We hit 73,000

July 10, 2021 • 1:30 pm

I’m sufficiently vain that I do enjoy it when the number of subscribers to this website goes up—especially when they hit a round number. I don’t get money, but I do get naches. (Yes, I know “round numbers” mean noting.) However, we just reached this mark, and I never thought it would be this high.  Thanks to the many readers who stick with the site, and maybe we’ll get to 75,000 before this site sleeps with the fishes.

(Somehow I think someone is going to unsubscribe to ruin this figure!)

Professor Ceiling Cat (Emeritus): “Ask me anything”

April 14, 2021 • 9:45 am

When Why Evolution is True came out, part of the publicity was to do a reddit “Ask me anything” feature, or “AMA”.  People post questions and you choose which ones to answer. It was fun, but a bit frantic, as it was time-limited and you have to answer quickly.

There’s not much to write about today save John McWhorter’s latest installment of The Elect (stay tuned), so I’ll do an AMA here.  Each reader can pose one question (with one related followup) in one comment, and I’ll try to answer as many as I can. The rules: no personal questions beyond those relating to food, travel, tastes in music and literature, and non-intrusive inquiries of that ilk. Science questions are encouraged, though of course I am likely to say “I don’t know” to some of them. And that’s about it.

I’ll check in throughout the day, and perhaps in the evening, and do what I can. I’m doing this not because I think my life has been especially notable or interesting, but because interaction here is usually one way: readers often write or comment about themselves, and I enjoy that. I’ll turn the tables this time.

You may fire when you are ready, Gridley.

In which PCC(E) tells people how to get rid of fruit flies

April 7, 2021 • 2:00 pm

This is not the first time I’ve been asked “how to get rid of fruit flies,” but this time it’s by a reporter for Chicago Magazine in the article below.

The first thing I had to ask when they queried me, was “what kind of ‘fruit flies’ are you talking about?” For the true fruit flies, the tephritids that endanger California’s fruit industry (that’s why you get inspected at the state border), aren’t a problem to homeowners.

What the reporter was asking me about was what geneticists call “fruit flies” but are better known to entomologists as “vinegar flies”. These are in the sister family Drosophilidae, and are the familiar Drosophila used in the lab. When you see little yellow flies buzzing around your fruit bowl, they are drosophilids, most likely Drosophila melanogaster or D. simulans.

And Drosophila are harmless, except to winemakers, and only because they’re attracted to the smell of alcohol and fly into the wine vats to die a happy death. (Flies love the smell of alcohol, as it denotes their real love, rotting fruit, in which they lay eggs.) Winemakers use pyrethrins, a fairly harmless pesticide derived from chrysanthemums, to control them.

If you see Drosophila buzzing around your fruit bowl or a glass of beer, don’t kill them, just shoo them away. They shouldn’t be breeding in your house unless you have a bunch of rotting fruit that’s sitting around for 12 days or so—and who has that?

(When I lived in Davis, I was called by a bar in Sacramento that really did have a Drosophila problem. A quick investigation showed that there was a huge bin of leftover, rotting lemons and limes from the bartender behind the building, and that was the source of the flies. For solving that problem, I got free drinks!)

But a reporter from Chicago Magazine was interested in how to get rid of them, along with three other “problems”: hiccups, alley rats, and hangovers. Somehow I was picked to be the fruit fly expert, and here’s my answer (click on the screenshots below to see the others, each with a different expert:

Well, this is advice for those with dipteraphobia. If you see fruit flies, just gently shoo them outside!

A retrospective look at a paper: Coyne and Orr (1989)

April 4, 2021 • 12:00 pm

The two best-cited pieces of scientific work bearing my name were both done in collaboration with my graduate student, Allen Orr, who was recommended to me by Bruce Grant, my undergrad genetics teacher at The College of William and Mary. Allen had gotten a B.A. in philosophy there, and went on to do a master’s degree with Bruce in Drosophila genetics. Bruce recommended him to me as a good prospect, but wasn’t sure how he’d work out as a Ph.D. student.

