Category: biology

Scientific American attacks the “cult of the penis”

March 9, 2022 • 12:15 pm

There’s a new Scientific American article that presents some interesting biology, but does it tendentiously, for its aim is to show, by citing a few cherry-picked examples of odd biology, that interest in the penis among biologists, and the relative neglect of the vagina, reflects the patriarchy. It’s time, says author Rachel Gross to take the penis off its pedestal.

Now I freely admit that males often have an obsession with penises and their size, but I don’t think that the study of animal penises, as opposed to vaginas, reflects the patriarchy, despite a Vox Magazine article called “How a pseudo-penis packing hyena smashes the patriarchy’s assumptions.” (Read Steve Gould’s explanation of the spotted hyena female’s “pseudopenis”, a modified clitoris, though Gould’s hormone-based explanation is probably wrong.)

Gross’s article is loaded with examples of the naturalistic fallacy (or should I say “phallusy”?)—the idea that we can derive lessons about what is “good” or “moral” in humans from observing the behavior other species that lack our kind of culture (i.e., all other species). We may learn something about the evolutionary roots of our behavior, but not its lessons for sexual equality.

Click on the screenshot to read:

Here’s one example from the article, which begins by discussing two new books, Phallacy: Life Lessons from the Animal Penis, by Emily Willingham, and GUYnecology: The Missing Science of Men’s Reproductive Health, by Rene Almeling:

. . . the flashy focus on the male member serves as a Trojan horse (pun intended) for a very different message: that a culture of phallus-worship has slanted the science in crucial and sometimes unexpected ways. On the one hand, we’ve inflated the role of the penis in genital evolution; on the other, we’ve left the male contribution to infertility, genetic abnormalities and other reproductive consequences unexamined. The result is stunted, lopsided science that shows only one side of the story.

But if this all be motivated by the patriarchy, why are medical problems with male genitalia neglected and “unexamined”? But here’s one example:

Consider that myriad beetle species are classified solely by their penis shape, while the true breadth of vaginal diversity has yet to be explored. This tradition has deep roots: Going back to Charles Darwin, who waxed poetic on the wonders of barnacle dongs, biologists have trained their lens on the penis while remaining largely uninterested in what vaginas were doing. Yet penises don’t evolve in a vacuum. All those traits we ooh and aah over—length, girth, bristles—are shaped by vaginal evolution, and the mutual dance between the two that plays out over generations.

Now this is a straw insect. The reason why many species of insects (not just beetles) are identified by their penis shape is because that is the structure that is most likely to be clearly different between species. It’s not because biologists have an obsession with penises. In many Drosophila, for example, you can tell closely related species apart only by examining the male genitalia (even dissecting the female ones show no difference). As all entomologists know, “if there is only one trait differentiating closely related species, it is almost surely the shape of the male genitalia or genital apparatus.”

Now the reason for this probably reflects the action of sexual selection during the origin of new species, just as in many species of birds it is the male ornamentation and color and not the appearance of the female that is the most obvious species-distinguishing trait.

In insects, for example, the females of an isolated population may come, for reasons I won’t discuss, to prefer a slightly different genital shape in their mates, perhaps because it “feels better”. (We just don’t know the reason for this; I’m speculating here.) Eventually, because of this preference difference, you may get a snowballing difference in the shape of male genitals, and with it a big change in the female preference.

In the end, the two populations, via the action of sexual selection, come to differ from one another in both male genitalia and in female preference for the conspecific male genitalia—up to the point that females from one population will no longer mate with males from the other. We then have two reproductively isolated populations: new biological species.

Note that both sexes of the new species differ profoundly, but it’s dead easy to tell the species apart by the male genitalia, while it’s impossible to tell the species apart by looking at female genitalia. (Note: female genitalia may differ in some species, but to see that you’d have to do very elaborate dissections.)

You can tell the species apart by simply using a microscope to examine the male genitalia, but not the females. In fact, the females may differ in a way impossible to tell apart by looking at them, for their difference in preference may reflect how the different genitalia “feel” during copulation,  and “tactile feeling” is a preference impossible to see because it’s coded in the female’s neurons.

I’ve made this point repeatedly, most notably in my book Speciation with Allen Orr, and others have as well, especially William Eberhard in his unjustly neglected book Sexual Selection and Animal Genitalia. This concentration on male rather than female genitals does not reflect sexism at all: it reflects both the way that sexual selection works and the fact that the selection manifests itself as morphological differences between species in male but not in female genitalia.

(A side note: in groups like squid in which sperm is transferred not through a penis but through another organ, it is those organs that tend to differ among species. This again supports the idea that during speciation, male morphology changes but what changes in females is often neuronally-based “feeling preference”.)

The idea that female preference is unduly neglected because of the patriarchy is not a fair charge because nearly every theory of sexual selection involves a concomitant change in both male trait and female preference for that trait.  It is a hell of a lot easier to see trait differences than preference differences, which can be tested only by behavioral studies exposing females to males of different morphologies or of different species.

Author Rachel Gross emphasizes that it’s only the new activity of women scientists and LGBTQ scientists (!) that has led to an interest in female vaginal evolution. This simply isn’t true (well, it may be 2% true): many of the discoveries she emphasizes below were made by men, including the fascinating “pseudopenis” of the spotted hyena, repeatedly used as an example of a species whose females are “empowered” (another example of the Naturalistic Phallusy). The author says this:

Today, as more women and LGBTQ scientists enter the field, we’re finding that vaginas, far from passive tubes for ejaculate, are active organs that sort, store and reject sperm. Kangaroos have three vaginas (two for sperm reception, one for joey ejection); swallowtail butterflies see out of theirs; and duck vaginas spiral and curve in a penis-repelling labyrinth. Even for non-vagina-lovers, these facts help us understand how genitals evolve as a whole. Both are part of the same unified story—a much richer tapestry than just one body part can tell. Leaving one out, whichever one, blinds us to the fuller picture of sex and sexuality.

