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.

_______________

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.

How should I get my hair cut?: a poll

June 11, 2020 • 8:30 am

Well, the tonsorial parlors, salons, and barbershops are now allowed to reopen in Chicago, and I’m thinking of getting a trim, as my hair is quite wild and unruly (see second photo below). But some people say they like the longer look, so I’m contemplating leaving it longer but neatening it up.  I’ll give two photos and crowdsource an answer, though there’s no guarantee I’ll go with the majority.

Have a look at two choices:

Thie is pretty short (photo taken in Shakespeare & Co. bookstore in Paris, petting the resident cat):

Pandemic hair, taken this morning. I wash it and run a brush over it, but that’s all I do. It’s definitely unruly.

 

“The Duckling Professor”

May 12, 2020 • 11:15 am

On Sunday, the local ABC News ran a story about the pond, the ducks, and yours truly. You can see the 3.5-minute video (and a transcript) of the piece below, shot and reported by ABC correspondent Zach Ben-Amots.

It’s a nice piece, I think, but I always cringe when I see myself. And it’s worse this time because I’m all shaggy from a lack of a haircut. And, in the second bit, I admitted to being stressed out (I was!), even though I greatly enjoy tending the waterfowl. This was right after we had another duckling death and the hens were fighting. So I’m not going to watch it again.

Oh well, I submit it for your approval. Just ignore the (lack of a) haircut.

 

The Chicago Tribune does a story on my ducks

April 1, 2020 • 9:30 am

UPDATE: Mary emailed me saying that she’d gotten a lot of email from people saying, in essence, “Thank you for making me cry and feel more hopeful this morning.”  Such is the power and value of good journalism!

**********

 

A few days ago, Colleen Mastony, the Director of Media Relations at the University of Chicago, contacted me, saying that she’d heard about my duck-feeding activities as well as the letter from our Provost and President allowing me access to Botany Pond during the lockdown. Colleen used to work for our biggest local paper, the Chicago Tribune, and wanted to pitch the story to the Trib, saying that she thought it would make a nice “feel-good” story for these troubled times.  She wrote up a prospectus and sent it to her former colleague Mary Schmich, who writes a regular column for the Trib.

Schmich is a big presence in Chicago media (indeed, nationally): she writes a regular, widely-read, and nationally syndicated column for the paper for which she won a Pulitzer Prize in 2012. On top of that, she wrote the comic strip “Brenda Starr, Reporter” from 1985 to 2011, and penned one of the most famous “advice” pieces of our era, a column called “Wear Sunscreen“, incorporating the advice that she’d give were she asked to deliver a commencement address. That column became an eponymous book and was turned into a piece of mix music by Baz Luhrmann, which you can see and hear here (I can’t find the column online, but its words are in the video).

At any rate, Mary liked the idea of the story, interviewed me about Honey and the ducks over the phone, and, two days ago, appeared at the pond with a Tribune photographer, Terrence James. Mary asked lots of questions while Terrence snapped Honey, Dorothy, and Wingman, who cooperated by eating duck food for the camera and then preening on the center “bathtub ring”. He also photographed me feeding the birds. Fortunately, no other ducks showed up to cause trouble.

After those two interviews, Mary texted me with more questions: she was punctilious about getting all the details correct. And then, that same day (yesterday), her story on Honey, me, the ducks, and the University went online. And today it’s in the paper version of the paper. If you’re in the U.S. you’ll be able to access the story from the links below, but if you’re overseas those links won’t work and you’ll have to use this “wayback” link.

Yanks can read the online story, complete with two photos, at either the Tribune link below or the Effingham Daily News link below that (click on the screenshot).  Note that you can get one free Tribune story per month, but can subscribe for only 99 cents for three months.

I won’t reproduce the story; see it by clicking on these headlines or on the link above.

Tribune:

 

from the Effingham Daily News:

Mary did a terrific job synthesizing everything and giving it the necessary background, atmosphere, and feel-good patina (see the ending). I went down to the pond a few minutes ago and told the ducks, but they seemed more interested in their mealworms than in their newfound fame.

The original online story had two photos by Terrence (below), but the new online story, as well as the paper edition, has only the photo of me. Here they both are, along with the Trib’s original online captions:

Jerry Coyne, a widely respected evolutionary biologist and an emeritus professor at the University of Chicago, feeds migratory ducks on Botany Pond on the University of Chicago campus March 30, 2020. He feeds the ducks three times a day.(Terrence Antonio James / Chicago Tribune)

Here, in order from left to right, are Dorothy, Wingman, and Honey:

Migratory ducks return to Botany Pond on the University of Chicago campus in Chicago’s Hyde Park neighborhood, where they are seen preening on March 30, 2020. (Terrence Antonio James / Chicago Tribune)

Finally, I sneaked a peek at the neighbor’s version in front of their door, and found that the story occupies half of page three. This is what you see when you turn the front page. Truth be told, I know why they used a photo of me but they should have had one of the ducks!

Anyway, now that Honey and her friends are famous, perhaps it will lead to more people visiting the pond. That carries the risk of them feeding bad stuff to the ducks, but the University has promised me a swell new “Do not feed the ducks” sign that will go up by the pond next week. It will say “Please do not feed the ducks. They are well taken care of” (my wording). More on that later.

My last research paper is published

January 23, 2020 • 11:45 am

Thie paper below is the culmination of research started at least ten years ago in Chicago, but, due to various glitches and re-doing the research in a more thorough way, it didn’t see light for a decade. The paper also represents a collaboration between several investigators, starting with my last NIH grant, but was delayed because of the need to do DNA sequencing (which I couldn’t do), and then the arrival of better, faster, and cheaper DNA-sequencing methods, which allowed us to sequence 20 million bases of DNA for the final paper.

