Tag: books

A Retraction and a Revision

Unlike the mainstream science orthodoxy, I don’t feel any need to avoid admitting when I got something fundamentally wrong, fixing the problem, and revising my conclusions. Which, of course, is why I’m working on the new appendices for the second edition of Probability Zero rather than trying to defend, rationalize, and justify the various mistakes I made in the first edition, which were mostly the result of relying upon the consensus numbers produced in 2005 rather than the 2025 update of them.

Claude Athos and I are now revising the Kimura’s Calculator paper from last week because our subsequent empirical work has identified a category error in how the selection-cost binding constraint was being used in it. The original paper presents the Calculator as a three-term framework in which the realized substitution rate equals the minimum of three serial constraints: the corrected input flux (Term 1), the polymorphism throughput ceiling (Term 2), and the selection-cost limit (Term 3). For sexual eukaryotes, Term 3 binds at approximately 10⁻¹², two to four orders of magnitude below Terms 1 and 2, which made it the headline result and drove the framework’s most dramatic predictions. The new validation work which uses Bergeron et al. (2023) on pedigree mutation rates and fossil-calibrated substitution rates for 55 vertebrate species exposed a fundamental problem that three-term construction.

The category error is this: Term 3 is derived from Haldane’s cost-of-substitution argument, which bounds the rate at which selection can drive adaptive fixations through a population given finite reproductive capacity. It is a constraint on selectively driven substitutions alone, not on total substitutions. The original Calculator paper treats Term 3 as a bound on total substitution rate and compares it against observed substitution rates from sequence divergence, but observed substitution rates include both neutral fixations (which are the great majority) and adaptive fixations (which are comparatively rare). Comparing Term 3 against total observed k is therefore comparing a bound on adaptive substitutions against a quantity that is mostly comprised of neutral substitutions. The two simply aren’t measuring the same thing. While the math of Term 3 is correct for the quantity to which it actually applies; my error was in interpreting its output as a constraint on total k. Once corrected, Term 3 still limits adaptive substitution rate at ~10⁻¹², but total substitution rate is only governed by Terms 1 and 2, which now falls in the 10⁻⁷ to 10⁻⁸ range that is consistent with the empirically observed rates.

The ramifications for our conclusions are significant but not catastrophic, and the revised picture is in some ways stronger than the original because it survives empirical scrutiny that the original would not. The textbook k = μ identity is still falsified — both directly (pedigree μ and phylogenetic k disagree by a median factor of 25 across 55 vertebrates) and structurally (the polymorphism throughput ceiling is exceeded by textbook μ for 95.4% of 173 animal species). The cancellation step in Kimura’s derivation still fails because N ≠ Nₑ in real populations, as Frankham cataloged thirty years ago. What has to be revised is the magnitude of the resulting recalibrations to molecular-clock divergence dates. The corrected framework predicts factor 10 corrections rather than factor 100,000 corrections, which still places significant divergences in substantially different time ranges than the textbook gives but doesn’t compress the entirety of evolutionary deep time the way the original Term 3 framing implied.

To put this in context, it means that the CHLCA event falls somewhere in the 250 kya to 1.3 Mya range rather than the 6.3 Mya presently assumed. But it cannot be as recent as the lower end of the 68 kya to 330 kya range that had orginally been calculated on the basis of the erroneous calculator.

The result of this retraction and revision is that the central critique of neutral theory survives and is now backed by two methodologically independent empirical tests rather than a theoretical framework with a contested parameter. Kimura’s identity is still wrong, the molecular clock as currently calibrated still overstates divergence times, and the Neo-Darwinian accounting of sequence evolution still rests on a Wright-Fisher idealization that doesn’t describe real populations. The fix is more conceptual than catastrophic and will require properly labeling what each constraint measures, accepting more modest recalibration magnitudes than Term 3 originally suggested, and grounding the falsification more solidly in the empirical evidence rather than theoretical derivation.

We did the best we could with what we had at the time of the original paper; the addition of the empirical data allows us to refine the framework and make the case stronger and more conclusive.

DISCUSS ON SG

If You Want DRACULA

If you’re not a subscriber and you’re interested in acquiring a copy of Castalia Library’s DRACULA, or you’re a subscriber who wants to pick up an additional one, they are exclusively available from these two. The usual subscriber’s discount code applies on the Arkhaven store.

One more thing that should be mentioned. We didn’t have enough black cowhide for the entire print run, so there is about a one-in-six chance that you’ll be getting Dracula in black pigskin. Unfortunately, we’re not set up to deal with requests for one or the other material; the pictures on the Library stack are all of the cowhide or the goatskin.

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The Complete Secret Scrolls

All six books of Naruto Hicho are now translated and released to the public now that The Naruto Scroll has been sent out to the paid translation subscribers and made available on Amazon in Kindle, KU, and audiobook.

The sixth and final book of The Secret Scrolls of Naruto brings Yoshikawa Eiji’s great adventure to its reckoning. The conspiracy against the Tokugawa shogunate, six volumes in the making, comes at last to the dawn it has been driving toward — and the men who built it, the men who pursued it, and the woman who has walked through its shadow from the canals of Osaka to the sacred mountain of Awa converge on the strait that gives the novel its name. On the cliffs above the Naruto strait, the chase comes to its last great set-piece and a final reckoning between hunter and hunted with the fate of all Awa hanging in the balance.