This is, I think, a gross distortion of the history of genital evolution. There’s more, and here her ideological lesson comes into view:

Both examples [JAC: the presence of multiple vaginas in kangaroos and “the neglect of guys in gynecology] reflect a deeper flaw in science’s approach to sex: the assumption that sex can only be either/or, two trains that run along separate, parallel tracks. Again and again, biology has proved this not to be the case—chromosomally, hormonally or genetically. For instance, we usually consider the presence of a penis to indicate a male, yet the hyena famously gives birth through her clitoris, which is so large that she can use it to mount the male. The female seahorse wields a long tube that looks an awful lot like a penis, which she uses to deposit eggs in the male’s pouch. So much for the penis as “the throbbing center of masculinity,” as Willingham puts it.

The lesson seems to be that sex is not binary IN HUMANS because of weird genitalic differences in other species. But sex is indeed binary in humans as defined biologically: males are the group that produce small, motile gametes (sperm) or have the potential to do so, while females are the group that produces large, immotile gametes (eggs) or have the potential to do so. THAT is the way, not penis shape or egg-delivering tubes, that biologists tell males from females, and the reason is because evolution forged sex that way: in animals, largely onto two tracks. The fact that a female seahorse deposits her eggs in the male’s pouch, and that he gestates the eggs and gives birth, says nothing about what obtains in humans, nor does it even say that “sex is not binary in seahorses.”  No, sex IS binary in seahorses:a male seahorse makes sperm and a female makes eggs.  What differs from most animals is which sex carries the fertilized eggs. But we’ve known that forever.

Finally, Gross gives us this message (my emphasis):

Here’s why: because human biases shape scientific knowledge, and much of what we know about our nether regions has been shaped by lazy, antiquated stereotypes about what men and women are. Looking past the penis and beyond the binary categories of male/female, penis/vagina (or, more accurately, penis/clitoris) opens our eyes to the full spectrum of gender and genitalia in all its glorious permutations. It makes for better science, and a deeper understanding of genital evolution and reproductive health.

Well, I’m not sure that Gross realizes that she’s given the game away by admitting flat out that yes, male/female is indeed a binary in humans.  Sex is binary. But yes, its manifestations, its twists and turns—like a duck’s penis—are fascinating to the biologist. Yet this does not mean either that the study of female genitalia have been of interest only to LGBTQ+ or female scientists, nor that we should draw any kind of lessons about how to best treat human males and females based on observing other species.

For another argument of the same stripe—that the diversity of nature tells us how patriarchal and sexist humans have been—see the article below from The Guardian. It, too, relies on a combination of anecdotes and the Naturalistic Phallusy, completely neglecting the great generalizations about the sexes first noted by Darwin. Once again the bonobos (who aren’t as nice as everyone thinks) are trotted out as an example of how females can be dominant in humans:

Ah yes, bonobos: these peaceable primates use sex toys, practise oral sex and establish and maintain female-led social structures through “genito-genital rubbing”. That’s entertaining, but it also matters: as Cooke says, it challenges the clichéd narrative on sex roles in primates, our closest animal relatives.

But why doesn’t the fact that the rest of the primate species show male aggression and “patriarchy” buttress the idea that males are the “dominant sex” in humans? Once again, it’s ludicrous to tell humans to right way to behave towards the sexes by pointing at other species. Nature is what it is, but human society, because of culture, can be made to abrogate what we see in nature—to circumvent evolution. The invention of contraception is one example.

As the biologist said who sent me the link below (a woman, by the way), “I suppose a more balanced account wouldn’t sell many books or warrant a big splash in a Sunday.”

(Lucy Cooke has a new book of “female myth-busting female-centered” stories,  Bitch: A Revolutionary Guide to Sex, Evolution & the Female Animal).

Taking a stand: Lucy Cooke by the giraffe enclosure at London Zoo. Photograph: Dan Burn-Forti/The Observer

 

 

Vox analogizes invasive species with human immigrants

November 30, 2021 • 9:15 am

I suppose it was inevitable that “invasive” species—species that take over a new area, often far from their native habitat—would be compared by the “progressive” Left to human immigrants, and thus the impact of these species minimized or even lauded. That’s the conclusion you can draw from the headline at the uber-woke Vox website below.

Actually, the article isn’t all that bad, as it does point out that some invasive species destroy ecosystems and must be controlled; other species are moving due to climate change; draws a distinction between true invasives and those deliberately introduced (see Wikipedia’s list of 100 of the World’s Worst Invasive Alien Species; the name “alien will alienate many here, lacking only the adjective “illegal” to enrage the woke); calls attention to the cruel way many invaders are destroyed (poisons can cause an agonizing death), and raises moral issues that should be considered (how do we trade off the death of sentient animals, or nonsentient plants, against native habitat and wildlife)? Those are all things to consider.

But the tenor of the article is one of equating human immigrants with invading species. As a biologist, I admit my biases that when trading off an invader that destroys native species and ecosystems, I give precedence to the natives. Each extinct species is a book that tells us not only about its ancestry, but also can impart fascinating facts about biology. Think of the Hawaiian Islands, where 95 out of the 142 endemic bird species (those found nowhere else) have gone extinct, not just because of habitat damage but because of introduced predators like rats and mongooses who destroy eggs, or feral pigs that destroy habitat. My solution would be, if possible, to get rid of the predators and pigs (as humanely as possible) and try to stem habitat loss.  Problems like this exist all over the world, and unless you have no appreciation for nature at all, you must think about invasion vs. conservation.

I have to say, though, that although the Vox article gives lip service to some truly damaging invasive species (e.g., cats and foxes that kill Australian marsupials), they tend to downplay many cases, like the interbreeding of coyotes with endangered red wolves (see below), my impression is that the article is written by a Leftist who favors open borders for the U.S. But of course the most invasive species of all, and the greatest danger to native species, is Homo sapiens.

Read and judge; you might take issue with my claims above.


