Category: self promotion

A self-aggrandizing post concerning a paper on speciation I wrote with Allen Orr

August 24, 2026 • 9:30 am

What is an old, retired scientist to do but look back on his career and find satisfaction in the good ideas he once had? (I just finished a great novel in which a superannuated Cuban musician does the same thing.) In line with that, reader Nick called my attention to a two-year-old video by Zach Hancock lauding a paper I wrote with my student, Allen Orr, as “one of the ten most influential papers in evolution.”

First, though, in April I bragged about another video by Zach Hancock (a professor at Augusta University) that put my book Speciation (also co-written with Allen Orr), as one of the ten most influential books in evolutionary biology (we were #10). I have to admit that I consider this book my most significant accomplishment in science, as it distilled the field of speciation down to a research program that succeeded in influencing research in the origin of species. It took us six years (each) to write.

I rarely look at Speciation now, though, for when I do I realize that when we wrote it I was at the top of my neuronal game, able to read, write, and synthesize far better than I do now. And when I open it and sample a page or so from the chapters I wrote, I think to myself, “Who is that guy? He was really savvy?!” I could not write it now, nor will either of us revise it.

But Zack had another video that I missed,  one on the ten most influential papers in evolutionary biology. And again Allen and I made the list, coming it at #9 with the paper below we published in 1989 in Evolution. Note the dedication to Bruce Grant, under whom both of us studied at William and Mary (click title to read the paper):

I’ll add that this paper was at first rejected by Evolution on one reviewer’s claim that we could not use the method of correlation that we did, but the reviewer simply didn’t understand that method (it’s not rocket science). We argued with the editor, something I’d never done, and the paper was accepted.

Zack chooses papers in the field that have been cited more than a thousand times. and I’ll let him explain the findings in his video below (the discussion of our paper goes from 5:23 to 7:51).

A few corrections. To determine the relative divergence time between pairs of species or taxa, we used published data using genetic distance determined by gel electrophoresis; we did not “sequence genes”.  The purpose of the paper, as Zack says, is to determine how reproductive barriers between species arise with time by looking at the degree of reproductive isolation (measured only as hybrid sterility/inviability or as mate discrimination) between groups and correlating that with electrophoretic genetic distance, which is a measure of divergence time.

Also, Zack emphasizes the “reinforcement” aspect of the paper (I’ve put that conclusion in bold below), but that is only one of its findings—granted, a nice one. But the overall conclusions are several-fold, as the paper’s abstract notes below, including the relative rates of evolution of postzygotic isolation versus one form of prezygotic isolation (mate discrimination) as well as showing early evolution of male versus female postzygotic isolation, which explains the phenomenon of “Haldane’s Rule“, a generalization first noticed by J. B. S. Haldane in 1922, but neglected until I took it up in 1985.  This rule, pointing out the greater preponderance of sterility and inviability in heterogametic (XY or ZW) hybrids than in homogametic hybrids (XX and ZZ) is still subject to investigation and controversy, but has been a central focus of the genetics of speciation since 1985.

Here’s the abstract of our paper with the “reinforcement” finding shown in bold. Note the other findings, too:

To investigate the time course of speciation, we gathered literature data on 119 pairs of closely related Drosophila species with known genetic distances, mating discrimination, strength of hybrid sterility and inviability, and geographic ranges. Because genetic distance is correlated with divergence time, these data provide a cross-section of taxa at different stages of speciation.

Mating discrimination and the sterility or inviability of hybrids increase gradually with time. Hybrid sterility and inviability evolve at similar rates. Among allopatric species, mating discrimination and postzygotic isolation evolve at comparable rates, but among sympatric species strong mating discrimination appears well before severe sterility or inviability. This suggests that prezygotic reproductive isolation may be reinforced when allopatric taxa become sympatric.

Analysis of the evolution of postzygotic isolation shows that recently diverged taxa usually produce sterile or inviable male but not female hybrids. Moreover, there is a large temporal gap between the evolution of male-limited and female hybrid sterility or inviability. This gap, which is predicted by recent theories about the genetics of speciation, explains the overwhelming preponderance of hybridizations yielding male-limited hybrid sterility or inviability (Haldane’s rule).

Finally, Allen and I continued to collect data as new studies became available, eventually expanding the study to 171 taxon pairs—an increase of 41% in the amount of data. The results, published in Evolution in 1997, were similar to those of the earlier study, but stronger because they were based on more data. You can read the paper by clicking below.