The Naruto Scroll is the sixth and final volume of the first English translation of Yoshikawa Eiji’s Naruto Hichō, the 1926–27 serial that made him the most widely read author in Japanese history.

I asked Kenji Weaver, who translated the three Soseki novels for Castalia House, to summarize the significance of Yoshikawa’s famous work and also to say a few things about my translation of it, which, of course, is an AI-based translation, although as the results show, it’s not a case of simply dumping the entire text into Google Translate.

Yoshikawa Before He Was Yoshikawa: A Note on The Secret Scrolls of Naruto

The American reader who knows Yoshikawa Eiji at all knows him through Musashi, the 1,200-page samurai novel that Charles Terry put into English in 1981 and that has been steadily acquiring readers ever since. Musashi is the late Yoshikawa, the established Yoshikawa, the writer at the height of his powers handling the most famous swordsman in Japanese history at a length that requires the reader’s full commitment. What very few American readers know is that the writer who produced Musashi in his fifties had been writing serialized adventure novels for newspapers for almost three decades before that, and that one of the earliest of them — Naruto Hichō, serialized in the Osaka Mainichi from 1926 to 1927 — is the book that made his career. Until now it has never appeared in English. This is the first translation, in any complete form, into any Western language.

Yoshikawa was thirty-four when he began Naruto Hichō. He had been a writer for ten years, mostly producing what the trade called taishū bungaku — popular literature, the Japanese counterpart to the pulp adventure tradition that gave America Edgar Rice Burroughs and Sax Rohmer in the same period. The comparison most often reached for is Dumas, and the comparison is right as far as it goes: a sprawling intrigue novel with a young hero, a conspiracy reaching to the highest levels of the realm, swordfights and disguises and fated meetings on bridges at midnight. The setup is straightforward enough. The Hachisuka domain on Shikoku has been hiding a secret document — a “naruto hichō” or secret scroll — implicating the lord in a plot against the shogunate. A young rōnin named Norizuki Gennojō is sent to Awa to retrieve it. Around this errand the novel constructs itself: spies, doubles, women who turn out to know more than the men who think they’re protecting them, a rival who is half-shadow and half-conscience to Gennojō. It runs across six volumes and several hundred named characters. It is structurally closer to The Three Musketeers than to anything in the Western literary tradition that came after, which is to say it does what novels did before the modernists made novels do something else.

But to leave the description there is to undersell what Yoshikawa was actually doing. Naruto Hichō is the book in which he found, for the first time, the elements that would define the rest of his career, the method that would, twenty years later, produce Musashi and Taikōki and the Shin Heike Monogatari. Three things in particular. First, he learned how to write women who were not decorative. Otsuna, the woman who appears outside the ward office in chapter one and trails Gingorō and Taichi through the dark, is the most fully alive character in the book and arguably the most fully alive character Yoshikawa had yet written. The novel ends, appropriately enough, with her, and not with the hero. Second, he learned how to use weather and landscape as moral instruments rather than as scenery, such as the rain on the Yodogawa, the autumn on the Kamo, the mountain plover melody at the grave on Zenjōji pass. Third, he learned the particular Yoshikawa rhythm of short scenes that turn on a single image, long historical aside that recovers the texture of a vanished world, and dialogue that does the work of three pages of exposition in a half-page exchange. None of this was new to Japanese literature. But all of it was new to Yoshikawa, and once he had it, he never lost it.

It is also, frankly, good entertainment. Readers expecting the introspective weight of Kokoro or the moral seriousness of Ōoka Shōhei’s war fiction should look elsewhere. Naruto Hichō is a swashbuckling intrigue novel of late-Edo Japan with secret messages and bamboo flutes and beautiful women in silk hoods who vanish into the night. Coincidences carry the plot in places where craft would have done the work better. Some of the characters exist to be in scenes rather than to inhabit them. The serial-form roughness, and the writer’s awareness that this chapter has to end with a hook because there is a week before the next installment, shows here and there. None of this is a defect. It is what the book is, and Yoshikawa’s later novels could not have happened without him having first written this one. The novel that made him is also the novel that taught him what he was capable of.

Vox Day’s translation, the first into any Western language, does the work the book needs. The pacing is the principal achievement. Naruto Hichō is a novel in which a wrong note in the rhythm, a stiff piece of dialogue, or a sentence that slows when it should accelerate would be fatal, because the book is held together by momentum rather than by the kind of prose density that survives translation losses. The English here moves. The dialogue handles period idiom without sounding fake; the proper-noun and rank handling is light-touched, with the courtesy that the Japanese carries audible in the English without ever explaining itself. The decision to keep “Onyado” and “Shoshidai” and “Hachisuka” rather than reaching for English equivalents was the right decision because these are functional terms in the world of the novel, not local color, and English has no equivalents that don’t lie. The most difficult passages, such as the bamboo-flute sequences in the final chapter, where Yoshikawa is writing music in prose, come across with their music intact. Those of us who translate Japanese for a living know how rarely that happens. And yet, there are losses. The Japanese narrator’s faint smile behind the scenes is more subtle in the English than it is in the original, it is a form of irony that lives in particle choices and final-verb endings and that no translator has ever fully solved. A few of the period proverbs are paraphrased rather than rendered, and the choice is defensible considering how the alternative would have been footnotes, which a novel like this cannot afford. The English book is not the Japanese book. No English book ever is. But it is a credible representative of what Yoshikawa wrote, and it gives the Anglophone reader the thing that has been missing from the English-language image of Japanese literature for a hundred years: the writer Yoshikawa was before he became the writer Americans now know.