As I said, the article isn’t as bad as it could be, but that’s not saying much when it comes to Vox.  Here’s a list of sentences and phrases where author Bolotnikova explicitly use the human/invasive species analogy:

For example, invasives can be considered a threat not only by killing or outcompeting native species but also by mating with them. To protect the “genetic integrity” of species, conservationists often go to extraordinary lengths to prevent animals from hybridizing, environmental writer Emma Marris points out in her book Wild Souls: Freedom and Flourishing in the Non-Human World. Consider the effort in North Carolina to prevent coyotes from breeding with endangered red wolves, which bears uncomfortable parallels to Western preoccupations with racial purity that only recently went out of fashion.

Good Lord! Only those who are looking for offense would find these “parallels”. Wolves and coyotes are different biological species, for one thing.

. . .That’s why some scientists look askance at the influence of invasion biology and argue that the field has a baked-in, nativist bias on documenting negative consequences of introduced species and preserving nature as it is. Invasion biology is like epidemiology, the study of disease spread, biologists Matthew Chew and Scott Carroll wrote in a widely read opinion piece a decade ago, in that it is “a discipline explicitly devoted to destroying that which it studies.”

Historically, the term has erroneously expanded to the idea of, “‘If you’re not from here, then you are most likely going to be invasive,’” Sonia Shah, author of The Next Great Migration: The Beauty and Terror of Life on the Move, said on a June 2021 episode of Unexplainable, Vox’s science-mysteries podcast. Conservation policies have been crafted around the idea that if something is not from “here” — however we define that — “then it is likely to become invasive, and therefore we should repel it even before it causes any actual damage,” as Shah says, which is part of the nativist bent that pervades ecological management.

Now these are uncomfortable parallels, but they’re between human immigration and animal invasions (animals are often moved deliberately by humans). This could—and may well have intended to—be an argument for letting immigrants go wherever they want. But wait! There’s more!:

. . .What’s more, the very notion of “invasion” draws on a war metaphor, and media narratives about non-native species are remarkably similar to those describing enemy armies or immigrants. For example, a recent news story in the Guardian about armadillos “besieging” North Carolina described them as “pests” and “freakish.” It also gawked at the animal’s “booming reproduction rate,” an allegation that, not coincidentally, is leveled against human migrants.

Well, we use invasion and war as metaphors for disease to. Is the “battle against covid” an alt-right slur on immigration?

We always have to be wary of teaching “indigenous knowledge” as equivalent to Western science. (New Zealand is having a real issue with that right now.) Here’s a confusing paragraph about that:

Indigenous knowledge is increasingly being recognized as essential to conservation, write Nicholas Reo and Laura Ogden — Dartmouth University professors of Indigenous environmental studies and anthropology, respectively — in an ethnographic study of Anishinaabe perspectives on invasive species. (The Anishinaabe are a group of culturally related First Nations peoples in the Great Lakes region of Canada and the US.) Anishinaabe ideas, Reo and Ogden found, reflect a worldview that sees animals and plants as belonging to nations with their own purposes and believes people have the responsibility to find the reason for a species’ migration. The authors’ sources recognized parallels between the extermination of species deemed invasive and the dark history of colonial violence against Indigenous peoples. The interviews “helped me recognize the ways in which different philosophies of the world shape our ethical response to change,” Ogden says.

But do the Anishinaabe try to find out the reasons for species migrations? If they do, then they have to use modern science. If they don’t, then this is irrelevant to the issue of conservation.

Finally, the article couldn’t resist using the word “diaspora”, which is usually applied to Jews but refers to any people dispersed widely from where they originally lived. This is the first time I’ve seen it applied to animals:

In Tierra del Fuego, at the tip of Chile and Argentina, a particularly dramatic novel ecosystem is taking shape. In 1946, beavers were introduced there in a futile attempt to create a fur industry. Instead, the animals proliferated and munched down the region’s Nothofagus — southern beech — forests, creating dams and ponds. “They are these miraculous world builders,” says Ogden, who wrote an essay imagining the beavers not as invaders, but as a diaspora. (Beavers have also been a boon for ducks and other marine species.) The invasive species paradigm, Ogden adds, is devoid of nuance, history, and politics; she prefers a concept that gives expression to the moral complexity of the beavers’ presence in South America, as well as the fact that they had no choice in being moved there.

Ecologist Dan Simberloff, however, deems this invasion a “disaster” for the native habitat.

As I said, this article is not without merit. It raises questions about invasive species (do they really damage native habitat or fauna?) that laypeople may not have considered, but, believe me, biologists have considered. But there are moral questions that biologists haven’t considered: is it worth the lives of 10,000 beavers, for instance, to save the Patagonian forests? Biologists say “yes”, for we’ll always have beavers, but Patagonian forests (or Hawaiian birds), once gone, are gone for good.  (Yes, the beavers should be exterminated humanely, which I suppose the Vox article would consider “genocide”.)

But in general, this article, conflating the problem of human immigration and crossing of politically determined borders with the invasion of animals and plants into novel areas, is a good example of the naturalistic fallacy. We learn nothing about how to deal with human immigration from studying invasive species. Not only that, but if you want to be more accurate in your analogy, you’d liken invasive species not to Central Americans crowded at the American border, but to Cortéz genocidal extinction of the Aztecs.  After all, human immigrants don’t wipe out the population into which they meld.

Here are four extinct species once on Oahu, one of the Hawaiian islands:

 

h/t: Luana

The most beautiful experiment in biology

September 19, 2021 • 9:45 am

John Cairns called “the Meselson-Stahl experiment“, published in 1958, “the most beautiful experiment in biology.” (Click on the first screenshot below to see the original paper, but what I really want you to do is watch the video at the bottom).

The paper was by Matt Meselson, who became a Harvard professor and distinguished researcher, and Frank Stahl, who was equally distinguished and worked at The University of Oregon. Both men are now 91, and both are still with us. The videographers shot both men together, 63 years later, to discuss this most important work, one that, in an unbelievably simple and clever experiment, revealed how DNA replicated. (There were several theories about how the genetic material was duplicated.) I always thought they should have won the Nobel Prize for this experiment, but it was not to be.

