Category: biology

London’s Natural History Museum commits the naturalistic fallacy—repeatedly

June 30, 2022 • 9:15 am

It appears, from the tweet below, that London’s famed Natural History Museum has taken its place in the Woke Parade, for the tweet below clearly means to validate different human gender identities and parade the Museum’s pro-LGBTQ+ credentials by publicizing the several lizard species that don’t require male sperm to have offspring. This phenomenon is called parthenogenesis, meaning “a form of asexual reproduction in animals that does not require fertilization by sperm.” In effect, all members of a parthenogenetic species (if one can call them “species”) are female.

What irks me is that this has NOTHING to do with LGBTQ+ people, who do not reproduce without fertilization. None of us do! This is simply virtue-signalling using animals to support human behaviors (I suppose it’s relevant to gender identity in this case, or if you are an extremist, the superfluity or toxicity of males). And vindicating human behavior by pointing to animals is a form of the “naturalistic fallacy“: the view that “whatever is natural must be good.” If you think I’m overinterpreting the intention of this series, have a look at the second video below or full Monty tour (a 26-minute video) produced by the Natural History Museum.

Of course humans don’t have parthenogenesis, so connecting it with LGBTQ+ in a video tour (see below) is simply mistaken. The naturalistic fallacy, too, is mistaken: that’s why they call it a “fallacy”.  There are plenty of natural animal behaviors that we would not want to see in our species, including infanticide, murder of conspecifics, cannibalism, eating one’s mate after copulation, robbery, adultery, theft, and the whole gamut of crimes and sins.

Yet Leftist biologists in particular are prone to this fallacy, constantly pointing to the diversity of sexual behavior in animals to somehow justify the diversity of sexual behavior in our own species. If I hear one more person bang on about how the clownfish—a sequential hermaphrodite that can change from male to female when a female in a group dies—I’ll scream. (Note that there is a definite change from one binary sex to another: a change from producing sperm to eggs.) Gender or sex change in humans need not be justified by pointing to its occurrence in nature: it’s something to accept and respect regardless of whether it occurs in nature. (And if it didn’t, would that make transsexuality bad because it’s “unnatural”?)

The orange clownfish (Amphiprion percula) much beloved by biologists who commit the naturalistic fallacy. Nemo is of course one of these.

But I digress. Offspring produced without male fertilization are common among invertebrates, especially insects. Vertebrates can have it too: it’s been seen not just in lizards, but in snakes, sharks, fish, and birds. In some of these (like the Komodo dragon), parthenogenesis may occur alongside normal reproduction, and so two sexes are not just present, but “needed”, for without males, the parthenogenetic variant would eventually disappear. (Whether to call parthenogenetic lineages that are genetically different as “different species from each other” is, as I implie above, a matter of taste.)

Komodo dragons MATING. Yes, males are needed to keep the species going.

Parthenogenesis in reptiles, is, as the video below shows, usually results from hybridization between two species. The hybrid offspring have two different genomes, one genome from each of the parental species, and this may mess up the normal process of meiosis that forms sperm and eggs. If it gets messed up in hybrids that, without fertilization, eggs can go on to develop into adults (and these eggs must still have two genomes), we have parthenogenesis.

Sometimes the asexual reproduction persists and we get a new “species”, but a feature of parthenogenesis like this is that it is very often an “evolutionary dead end.” For reasons probably connected with a lack of genetic variation, parthenogens don’t hang around for long as a group. They tend to go extinct well before other species. We know this because looking at the genes of the parthenogenic individuals show that they’re very similar to those of the parental species, which means that the new asexual form hasn’t been around long enough to genetically diverge from the two parental species. The “dead end” nature of this asexual process isn’t mentioned by the Natural History Museum!

Even in parthenogenesis, two sexes are sometimes “needed”, because in many forms of the trait, even in reptiles, sexual activity is needed, even without fertilization. This can take the form of a female mounting another female (“pseuocopulation”), or even copulation with males from one of the parental species—copulation that doesn’t cause fertilization. For some reason we don’t understand, the process of egg development may require a behavioral trigger of copulation or pseudocopulation. Thus the Natural History Museum is also misleading in saying that “two sexes aren’t needed.”  In some cases they are, though they’re needed in one of the two parental species.