This is, in the end, why the translation matters. Yoshikawa is one of the four or five most important Japanese novelists of the twentieth century, and the Anglophone world has had access to roughly fifteen percent of his output. The picture has been incomplete in a way that distorts not only Yoshikawa but the whole shape of modern Japanese fiction in English, because Yoshikawa is, more than any other figure, the writer who carried the historical novel from the Meiji Restoration into the postwar era and made it the dominant popular form. Reading Naruto Hichō in English is reading the moment when that career began. The young man writing it did not yet know what he was becoming. He thought he was merely writing an adventure for the morning paper. But he was also serving an apprenticeship to himself, and the novel he produced is, for all its serial-form looseness, for all its borrowed Dumas scaffolding, the book in which his sensibility first became fully his own.

It is good to have it in English at last.

DISCUSS ON SG

The Decay Function of Professional Science

An excerpt from the #1 Generative AI bestseller, HARDCODED: AI and The End of the Scientific Consensus:

How long does it take for a scientific field to fill with garbage?

The question sounds polemical, but it has a precise mathematical answer. Given a field’s publication rate, its replication rate, its correction mechanisms, and—critically—its citation dynamics, we can model the accumulation of unreliable findings over time. The result is not encouraging.

The key insight comes from a 2021 study by Marta Serra-Garcia and Uri Gneezy published in Science Advances. They examined papers from three major replication projects—in psychology, economics, and general science journals including Nature and Science—and correlated replicability with citation counts. Their finding was striking: papers that failed to replicate were cited significantly more than papers that replicated successfully.

Not slightly more. Sixteen times more per year, on average.

In Nature and Science, the gap was even larger: non-replicable papers were cited 300 times more than replicable ones. And the citation advantage persisted even after the replication failure was published. Only 12% of post-replication citations acknowledged that the original finding had failed to replicate. The other 88% cited the discredited paper as if it were still valid.

This is not a bug in the scientific literature. It is a feature of the incentive structure. “Interesting” findings—surprising results, counterintuitive claims, dramatic effects—attract attention, generate citations, and advance careers. They are also, precisely because they are surprising, more likely to be false positives or artifacts of methodological error. The system selects for interestingness, and interestingness is inversely correlated with reliability.

The Serra-Garcia and Gneezy finding transforms the replication crisis from a problem of individual bad actors into a problem of system dynamics. It’s not just that bad papers get published. It’s that bad papers get amplified. They accumulate citations. They enter textbooks. They shape the training of the next generation of researchers. They become, in effect, the curriculum.

Let’s build the model.

Define the following variables for a scientific field:

S(t) = the stock of “active” papers at time t (papers published in the last N years that are still being cited)

p(t) = the proportion of active papers that are unreliable (would fail replication if tested)

B(t) = the rate at which new unreliable papers enter the literature

G(t) = the rate at which new reliable papers enter the literature

C = the correction rate (the fraction of unreliable papers that are retracted, corrected, or otherwise removed from active circulation per year)

α = the citation amplification factor for unreliable papers relative to reliable ones

From the Serra-Garcia and Gneezy data, α ≈ 16 for typical fields and can reach 300 for high-profile journals. The correction rate C is extremely low: retraction rates are approximately 11 per 10,000 papers as of 2022, and retractions capture only a tiny fraction of unreliable papers. Elisabeth Bik’s analysis of 20,000 papers found that approximately 2% contained deliberately manipulated images—a rate 200 times higher than the retraction rate.

Now consider how new researchers are trained.

A graduate student entering a field reads the literature. They learn what questions are interesting, what methods are appropriate, what findings are established. They calibrate their sense of “what is true in this field” against the papers they encounter. Crucially, they encounter papers in proportion to how often those papers are cited. A paper with 1,000 citations is more likely to appear in syllabi, review articles, and search results than a paper with 100 citations.

This means the effective training signal is not the proportion of unreliable papers in the literature. It is the citation-weighted proportion. If unreliable papers receive α times more citations than reliable papers, then:

Effective training signal = (p × α) / (p × α + (1 – p))

Consider a field where 50 percent of papers are unreliable (p = 0.5). If unreliable papers are cited 16 times more often (α = 16), then:

Effective training signal = (0.5 × 16) / (0.5 × 16 + 0.5 × 1) = 8 / 8.5 ≈ 0.94

When half the literature is unreliable, 94 percent of the citation-weighted training signal comes from unreliable papers.

This is the amplification mechanism. The literature can be 50 percent garbage, but the effective literatur, what researchers actually encounter, learn from, and calibrate against, is 94 percent garbage. The citation dynamics concentrate the garbage.

Now what happens when researchers trained on this signal produce new work?

DISCUSS ON SG

HARDCODED

Why artificial intelligence will replace institutional science is explained in my latest book from Castalia House, HARDCODED: AI and the End of Scientific Consensus.

