charles Darwin, not in Jesus Christ. It wasn’t just the wrong bet, it was a very foolish one:

On Oct 2 it will be 20 years since The God Delusion was published. Coincidentally, books by Sam Harris, Dan Dennett, and Christopher Hitchens came out at around the same time. This led someone (not any of the four of us) to invent “New Atheism” as a “project”. We wrote our books independently without collusion, and as far as we were concerned there was no such project. It was sad that the old arguments needed to be restated. Even sadder, they still need to be re-stated, in 2026.

They don’t need to be restated. They were demolished in 2009 by The Irrational Atheist. Ever notice that no one claims religion causes war anymore, Richard? Yeah, that wasn’t The New York Times or Nature. They were literally quoting me. Ever notice that no one cites the Red State argument anymore? Also me.

Not all physicists accept the premise of the fine-tuning argument. See Victor Stenger’s The Fallacy of Fine-Tuning. Some suggest that it works only if you twiddle one knob at a time. If you turn several knobs together, there could be a very large number of combinations of settings that yield biologically promising universes.

Other physicists, including Martin Rees himself, point out that the currently favoured theory of universe inflation predicts the existence of a multiverse embracing huge numbers of universes. A small minority of these universes happen to have their knobs set to biology-favouring values. We obviously have to be sitting in one of that minority, because here we are – the so-called anthropic principle.

As a biologist, I lack authority to enter this debate. I agree with Paley that the biological argument from design was the big one. Darwin’s solution has correspondingly huge significance. It inspires confidence that the relatively minor cosmological version will in due course yield.

Darwin’s solution has no significance. Darwin is irrelevant. It’s now logically, mathematically, and empirically proven that evolution by natural selection never happened. It couldn’t have ever happened and it didn’t happen. The scientific case is closed, Richard Dawkins just doesn’t know it yet.

Christians don’t just know some hymns, or think it might be a rather nice idea if people loved their neighbours a bit more. Christians believe. They believe that a man called Jesus died to redeem our sins and walked three days later. If, like me, you reject such tosh, you are not a Christian.

I pay God the compliment of taking the hypothesis of his existence seriously. If verified, God would be the most exciting hypothesis in the entire history of science. A universe conceived and designed by a superhuman intelligence would be a totally different kind of universe from the one which, in my opinion, we actually inhabit. At a stroke, the whole of science would have to be rewritten, from the bottom up.

That “tosh” is exactly what we believe. And rewriting the whole of science is exactly what we’re doing. Starting with evolutionary biology.

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Snikker-Snak

Since Erika isn’t a sufficiently big girl to defend her own field of science from a game designer with no academic or scientific credentials at all, I’m reliably informed that she’s going to have DOCTOR ZACH HANCOCK white-knight for her and offer his no doubt Very Serious and Very Credentialed Critique of Probability Zero.

That’s right, THE DOCTOR. ZACH HANCOCK! I’m sure you’re all aquiver with dread and awe.

And since Dr. Hancock, like the intrepid Brian, is a POPULATION GENETICIST, it should be very amusing to watch him demonstrate that he doesn’t know the first thing about the math that serves as the sand beneath his science. But I’m anticipating we’re going to hear all about ISLANDS and DEMES and STEPPING STONES, which should not only offer us an expanded vocabulary, but entirely new ways of amusing ourselves at the expense of midwits in labcoats who never realized there was rather more to understanding science than memorizing the textbook.

It truly amazes me that these people never, ever, stop to consider who and what they’re dealing with. First, they claim that I’m a white supremacist… and they think that’s some sort of sign that I don’t know the math? Correct me if I’m wrong, but I seem to recall a certain group of Aryan supremacists who were very, very good with math, so much so that the US science community imported a whole collection of them in the middle of the 20th Century for one reason or another.

Second, they know I’m a game designer. Not only that, but a game designer who is very heavily involved with artificial intelligence. And yet, they keep being surprised that I know what they’re going to say on the subject before they say it. Which is amusing, considering that I can already tell what Zach Hanson will have for lunch next Thursday with a 87 percent chance of success.

If you doubt that these credentialed scientists are really as dumb and innumerate as I’ve been pointing out, consider this lunatic trying to correct someone who is explaining the concept of an AVERAGE to him. Like JFG, he literally doesn’t understand what an AVERAGE RATE is.