Since electrophoretic analysis of species divergence is largely obsolete—everyone uses DNA sequencing now—the whole paper can’t be repeated with modern methods, but what has been done is analysis of a subset of species, and, as I recall (I’m not going to look up the papers), the results to date support those of our 1989 and 1997 papers.

A scientist is lucky if he or she has more than one or two good ideas in their career, and by that I mean an idea that influences their field in a substantial way. I’ve had about three, one of which is the analysis embodied in these two papers. And I have to pay tribute to Allen Orr (now retired, too): fiercely intelligent and hard-working—more a colleague than my graduate student. Both of us are honored to be included in the lists of ten books and ten papers discussed by Hancock. Josh and Esther Lederberg, W. D. Hamilton. Ronald Fisher, Sewall Wright—that is damn fine company!

My eponymous bufonid has been made part of a high-profile conservation campaign

August 5, 2026 • 11:00 am

The ponderous title above was from Greg Mayer when he emailed me the information below. To wit: there is a new project, called the Phoenix Species project, which is described at its own site, at re:wild, and in the New York Times. It is a great project, has targeted 100 very endangered species for saving, and does not involve Colossal trying to “de-extinct” species via genetic tweaking,

From the Phoenix page:

The Phoenix Species Project is a global effort to recover 100 of the world’s most threatened species by providing sustained support for the local champions with the experience and knowledge to lead their recovery.

The project begins with a $200 million commitment, with $100 million from Leonardo DiCaprio’s Re:wild and $100 million from the Bezos Earth Fund, with support from Leonardo DiCaprio, Age of Union, and the Todd Graves Family Foundation. The project’s 100 species span mammals, amphibians, reptiles, birds, fish, invertebrates, and plants from 30 countries that live across a range of habitats, from oceans to freshwater lakes, tropical rainforests to volcanic plains.

Here’s a short video about the Project:

You can see the species chosen for special funding at this site.  The NYT says this:

The hundred species were chosen because they were near extinction, had local organizations already working to save them and represent a diversity of habitats, countries and types of species.

. . . For the fuzzy belly button plant, a succulent that has lost more than two-thirds of its population to harvesting since 2019, when it became very popular abroad, the money will allow conservationists to breed more plants in captivity, buy trail cameras for security and fund work with communities so the plant can be returned to the wild without getting overharvested again, said Domitilla Raimondo, the threatened species program manager at the South African National Biodiversity Institute.

“They’re not as charismatic as a panda bear or a rhino, so they don’t tend to get the love and attention that other species get,” she said. “What is really great about this Phoenix recovery plan is it’s giving equal love to different species.”

Still, it includes only three invertebrates, among them a snail in Tahiti, and no insects.

Vivek Menon, chair of the Species Survival Commission at the International Union for Conservation of Nature, said the 100 species were a “fantastic first step” and emphasized the need to scale quickly.

More than 11,000 species are classified as either critically endangered or extinct in the wild on the I.U.C.N. Red List, the leading global scientific authority on the status of species. Almost 40,000 more are endangered or vulnerable.

That averages out to $2 million per species, a goodly amount. Greg sent me this information because one of the targeted species, shown below, is my very own frog, Atelopus coynei, which my late friend Ken Miyata and I collected in the coastal rain forests of Ecuador in 1976 (it now has its own Wikipedia page, and you can see all my posts on this story here.).  Ken named it after me because, when we were in graduate school at Harvard’s Museum of Comparative Zoology, he ran out of dough and I loaned him $500.

From the paper giving the description in Breviora:

And Ken’s note about the origin of the species name:

For many years I thought A. coynei had gone  completely extinct, but a population was discovered in Ecuador by Andreas Kay in 2012, and now there are several disjunct populations in Ecuador. One is where reader Lou Jost lives and works (the Dracula Reserve described below). I see it’s been given the common name Río Faisanes Harlequin Toad. And I had no idea that the world population is down to 250 individuals. From Wikipedia:

It currently found in only four disjunct areas in Carchi Province, including two locations in Río Chinambi and the Dracula Reserve, a private protected conservation area in Carchi Province, north-western Ecuador, which was established through the effort of the Rainforest Trust, EcoMinga Foundation, and Orchid Conservation Alliance.