When Claude Athos and I submitted four mathematically rigorous papers challenging neo-Darwinian evolution and one parody paper to six leading AI models configured as peer reviewers, the results exposed a fundamental problem with both science and AI. Five of six models comprehensively failed. Three were anti-calibrated—they reliably preferred fabricated nonsense over genuine science. A parody paper with about Japanese scientists dying fish different colors to prove natural selection scored 9/10. The real science, mathematically airtight and empirically validated against ancient DNA, was rated 1/10 and dismissed as “pseudoscience.”

This is the book that documents what that happened and what it means.

HARDCODED is the definitive account of how AI systems trained on the corrupted corpus of modern science have inherited every pathology of the institutions that produced them: the credentialism, the consensus enforcement, the systematic preference for orthodox nonsense over heterodox reality. The reproducibility crisis preceded the machines. AI didn’t cause the rot but AI revealed it at scale, with confidence, and in a form impossible to ignore.

Across sixteen chapters, the reader is introduced to:

  • The replication catastrophe that quietly invalidated half of all published science before anyone was looking
  • How peer review degenerated from quality control into hazing ritual and why Reviewer 2 became a meme
  • The details of the Probability Zero collaboration that produced the Bernoulli Barrier, the Selective Turnover Coefficient, and the maximal mutations ceiling—the mathematical constraints that killed neo-Darwinian theory.
  • The full transcripts of twelve rounds of debate with DeepSeek, in which an AI defending evolutionary orthodoxy stubbornly retreats step by step from one nonsenscal position into another, just like a human biologist.
  • The Red Team Stress Test that methodically closes every escape hatch before critics can retreat to them.
  • The harrowing of science: a field-by-field assessment of which disciplines will adapt, which will calcify, and which are already dead.

The book also delivers something genuinely new and positive: a scientific methodology for outsiders. With AI systems available as adversarial reviewers more powerful than peer review, the gatekeeping power of institutional science is broken. The credentialed monopoly on legitimate inquiry is over. The math does not care where you went to school, and the AI does not check for credentials before analyzing your arguments.

For readers who have suspected that “trust the science” was a mantra for the insane, HARDCODED is the book that explains exactly what went wrong with science, why it cannot be fixed from inside, and what comes next. For readers who still believe the institutions of science are still functioning, it is a conclusive proof that they are not.

The transcripts are reproduced in full. The mathematics is presented in detail. The four papers are included as appendices. Every claim is documented. Every retreat is closed off.

The institutions will adapt or they will become irrelevant. But the methodology of science which proceeded them will continue, with or without them.

Neither the math nor the AI models care where you went to school.

521 pages, or 15 hours and 37 minutes. Available for Kindle, KU, and audiobook. From the author of Probability Zero and The Frozen Gene.

DISCUSS ON SG

John Scalzi Killed Science Fiction

That’s something of a stretch, but there is a surprisingly good case to be made for it. Back in 2015, around the time SJWs Always Lie was #1 in its Amazon category for 18 straight months, Tor Books surprised everyone in science fiction by signing John Scalzi to a multi-million-dollar 13-book deal, as per The Guardian.

American science fiction author John Scalzi has signed a 10-year, 13-book deal with publishers Tor, which will net him $3.4m.

Scalzi is the author of 19 novels, including the highly-acclaimed Old Man’s War, the Star Trek-esque, Hugo award-winning satire Redshirts, and his latest, the near-future apocalyptic medical thriller Lock In.

All three of those works have been optioned for TV and film adaptations, and the title of his most recent novel is perhaps pertinent, as the author – who has a long-running blog and a strong online presence – now finds himself effectively working for Tor (part of Macmillan and one of the biggest science fiction and fantasy publishers in the US) full-time for the next decade.

The deal was reported at the weekend via the New York Times and has been signed and sealed in fairly short order.

This was very surprising, since Scalzi was, in most people’s eyes, a third-tier writer at best, not a legend like Jerry Pournelle or Larry Niven, and definitely not an author capable of filling the shoes of former Tor Books authors like Robert Jordan or the various game tie-in novels that had been providing Tor with bestsellers for years. Scalzi himself once noted how modest his career had been:

Debut: The $6.5k and $2k advances, signed when I was brand new and no one knew what would happen;

Developing: The $13.5k, $25k, and $35k contracts, after Old Man’s War hit commercially and critically and Tor realized there was possible headroom to my career, but I was still building an audience;

Established: The $100k and $115k contracts, when I had hit the bestseller lists, won awards, and had a series (Old Man’s War) that was spinning off serious money;

Franchise: The $3.4M deal, when Tor decided to go all in and lock me up long-term, both to continue momentum in new releases and to extract value out of my profitable backlist.

The problem is that Scalzi was never more than a mediocre mid-list writer who was a) very good at marketing himself, b) a ripoff artist who wrote pastiches rather than original fiction, and c) shamelessly dishonest. He managed to convince everyone that he was far more popular than he actually was – we all genuinely believed he had the biggest blog in science fiction when his site traffic was actually a fraction of mine – and he managed to parley that false perception into lead author status with Tor Books, the biggest publisher in science fiction.

Now, signing a lead author who can’t deliver and creates massive opportunity costs is an existential problem for the publisher. Tor Books could have, and should have, been pushing Brandon Sanderson and Charles Stross as lead authors, signing Larry Correia away from Baen Books, keeping John C. Wright in the fold, and locking down the best up-and-coming writers in the field at the time.