At the time I was at the University of Maryland, took Allen on, and the rest was history. I had no idea how to mentor graduate students—Allen was my first—but it turned out he needed no mentoring: he was a self-starter. Over his few years in my lab, he published about ten papers and won the Society for the Study of Evolution’s Dobzhansky Prize in 1993, given to the person the SSE’s committee considers the best young evolutionary biologist.

The two most cited works include a pair of related papers (Coyne and Orr 1989, 1997), and our coauthored book Speciation (2004).

I summarized the main findings of the two papers, and gave a bit of their history, in a post from October of last year, which includes an interview I did about it in 2017 for Reflections of Paper Past.  At that time I didn’t know that two people, including my last student, Daniel Matute, were writing a retrospective of the 1989 and 1997 papers.

At any rate, in honor of the 75th anniversary of the journal Evolution, it’s been publishing retrospectives of notable papers that have appeared there. One chosen for this treatment was the Coyne and Orr duo. The retrospective paper, by Daniel Matute (UNC Chapel Hill) and Brandon S. Cooper, now at the University of Montana, can be accessed by clicking on the screenshot below, or you can get the pdf here. The reference to the retrospective is at the bottom. It will probably be of interest only to evolutionary geneticists, but it’s here for the record.

I have to say that Daniel and Brandon did a terrific job. It’s far more than a “retrospective” of our papers, but a new meta-analysis of existing data on how reproductive barriers between incipient species grow with time. (That was the subject of our original papers, and you can read the summary at the link above.) The new paper highlights where we were right, where we were wrong, what gaps there are in our knowledge about reproductive isolation, and what directions future research on the time course of speciation should take. In other words, it’s a review paper on a growing area of research rather than a discussion of just two small papers.

I’ll end by giving their abstract, which shows what the paper is about. But if you work on speciation, you’ll want to read their whole paper:

Abstract

Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr’s influential meta‐analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.

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Matute, D.R. and Cooper, B.S. (2021), Comparative studies on speciation: 30 years since Coyne and Orr. Evolution. https://doi.org/10.1111/evo.14181

Ask me anything

February 14, 2021 • 9:00 am

I’m still doing writing that requires braining (for another assignment to be divulged), and although I have a science post scheduled for later today I thought I’d do a reddit-like “AMA”.

Readers are welcome to ask all sorts of questions, with the proviso that the questions not be really personal ones. Exceptions: my life in science, food, travels, perhaps some philosophy, or things of that ilk. I can’t guarantee to answer every question (assuming there are some), but I’ll have a look from time to time and satisfy people’s curiosity.

Oh, and please, nothing rude or uncivil (as always!).

A recurrent dream

November 27, 2020 • 11:30 am

You’ve probably noticed that the site has a new look, which is similar to the old one but has eliminated many of the glitches. It’s still a work in progress. Do have a look on your mobile device and see how it looks there as well. And email or comment below if you have any beefs or suggestions.

I wanted to relate a recurrent dream I’ve had, which has replaced my old recurrent dream in the last five years. The old one is familiar to many academics, and involves being late for a class or an exam, or being in an exam and not having studied for it. I had that dream every week or so for decades after college. I later learned that my old Ph.D. advisor, Dick Lewontin, had it every night. Other academics have told me of such dreams as well, which shows that a). dreams are not completely meaningless, and b). we’ve internalized the anxiety that comes along with being a teacher and a professor, and that’s expressed in our dreams. Or so I think.

But I no longer have “college dreams”. Rather, I have a dream related to the “can’t-find-the-exam-room” dream. In this one, I’m in one locality and have to get to another one, and am severely time limited. Sometimes I’m with someone (usually a woman I don’t know), but often not.  Last night I was alone somewhere in New York City, but it was a city with very narrow, twisted streets, all confusing, and I had to get to Grand Central Station by a certain time. (I have no idea why.) I kept trying to make my way there, but kept getting lost. One time I found myself in a miniature suburbia, complete with cute houses, lawns, and picket fences, occupying a single street in the city. Then I found myself in a Chinatown, with narrow streets filled with Chinese restaurants.

In none of these dreams do I ever make it to my destination; I always wake up knowing that I didn’t make it on time. In this way the dreams resemble the “frustration dreams” involving exams and classes.