A bit of backstory: on p. 166 of Horace Freeland Judson’s wonderful book about molecular biology, The Eighth Day of Creation, you can read this:

Soon after Meselson got back to Pasadena that winter, Max Delbrück and his wife carried [Meselson] and Stahl to the Kerkhoff Marine Station, run by Caltech, on the sea at Corona del Mar, and locked them into an upstairs room with two sleeping bags and a typewriter until they wrote the paper.

You can read the Wikipedia link to the experiment, but first watch the video at the bottom first, which explains this lovely bit of experimental molecular genetics. It’s a really wonderful view of two aging scientists remembering their greatest moment.

This video truly conveys the excitement of the early days of molecular genetics in the 1950s after Watson and Crick had published their proposed structure. W&C had suggested a method of replication of DNA, but it wasn’t really “proven” until the Meselson/Stahl experiment.

.  At the end, the two collaborators and friends visit the llamas that Stahl now farms

h/t: Matthew

A new way of visualizing cells

December 13, 2020 • 2:30 pm

This is a lovely video showing a new way of visualizing cells as they are living and operating. The “microscope” that does this is extremely large and complex. I don’t know much about it, and don’t fully understand the principles, but this video probably tells you all you need to know. The images are stunning, and I love the enthusiasm of the researchers.

Has the problem of protein folding been solved?

December 1, 2020 • 1:00 pm

One of the biggest and hardest problems in biology, which has huge potential payoffs for human welfare, is how to figure out what shape a protein has from the sequence of its constituent amino acids. As you probably know, a lot of DNA codes for proteins (20,000 proteins in our own genome), each protein being a string of amino acids, sometimes connected to other molecules like sugars or hemes. The amino acid sequence is determined by the DNA sequence, in which each three nucleotide bases in the “structural” part of the DNA sequence codes for a single amino acid. The DNA is transcribed into messenger RNA, which goes into the cytoplasm where, connected to structures called ribosomes, and with the help of enzymes, the DNA sequence is translated into proteins, which can be hundreds of amino acids long.

In nearly every case (see below for one exception), the sequence of amino acids itself determines the shape of the resultant protein, for the laws of physics determine how a protein will fold up as its constituent bits attract or repel each other. The shape can involve helixes, flat sheets, and all manner of odd twists and turns.  Here’s one protein, PDB 6C7C: Enoyl-CoA hydratase, an enzyme from a bacterium that causes human skin ulcers.  This isn’t a very complex shape, but may be important in studying how a related bacterium causes tuberculosis, as well as designing drugs against those skin ulcers:

And here’s human hemoglobin, formed by the agglomeration of four protein chains, two copies each from two genes (from Wikipedia):

Knowing protein shape is useful for many reasons, including ones related to health. Drugs, for example, can be designed to bind to and knock out target proteins, but it’s much easier to design a drug if you know the protein’s shape. (We know the shape of only about a quarter of our 20,000 proteins.) Knowing a protein’s shape can also determine how a pathogen causes disease, such as how the “spike protein” or the COVID-19 virus latches onto human cells (this helped in the development of vaccines). Here’s the viral spike protein, with one receptor binding domain depicted as ribbons:

And there are many questions, both physiological and evolutionary, that hinge on knowing protein shapes. When one protein evolves into a different one, how much does that affect shape change, and can that change explain a change of function? (Remember, under Darwinian evolution, gradual changes of sequence must be continually adaptive.) How do different shapes of odorants interact with the olfactory receptor proteins, giving a largely one-to-one relationship between protein shape and odor molecules?

Until now, determining protein shape was one of the most tedious and onerous tasks in biology. It started decades ago with X-ray crystallography, in which a protein had to be crystallized and then bombarded with X-rays, with the scattered particles having to be laboriously interpreted and back-calculated into estimates of shape. (This is how the shape of DNA was determined by Franklin and Wilkins). This often took years for a single protein. There are other ways, too, including nuclear magnetic resonance, and new methods like cryogenic electron microscopy, but these too are painstakingly slow.

Now, as the result of a competition in which different scientific teams are asked to use computer programs to predict the structure of proteins that are already known but not published, one team, DeepMind from Google, has achieved astounding predictive success using artificial intelligence (AI), to the point where other technologies to determine protein structure may eventually become obsolete.

There are two articles below, but dozens on the Internet. The first one below, from Nature, is comprehensive (click on screenshot to read both):


This article, from the Deep Mind blog itself (click on screenshot), is shorter but has a lot of useful information, as well as a visual that shows how closely their AI program predicted protein structure.

 

In a yearly contest called CASP (Critical Assessment of Structure Prediction), a hundred competing teams were asked to guess the three-dimensional structure of about a hundred sections of proteins (“domains”). The 3D structure of these domains were already known to those who worked on them, but was unknown to the researchers, as the structures hadn’t been published.

The method for how Deep Mind’s AI program did this is above my pay grade, but involved “training” the “AlphaFold” program to predict protein structures by training the program with amino-acid sequences of proteins whose 3-D structure was already known. They began a couple of years ago in the contest by training the program to predict the distance between any pair of amino acids in a protein (if you know the distances between all pairs of amino acids, you have the 3D structure). This year they used a more sophisticated program, called AlphaFold2, that, according to the Nature article, “incorporate[s] additional information about the physical and geometric constraints that determine how a protein folds.” (I have no idea what these constraints are; the procedure hasn’t yet been published but will be early next year.)

It turns out that AlphaFold2 predicts protein structure with remarkable accuracy—often as good as the more complex laboratory methods that take months—and does so within a couple of hours, and without any lab expenses! In fact, the accuracy of shape prediction wound up being about 1.6 angstroms—about the width of a single atom! AlphaFold2 also predicted the shape of four protein domains that hadn’t yet been finished by researchers.  Before this year’s contest, it was thought that it would take at least ten years before AI could be improved to the point where it was about as good as experimental methods. It took less than two years.

Here’s a gif from the DeepMind post that shows how accurately DeepFold 2 predicted two protein structures. The congruence of the green (experimental) and blue (AI-predicted) shape is remarkable.