“When dealing with average rates, it really doesn’t matter if particular fixations happen parallel or in sequence. We could have 25 fixations in sequence over a timeframe, or we could have 20 parallel and five in sequence over the same timeframe. The average is the same “

This is mathematically false.

No. It’s not mathematically false. It’s not false at all. It’s literally what an average rate means!

If you drove ten miles and it took you an hour, then it makes no difference if you were driving sixty miles an hour part of the time or you were stopped part of the time, or even if you turned around and drove back home to pick up something you forgot. The AVERAGE RATE of 10 MPH covers all of those possibilites and more.

And don’t forget, we already know how many of those fixations happened in parallel and how many did not because the data is available in 500-generation slices. For example, Ara+2 had 66 fixations in 60,000 generations. At 909 generations per fixation, this was one of the fastest still-viable populations. There were 14 fixation events and every single one of them was sequential. The smallest gap between fixations was 1,500 generations. The largest gap was 9,500 generations.

So there were zero parallel fixations in 60,000 generations. None whatsoever. That’s not theory. That’s the actual empirical evidence from the most famous experiment in evolution. And to answer the obvious question how you can get 66 fixations out of 14 fixation events, the answer is simple: sweeps. Each selective serial fixation carried along an average of 5.3 neutral mutations to fixation with it.

I ran the numbers across all 12 of the populations to make sure this wasn’t an anomaly. There were ZERO parallel events, none in any of the five viable populations and none in the seven hypermutating populations. The smallest gap between fixation events was the 1,500 generations in Ara+2. The largest gap was 10,500 generations in Ara-6.

In fact, what we’re seeing here is empirical evidence for what I mathematically demonstrated with the Bernoulli Barrier. Which means the third edition of Probability Zero is going to be a doozy.

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They Never Stop Lying

It’s truly remarkable how evolutionists will keep repeating obviously false statements over and over again, even after they have been a) shown that the statement was always false and b) told directly that they are repeating a false statement. A woman named Rebekah with a YouTube channel called Examining Origins has obviously read Probability Zero and challenged evolutionists to address its arguments there. The video already has 598 comments, and not one single one of them even demonstrates a basic grasp of the issues involved, let alone presents a coherent response.

Philalethist_Physikos: I respect your work, Rebekah! A quick word of caution to the audience on Vox Day’s formula in Probability Zero: his math assumes mutations fix strictly one after another in a single-file line. In real biology, sexual reproduction and recombination mean mutations sort across the genome simultaneously in parallel, so the math doesn’t hold up in population genetics. If you want rigorous mathematical challenges to evolutionary timescales, stick to researchers like Douglas Axe (coordinated mutations) or Walter ReMine and Royal Truman Haldane’s Dilemma and selection cost). They address real population genetics without making the single-file error!

No, literally none of my math assumes serial fixation. Not MITTENS, not the separate and unrelated math addressing the misapplication of Kimura’s steady-state identity, and not the separate and additionally unrelated math proving the impossibility of punctuated equilibrium. To the contrary, serial fixation with sweeps and ancestral drift are about all that is left AFTER the math eliminates various mechanisms that are not viable.

I quote from yesterday’s post: The LTEE runs twelve identical populations of bacteria in parallel from the same ancestor. Every single evolutionary mechanism from natural selection, genetic drift, mutation, hitchhiking, epistasis, compensatory mutation, and frequency-dependent selection, to clonal interference operates simultaneously in all 12 populations for 85,000 generations and counting.

Which is how we know Philalethist_Physiko isn’t merely ignorant, but dishonest. He appears to have read my post, which is why he mentions “sexual reproduction and recombination” and therefore knows that recombination isn’t included in the LTEE calculations, but he still claimed that I assumed serial fixation which is not at all the case. And he also assumes that recombination will help speed up the fixation rate, which it won’t. the recombination appeal is the signature of someone who learned evolutionary biology from the adaptive narrative rather than from the math. In the evolutionist narrative, recombination is always a good thing. In the math, recombination is a double-edged sword that also breaks linkage, imposes segregation costs, and exposes deleterious recessives. But any positive effects of recombination are massively overwhelmed by the much larger negative effects imposed by sexual reproductive limits.