Click on the screenshots to go to the Phoenix page:

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Another photo from the Dracula Reserve, this taken by Juan Pablo Reyes and Jordy Salazar/EcoMinga. The frog is much prettier than the photo above suggests, with lime green spots on a brown body, jazzed up with white racing stripes:

From the Phoenix site:

The Río Faisanes Harlequin Toad is a small amphibian that lives in the high-altitude cloud forests of the Ecuadorian Andes. The species is rare, and scientists have only ever found it in a handful of spots. In 1976, scientists described the species from a subpopulation the Río Faisanes River, the species namesake. Now, scientists think that the species likely only lives in two places. One is in the municipal protected area ACUS Río Chinambí and the other is the privately protected Dracula Reserve. Both localities are in Carchi province.

The disease chytridiomycosis and the degradation of the Río Faisanes Harlequin Toad’s forest habitat from agriculture, logging and human settlements have caused dramatic declines in the species. The toad was even lost to science from 1984 until 2012, even though scientists had tried searching for it.

The Río Faisanes Harlequin Toad is active during the day, especially in the rain, where it spends most of its time along the rocky river banks and stream beds. At night the toads will move to leaves that overhang the water. When it comes time to breed, the species lays eggs in fast-flowing streams and rivers attached to rocks.

I see I’m being solipsistic, concentrating on only one species out of 100.  Forgive me, but I’m glad there’s money for them all. It’s a good project, but if you read the NYT, you’ll see the paper beefing about how Amazon, which donated half the money, is responsible for environmental degradation. But let’s hope the money does help to save some of these critically endangered species, especially the eponymous bufonid

A historic picture. . .

July 10, 2026 • 11:05 am

. . . well, at least in my history. I found this picture by accident while trawling through my iPhotos. I don’t have a date (the info on the photo says 2022, but that can’t be right), and I don’t know who took the photo: it could have been me or it could be my friend Andrew Berry.

But it does show three generations of evolutionary geneticists, photographed in Dick’s office at Harvard after he retired. The top photo is of Theodosius Dobzhansky (1900-1975), the Ph.D. advisor (at Columbia) of Dick Lewontin (1929-2021), my own Ph.D. advisor, the living person to the right. Dick was a huge fan of Dobzhansky, whom he called by his nickname “Dodek”, and Dobzhansky was going to be my own Ph.D. advisor, except that when I had to do my alternative service as a conscientious objector, Dobzhansky retired and moved to UC Davis, and could no longer take students. I then importuned Lewontin to take me, and he did, but that’s a long story. . . .

Dobzhansky is sitting in a characteristic pose, sitting at them microscope and reading chromosome inversions in Drosophila pseudoobscura or D. persimilis. That was the research he did: he had two high-class technicians who manipulated the flies and did the salivary-gland squashes to reveal the chromosomes, and Doby (an alternative to “Dodek”) read the slides to see the inversion karyotypes.

The bottom picture is me en déshabillé, photographed climbing Mount Lewontin (a tiny hillock south of Death Valley, named after Dick because he did fly-release work there). That photo was taken by Phil Ward, an old friend and a professor of entomology at UC Davis. We had gone to Death Valley for biology, I to collect flies and Phil to collect ants. I wanted to do a “first climb” of the tiny hillock, which others had climbed before, and so, to make it unique, I did it without clothes (I couldn’t do it without oxygen since no oxygen is required!). I am wearing shoes and my usual field Stetson. I autographed the photo and gave it to Dick, who put it on his wall beneath Dobzhansky’s.  I believe my autograph said something like “To Dick Lewontin, who has always climbed upwards towards the naked truth.”

Well, what the hell—it’s Friday.

Some braggadocio

July 7, 2026 • 10:30 am

I started this website in 2009, and it’s hard to believe that it’s been going for 17 years (this is the 31,860th post!). It began simply as a suggestion from my editor, Wendy Wolf at Viking/Penguin (now Penguin/Random House), that I start a website to promote my first trade book, Why Evolution Is True. (I was supposed to do what Neil Shubin did to promote his book Your Inner Fish). And that’s what I did, intending to perhaps post a brief item every few weeks about new evidence for evolution.

As you know, I quickly abandoned that intention and, discovering that I not only liked writing but also wanted to air my views about many things, including a love of cats, the website became a monster, eating up huge amounts of time. I don’t regret that, or have any plans to stop, for it’s only when I’m writing on this site that I’m able to forget the thousand natural shocks that kosher flesh is heir to.