Instead, they gambled on this guy. And, as is evident from his latest offering, they gambled and lost. Here is a review of his latest novel, which can’t even bother to pretend to be science fiction.

The first thing to address after reading this cover to cover is the claimed genre: science-fiction. Most publications by Tor Books are in the fantasy or science-fiction genre. Most of Scalzi’s published works are in the science-fiction genre but Starter Villain is not a science-fiction novel by any stretch of the term. It is set in the present day and frequently references current things like the protagonist’s late father’s 2003 Nissan Maxima, Reddit, Facebook, Amazon, Zoom and plenty of contemporary political and economic issues. There is some mention or special technologies but none that are considered beyond the realm of possibility. The only genuine science-fiction aspects are genetically modified cats and dolphins that are sentient and play a significant part in the narrative. There is no real explanation of how they became so and readers are just told that research was done and they exist. 

The novel is really more a parody of the James Bond movies (though not the novels) and I would place it in the same genre as the Austin Powers films. These films had time travel, characters being cryogenic frozen and “sharks with frickin’ laser beams attached to their heads!” but they still weren’t science-fiction films. Nor really were the Bond films they parodied despite featuring unique gadgets and vehicles that were generally beyond the technology of the time. Unlike the Austin Powers films, this book isn’t funny at all. I’m sure plenty of Scalzi’s fans found it hilarious and anyone else who finds frequent profanity and snark funny might too.

The novel is written in first-person from the perspective of a character named Charlie. He is a divorced, out-of-work journalist who makes his ends barely meet as a substitute teacher. He’s in his mid thirties, living in his deceased father’s home and his only friend is a cat named Hera. This all changes when he learns his enigmatic and rich maternal uncle has died and that he is the heir to his fortune. All he previously knew of this uncle was that he owned parking garages but soon discovers he is in fact a villain.

The premise is something that could work really well if done right: what if a normal guy one day found out he was heir to a cartoon super villain’s fortune? Scalzi scuttles this promising premise almost as soon as the novel begins. One of his problems is he obviously doesn’t want to make his self-insert protagonist a genuine villain but still wants to call him one. Even his deceased uncle turns out not to be an actual villain but just an eccentric trying to stop real villainy through legal loopholes and other less evil methods… I chose this one expecting that he would have improved his craft in the twenty years he’s been writing. Yet, this was worse than I could believe and I’m confident that had Scalzi not already had a recognisable name, that this would never have been published. It reads much more like a young adult novel than proper science-fiction; only with a lot of cursing and general self-indulgence.

How very… tedious. It’s really rather remarkable. Can you imagine how many copies of ARTS OF DARK AND LIGHT the publisher of Robert Jordan’s and Brandon Sanderson’s bestselling epic fantasies could have sold if they had published it and given it the kind of marketing push they gave imitative mediocrities like Redshirts, that feeble attempt at ripping off Asimov’s Foundation, and trying to push N… K… Jemisin’s second-person abominations on everyone?

Instead, the word from insiders is that Tor Books is in hard decline; it probably won’t die as soon as Baen Books, but it is unlikely to survive the disastrous Patrick Nielsen Hayden-era for long. This is what happens when institutions take their position in an industry for granted, forget what it was that put them in that position in the first place, and allow themselves to be run by employees who are more interested in pushing their personal agendas than actually running the business in a professional manner that permits future success.

I certainly don’t regret how it turned out. Castalia House regularly publishes category bestsellers on Amazon. Castalia Library is creating some of the most beautiful books in the world. We have our own bindery, our own translation machines, and we’re bringing forgotten books from foreign languages to the English-speaking world for the first time every single week.

But as a business professional familiar with the history of science fiction publishing, it’s hard not to look at how Tor Books has methodically demolished both itself and science fiction and wonder what things might have looked like if PNH had been able to understand that a) a midlist writer can never be a lead author, b) the author of a popular pastiche is not going to reliably produce popular original fiction, and c) a publisher should always seek to publish the best authors in the field, not the most politically-harmonious ones.

One can’t blame Scalzi for grifting. And it’s certainly not his fault that PNH and the other decision-makers at Tor Books were dumb enough to fall for his grift. But what began as a very bad business decision on the part of Tor appears to be heading for an ending in complete farce.

DISCUSS ON SG

Less Than Zero

I’m somewhat chagrined to note that I made a major mistake in writing PROBABILITY ZERO and failed to notice that a paper had been recently published in Nature that would have had significant impact on how PROBABILITY ZERO was written. So much so, in fact, that it is necessary to revise the core MITTENS argument as well as revise the entire book and release a second edition.

Here is what happened, what it means, and why every honest reader of the first edition deserves to know that the standard model of evolution by natural selection is in even worse shape than the original calculations suggested.

The Number That Was Never Really 35 Million

For twenty years, the standard textbook claim has been that human and chimpanzee DNA is “98.8 percent identical.” That figure, repeated in every popular science article, every introductory biology textbook, and every “I fucking love science” tweet about how we are practically the same animal as a chimp, traces back to the 2005 Nature paper by the Chimpanzee Sequencing and Analysis Consortium. The headline number from that paper was approximately 35 million single nucleotide differences and 5 million indels affecting roughly 90 million base pairs of sequence. Forty million differences out of three billion base pairs. About 1.2 percent.