To demonstrate how wildly ignorant the scientists themselves are, consider this comment from someone who claims he is a research geneticist.

brianmansfield6912: This is not ‘unresolved’. I’ve been a research geneticist for almost 40 years, perhaps I can explain the basic problem. There is a critical error in the calculations in that book. The approach he uses calculates the probability of the occurrence of the 20 million SPECIFIC substitution differences that exist between human and chimp. The correct method is to calculate the probability of ANY 20 million differences. That is, how many substitutions are expected to accumulate over 9 million years? Basic mutation rates and probability theory predict about 20 million. The problem isn’t with evolutionary theory. It would be interesting to someday find an honest creationist….

First, the Kimura equation he’s citing is inapplicable and he’s using the wrong one. The applicable Kimura equation, the time-related one, predicts six neutral mutations, not 20 million. The other Kimura equation, the steady-state identity to which he is appealing, has been mathematically and empirically proved to be irrelevant and all the calculations based upon it are totally wrong. Genetic drift simply doesn’t happen in any population over 10,000. This guy has literally no idea what he’s talking about, for all that he’s waving his credentials and Dennis McCarthy’s erroneous babblings around like a flag.

Here’s another demonstration of an inability to grasp what is being analyzed by someone named Taylor:

Just took the time to actually review the paper cited at the 2 minute mark (2009, Barrick et al), and the quote is a blatant lie.

By generation 20,000, that lineage had picked up 45 mutations, or about one per 440 generations. That’s roughly three times faster than the quote says. Then a mutation that sped up mutation across the whole genome appeared around generation 26,000, and the total climbed to 653 by generation 40,000. Vox Day’s own blog attributes the 1,401 figure to a 2017 paper, not the 2009 one, and counts only beneficial fixations, which is just so clearly biased it’s unthinkable that anyone would dare actually publish it. Human genes have evolved traits like near/far sightedness, derpression, anxiety, schizophrenia, endometriosis, sickle cell anemia, and a million other non-beneficial traits. Then there are our different eye colors, hair-growth rates, toe shapes, etc. that are closer to the neutral side… So counting only “beneficial” mutations is just plainly stupid.

The other side of the problem with this quote is that it’s clearly attempting to trick readers into thinking that this observation should be understood to be some kind of universal speed limit for mutations. It’s not. The fastest rate we’ve ever “observed” is hilarious because on one had, it proves that we’ve observed evolution occurring under lab controlled conditions, AND it only sets the bar for what we’ve literally observed in lab, not what we might observe in any and every other species. For example, the largest start we’d ever observed by the early 1700’s was our own, but that didn’t mean that our sun was the largest star we could ever see.
Observing mutation rates in a lab is a massive undertaking, unless you use something incredibly small that reproduces quickly, like bacteria or mice. But also, just because we don’t observe mutations under lab controlled conditions doesn’t mean we haven’t observed them. A human newborn carries about 60 new mutations. That puts the expected human rate at tens of substitutions per generation, which just so happens to be the EXACT order of magnitude that the human–chimp divergence requires.

TBH, I’d be shocked if you even take the time to read this. I’d be astounded if you listened closely enough to consider changing your mind, but I expect, like all other facts that contradict your religious beliefs, that you’ll simply ignore it and continue building your empire of willful ignorance.

It’s not “a blatant lie”. It’s a demonstration that the critic doesn’t have the first clue about the LTEE, how it works, or what it is measuring. First, the number that I have cited, 1,322 generations per fixation, is the AVERAGE number of fixations across the still-healthy populations for 60,000 generations each, confirmed directly from the lab’s raw data. This guy is citing the Barrick 2009 paper’s results for one population: Ara-1. The critic saw that there were 45 mutations detected in that lineage. But those are total mutations detected in a single lineage, not fixations across the entire population, and it doesn’t even begin to take into account what happened in the other 11 populations. The MITTENS figure of ~1,322 generations per fixation is derived from what is now the remaining five viable populations through 60,000 generations to count mutations that actually reached ≥95% frequency in any of those five populations. Taylor is comparing apples to automobiles.

UPDATE: Sometimes I can’t tell if they’re lying or if they’re just retarded as with this comment by CreationMyths.