There aren’t many cases where computers can make a whole experimental program obsolete, but this appears to be what’s happening here.

There is one bug in the method, though it’s a small one. As Matthew Cobb pointed out to me, in a few cases the sequence of amino acids doesn’t absolutely predict a protein’s shape. As he noted, “Sometimes the same AA [amino acid] sequence can have different isoforms [shapes that can shift back and forth], which can have Very Bad consequences—think of prions, in which the sequence is the same but the structure is different.” Prions are shape-shifting proteins that, in one of their shapes, can cause fatal neurodegenerative diseases like “Mad cow disease”. These are fortunately rare, but do show that the one-to-one relationship between protein sequence and protein shape does have exceptions.

Here’s a very nice video put out by DeepMinds that explains the issue in eight minutes:

We’ll have to wait until the paper comes out to see the details, but the fact that the computer program predicted the shapes of proteins so very well means that they’re doing something right, and we’re all the beneficiaries.

It’s the end of the world as we know it

November 19, 2020 • 3:30 pm

Noted in passing, here’s an “exhibit” put up by the National Park Service itself.

Indeed, things are rarely simple in nature. Queer ecology has put paid to the notion that there are two discrete biological sexes in humans (and in other mammals, birds and fruit flies), as well as to the idea that an American Robin is a “box” differentiated from a Northern Cardinal “box”.

What a great new way to view the world! Thanks to the biologists at the National Park Service, I am freed from my subservience to colonialist and essentialist biology.

Your tax dollars at work . . . .

h/t: Luana

 

A good article on the meaning of biological sex

September 23, 2020 • 1:30 pm

There’s lot of confusion among laypeople, and even among scentists, about what “sex” is, in the sense of “what do we mean by a biological sex?” This goes along with questions like “Is sex binary?”, “How many sexes are there?” and so on.

For a scientific but accessible discussion of how biologists construe sex, the article below from Aeon (click on screenshot) is quite good.

There’s not much to quibble with in the piece, as it’s a straightforward discussion about how biologists regard sex, so I won’t do anything except list some of the questions it takes up:

  • What do biologists mean by “the sexes” of an animal or plant?
  • Why do we have sexes in the first place? Why doesn’t everything just reproduce asexually by budding or parthenogenesis (production of an offspring from an unfertilized egg)?
  • Why are there only two sexes in the vast majority of animal species? Why can’t there be three or more sexes?
  • Are hermaphrodites or developmental anomalies members of other sexes?
  • Why do biologists define the sexes by gamete size rather than by chromosomal constitution or characters like sexual organs?
  • Why doesn’t the existence of individuals with combinations of male and female traits prove that sex is a continuum?
  • Why we can’t necessarily extend biologists’ views of sex to questions like “who participates in women’s sports?” or “who goes to a women’s prison?”

I have a few minor quibbles with the piece, but they’re so trivial that they’re not worth mentioning. What especially interested me was the evolutionary question. Biologists have long wondered “Why did sexual reproduction evolve in the first place?”, and, truth be told, we don’t have an answer everyone agrees on. There is more agreement on why there are just two sexes in the vast majority of animals, although some organisms like protists have dozens of “mating types” that might be seen as sexes (Griffiths doesn’t).

Have a read of the piece if you want to be informed about biological sex before you wade into the gender wars.

Matt Meselson describes his most famous experiment (with Frank Stahl)

July 18, 2019 • 11:00 am

In 1958 Matt Meselson, whom I knew slightly at Harvard (he was a terrific guy), performed, along with Frank Stahl, an experiment that John Cairns called “the most beautiful experiment in biology”. What he and Stahl did (see description here) was to use density-labeled components of DNA to choose among which of the three methods of DNA replication floated at the time was correct (people didn’t know how DNA replicated in 1958; this experiment settled the issue):

In “semi-conservative replication”, each strand of DNA unwinds and makes a copy of itself, so that each DNA helix in the next generation of DNA has both a parental strand and a new strand synthesized from nucleotides and sugars. “Conservative” replication involves each double strand making another whole double strand.  “Dispersive” replication involved the DNA breaking, with each break synthesizing new DNA, matched to the other strand, in bits. They’re portrayed above.

Meselson and Stahl’s genius was to use an in vivo replication in E. coli producing DNA strands labeled with heavy isotopes (15N) that, while chemically identical to non-radioactive nucleotides, would be distinguishable from the non-labeled strands because the former were heavier and could be separated by vigorous centrifugation. (They used labeled nucleic acids as the components of the original strands; those labeled nucleotides were themselves synthesized by growing the starting bacteria for a few generations on “heavy” ammonium chloride—the only source of nitrogen—a component of nucleic acids—in the bacterial medium.)

The beauty of the experiment is that the results—confirming semi-conservative replication—were visible in a single photograph (below), and were unambiguous. It was a lovely experiment, and I think deserved a Nobel Prize (sadly, one wasn’t given for this).

This nice 13-minute talk by Matt, taken from an iBiology talk website, describes this experiment. He and Stahl started by putting bacteria containing fully “heavy” DNA into medium with non-heavy ammonium chloride, so that all the new DNA synthesized would be light.

Under the semi-conservative hypothesis, the next generation of DNA would be “half heavy”, as each helix would have both an original heavy and new light strand, with the latter containing nucleic acids synthesized from the lighter nitrogen in the medium.

Under the conservative hypothesis, the next generation of DNA would consist of fully light double strands and fully non-heavy original double strands. There would only be two types of strands detectable, and those would stay, with the heavier ones eventually disappearing as their carriers died and new DNA was formed. And under the “dispersive” hypothesis, the next generation of DNA would be not fully heavy or not fully light, but a schmear of ‘partly-heavy helices”. You’d get a mess of mosaic strands in subsequent generations.

Well, listen to Matt describe this pathbreaking experiment below. I’ll give a link to their paper and the famous figure that convinced everyone below the video.