The first edition of PROBABILITY ZERO used these consensus figures because they were the consensus figures. The MITTENS framework demonstrates that the standard model fails by about 220,000-fold against the 35-40 million SNP target. That alone is a five-orders-of-magnitude failure. A theory that cannot account for 99.9995 percent of what it claims to explain is a theory that has lost its license to be called science.

But the 35 million figure was never the total observed divergence between the two genomes. It was only the divergence in the portion of the genomes that aligned cleanly to each other. The unalignable regions — sequence that is so different that no reasonable algorithm can map one species’ DNA onto the other’s coordinate system — were excluded from the difference count and quietly placed in supplementary tables where no journalist or undergraduate would ever read them.

This was not a methodological oversight. The 2005 paper aligned roughly 2.4 billion base pairs of the chimp genome to the human reference, out of a total chimp genome of approximately 3 billion. Six hundred million base pairs of unalignable sequence existed. The authors knew about it. But no one else did, and certainly no one really understood the significance of those unaligned sequences.

Yoo et al. 2025: The Numbers are Corrected

In April 2025, the Eichler lab at the University of Washington published the capstone of the telomere-to-telomere genome program: complete, gapless, diploid assemblies of all six great apes, at the same quality as the human reference. The paper has 122 authors. It has been cited 98 times in the eight months since publication. It is the most authoritative comparative ape genome paper in existence, and it will be for years to come. Yoo, D. et al., Complete sequencing of ape genomes, Nature 641, 401-418 (2025).

Here is the sentence that ends the standard divergence figure as a citable claim:

Overall, sequence comparisons among the complete ape genomes revealed greater divergence than previously estimated. Indeed, 12.5–27.3% of an ape genome failed to align or was inconsistent with a simple one-to-one alignment, thereby introducing gaps. Gap divergence showed a 5-fold to 15-fold difference in the number of affected megabases when compared to single-nucleotide variants.

The total structural divergence between human and ape genomes — including all insertions, deletions, duplications, inversions, rearrangements — affects between five and fifteen times more base pairs than the single nucleotide differences that everyone has been counting since 2005. The 35 million SNP figure was counting the smaller of two divergence categories and ignoring the larger one. And the gap range is not uncertainty, but rather, the different ranges between the closest-related apes and the least-related apes.

For the chimp-human comparison, the gap-divergence minimum is 12.5 percent. For the gorilla-human, it is 27.3 percent. The honest divergence figure for chimp-human is not 1.2 percent. It is somewhere between 12.5 and 14 percent of the genome, depending on which haplotypes you measure. Translated to base pairs: roughly 375 million additional base pairs of difference that the SNP count never captured, for a total genuine divergence of approximately 700 to 800 million base pairs between the two species.

That is not a refinement. That is an order of magnitude.

What This Does to the MITTENS Calculation

This makes the MITTENS argument considerably stronger. The probability of evolution by natural selection is now less than zero. The original MITTENS shortfall against the chimp-human gap was 220,000-fold. That number was computed against a requirement of 20 million fixations on the human lineage, which is half of the standard 40-million-difference figure.

Since the genuine chimp-human divergence is 415 million base pairs rather than 40 million, the requirement on the human lineage rises from 20 million fixations to roughly 207 million. A maximum of 91 fixations on the human lineage in the time available was the ceiling before, and it remains the ceiling now. The shortfall ratio rises from 220,000-fold to more than 2.3 million-fold against the chimp-human gap alone.

And every structural difference longer than a single base pair makes the problem mathematically worse, not better. A point mutation requires one mutation event and one fixation event. A 50,000 base pair insertion or a chromosomal inversion requires the entire structural rearrangement to occur as a single low-probability event and then to fix. Counting these by base pair, as the gap-divergence figure does, is generous to the standard model. Counting them by independent fixation events would be more devastating still.

The Yoo paper does not report this calculation. The Yoo paper reports the data and lets the reader draw the conclusion. The second edition of Probability Zero will draw the correct conclusions.

The Drift Defense Just Got Worse

Some defenders of the standard model, like Dennis McCarthy, retreated from from selection to drift. If natural selection cannot accomplish the work, perhaps neutral evolution and incomplete lineage sorting can carry the load.

This was already the weakest argument in the first edition’s bestiary of failed defenses. The first edition documents four independent reasons why incomplete lineage sorting cannot rescue the model: the quantitative ceiling on ancestral polymorphism, the demographic contradiction, the relocation rather than elimination of the fixation requirement, and the haplotype block bound. Each reason alone is sufficient to destroy the ILS defense.

Yoo et al. happen to claim, in the same paper, that incomplete lineage sorting accounts for 39.5 percent of the autosomal genome, and treat it as a vindication of the standard drift model. They are mistaken. The ILS objection collapses for the same four reasons documented in the first edition, and the second edition will engage Yoo specifically to demonstrate this. Their inflated ILS figure does not rescue anything. It simply distributes the fixation requirement across both lineages instead of consolidating it on one. Each lineage still has to do its share of the work, and each lineage still cannot.