He claimed he addressed this, but he hasn’t. His math clearly doesn’t, and apparently either Day nor anyone defending him understands that math well enough to realize that. Day says his math accounts for simultaneous mutations and recombinations but if you actually look at his math, it doesn’t. He explains that this is the case, apparently without realizing so, several times in his book. He’s very clear on this.

The math OBVIOUSLY does address this because parallel fixation is built right into the numbers being averaged due to the nature of the LTEE experiment. And it should be immediately obvious that parallel fixation is included in the math because the average includes all the different populations evolving separately at the same time! And the math also obviously does NOT account for recombinations because bacteria do not reproduce sexually. Once more, we have a would-be critic who has no idea what he’s babbling about. He literally doesn’t know what is being measured or how it is being measured.

UPDATE: Correction: CreationMyths is neither lying nor retarded, he’s merely confused MITTENS math with Bernoulli math.

Nope. He specifically explains this in the book. Several times. His math is for sequential fixation. He does not account for the the fact that recombination allows multiple beneficial alleles to fix at once, nor for the fact that selective sweeps fix multiple alleles at once (mostly neutral). For real, you’re all just repeating what he says as though that’s a response to all the reasons he’s wrong. By all means, keep taking his word for it. There’s a reason real biologists take this stuff seriously. It’s just the “waiting time problem”.

Now I understand why he’s confused. He’s confusing the math of MITTENS, which specifically includes and incorporates parallel fixation, with my subsequent disproofs of parallel fixation. Now, I can assume that you think there is somehow a contradiction there. But there isn’t for a simple, but non-obvious reason: neither the Bernoulli Barrier nor the Hard Limit on neutral drift apply to the LTEE experiment because a) the math is an average of 12 different populations and b) there is no time for neutral drift to have occured yet in the 85,000-generation time limit of the LTEE. The MITTENS generations-per-fixation rate includes parallel fixation due to the structure of the experiment. It is literally built into the structure since it utilizes 12 completely separate populations all running simultaneously in parallel. That’s not how real-world species work.

This is the section that has him confused. It’s from Appendix A and he doesn’t realize that it’s referring to different, non-MITTENS math.

The theory of evolution by natural selection fails its own quantitative test, by its own mathematics, against the data its own practitioners have produced and published. The logical structure of the result is as follows. The Bernoulli Barrier proves that parallel fixation—millions of mutations simultaneously reaching fixation—is physically impossible (pn ≈ 10−34,000,000). The Averaging Problem proves that the polygenic rescue—gradual frequency shifts at many loci under selection on aggregate fitness—is logically impossible, because the mechanism destroys the variance it requires to operate. Therefore fixation must be sequential. And sequential fixation is empirically falsified: the fastest rate ever measured in any organism, applied to the most generous generation count, yields 180 fixations where 205 million are required. The impossibility is in the structure—parallel is ruled out a priori by probability and by logic. The empirical falsification is in the throughput—sequential cannot do the work in the available time by a factor of 10⁶.

Now, perhaps I could have worded it better, but the statement is nevertheless correct because the all-cause rate is obviously faster than a sequential rate. They don’t realize that I am implicitly acknowledging the whole basis of their critique there, because it’s totally irrelevant. This is what I meant by the evolutionists not understanding that there are multiple levels to the disproof of evolution by any and all mechanisms. They’re still wrestling with stage one and trying to defend natural selection, so pulling in elements from later stages is only going to confuse them. They don’t realize that I’ve not only incorporated parallel fixation at the most naive level, I’ve subsequently demonstrated why it doesn’t operate the way they imagine it should.

Anyhow, the MITTENS 3.0 paper renders those complicating elements moot to such an extent that I omitted both the Bernoulli Barrier and the Averaging Problem, even though both of them remain entirely correct.

UPDATE: More hilarity forthcoming.

GraysonHawk: We’re all reading Vox Day’s book right now and laughing at how stupid his math is. Video incoming.

It should be amusing to catalog all of the various things this retard is going to get wrong in his desperate attempt to prove that math which has been confirmed by every major AI system and more than 10 math PhDs is “stupid”. They have absolutely no idea how far ahead of them I am; it appears they still genuinely believe that k=u over time even though it was both mathematically and empirically disproved more than a decade ago by mathematicians and scientists who are not me.

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