It was observed ages ago that Yud completely whiffed Mendelian genetics. Here’s the explanation in the su3su2u1 review, to refresh:

The other model Hariezer lays out is that magic lies on a single recessive gene. He reasons squibs have one dominant, non-magical version, and one recessive magical version of the gene. So of kids born to squibs, 1/4 will be wizards. In this version, you either have magic or you don’t, so if wizards married the non-magical, wizards themselves could become more rare, but the power of wizards won’t be diluted. […] Squibs are, by definition, the non-wizard children of wizard parents. Hariezer’s model 2 predicts that squibs cannot exist. It is already empirically disproven.

Hariezer, of course, does not notice this massive problem with his favored model, and Draco’s collected genealogy suggests about 6 out of 28 squib born children were wizards, so he declares model 2 wins the test.

Which goes to show that you shouldn’t try to learn science from HPMOR: the facts are bad, and the reasoning is bad. It doesn’t matter pedagogically whether it’s the author’s mistake or the character’s. And, really, having an 11-year-old boy who has done nothing but read books be the conduit for explanations of science is just a bad structural choice, for the same reason that you don’t see textbooks with unreliable narrators.

Yud is still throwing words at this:

the genetically literate mind informed by canon will now inquire how two Wizard phenotypes ever yield a Squib phenotype when Wizards are Magical-Magical homozygous.

Ooh, do tell.

The answer is not fully given in HPMOR proper

Ooh, do fuck off. You don’t get points for the story you didn’t write. And adding lore after the fact doesn’t change that your characters made the wrong decision from the information they had available at the time.

There is not a Magical gene complex that creates magic, but a Mundanity gene complex that suppresses it. After all, from pure physics we can never get to magic, but in an innately magical universe somebody could cast a spell to create the local appearance of mostly physics.

This is weird and arbitrary. Plenty of science-fiction stories have magic (or that which is effectively magic) operating by unknown-to-us physics. For example, the Laundry Files books are full of sigils and geases and summonings, and they explicitly say that the physicists are right, in the domain they’ve studied.

Similarly if all beings start out mundane then no gene complex can possibly create magic in them, but if all beings start out magical some gene complex could suppress their magic. Squibs and ultimately Muggleborns then arise naturally from a population of Muggle phenotypes as mutations damage the Mundanity gene complex, and in turn Wizard phenotypes sometimes yield Squibs as the Mundanity gene complex sometimes repairs itself by chromosomal crossover, with the phenomenon being more commonly observed in wizarding families with recent Muggle ancestry, to the alarm of genetics-illiterate purebloods.

From the Mendelian pattern implying the Mundanity gene complex is all on one chromosome, the gene complex can be inferred to be artificial in nature.

For Yudkowsky, operons must be evidence of Intelligent Design.