Once more unto the breach

I’m preparing to teach genetics again, and as usual, I’m trying to rework some of the lectures, because I don’t care to say the same thing every year. I had one odd thought that I’m probably not going to squeeze into the lectures this year, but thought I’d bounce it off people here.

Evolution and genetics were on parallel tracks in this very interesting period of 1860-1910. While the American Civil War and the Franco-Prussian War and the Boer War might have been distracting most people, biologists had their own obsessions. Charles Darwin published in 1859; Gregor Mendel in 1863. Darwin had immediate popular success, while Mendel was basically ignored and neglected. I was contemplating why the difference was there, and had a random idea.

Darwin started with a phenomenological and largely descriptive foundation, no significant math anywhere in The Origin. Mendel’s brief paper was little more than a mathematical hypothesis, with limited qualitative description — it was just peas, one model system, and the traits weren’t even particularly interesting, except for the fact that their inheritance was so discrete.

Evolution took off fast, and rather erratically. There were so many bad hypotheses built on the framework of natural selection (for instance, all of Haeckel’s work) that by the end of the 19th century, Darwinism (and in this case, that was an appropriate name for it) was fading, and people were finding flaws and poking holes in the idea. The absence of a quantitative basis for analysis was killing evolutionary theory.

Meanwhile, Mendel’s laws of inheritance weren’t getting any attention, but there was all this foundational qualitative work getting done — cell theory was being established, microscopy was taking off (instruments were reaching the physical limits of optics), Weismann had worked out the limitations of cellular inheritance, Sutton and others were publishing all this tantalizing stuff about chromosomes. When 1900 rolled around and Mendel was rediscovered, everyone was primed for his statistical/probabilistic theory of inheritance. We could do math on it!

Also, evolution was rescued by it’s happy marriage to genetics and in particular, population genetics. We could do math on evolution, too!

Everything is better with mathematics, is my conclusion. Except maybe individual success — before 1900, someone could come up with a hot theory and get it named after themselves. Afterwards, there’s too much detailed quantitative thinking going on for any one person, and eponymous theories went out of style, being regarded with suspicion, even.

Along comes SMBC to correct me:

OK, OK, it’s not just mathematics, it’s thinking precisely. But isn’t that what math is? How do you think precisely without the application of math and statistics and quantitative reasoning?

We’re home at last!

We’re back from our excursion to Madison — a day driving there, two days with Iliana, and a day driving back, but totally worth it. You may recall that I mention the distinct change at the border with Wisconsin (“adult novelty stores, billboards for cheese, and roadkill as far as the eye can see”), but we also saw something in common: so many “Pro Life Across America” billboard spread across both Minnesota and Wisconsin. They’ve gotten more condensed over the years, at least. Nowadays they’re just a photo of a cute, plump 6-month old babies with the words Heartbeat 18 Days. That’s all. Not even grammatical. We’re just supposed to leap to the conclusion they want.

I have a much more interesting statement: Poop 19 Seconds.

That’s from Bethany Brookshire’s Insomniac Academy of brief YouTube shorts with fascinating facts about anatomy. Check it out!

I reaffirm my support for the Freedom From Religion Foundation

Now, both Jerry Coyne and Steven Pinker have announced their resignation from the honorary board at the FFRF. Good. They were a terrible influence, and their departure strengthens the FFRF as a defender of reason.

Their latest post on their website declares Freedom From Religion Foundation supports LGBTQIA-plus rights. They admit that they erred in permitting someone (Coyne, of course) to publish an article in their newsletter that was ignorantly prejudicial against transgender individuals.

However, advocacy is rarely perfect, and progress is not always linear. Recently, we published a guest blog post as part of an effort to provide a forum for various voices within the framework of our mission. Although we included a disclaimer that the viewpoints expressed within the post were not necessarily reflective of the organization, it has wrongfully been perceived as such.
Despite our best efforts to champion reason and equality, we recognize mistakes can happen, and this incident is a reminder of the importance of constant reflection and growth. Publishing this post was an error of judgment, and we have decided to remove it as it does not reflect our values or principles. We regret any distress caused by this post and are committed to ensuring it doesn’t happen again.
Moving forward, we are reviewing our content guidelines and internal processes to ensure our public messaging consistently reflects our values. We are committed to learning from this experience.
We stand firmly with the LGBTQIA-plus community and their allies in advocating for equality, dignity and the freedom to live without fear of religiously motivated discrimination. Our mission to keep religion out of government is inextricably linked to preserving and advancing these fundamental rights.
Together, we will continue to champion a society where all people — no matter their sexual orientation, gender identity, beliefs or nonbeliefs — are treated equally under the law.