What does this mean? Beats me.

If you have a recurring dream—and I’m sure many of you do—by all means share it with us.

Moar photos from the proprietor

November 17, 2020 • 2:15 pm

There is much to brain about, but although the neurons are willing the flesh is weak. Perhaps tomorrow, but, for the nonce, here are some pictures I’ve taken. These are just random photos as I scroll through the years. Some of these I’ve posted before

Three from St. Petersburg, July 2011, during the Littorina (marine snail) meetings. Somehow I fell in with this great group of researchers, who love to have fun and hold good meetings in nice places. First: Dostoyevsky’s cigarette case, inscribed by his young daughter the day he died:  “28 January. Papa died today.” He died on February 9, 1881, so I assume that the written date is the Julian calendar date.  This is in his apartment home in St. Petersburg:

One of my favorite pictures I ever took, at Peter the Great’s Peterhof Palace (they took us all out there; the meeting organizers were fantastic). When I saw this scene I knew it was a Cartier-Bresson “decisive moment” with all the children posed as if in a dance. It might be better in black and white:

The locomotive and tender of the train that brought Lenin to the Finland Station from Switzerland on April 16, 1917, before the October Revolution. Not many people know this locomotive is there, and it took me nearly an hour to make myself understood that I wanted to see it. There were no English-speakers, and I finally drew a locomotive with a picture of Lenin on top to show a ticket-taker, which twigged him to my request. You have to get special permission to see it, and it’s under glass.

August, 2011. Lunch at Allen & Son, a ramshackle BBQ joint in the middle of nowhere near Chapel Hill, North Carolina. My companion was John Willis, a professor at Duke, who, like me, loves BBQ. Note the chopped North Carolina version, with slaw and hush puppies, as well as fried okra as a side dish. Banana pudding for dessert is served only on Fridays, and therefore we went on a Friday:

 

Alas, Allen and Son is no more. Genuine BBQ joints are an endangered species.

Chicago, September 2011:

October, 2011: What many think is America’s best pizza: the white clam pie at Pepe’s in New Haven, made with lots of garlic and fresh clams. It’s not available every day. I made my friend Fred Cohan take me there after I gave a seminar at his school,  Wesleyan.

November, 2011: eating the best paella I’ve ever had, and in Valencia, of course. I gave a talk at the University, and then my best friend Kenny and his wife Jane, whose son Adam was living in Valencia, came down to take me to this joint far out in the country. An old man tends the paellas over a wood stove. Lord, was it good!

On to another seminar in Madrid, where I visited one of the most famous places to get chocolate and fresh, hot churros. (This is one of the best things about being an academic: you get local hospitality and travel as part of the job.)

The chocolate is thick and rich, and you dip the hot churros into it.

Costa Rica, January 2012 for a meeting of the officers of the Society for the Study of Evolution. (I did a lot of traveling that year!) After the meeting, I traveled around with our Secretary, Judy Stone, to act as her companion while she collected plants:

Overlooking the Pacific:

Oophaga pumilio, known as the strawberry-poison-dart frog, or “blue jeans frog”. It’s tiny (this is an adult), and I photographed one in my hand.

The greatness of PCC(E)

November 13, 2020 • 2:15 pm

This CNN bulletin gives what’s likely to be the final Electoral College tally for Biden (306 votes) and Trump (232 votes). (Click on the screenshot.)

I’m letting you know because I was the first person to call the election for Biden AND to give the correct final Electoral College vote for Uncle Joe. This was in a post on November 5.  I ask all the readers to avoid false idols like Nate Silver and recognize the prescience and wisdom of your host, who will now celebrate by taking a nap.

Miscellaneous photos

November 9, 2020 • 1:45 pm

I’m off to look for hooded mergansers, which have been sighted not far away in Hyde Park.  In the meantime, while looking for photos this afternoon, I came across some old ones of interest—at least to me. I’ll share them. TRIGGER WARNING: Some self aggrandizement.