It’s finally appeared as an “early online” paper in Genetics, and will be in the journal soon (I hope). Click on the screenshot to see the online version (pdf here), which isn’t as spiffy-looking as the published version will be. Since I’m not doing any more research with my own hands, this represents what I think will be my last research paper, but perhaps not my last refereed scientific paper.

I’ll explain the results as briefly as I can when the paper appears in final form, but if you want to read it now, it’s free.  I want to say two things, though.

First, I think it’s a really cool experiment, and a good way to go out. It’s the sort of experiment that every evolutionary geneticist thinks of, wants to do, but realizes that it’s dicey because it takes a long time and you might not get the answer before applying for your next grant. Fortunately, this was a major part of what I knew would be my last NIH grant, so I was under no pressure to finish the experiment in the three-year granting period. The question involved was this: if you thoroughly mix two different species of Drosophila, producing a “hybrid swarm” that has the DNA and cytoplasm of both species in equal proportion, what happens to that swarm? Does it evolve into a new species? Or does it revert back to one or the other parental species, and, if so, does it revert to the same species over and over again when you make replicate swarms? And if there is such reversion, how much is reflected in morphology, behavior, and DNA sequence? (That is, does the evolved swarm superficially resemble one of the parental species but still contains DNA from both species?) Or does the admixture produce a swarm that is not a “new species” (like the hybrid parrots that the Washington Post got wrong), but simply a mixed population of mongrels that isn’t reproductively isolated from its parents?

The answer, it turned out, was very clear, repeatable, and quite interesting. But stay tuned.

Second, my very first real research paper, published in 1972 based on my undergraduate research at William and Mary—and also on speciation—appeared in Genetics as well, which is a very good journal. (That paper is free online here.) So there’s been a pleasing symmetry in my research career.

Lunch with Pinkah, and a preview of his next book

January 17, 2020 • 9:15 am

When I’m in Cambridge visiting old friends, I always try to get together with Dan Dennett and Steve Pinker—separately— for I enjoy the intellectual stimulation this provides (and, in the case of Dan, the inevitable stentorian arguing as well). Dan’s out of town this week, but yesterday I managed to dine with The Pinkah at Legal Seafoods near Harvard Square. (Coincidentally, a reader recommended that restaurant in a comment yesterday).

Pinker had just finished lecturing at the Kennedy School next door, and we had a longish lunch over seafood and brewskis. Since Pinker is wickedly smart, eloquent, and apparently remembers everything he’s ever read, lunch with him is not just a culinary experience, but a bout of cerebral ping-pong. While ingesting the food one must also try to absorb his arguments, which come fast and furious. We talked about determinism, free will, the evolution of music (Steve thinks that there is not an adaptive evolutionary basis for music and musicality, even though music is universal in all cultures), the penal system, evolutionary differences between the sexes, speciation, Sewall Wright’s shifting balance theory of evolution, evolutionary psychology in general, Steve Gould, and other diverse topics.

Below is my lunch: Legal Seafoods’ famous crabcake (sadly, only one in the lunch portion). I also had a Belgian sour ale. Steve had an IPA (as I recall) and salmon cooked as rare as they could. (I told him he should have just asked for lox.) My crabcake, which was fabulous—all crab and no filler—came with a salad that contained walnuts and cranberries:

Here’s Pinkah after lunch, resplendent in his dark suit and elephant cowboy boots (he immediately assured me that the elephant was legally culled to reduce population size, not to harvest its skin).

At some point I asked Steve what his next book will be (there’s always a next book for him). He first referred me to its nucleus, the article in Proc. Nat. Acad. Sci. below (click on screenshot to see the whole article). I’ve also put up the abstract:

So I told Steve that I wouldn’t reveal the topic of his next book, but he said it was more or less an open secret, and even sent me a summary of its topic, which I have permission to publish. Here’s what he said:

This PNAS paper is a preview of the ideas and the research from my group that will be the core of the new book. Its tentative title will make it sound more controversial than it actually will be:

Don’t Go There: Common Knowledge and the Science of Civility, Hypocrisy, Outrage, and Taboo.

Though I’ll discuss outrage and cancel culture and social media shaming mobs, they won’t be the focus of the book—there is no shortage of articles documenting and deploring them, any day of the week. This one will probe the game theory and psychology behind them, together with other example of coordination like fads, bank runs, political protests, network externalities, moral norms, social conventions, and everyday informal cooperation. I’ll probe at the psychological phenomena beneath them, including the sense that certain things are public (“out there”), emotions such as shame, embarrassment, guilt, and outrage, and nonverbal displays including blushing, cringing, crying, laughter, and eye contact.

So you can look forward to that (as usual, the Pecksniffs will come out in force to criticize it, no matter what he says). Steve said he’ll start writing it in about a year, and I suspect it won’t be long after that until it’s finished (he wrote The Better Angels of Our Nature in only a year and a half).

Finally, before lunch I tarried for a while in the book section of the Harvard Coop, and found that they had moved the biology section down to the first floor, right inside the door—where it deserves to be. There’s even an “evolution” section (which, unaccountably, is missing WEIT). But several copies of Faith Versus Fact reside in the History of Science section, also where they should be. I’ve seen them in “Theology” sections, but they could also be comfortable in “Philosophy of Science” sections. (I have to tout my books because, unlike Steve’s, they’re not self-touting!)