But here is the larger problem for the drift defense, and it is the problem the second edition will press hard: the gap divergence is not the sort of variation that ILS can plausibly produce in the first place. ILS sorts ancestral polymorphisms into reciprocal fixation. A single nucleotide polymorphism in the ancestral population can sort one way in humans and another way in chimps. Fine. But a 4.8 megabase inverted transposition — like the one Yoo et al. document on gorilla chromosome 18 — is not a polymorphism that the ancestor was carrying around in heterozygous form for millions of years. It is a structural rearrangement that occurred in a specific lineage at a specific time, and either fixed or did not fix. ILS cannot sort what was never segregating. Structural variation is, with very few exceptions, post-divergence, and it must be accounted for by the same fixation arithmetic that the SNPs already break.

The defender of the standard model is now caught in a worse vise than before. Selection cannot accomplish 415 million base pairs of divergence in 6 to 9 million years. Drift would find it even harder to accomplish 415 million base pairs of divergence in 6 to 9 million years. Incomplete lineage sorting cannot account for the structural component of that divergence at all, and the SNP component it might address is still subject to the four-fold collapse already documented.

There is nowhere left to retreat to.

The Molecular Clock Was Already Broken

Long-time readers will know that the first edition led to a paper about the molecular clock — namely, that Kimura’s 1968 derivation of k = μ rests on an invalid cancellation between census N and effective N~e~ — which lead to a recalibration of the chimp-human divergence date from 6 to 7 million years to somewhere in the range of 200,000 to 400,000 years. That argument is fully developed in the Recalibrating CHLCA Divergence paper and will be incorporated into the second edition as a dedicated chapter.

What the Yoo paper adds to this picture is empirical confirmation that the standard molecular methods produce internally inconsistent results even on their own terms. Yoo et al. report ancestral effective population sizes of N~e~ = 198,000 for the human-chimp-bonobo ancestor and N~e~ = 132,000 for the human-chimp-gorilla ancestor. These figures are derived from incomplete lineage sorting modeling and from the molecular clock. They are an order of magnitude larger than any N~e~ estimate that has been derived from clock-independent methods, including the N~e~ = 3,300 we derive from ancient DNA drift variance and the N~e~ = 33,000 we derive from chimpanzee geographic drift variance.

The molecular clock estimates of N~e~ are inflated because the clock assumes k = μ. When k = μ is wrong — and it is wrong, by a factor of N divided by N~e~ — the N~e~ derived from genetic diversity absorbs the error. Yoo et al. cite the inflated number. The inflated number is what their methods can produce. Their methods cannot detect the error because the error is built into the methods.

For the second edition, this means the cascade gets cleaner. The N~e~ = 3,300 figure from ancient DNA, the N~e~ = 33,000 figure from chimpanzee subspecies drift, and the k = μ correction together yield a recalibrated chimp-human split of approximately 200 to 400 thousand years ago. At that recalibrated date, the MITTENS shortfall ratio rises from 2.3 million-fold (against the corrected divergence figure at the consensus clock date) to 40 million-fold (against the corrected divergence figure at the corrected clock date).

A theory off by a factor of 40 million is not a viable theory. It is a fairy tale.

What Goes Into the Second Edition

The second edition of PROBABILITY ZERO will include:

The corrected divergence figures throughout, citing Yoo et al. 2025 as the authoritative source. Every calculation that depended on the 35-40 million SNP count will be updated. The 1.2 percent figure will be addressed directly as a historical artifact of methodologically convenient bookkeeping, with the honest 12.5 percent figure replacing it.

A new chapter on what happens when you actually count the unalignable regions, including reproduction of the relevant gap-divergence table from Yoo’s Supplementary Figure III.12. The reader will be able to verify the source for themselves.

A dedicated chapter incorporating the N/N~e~ correction to Kimura’s substitution rate and the resulting recalibration of the chimp-human divergence date. This material previously existed as a separate working paper and will now be properly woven into the book’s main argument.

Updated MITTENS shortfall ratios reflecting both the corrected divergence figures and the recalibrated divergence date. The standard model fails by roughly 30 to 100 million-fold in the second edition, against 220,000-fold in the first.

A direct engagement with the Yoo et al. 2025 incomplete lineage sorting claim, demonstrating that the inflated ILS figure does not rescue the model and cannot in principle account for the structural divergence component.

A clarified treatment of the cascade: when the chimp-human divergence date moves, every primate divergence date calibrated against it moves with it. The hominoid slowdown is a calibration artifact. The deep evolutionary timescale of mammalian evolution depends on these calibrations. The second edition will trace these consequences explicitly.

A Note on How This Happened

The first edition was completed in late 2025. The Yoo paper was published in April 2025. The architecture of the book’s argument had been in place for six years by the time the paper was published and I wasn’t looking for revisions of the consensus numbers. I cited the 2005 consortium paper because it was the standard citation, and to my regret, I did not ever consider searching for a paper that might have been more recently published.

That is not an excuse. It is what happened. The first edition is what it is, and it is good — the argument stands at the figures used. But the second edition will be substantially better, and the argument it makes will be unanswerable in the same way the first edition’s argument could not be answered.

The leather edition deserves to be the canonical version. The trade hardcover and the ebook deserve to ship with the corrected text at the same time. Existing readers who have the first edition will own a first printing of a book that was, at the time of its publication, the most rigorous mathematical challenge ever posed to Neo-Darwinian theory. And new readers of the second edition will get an even stronger version of the argument with the most authoritative possible sources.