My landsmen uncles: Bernie and Moe. The brothers of my mom, they had a thriving auto parts business in Pittsburgh.  Look at those golf outfits! (I wonder how they got into the country club. . . )

My first student, Allen Orr, and I on the Great Wall of China at the International Congress of Genetics in 1998:

My dad (right) with Sophia Loren at a toy store in Athens, ca.  1956. Loren was there to film the movie Boy on a Dolphin, and my dad helped with the vehicle logistics (they used Army petrol and vehicles as there was a postwar shortage of both in Greece).

Feeding cats at a convent in Mystras, Greece, ca. 2000. I always carried a box of cat food in my backpack while in Greece. The nuns, who didn’t take good care of these hungry moggies, were peering out the windows:

At the Karni Mata “Rat Temple” in Deshnoke, Rajasthan, India, 2003. The rats (there are thousands who run loose in the temple) are eating one of the offerings: a pan of cream.

Pushing flies, 2005. My station at the lab bench. This is what I did for the vast majority of my career:

Beef brisket BBQ at the City Market in Luling Texas (2005)—in my experienced view, the best barbecue in America. No plates, just white bread, raw onion, pickles, beer (sausages if you want ’em), and their fantastic sauce.

Greg Mayer, who wrote this morning’s election post, in his office in 2005, cutting up a kringle for us to eat (this is a pastry speciality of Racine, Wisconsin):

A “Big Dat”, the monster donut that’s the speciality of Dat Donuts on the South Side. I see this is getting food-themed.

With my buddies at the end of a two-month field course in Tropical Ecology run by the Organization for Tropical Studies. Costa Rica, 1974:

Feeding a real Texas longhorn on the Hillis/Bull Double Helix Ranch, 2007

And shooting beer cans (I have never fired at a living thing!):

A ride on a tamed wild mustang, New Mexico, 2007. At last I got to put my cowboy boots to genuine use!

A beautiful feral kitten at the Şehzade Mosque, Istanbul, 2008:

Tasting wine with my oenophile BFF, Kenny. Denton, England, 2008.

Time to look for mergansers!

Revisiting an old paper, but a good one

October 13, 2020 • 9:30 am

I have to brag a bit in the title because if you say a paper is an “oldie,” you have to also say “it’s a goodie”. But I think this one is—it’s the first of two papers I wrote with my then-grad-student Allen Orr on the time course of speciation in Drosophila.  And it’s one of the few good ideas I’ve ever had. I don’t know how often it’s been cited—I don’t look up stuff like that—but it has been influential in inspiring others to do related work. I’m writing about this paper because I recently revisited it in an interview (see below).

Here’s a very brief summary of what we did. I realized one day, when I was at the University of Maryland, that there existed a tremendous amount of data about the sexual isolation and hybrid sterility/inviability of various Drosophila (fruit fly) species tested in the lab. There also existed, separately, a large amount of data on the “genetic distance” between these species as judged from gel electrophoresis. This genetic difference is a rough measure of the times since the species diverged. The more similar the electrophoretic profiles, the younger the species. (The actual real-time calibration of the distance is hard, as Drosophila has no fossil record, but we did our best.)

You could, I realized, take various pairs of species, see how much reproductive isolation they had between them—how much mating discrimination and whether the hybrids were viable and fertile—and correlate that with the genetic distance between members of each pair. If you plotted genetic distance against the degree of genetic isolation, you could get a “time course” of speciation, seeing which forms of isolation evolved earliest, what rate they evolved at, whether it would make a difference if the species lived in the same or different areas, and so on.

Of course there are lots of issues here, one being that measures of reproductive divergence between various pairs of species aren’t evolutionarily independent, so we had to do phylogenetic corrections. Further, sexual isolation and sterility/inviability are only two of the reproductive barriers that separate species, and we had to neglect types of genetic isolation that could operate in nature but couldn’t be measured in the lab (e.g., different preferences for food or microhabitats).

The results, though, were surprisingly clean and enlightening. For example, we found that sexual isolation—but not hybrid inviability—evolves ten times faster between species now found in the same area than those now found in different areas. This result, which has held up in repeats of our work, suggests that natural selection “reinforces”, or strengthens, mate discrimination between species when they live in the same place. That’s probably because there is a genetic penalty to be paid, in the form of hybrid problems, if you actually mate with the “wrong” species; and you only have that kind of selection operating in species that live in the same area, and have a chance to produce hybrids.