Here’s the famous figure, beginning with heavy DNA at the top from E. coli (right stripe in generation 0). The density of the centrifuge gradient increases to the right, and strands tend to settle where their density matches the density of the cesium chloride in the centrifuge tubes.

When the bacteria were put on non-labeled medium, and the tubes scanned with UV-absorption, which picks out the DNA, you see that in the first generation all the DNA is heavy (original bacterial DNA). As those bacteria replicate and form new DNA strands, the heavy helices begin to wane and we start to see half-heavy helices (lighter stripe forming in the left, lighter part of the gradient). This stripe gets darker after more “hybrid molecules” accumulate (generation time is shown on the right of the figure). After one generation of replication, you get hybrid strands which are lighter than the original ones (the bands show the position in the density gradient of the centrifuge). Then, after another generation, the hybrid stands themselves replicate, forming a double-light helix from the newly synthesized strand as well as the half-heavy strand containing the original heavy strand of DNA. By generation four, nearly all the helices are fully light (to the left), as the original strands are in a minority in the mix since their carriers have died or been outbred. In other words, the three bands predicted by the semi-conservative hypothesis were seen. The experiment ends three photos from the bottom, at generation 4.1.

The presence of the three well-demarcated strands forming in sequential order shows unambiguously that the semi-conservative model of DNA replication is correct. You don’t need statistics to get the answer here!

You can download the original paper by clicking on the screenshot:

I don’t know of a more beautiful—or unambiguous—experiment in modern molecular biology. And the stuff about Meselson and Stahl being locked in a room with food and a sleeping bag until they wrote that paper happens to be true. (For more, read The Eighth Day of Creation by Horace Freeland Judson).

An interview with E. O. Wilson: He’s still on about group selection

May 11, 2019 • 12:15 pm

Matthew sent me a link to this interview with the renowned biologist E. O. Wilson published in The Chronicle Review (part of the Chronicle of Higher Education). It’s generally okay but has some reportorial errors and, sadly, documents Wilson’s continued insistence that human altruism evolved by selection among groups (“group selection”).  The article appears to have come from The Wall Street Journal; click on the screenshot to read it.

The interviewer, Charlie Tyson, a grad student at Harvard, should have not made the errors below, especially because he’s right there at Wilson’s school. Granted, these errors aren’t important, but bespeak a lack of journalistic care.

Errors of fact

The claim that Wilson’s lab and office were right down the hall from those of his adversarial colleagues Steve Gould and Dick Lewontin, and the claim that during the “sociobiology wars,” a protestor dumped a pitcher of ice water on Wilson’s head.

Here’s what Tyson wrote:

Not since Alfred Kinsey has an entomologist’s career been so marked by controversy. Wilson became a public figure in 1975 with Sociobiology (Harvard University Press), which argued that social behavior, in humans as in other species, has a biological foundation. Some critics — most notably Richard Lewontin and Stephen Jay Gould, both just down the hall in Harvard’s biology department — saw the book as providing scientific cover for racism and sexism. In a well-known incident at the 1978 meeting of the American Association for the Advancement of Science, a demonstrator dumped a pitcher of ice water on his head, shouting, “Wilson, you’re all wet!”

No, their offices were not down the hall from each other, nor even on the same floor. Wilson’s office and labs were on the fourth floor of the MCZ labs, while Lewontin’s was on the first floor (for a year after he arrived at Harvard) and then on the third floor. Gould was located in another building: the Museum of Comparative Zoology proper, with his office on the ground floor. This would have been easy for Tyson to ascertain.

More important, it seem untrue that a pitcher of ice water was dumped on Wilson’s head at that meeting. That’s a biological urban legend that has been repeated many times. But it’s apparently wrong. The New Atlantis reports the truth: it was a cup of water, and was not dumped on his head:

 Most memorably, protesters rushed the stage at a February 1978 meeting of the American Association for the Advancement of Science just as Wilson was about to begin a talk. They chanted “racist Wilson you can’t hide, we charge you with genocide” and threw a cup of water at him (later embellished in legend into a full pitcher of ice water).

The cup-of-water version is the way I’ve heard it from those who were there, and David Hull concurs (though not Ulrike Segerstrale). Wilson could have clarified this, but I guess Tyson didn’t ask him.

But on to the science. In the interview, Wilson maintains, as he has before, that group selection is the explanation for the evolution of altruism in humans. In his most recent set of books, he’s also maintained that nearly all traits that ‘make us human’, including creativity, music, and so on, also came via group selection.  Further, he’s maintained that eusociality in social insects (the division of the colony into non-reproducing but cooperating castes, with a reproductive queen) also had nothing to do with kin selection, but was also the product of differential reproduction and extinction of groups.

Virtually every expert in insect social evolution has objected to Wilson’s view, given in a paper in Nature with Tarnita and Nowak. Apparently the only people who accept Wilson et al.’s view are the three authors of that paper, along with group-selection enthusiasts like David Sloan Wilson. You can see all my posts on this controversy here and here.) I also wrote a critical review of Wilson’s book The Social Conquest of Earth, which laid out his group selection ideas for humans, in the Times Literary Supplement; the review is paywalled, but I have copyright and posted my review here. Finally, you can see links to letters in Nature from the 140-odd evolutionists who objected to Wilson et al.’s view of group selection as the cause of eusociality in insects at this post. (I was one of the signatories.)

Here’s a snippet from Tyson’s interview:

Q. Your new book, Genesis, offers for the general reader an introduction to how complex societies evolve. But for the more specialized reader, it doubles as a manifesto for group-selection theory.

A. I realized we needed to get it straight on where advanced eusocial behavior comes from. I’ve felt, without fail, that it comes from group selection.

I had been a main proponent of kin selection. In fact, I was the guy who met W.D. Hamilton way back, who promoted him and helped him. And I think kin selection does in fact occur.