That article is currently flooded with comments criticizing the FFRF — many of them seem to be coming from the horde of haters at Coyne’s blog. The gist of many of their comments seems to be that the FFRF is the transphobic one, which is ludicrous and little more than a childish playground taunt. I think we can ignore that nonsense.

Some of them are claiming that Coyne’s claim that sex is totally binary is scientific, and that it is unscientific to argue for a more complex continuum of traits. This is also nonsense. Don’t argue with me, though, take it up with the Society for the Study of Evolution’s position on transgender identity from back in 2018.

We, the Council of the Society for the Study of Evolution, strongly oppose attempts by the Department of Health and Human Services (HHS) to claim that there is a biological basis to defining gender as a strictly binary trait (male/female) determined by genitalia at birth. Variation in biological sex and in gendered expression has been well documented in many species, including humans, through hundreds of scientific articles. Such variation is observed at both the genetic level and at the individual level (including hormone levels, secondary sexual characteristics, as well as genital morphology). Moreover, models predict that variation should exist within the categories that HHS proposes as “male” and “female”, indicating that sex should be more accurately viewed as a continuum.* Indeed, experiments in other organisms have confirmed that variation in traits associated with sex is more extensive than for many other traits. Beyond the false claim that science backs up a simple binary definition of sex or gender, the lived experience of people clearly demonstrates that the genitalia one is born with do not define one’s identity. Diversity is a hallmark of biological species, including humans. As a Society, we welcome this diversity and commit to serving and protecting members regardless of their biological sex, gender identity or expression, or sexual orientation.

*Here we are speaking of the multi-dimensional aspects that underlie male-ness and female-ness, including hormones, physiology, morphology, development, and genetic aspects. We acknowledge that many of these aspects are bimodal. Furthermore, some of these aspects are discrete categories (e.g., XX/XY, SRY presence/absence, gamete size, sperm production vs egg production, presence/absence of certain genitalia), but these categories don’t always align within individuals, are not always binary, and should be irrelevant to the determination of a person’s legal rights and freedoms.

There’s a second letter there, too.

As scientists, we write to express our concerns about the attempt by the Department of Health and Human Services (HHS) to claim that there is a biological basis to defining gender as a strictly binary trait (male/female) determined by genitalia at birth.

Variation in biological sex and in gendered expression has been well documented in many species, including humans, through hundreds of scientific articles. Such variation is observed at both the genetic level and at the individual level (including hormone levels, secondary sexual characteristics, as well as genital morphology). Moreover, models predict that variation should exist within the categories that HHS proposes as “male” and “female”, indicating that sex should be more accurately viewed as a continuum. Indeed, experiments in other organisms have confirmed that variation in traits associated with sex is more extensive than for many other traits. Beyond the incorrect claim that science backs up a simple binary definition of sex or gender, the lived experience of people clearly demonstrates that the genitalia one is born with do not define one’s identity.

Diversity is a hallmark of biological species, including humans. Our three scientific societies represent over 3000 scientists, many of whom are experts on the variability that is found in sexual expression throughout the plant and animal kingdoms. If you wish to speak to one of our experts or receive peer-reviewed papers that explain why there is a continuum of sexual expression, please contact us at president@evolutionsociety.org.

Sincerely,

Dr. Hopi Hoekstra
President, Society for the Study of Evolution
Professor, Harvard University

Dr. Sharon Strauss
President, American Society of Naturalists
Professor, University of California, Davis

Dr. Susana Magallón
President, Society of Systematic Biologists
Professor, Universidad Nacional Autónoma de México

Hmmm. Hoekstra has published with Coyne in the past, so maybe that will have some weight with him.

I look forward to Coyne’s resignation from the SSE, as well. Or maybe he’s waiting and hoping for a purge of all those woke scientists from the Society? He might get his wish, given the ascendancy of the ideology he favors in our government.

Breaking news: Richard Dawkins has also resigned from the FFRF! And there was much rejoicing!

You think spider sex is crazy?

I beg to differ about spider sex — it’s perfectly normally weird, but then I have been spending a fair amount of time trying to encourage spiders to have sex. Mainly what I’m concerned about is that it’s too infrequent, and they seem to have seasonal depression. But OK, it is interesting, as this video demonstrates.

You know what’s kinky, though? The video mentions that “some flies have a female who penetrates the male to collect sperm”. Not spiders, but barklice (Neotrogla), which aren’t flies and aren’t lice, but a kind of true bug, have completely reversed sex roles.