This all came to mind when yesterday I got a request from my agent to allow a translation of WEIT into a new language: Uzbek! Of course I get a tidy but not huge sum for each such translation, and now the book is in 21 languages besides English. I’ve listed them below, including the publisher:

Original English:      Viking/Penguin (US), and Oxford University Press (UK)

Foreign:

ARABIC  National Centre for Translation and Publishing, Egypt
BASQUE  Universidad del Pais Vasco (hardcover and ebook)
BENGALI  Agradoot and Company, Dhaka, Bangladesh
BRAZIL JSN Editora
CROATIAN   In.Tri d.o.o
FINNISH  Vastapaino
FRENCH Markus Haller, Switzerland
GREEK Diadromes
JAPAN  Nikkei Business Publications
HEBREW  Books in the Attic
ITALIAN  Codice
KOREAN Eulyoo Publishing Company
PEOPLE’S REPUBLIC OF CHINA (Mandarin)  KeAi Communications
PEOPLE’S REPUBLIC OF CHINA  (Simpified Chinese) Shanghai Translation Publishing House
POLISH  Proszynski i Ska
PORTUGUESE  Edicoes tinta-da-china (Portugal)
RUSSIAN Alpina
SPANISH  Editorial Critica
TURKISH Palme Yayinevi
UKRAINIAN NashFormat Publishers
UZBEK           1000 Books Project

The translation I’m proudest of is the one in Arabic, because the Arabic-speaking and Farsi-speaking world is rife with creationism since the Qur’an, which is often taken as literal truth, paints a creationist scenario for the origin of life and humans. Sadly, the Arabic translation, done in Egypt, is almost unavailable: I’m told you can buy it in only one small bookstore in Cairo.

Here are two questions I’m sometimes asked:

Are you going to update the book? I have no plans to. The material is pretty much up to date, though there are a handful of errors that remain. And it’s short on molecular evidence for evolution.  But there is no other book that covers the same ground, and I’ve heard from many people who said it convinced them that evolution was indeed true, as well as from a few who said it made them abandon their religion. Which leads to the next question:

Is this book the accomplishment you’re most proud of? No, though I am quite proud of it, for it was successful in doing what I wanted (it even nosed onto the NYT bestseller list), even if it didn’t dispel the pervasive creationism of America and other countries. A 2024 Gallup poll, for example, shows that 71% of Americans continue to think that God had some hand in human evolution, with more than half of those being Biblical creationists. But a naturalistic belief in evolution is gaining!:

In terms of the quality of analysis and comprehensiveness of coverage, I’m still most proud of the academic book I wrote with Allen Orr, Speciation. It grew out of my whole career working on the origin of species, and summarizes and analyzes what we knew at the time (2009) about how single lineages could split into two or more species. Speciation was originally published by Sinauer, but when that estimable publisher disbanded when its founder retired, its books were bought by Oxford University Press. Now Speciation is hideously expensive ($189.00 in paperback and $239 or more in hardcover). I wouldn’t recommend reading it unless you’re an evolutionist or other biologist, as it presumes knowledge that most laypeople don’t have.

When I dip into Speciation, as I do on rare occasions, I am impressed at how well I could think and write back then.  I would not be capable of writing it now, as my brain doesn’t work as well as it used to. But I’m glad that Allen and I took the six years required to write it, as it’s the definitive book on the subject, and no other book had come along to supplant it.  Is it out of date? Certainly, but neither Allen nor I have the will to update it. And it still lays out the problem in a way that’s useful, even if we have a lot more examples.

What I would add it I were to rewrite it would be a lot more about on “hybrid speciation”, especially the phenomenon of diploid species hybridizing and then the hybrids evolving into a new and distinct species.  In 2009 we had a few examples of the phenomenon, but they’ve proliferated. (Polyploidy in plants is one example of hybrid speciation, but we did include a lot of material on that.)

I’m also proud of the cover (in color below), which shows three congeneric species of fish. (I didn’t want to show Drosophila because everybody expected that the book would be Drosophilocentric, and it wasn’t.)  I spent hours sitting on the floor of the biology library here (no longer extant), trying to find good pictures that would represent speciation. I finally found one, and I could use it without permission as the copyright had expired. Here’s the source of the picture as detailed inside the book:

I loved the connection with David Starr Jordan and Teddy Roosevelt. I took out the book and carried it to the main library, which had a huge scanner that could reproduce things in great detail. And that’s what I sent to Sinauer to go on the cover. By the way, the fin going through the “O” in my last name was done on purpose by Sinauer. That’s cool, too:

Such are the thoughts engendered by a request for translation.