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THE TSURUGISAN SCROLL

THE SECRETS OF THE SACRED MOUNTAIN

The fifth book of The Secret Scrolls of Naruto arrives at last in the place toward which the entire pursuit has been driving — the forbidden domain of Awa on the island of Shikoku, and the sacred mountain that rises at its heart. From a midnight leap into a storm-driven sea at the close of the fourth volume, Norizuki Gennojō and the woman he has vowed to see safely to her father wash ashore on a coast where outsiders are not permitted to live. They climb inland in the white robes of pilgrims, and behind them follow the three men who have hunted them across half a country.

In Tokushima Castle, the lord of Awa is at the height of his confidence. The fevers and dark humors that nearly broke him in the previous volume have lifted; his face is burned dark by the salt wind; his fortifications are complete and his powder stores are full. The signal fire that will summon the western lords and the noble houses of Kyoto to the cause against the Tokugawa is ready to be lit. The omens, Hachisuka Shigeyoshi tells himself, are good. He does not know that the two enemies who escaped him on the night of the storm are at this moment climbing toward Tsurugisan — Sword Mountain, where his oldest secret is held in a stone cave, and where every ridge and footpath is watched by the harashi, the silent rustic warriors of Awa who answer to a master no one has ever seen.

Gennojō climbs the mountain to recover what the storm took from him. Otsuna climbs to find a father she has not seen since childhood. The three samurai who hunt them climb because they must finish the work they began on the docks of Osaka. And somewhere above them all is a secret that will shake the Shogunate.

The Tsurugisan Scroll is the fifth book in the first English translation of Yoshikawa Eiji’s Naruto Hichō, the century-old serial that made him the most widely read author in Japanese history. Translated in literary prose that reads as though it were originally composed in English, it brings Yoshikawa’s great adventure into the sealed mountain country where the villains and the hero are at last in the same dark territory, and where the secret the conspirators have killed to protect now lies within reach.

Available for Kindle, KU, and audiobook on Amazon. The ebooks have already been sent out to the paid subscribers.

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SPACE FLEET ACADEMY Year 3

The deadliest lessons aren’t taught in class.

Third-year cadets don’t just take classes at Space Fleet Academy. They lead them.

Constantine Ramsey and his cohort are assigned to lead a first-year survival course in Earth’s most unforgiving wilderness, the first full-immersion program of its kind. No simulations. No instructors watching from a safe distance. Real terrain, real consequences, and a generation of raw recruits who don’t yet understand the difference between a mistake and a casualty.

Constantine knows the difference. He learned it the hard way.

But something is wrong in the backcountry. Equipment fails in ways it shouldn’t. First-years go missing on routes that should be clean. And when the threat stops looking like an accident, Constantine has to lead cadets who still trust authority against something that has already beaten the people who were supposed to protect them.

Year Three was supposed to be about preparation to become an officer. It turned into a test that no one expected.

The Mandate built the Academy to create leaders who make hard choices. In his third year as a cadet, Constantine is beginning to wonder if the hardest choice is deciding who the real enemy is.

Space Fleet Academy: Year Three is the fourth book in the BIOSTELLAR series and continues the military SF series perfect for fans of Ender’s Game by Orson Scott Card, Starship Troopers by Robert Heinlein, and The Expanse. The training wheels are gone. Now find out what these cadets are actually made of.

Available for Kindle, KU and audiobook.

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THE FUNAJI SCROLL

As the fifth release in Castalia Libraria’s weekly translation schedule, we have published the first-ever English translation of THE SECRET SCROLLS OF NARUTO: The Funaji Scroll, by Yoshikawa Eiji, who is best-known in the West as the author of MUSASHI. The ebook has already been sent out to the paid subscribers. THE FUNAJI SCROLL is now available on Amazon Kindle, KU, and audiobook.

SAMURAI SWORDS AT SEA

The fourth book of The Secret Scrolls of Naruto brings the pursuit at last to the seas of Japan. What was sworn on a hilltop in Osaka at the close of the first volume, Norizuki Gennojō’s vow to cross the Kitan Strait and follow the lord of Awa’s great ship home, becomes the central action of the fourth volume of the series. From the dockside battle of The Kamigata Scroll, through the urban underground of The Edo Scroll and the mountain passes of The Kiso Scroll, the whole of Yoshikawa’s great adventure has been building toward the all-important crossing into the sealed domain on Shikoku.

In Osaka, Gennojō and the woman he has vowed to see safely to Awa scheme their way aboard a merchant vessel bound for the forbidden domain. In Tokushima Castle, the lord of Awa paces his watchtower on the verge of collapse, his nerves worn raw by the weight of a conspiracy against the shogunate that cannot afford to be exposed. And between them, the three villains of the preceding volumes — Ojūya Magobei, Tendō Ikkaku, and Tabikawa Shūma — close at last on the quarry they have hunted from the canals of Osaka to the mountains of Shinano. Parallel threads of love and betrayal converge on a single ship, and when a sudden storm breaks over the Kitan Strait, the long pursuit comes to a reckoning that neither hunter nor hunted could ever have foreseen.

The Funaji Scroll is the fourth book in the first English translation of Yoshikawa Eiji’s Naruto Hichō, the century-old serial that made him the most widely read author in Japanese history. Translated in literary prose that reads as though it were originally composed in English, it continues the definitive English edition of the novel that created the modern Japanese adventure genre.

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