Finally, the Natural History Museum errs by saying that all parthenogenic reptiles are clones (genetically identical to the mother). This isn’t true. There are a variety of ways that animals can produce offspring without sex. Some of these involve all the offspring being clones, producing eggs by simple development of an egg that happens to have the same genomic constitution of a mother, i.e. two copies of each chromosome. This form, called apomixis, produces offspring that are all genetically identical to themselves and to their mother. These are all clones.

But there’s another way of reproducing without sex that produces genetically diverse offspring. It’s called automixis, and can occur in several ways. One is that meiosis (production of gametes) produces genetically diverse egg cells, two of which can fuse to form a diploid egg that’s capable of becoming an adult. Since the eggs themselves are genetically different, the diploid eggs will differ from each other too, and  thus the offspring that result will not be clones of each other—or of the mother. Some lizards use this method of reproduction, and so the offspring are not “clones”.

That’s the biology lesson, so you can see that there are at least two errors in the Natural History Museum tweet that I’ve put below again.. However, the tweet’s purpose is not scientific accuracy, but to imply that reproduction without sex somehow supports LGBTQ+ people. As I said, it doesn’t, for no LGBTQ+ folks, or any other human, reproduces parthenogenetically. Readers may wonder what mindset made someone decided that parthenogenetic lizards are part of the “LGBTQ+ tour.”

The video below, labeled above and on YouTube as another part of the LGBTQ+ natural history tour, is pretty anodyne, and in fact doesn’t even mention the L+ sequence. But look at the one below that,designed to vindicate human homosexuality by showing that some beetles have same-sex behavior!

Oy vey! The advantage of the video below is that it’s short. It describes same-sex sexual behavior in insects. Why? Because it’s meant to show that homosexual behavior in humans. because it occur in animals, is “natural”. Ergo, we can’t criticize it. But as I said in my review of Joan Roughgarden’s book Evolution’s Rainbow, a review published in the Times Literary Supplement, this argument doesn’t hold water:

But regardless of the truth of Darwin’s theory, should we consult nature to determine which of our behaviours are to be considered normal or moral? Homosexuality may indeed occur in species other than our own, but so do infanticide, robbery and extra-pair copulation.  If the gay cause is somehow boosted by parallels from nature, then so are the causes of child-killers, thieves and adulterers. And given the cultural milieu in which human sexuality and gender are expressed, how closely can we compare ourselves to other species? In what sense does a fish who changes sex resemble a transgendered person? The fish presumably experiences neither distressing feelings about inhabiting the wrong body, nor ostracism by other fish. In some baboons, the only males who show homosexual behaviour are those denied access to females by more dominant males. How can this possibly be equated to human homosexuality?

Ironically, while narratorJosh Davis, says that the early entomologists describing same-sex copulation in insects did so to justify homosexuality as “natural” in humans, Davis doesn’t go on to say that this whole endeavor is meaningless.  What if there were no same-sex behavior in insects or other animals? Would that mean that human homosexuality should be deemed abnormal and deplorable? Of course not!

This whole “LGBTQ+ four of the Natural History Museum appears to rest entirely on the naturalistic fallacy (see the  26-minute video, too). Whatever happens vis-à-vis sex in animals has nothing to do with how we regard homosexuality (or any other non-cis sexual behavior) in humans. We do lots of things that animals don’t, and judging our behavior, morally or otherwise, must rest entirely on human considerations like the morality we’ve developed that isn’t seen in animals. It’s ironic that in their desire to be au courant with woke ideology, biologists have reverted to adopting a fallacy that they rejected long ago.

The Natural History Museum has fallen into a real trap here, and it’s embarrassing that it are producing these videos. But of course science is now increasingly prey to “progressive” ideology, and so much worse for science.

Be sure to watch the long video that claims that “some sheep are homosexual”—in the human sense. That is, they choose to be homosexual—as if human gay people choose. It’s all a big mess.

h/t:  Luana, Greg Mayer

 

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