The female has a penis-like protrusion called a gynosome, which is erectile and curved. The male has no such organ; he has an internal chamber instead. When she penetrates him during sex, he delivers sperm into a duct in her gynosome, which leads to a storage organ. He still ejaculates, but he does so inside his own body, not hers.

Neotrogla sex can last for days, so it’s important for the duo to stabilise themselves. The female does it by inflating the base of her gynosome inside the male. It’s covered in patches of tiny spines, which help to anchor her in place for her sexual marathon. You can find similar spines on the penises of many male animals where they provide extra stimulation during sex (as in cats, mice and chimps) or inflict horrendous wounds on the females (as in the seed beetle).

In Neotrogla, the spines are such good anchors that it’s impossible to separate a mating pair without killing the male. As Yoshizawa writes, “Pulling apart coupled specimens (N. curvata; n = 1) led to separation of the male abdomen from the thorax without breaking the genital coupling.” In other words: We tried yanking one pair apart; it didn’t work and the male kinda broke.

See? Spiders are perfectly ordinary, mundane, familiar little creatures. No pegging involved.

It’s a wrap

Portrait of the Fall 2024 semester

The grades for all of my classes, Fundamentals of Genetics, Evolution, and Development, and History of Evolutionary Thought, and Cell Biology lab, and Biological Communication II, have been submitted. I am done. This was not my favorite semester of the 50-some semesters I’ve taught here.

Now I’m getting ready for spring semester — or rather, I have been getting ready. I set up fly stocks way back in early November, I have to do one more generation, and then I set up all the flies for our first lab. Bonus: next semester, I have no classes on Fridays. Three day weekends every week! That might make up for all the grading I’ll have to do in the writing class I’ll be teaching.

The journal Intelligence really needs to change its name

That’s a journal I would never trust — after all, they were responsible for publishing Richard Lynn’s hacky paper on the IQ of nations. Now here’s another example of a terrible racist paper from it. It’s an evolutionary psychology paper by Kanazawa, a terrible combination that ought not to ever pass peer review.

On the basis of his theory of the evolution of intelligence (Kanazawa, 2004), Kanazawa (2008) proposed that, during their evolutionary travels away from the relatively stable and hence predictable environment of evolutionary adaptedness (EEA; i.e., the African savanna of the late Pleistocene), the ancestors of Eurasians encountered evolutionarily novel environments that selected for higher intelligence. Therefore, Kanazawa (2008) predicted higher average IQ scores in countries located farther away from the EEA. Kanazawa (2008) tested this hypothesis against data gathered by Lynn and Vanhanen (2006), who estimated so-called “national IQ-scores,” i.e., the average IQ of the inhabitants of nations in terms of western norms. Kanazawa (2008) found a significant negative correlation between countries’ national IQs and their distance from three geographic locations in and around sub-Saharan Africa.

This is from a paper analyzing the problems of peer review, using Kanazawa’s paper as a case study. That evo-psych paper flew through peer review, with reviewers missing a number of deep problems.

We point to a number of indisputable issues that should have precluded publication of the paper as constituted at the time of review. First, Kanazawa’s (2008) computations of geographic distance used Pythagoras’ theorem and so the paper assumed that the earth is flat (Gelade, 2008). Second, these computations imply that ancestors of indigenous populations of, say, South America traveled direct routes across the Atlantic rather than via Eurasia and the Bering Strait. This assumption contradicts the received view on evolutionary population genetics and the main theme of the book (Oppenheimer, 2004) that was cited by Kanazawa (2008) in support of the Out-of-Africa theory. Third, the study is based on the assumption that the IQ of current-day Australians, North Americans, and South Americans is representative of that of the genetically unrelated indigenous populations that inhabited these continents 10,000 years ago (Wicherts et al., 2010b). In related work by others who share Kanazawa’s (2008) views on the nature of race differences in IQ, the latter issue was dealt with by excluding countries with predominantly non-indigenous populations (Templer and Arikawa, 2006). Thus, although Wicherts et al. (2010b) raised additional issues that may the topic of debate (see below), these three problems are beyond dispute.

I am amused that Kanazawa’s methodology assumed that the Earth is flat and that all peoples ignored geographical obstacles, like mountains and oceans, to make a beeline to their modern location. I am horrified that anyone would use Lynn’s deeply racist and wrong paper to make any estimates of a population’s intelligence. I reject the whole notion of IQ as a useful measure of intelligence in the first place.

The authors propose some changes towards a more open peer review process, which sound good to me. My simpler solution is to simply throw out the whole goddamn journal of Intelligence, along with anyone who publishes in it.