Having introduced kin selection, Hamilton had, in my view, explained the origin of nepotism. But then he came up with something called “inclusive fitness.” He said: Maybe societies as a whole originate when a lot of individuals together are helping one another, or cooperating, to the degree that they are related to them. If they were all closely related, then there would be a lot of individuals cooperating, and you might have the origin of a society — particularly a society based on altruism. I favored that idea and mentioned it as far back as The Insect Societies (Harvard University Press) in 1971.

Inclusive fitness carried the day. But it just wasn’t working. I saw that there were big flaws in it.

Nope, there are no big flaws in inclusive fitness arguments. And they still carry the day. The idea of group selection creating major features of human evolution, or of evolution in general, is not widely accepted, for it has major flaws. Although Tyson characterizes Wilson’s argument accurately, saying “Within groups, selfish individuals beat altruistic individuals — but altruistic groups beat selfish groups”, this is deeply flawed. As I wrote about Wilson’s words to that effect in his Chicago discussion with Alan Alda:

Wilson then said he was going to give the audience an equation about how group selection worked, and my heart sank as I imagined him trying to spout math. Fortunately, he said just this: “Within groups, selfish individuals outcompete altruistic ones. But altruistic groups outcompete selfish ones.” The audience applauded loudly, but of course didn’t realize that that is one of the big problems of group selection. Not only is the turnover of individuals within groups faster than the turnover of groups themselves (via splitting and extinction), but once you have a group of all altruists, it’s unstable to the invasion of selfish individuals who gain but do not give. One selfish person in an altruistic group will begin breeding like rabbits compared to the others. It’s thus quite problematic to assert that some many aspects of human behavior and morphology evolved by selection among groups rather than among individuals. If you want to read a comprehensive critique of the problems with group selection, you couldn’t do better than Steve Pinker’s Edge piece, “The false allure of group selection.”

Pinker’s essay lays out far better than I could the problems with group selection, including the fact that there’s no evidence for it playing a role in the evolution of a single biological trait (I hold out sexual reproduction as a possible exception). The unfortunate situation is that Wilson is the best known evolutionary biologist alive, and has won two Pulitzer Prizes. When he speaks, people listen, and when he extolls group selection, the layperson believes him. They don’t know the problems with Wilson’s Big Hypothesis.

I’m not sure why Wilson, at the end of his career, has fixed his colors to the leaky vessel H. M. S. Group Selection. I’ve heard some of his colleagues give explanations, but I won’t repeat that gossip. It’s just sad that a man who became famous for having so many good ideas is chaining himself to a very bad one to ensure his legacy. But his legacy was assured a long time ago, and will only be tarnished by his tenacious clinging to group selection.

One other error in the interview, this time made by Wilson himself when discussing the opponents to his view of human sociobiology (now called “evolutionary psychology”):

Sociobiology got a book review on the front page of The New York Times. I think — well, I know — that some very small number of professors at Harvard, in my own department, were upset, because they thought that theories they were working on were the kind that should get recognition.

Wilson is wrong here. He’s referring, of course, to Steve Gould and Dick Lewontin. I knew both of them, for Dick was my advisor and Gould was on my thesis committee, and I never got any inkling that they objected to sociobiology because it dimmed their own professional lights. That’s an uncharitable statement, and not true. Lewontin and Gould fought against sociobiology (along with a lot of other students who then had no lights to dim) because they were ideologically opposed to it: they were pretty much blank-slaters and opposed to biological determinism, thinking that sociobiology would somehow justify a hierarchy of races and sexes and buttress the status quo. I heard Dick and Steve talk about this many times, and also knew Dick very well—certainly well enough to know that the man didn’t have a jealous bone in his body. Steve was more ambitious for public acclaim, but even so I don’t see him going after Wilson because he was jealous.

But what is true is Wilson’s claim that he won the sociobiology debate. In the end, people have accepted sociobiology for many species, and even in humans the discipline of evolutionary psychology is well established, though sometimes prone to exude weak papers.

And the good stuff in the interview. I like how Wilson says people should get into biology:

Q. What are some questions that scientists today should be asking but aren’t asking? What’s causing our blind spots: Funding? Overspecialization? Politics?

A. You’re asking me an impossibly large question. Let me make one suggestion, and maybe that’ll lead to another.

I am unhappy about STEM. That is, I’m unhappy about how it’s presented as the principal portal for careers in science and technology. Young people — in some cases, young enough to be as far back as grammar school — are presented with this intellectual triathlon in order to go into science and technology.

There’s no question that we need all the ablest people that can be recruited to go into science and technology to keep this country strong. But STEM is an unnecessarily forbidding set of stairs.

Consider a young person who’s thrilled by seeing a natural system, a remarkable geological formation that stirs the imagination, or a group of animals or plants. This youngster says, Boy, when I get to college, I would like to move on to a career in science, and biology especially. Now, the STEM-oriented teacher — if we are following the STEM ideology as we hear it — says: “I think that’s a good ambition. But remember that biology is based substantially upon chemistry. So, I advise you to start getting a good background in chemistry. Oh, and while you’re at it, you should keep in mind that chemistry is based upon, to a major degree, principles of physics. So consider starting to get a background in physics, too. And, oh, I almost forgot: To get into physics, and a lot of the best parts of chemistry, you’re going to need ‘M,’ mathematics. So I want you to get started on math courses right now.”

Now, I’m going to say something startling. And I’m going to get myself in trouble. But heck, that’s why you’re here.

Q. Yes.

A. And I’m going to say: Nonsense!

The right way to create a young scientist who’s going to be on fire by the time they’re in college is to let them pick something, some subject, that has really excited them. If they dream of space exploration, if they dream of curing a cancer, if they dream of going to distant jungles and discovering new species — whatever their dream is, let them dream.

Indeed: let them dream! And give them the resources to fulfill their dream!

While I don’t think that science is going to claim hegemony over art, literature, and all the humanities, I also like Ed’s discussion about how consideration of animal perception and consciousness might give art and literature a shot in the arm. This is the kind of poetry that I admire in Wilson’s writing. Here’s his discussion how an infusion of science in the creative arts could create A Great Leap Forward:

Let me give an example. A female moth comes out from the pupa. She’s got to mate. She releases a sex-attraction pheromone that’s carried downwind. In some moths, that pheromone can go downwind for kilometers. The males pick up on it and head upwind. In some species they start flying zigzag.