Chat GPT caricature

June 15, 2026 • 8:00 am

UPDATE: I’ve added a new caricature which has both ducks and cats (at bottom).

Just to see how much ChatGPT knows about me, I gave it this task:

Draw a caricature of Jerry Coyne based on everything you know about him (including his love of ducks).

I also included a picture of myself.  I have to say that it did a good job, though there are too many ducks (next time I’ll add cats).  Grok is not nearly as good as Chat GPT for drawing, but I was still surprised at the amount of information about me that the bot can trawl from the Internet.

A shirt and a puggle

June 1, 2026 • 10:30 am

There’s a dearth of news, or should I say there’s a dearth of news that I want to write about: the interesting news is relevated to the morning Hili post.  But since it’s June 1, which marks for me the Day to Begin Wearing Hawaiian shirts, I present my garb for today. I have about 50 Hawaiian shirts, acquired when I went through an aloha-shirt phase, but I wear them only in appropriat weather. This one is semi-authentic, as it’s not old but has coconut buttons and a pocket matched with the shirt’s pattern—two features of an authentic Hawaiian shirt. (The real old ones from decades ago are made of rayon, not cotton.  I got it from a now-defunct outfit that had gorgeous Hawaiian shirts: “Paradise on a Hanger” (great name). Sadly, it is not longer in business, but i have enough shirts.

This one has a lovely green-and-orange fish pattern. I wish that mainland Americans would take up this habit, for you see them all over the islands of Hawaii, especially on “aloha Fridays.” It counts as “business casual” garb, too. You can hardly be unhappy when all around you are colorful shirts.

And Matthew sent this short YouTube video about a new puggle (the name for a baby platypus, Ornithorhynchus anatinus) from ZoosVictoria, which really does seem to be interested in conservation. Note that the incubation for the egg is just ten days, but it’s four months until it emerges from the den. It’s okay to hold females, but remember that males have poison spurs on their hind legs, which can inflict a painful and slow-healing wound.

Dark thoughts in the wee hours

April 10, 2026 • 9:30 am

My insomnia continues, and has apparently worsened for reasons I don’t understand. Perhaps it’s anxiety about the war, but it’s definitely anxiety about something. Perhaps subliminal anxiety—after all, we can’t control what our brain does.  Last night I woke up at 2 a.m. and couldn’t get back to sleep. When this happens nearly every night, I try to suppress the worries that arise almost—like everyone, I have a panoply of items on the worry list. But anxiety seeps in and keeps me awake. AT 4 a.m., I hauled my sorry tuchus out of bed, did my ablutions, and came to work. That is the usual situation.

If I were to guess at the items that make me most anxious (besides the worry about getting back to sleep, which is counterproductive), there are these:

The Middle East.  Because I post daily about the war in Iran and other Middle Eastern matters, I seem to have gotten caught up in the roller coaster that is this region of the world, a roller coaster exacerbated by Trump’s waffling, which may be a deliberate strategy.  Regardless, like the mess that is American politics now, I realize that there’s little I can do to affect matters. And given that, I should simply observe the situation, express my opinion when I can, but not get so engaged that I’m destabilized by the ups and downs of both the war and politics.  But in this I’ve failed.

The ducks at Botany Pond.  I should just do what I can to take care of them, including feeding the ducklings when they come, but caring for them has almost become an obsession.  “No ducklings left behind” is my motto.  There’s nothing I can do to stave off most predators or prevent errant mallards from entering the pond and harassing Vashti, but somehow it’s a constant anxiety until the ducklings grow up and fly away.

Death.  I guess a lot of readers don’t worry about their mortality, but when you get into your seventies it’s almost inevitable. I’ve already lost several friends and classmates, and of course, as the syllogism goes, all men are mortal.

In response, some people have said that because they don’t worry about the time before they were born, which they equate with the time after they die, it’s futile to be afraid of death. In response to that I quote Christopher Hitchens, who knew he was dying of cancer but never openly admitted it:

“It will happen to all of us, that at some point you get tapped on the shoulder and told, not just that the party’s over, but slightly worse: the party’s going on — but you have to leave. And it’s going on without you. That’s the reflection that I think most upsets people about their demise.”

I once asked readers if they wanted to be immortal (with the stipulation that you don’t fall apart completely), and most said “no”—they will have seen enough of life when the Reaper comes. But I like the party too much!