Speaking of flat earth follies, I see that YouTube is in a tizzy because someone is doing something called “The Final Experiment” — a group of people are flying to Antarctica to witness the fact that there is a period where the sun never sets, which ought to be impossible if Antarctica is actually a ring of land surrounding the whole planet. It’s ridiculous. No, flat earthers will find a new excuse and will not be persuaded by a “final” experiment — it’s not as if they reached their beliefs by experiment and reason in the first place, or as if all the other evidence that the earth is roughly spherical were insufficient.

Can you imagine someone proposing a “final experiment” to “prove” that life on earth evolved? I can’t. I know the idiots who are creationists far too well to think that.

Sexual dimorphism — it’s scary

This is a female Latrodectus mactans.

This is a male Latrodectus mactans.

I brought them together this morning. The female is plump and mature. The male has large, engorged palps. This is what they look like together.

They did not mate today, although the male spent a lot of time scurrying around and tentatively plucking at the web. At least she didn’t eat him. I put a video of the anxious, fruitless male on my Patreon.

I left them to honeymoon overnight. I’ll check on them tomorrow.

Reading the Daily Mail is not how to do research

Potholer54 has a new video, in which he explains the error of all those people who say “do your own research,” a phrase so heavily abused by conspiracy theorists and cranks that it has lost much of its meaning. To me, “do your own research” means digging heavily into the background science and reading the journals; to them, it seems to mean finding a Daily Mail headline that fits their preconceptions and running with it.

It’s like he’s talking about me, a little bit. When I got into arachnology 6 or 7 years ago, I was a near total n00b — I could apply what I knew about developmental biology and evolution to them, but I couldn’t just catch a spider in my garage and claim to now be an expert on spiders. I have read so many books and papers on them, in addition to continuing to chase spiders all over the countryside, but I feel like I’ve just scratched the surface. I think real scientists have to approach any field with a sense of humility, even if they’ve been working on it for decades.

What really amused me, though, what that this was the latest comment on the video, at the very top of the page.

too bad everyone has randomly decided that human minds aren’t subject to evolution. there might be an answer in evolutionary psychology as to why an animal with nothing but sapience to defend itself has to decide it knows what it’s doing pretty early on in a novel situation if it wants to survive… but of course we all know that’s bunk, right? humans didn’t evolve. we’re special snowflakes. god’s dandruff

What a lovely example of a bad scientific argument! I’m pretty sure that potholer54 understands that humans, and human brains, are the product of evolution, and sarcastically suggesting that he has overlooked an explanation that every right-thinking evolutionary psychologist has deduced is a serious error of comprehension. It is a classic example of evo-psych argumentation, though — I have been told many times that because I find evo-psych to be facile, superficial, and a swamp of bogus reasoning that I must be a creationist.

To be fair, though, not all the people who were offended by the video are incapable of following a simple train of thought. For example, this person at least got the gist of what was said:

Does insulting the “do your own research” group have a positive effect on anyone?
What’s the purpose of this video? Genuine question.

Yes, it was a criticism of the “do your own research” group. Very good! Sirtra understood something.

It was not about insulting them, though. It was explaining that they don’t know what they’re talking about, that they’re pursuing information in a wrong and misleading way, and that maybe “doing your own research” ought to involve cracking open an introductory textbook and actually studying the basics of the topic first, and understanding how the authorities in a field derive their conclusions. The purpose is to explain how to do research properly.

Like how zEropoint68 could benefit from knowing the basics of evolutionary biology before explaining tendentiously what evolutionary biologists believe about the human brain.

Here we go again

Are you ready for another pandemic?

No, you are not. And this one has the potential to be worse than COVID.

Cases of H5N1, the bird flu, are on the rise. Bird flu is bad — the cases are limited right now, because most of the transmission is from birds/cows to humans, and not human to human, and most of us don’t cuddle chickens that often. Please don’t start.

We’re definitely not at the point where we should panic and shut everything down, but we are at the point where we should be preparing, building up stockpiles of vaccines, and developing new vaccines (there is no commercially available RNA vaccine for bird flu yet). If the virus mutates, as viruses are wont to do, a variant could spread with stunning speed.

But don’t count on those vaccines saving us if this virus does what flu viruses sometimes do, and turns into a pandemic form. It won’t oblige humanity by slowly mutating, giving people a chance to ramp up vaccines quickly.

“It is going to happen fast,” says Ali Khan, dean of the University of Nebraska Medical Center College of Public Health and a veteran of numerous disease outbreaks, from influenza to Ebola.

The world just saw this happen. COVID appeared suddenly and spread globally before alarm bells rang. Even with the new, quick-turn technology of mRNA vaccines, it took just about a year after SARS-CoV-2 started its global spread to get the first doses into arms. By that point, 300,000 people had died in the U.S. and hundreds of thousands more—possibly millions—died around the world before vaccines were fully deployed.