Here’s a graph from the second of our paper of papers showing two plots of the degree of sexual isolation between pairs of species (y axis) against their electrophoretic genetic distance (a measure of the divergence time between members of each pair). “Allopatric” taxa are pairs of species that are geographically isolated at present, while “sympatric” taxa are pairs of species that live in the same general area. (These data are phylogenetically corrected.) You can see that the degree of sexual isolation appears much earlier (at lower genetic distances) when the taxa live in the same area. This is a very striking result that is highly statistically significant. It suggests that natural selection operates on species living in the same place to “reinforce” their sexual isolation. You don’t see this difference for hybrid sterility or inviability, which are not expected to be reinforced by selection.

I digress, but it’s nice to think about this good old work.  Allen came on board the project at the beginning, and we spent several years collecting the data (which was scattered all over the literature), calculating statistics when only raw data were given, and analyzing the data. Thus the paper didn’t come out (in Evolution) until 1989, three years after we’d moved to Chicago.

Then electrophoretic data and reproductive-isolation data continued to accumulate, so in 1997 we published an update of the 1989 paper. The additional data confirmed the patterns we’d seen before. And now, since nobody does electrophoresis any more, and estimates of genetic divergence come from DNA sequences, we can’t do this analysis further. (DNA-sequence data does not exist for most of the species we used.)  Similar work has been done in fish and tomatoes, and at least two researchers have redone our analyses in flies using different techniques (the conclusions remain good).

The references to our two papers are given at the bottom, along with the links to them (free access).

This long introduction just wrote itself, when what I really want to do is call your attention to an interview I did about that first paper with Hari Sridhar at his site Reflections on Papers Past. Hari, a a post-doctoral researcher at the National Centre for Biological Sciences, Bengaluru (formerly Bangalore), India, has been interviewing scientists about well known papers in ecology and evolution since 2016.  He was kind enough to interview me about the first Coyne and Orr paper, and you can see the interview by clicking on the link below. I haven’t read the final version, which is a transcript of an audio conversation, so be aware that it’s spoken language. I did read a draft and corrected a few phrases that were unintelligible over the phone.

If you’re interested in papers in ecology and evolution, you might have a wander round Hari’s site; there are lots of interesting papers and interviews, many with people I know.

Click below to see the interview.

I want to add that although Allen was my grad student during much of the time we wrote these papers, it was a total collaboration. As with all my students, I don’t micromanage their work or ever tell them what research to do. Allen was interested in the project from the beginning, and contributed tons of work and many ideas to the two papers. And our collaboration continued in what I consider my most important scientific accomplishment, the book Speciation (Coyne and Orr, 2004; note that the book is now expensive but was about $50 when it first came out).

Here are Allen and I at the Evolution meetings in Portland in 2010. Allen was president of the Society for the Study of Evolution, and I was an incoming President, so he briefed me about the job. We had a great time in Portland, as that was before the city went nuts.

And as a measure of the fame of our work, you can’t get bigger than this. My collaboration with Allen was featured in the 2001 movie “Evolution” (a dreadful film!), as a scrawled reference on the blackboard behind two of the stars, David Duchovny and Orlando Jones. See below. It says “Read Coyne and Orr.  ‘Drosophila’ pp. xx8-450”. Note that the page numbers don’t correspond to either paper that we wrote, though it may refer to the book. But even in the book those pages don’t correspond to anything that would be a reading assignment.

Another ex-student of mine, Mohamed Noor, called me up and said he’d seen the movie and noticed a reference to our paper on the blackboard. I didn’t believe him, so I had to go see the movie myself. Sure enough, we were in there! Someone later sent me a screenshot (below).

I would call that real fame! Pity they got the page numbers wrong. I’ve always wondered who wrote that on the board and how they knew about our work.

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Coyne, J. A. and H.A. Orr.  1989.  Patterns of speciation in Drosophila.  Evolution 43: 362-381.

Coyne, J. A., and H. A. Orr. 1997. “Patterns of speciation in Drosophila” revisited. Evolution 51:295-303.