Imagine those puffs and ellipses of odor: spreading and dying away, spreading and dying away. If you could visualize all of that and walk into nature, you would see an entirely different picture. On the ground, the smallest of the creatures finding one another. Prey. Rival males. Females. A constant maelstrom of chemical communication.

Humans don’t have the capacity to understand the chemical communication going on around us that makes up the real world. We are dumb to that, or anosmic.

But the other thing is that we can’t see beyond a tiny fraction of the electromagnetic spectrum. Other organisms can see ultraviolet, or the infrared on the spectrum. Here is a whole opportunity in the humanities. It would be interesting if you could create the optical world of a spider or a bird, and show the world what would be seen or heard by them. You’d be painting an entirely different landscape. You could have a cottonmouth landscape, or a timber rattlesnake landscape. It would be nice to have a gallery of visual representations with the electromagnetic spectrum shifted over, from the point of view of a butterfly or an ant, translated into our narrow human sphere of perception so that we can see what they feel or see.

The humanities should not tolerate limits on themselves. There are so many exciting things to be done with the arts.

I don’t share Wilson’s optimism here, but I like the approach. Still, I don’t think it will replace anthropocentric art and literature.

Finally, Ed emphasizes the importance of collections in museums and—something I especially mourn—the loss of taxonomists and other specialists on groups of organisms. Take Drosophila, for example: perhaps the most studied group from an evolutionary-genetic point of view. If you’re studying biodiversity and speciation in that group, as I have, it’s crucial to have specialists who can help identify and place new species. Yet I can think of only about two Drosophila taxonomists on the planet. There’s no professional acclaim or recognition for such work, which is a damn shame given its importance. You can’t catalogue biodiversity without such people, and biodiversity is something we really need to understand now.

More scientific puffery at The New Yorker

April 6, 2019 • 12:30 pm

I’ve often carped about the New Yorker‘s science writing (see here and here, for instance), something that became a pet peeve when it published Siddhartha Mukherjee’s wonky ideas about epigenetics and then refused to correct them after many famous geneticists called it to their attention.   After I was getting tired of its attempt to wrap every subject in baroque and orotund prose, including science, I finally gave up my subscription when its self-important editor, David Remnick, caved in to public pressure and disinvited Steve Bannon from the New Yorker Festival (writer Malcolm Gladwell dissented). The magazine was also becoming increasingly Woke, as its target audience, rich Leftists, wanted the rag to flaunt more virtue.

But I still have a stack of back issues, and have been working my way through them, feeling most of the time that canceling my subscription was the right thing to do. For one thing, I can read a lot more books.  On the plane to Amsterdam, I read the January 14 issue, which included this article by Jerome Groopman, a staff writer and physician. It’s a review of a new book, Nine Pints: A Journey Through the Money, Medicine, and Mysteries of Blood, by Rose George, which describes the history of research on blood, starting with ancient mythology through the first transfusions and on to modern knowledge. The book sounds good, but Groopman has to trick out his review, à la New Yorker style, with irrelevant flourishes. You can read the article, which does contain some fascinating facts, by clicking on the link below.

Perhaps I’m being captious here, but after reading the article, a piece that recounts some good history of science and interesting medical facts (the account of Harvey’s discovery of blood circulation is fascinating), it winds up saying that the Big Mystery of Blood remains. Yet what that “profound mystery” actually is is never elucidated.

Groopman begins with a literary flourish, referring to Leviticus:

During my training as a hematologist at U.C.L.A., forty years ago, a senior faculty member introduced the program of study by citing a verse from Leviticus: “The life of the flesh is in the blood.” For the assembled young physicians, this was a biological truth. Red cells carry oxygen, required for our heart to beat and our brain to function. White cells defend us against invasion by lethal pathogens. Platelets and proteins in plasma form clots that can prevent fatal hemorrhages. Blood is constantly being renewed by stem cells in our bone marrow: red cells turn over every few months, platelets and most white cells every few days. Since marrow stem cells spawn every kind of blood cell, they can, when transplanted, restore life to a dying host.

. . . and, in a literary trope of circularity, Groopman also ends his piece with Leviticus. But what on earth is the “oldest, most profound mystery of blood.” Groopman’s last sentence, which says that “the life of the flesh” could also mean “the soul of the flesh” in Hebrew, doesn’t clarify things a bit.

Last month, in San Diego, the American Society of Hematology had its annual meeting. The program featured new discoveries about blood’s biology and accounts of recent advances in patient treatments—including an alternative to chemotherapy for one of the most common and incurable forms of leukemia. But, even as the field probes ever more deeply into the ways that blood serves living tissues, my colleagues and I are no closer to unravelling the oldest, most profound mystery of blood. In the verse from Leviticus, the word nefesh, translated as “life,” also means soul.

This is an example of how not to write popular science: ending with a claim that The Big Mystery Still Remains. This is how the magazine’s penchant for the humanities at the expense for science actually corrupts the science in an almost metaphysical direction. For how else can you interpret “the oldest, most profound mystery of blood”? Clearly, science will not suffice.

*********

As an addendum, here’s how Groopman (and the New Yorker itself) often present the Jesus myth as if it were literally true, with no doubt cast upon it:

Yet, despite the firm proscription against ingesting blood, one breakaway Jewish sect of the first century A.D. made the idea of doing so central to its rituals. Its leader, Jesus of Nazareth, told his disciples that the bread and the wine at the Last Supper were his body and blood, and should be consumed thereafter in memory of him. The ritual of the Eucharist became a cornerstone of early Christianity, and with it the doctrine of transubstantiation—that a literal, not just figurative, transformation occurred during the sacrament.

Here we see the credulous acceptance that Jesus of Nazareth not only existed, but was leader of a Jewish sect, as well as the implication that the Last Supper really did happen. Where is the “reportedly” that should occur at least twice in this paragraph?