Viruses reproduce at a phenomenal rate, faster than we slow clumsy vertebrates can adapt. You just know, though, that the guy Trump wants to appoint to run the NIH is going to argue for “herd immunity” the instant a pandemic takes off. In fact, this country has been working to undermine even a minimally responsible pandemic response for the last few years.

When COVID broke out, people were largely open to vaccines. Then-president Donald Trump touted his government’s rollout of the vaccine, but he has since helped feed vaccine skepticism. Neither Trump nor his Democratic opponent for president, Vice President Kamala Harris, mentions pandemic preparedness in their respective campaign platforms.

Even uptake of routine childhood vaccines is falling. “The lack of trust around vaccines does put us in a very bad place. We do know that people are dying because they are not getting vaccinated against COVID,” Khan says. The U.S. Centers for Disease Control and Prevention reports that only 11 percent of adults and just 7 percent of pregnant women have received the latest COVID vaccine.

Some states have loosened vaccine requirements and recommendations, something that worries Khan and other public health experts. Vaccines cannot help anyone if people don’t get them. Politicians who don’t promote the need for pandemic preparations are gambling that the next one won’t hit during their terms in office. “This is all going to potentially come home to roost with the next pandemic,” Khan says.

I got my COVID vaccine. It won’t help against bird flu, though. Meanwhile, the idiots are pushing the public to take greater risks. Remember all the fools touting raw milk for some absurd reason? That had consequences in California.

The source for all those bird flu cases in California was a few cow herds, herds specifically raised to produce raw milk, from a company called Raw Farm, run by a guy named Mark McAfee. Remember that name; it could go down in history, just like that of Mrs O’Leary. McAfee has some political opportunities in the current climate.

As bird flu has spread among poultry and cattle in the US this year, raw milk has seen a new wave of interest and some high-profile supporters, including Robert F. Kennedy Jr., President-elect Donald Trump’s choice to lead the US Department of Health and Human Services.

Raw milk was on a laundry list of items that faced “aggressive suppression” by the US Food and Drug Administration, Kennedy said in a post on X in October. In a fact sheet shared with CNN on Monday, Raw Farm said its CEO, Mark McAfee, “has been asked by the RFK transition team to apply for the position of ‘FDA advisor on Raw Milk Policy and Standards Development.’ ” CNN has reached out to the Trump transition team for comment.

Imagine a pandemic with RFK jr and Jay Bhattacharya in charge. Or don’t, if you don’t like nightmares. We are so screwed.

Oh, and for those people who look at a table listing a mere 57 cases, who think that’s minor and nothing to worry about, that’s just human cases. The virus is thriving in herds of cattle and flocks of birds, you know, those animals most of us eat.

In updates since November 27, the US Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) confirmed 14 more H5N1 outbreaks in dairy cattle, all involving California herds. The latest additions push the state’s total to 475 and the national total to 689 across 15 states.

Also, APHIS confirmed more H5N1 outbreaks in poultry in six states. All involve commercial farms. In California, the virus struck poultry farms in three counties—a duck breeder and a broiler facility housing more than 266,000 birds in Fresno County, a turkey farm in Merced County, and a commercial hatchery in Tulare County.

In Minnesota, the virus hit two more turkey farms in Meeker County, one of which has nearly 242,000 birds.

Similar outbreaks were confirmed at turkey farms in North Dakota (Ransom County), South Dakota (Beadle and Faulk counties), and Utah (Sanpete County).

In the south, the virus was confirmed at a broiler farm in Tennessee’s Gibson County that houses 37,200 birds. The outbreak is Tennessee’s first since October 2023.

Think of those as vast culture dishes where H5N1 is proliferating and mutating at a furious rate. Give ’em time, we’ll get a deadly variant popping out eventually.

An hour of mathematical genetics homework

We Americans have all had a pleasant Thanksgiving and possibly an indulgent Black Friday, but it’s time to get back to work. Yesterday, Zach Hancock gave a presentation on why the hereditarian fallacy is a fallacy — the math doesn’t work. The video demonstrates an important truth: biology requires math. In this case, it’s a fairly simple level of math, so if you know a little algebra and maybe a little statistics, you should be able to cope.

It’s an important message, too. Racism and hereditarianism are built on a false premise, and anyone who tries to use population genetics to argue against evolution or for racism doesn’t understand some rather basic stuff.

It gets in some good digs against Steven Pinker, too, who clearly doesn’t understand genetics or basic math.

Now get to work. Your break is over.