A Leap of Faith, Part 2

My wife, infant son, and I moved to Amherst the first weekend of April 1982. A beautiful snow fell on Sunday. Then, early on Monday morning, my new boss Bruce Levin cross-country skied by the old house we were renting, knocked on the door, and asked me when I’d be coming to the lab!

I had much to learn, of course. I remember learning how to use a pipettor from a technician in Bruce’s lab, and how exciting it was to estimate the number of cells in a flask (typically many millions or even billions). That estimation is done not by counting the cells directly, but instead involves precisely diluting small amounts through a series of test tubes, each tube containing a large, known volume of a sterile solution. At the end of the dilution series, one takes a tiny amount from the final tube and spreads it across an agar plate. The plate is then incubated for a day or so, during which time each of the few hundred cells that survived the dilutions grows into a separate colony. A colony is a clump of millions of cells that can be seen with the naked eye, unlike the individual cells that can be seen only by using a microscope. One counts the colonies on the plate and, using that number and the dilutions that one made, one can then back-calculate the density of cells in the original flask.

In my first effort at this most basic procedure, I did three replicates from the same flask. I was thrilled when I counted the colonies on the first two plates, and the numbers differed by only a few percent. The third plate, however, differed by perhaps a factor of two, which meant I had done something wrong—maybe I’d let an air bubble into the pipettor’s tip, displacing some of the liquid—and I realized the importance of attention to details.

A little later, while I was still learning the ropes, Bruce had me perform a more complicated experiment to measure the rate at which a certain virus, called T6, adsorbs to and infects E. coli cells. The experiment required a lot of repetitive dilutions and plating of samples that I had to process quickly and accurately. The basic idea is that free viruses should decline in number over time as more and more of them enter cells. (This decline continues only until the first viruses to infect cells have had enough time to produce the next generation of viruses, hence the need to process the samples quickly.) Alas, my experiment was a total failure. What was I doing wrong? I think Bruce had me repeat the experiment, with the same lousy outcome. Though he never said it, perhaps he would regret hiring me. After all, given my lack of experience, Bruce had also taken a leap of faith.

After my second failure, Bruce checked his notes about the particular strain that we were using. As it turned out, he had given me a strain of E. coli that was resistant to T6! Hence, there were no infections, and that explained my failed experiments. Later on, I was able to use the same protocol to measure the rate at which a different virus, T2, adsorbed to and infected E. coli.

Oh, and what about my experiment to look for evolutionary changes that compensated for the cost of bacterial resistance to infection by viruses? That’s what I had proposed in my letter to Bruce asking about a postdoc. I never got to that experiment while I was in Bruce’s lab. However, it provided the seed for a project that I eventually conducted as an early-career faculty member at the University of California, Irvine.

[Bacterial colonies growing on agar plates. Photo credit: Brian Baer, MSU.]

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The Bacterial Allstars

I wrote about Stephen Jay Gould’s book, Wonderful Life, in a previous post. While that book wasn’t an inspiration for starting the LTEE, I often quote passages from it when I give talks on the LTEE, because those passages frame the big-picture question about the repeatability of evolution.

I first heard Gould speak at a multi-day conference in Irvine, California, in 1994. The conference was on Tempo and Mode in Evolution, with the talks celebrating and building upon the ideas in a landmark 1944 book of that same title written by the paleontologist George Gaylord Simpson (1902-1984).

Gould’s talk began with several pictures of dramatic newspaper headlines that read something like these:  Darwin Hammered, Darwin Rejected, and Darwin Trounced Yet Again. I remember nodding in agreement about the lack of respect for Charles Darwin and his ideas in the press, and I’m sure many of the others in attendance did as well.

But then Gould turned the tables to reveal his sly humor. These were all headlines from the sports section of Boston newspapers about ill-fated outings by Danny Darwin, who pitched for the Red Sox. Gould was not only an expert on fossils; he was an aficionado of baseball as well. In fact, he wrote many interesting and scientifically minded essays about baseball including, for example, a memorable piece on the extinction of the .400 hitter in his book Full House. (And see this interview with Gould on that subject.)

I had hoped to meet Gould at this meeting, or at least I hoped he might hear me speak when I gave a talk about the LTEE. (Here’s a link to the paper that I covered in my talk.) Alas, Gould gave his talk and then left the conference before my talk, and before I could meet him.

Luckily, though, I met Gould when he came to MSU, first as a commencement speaker in 1999, and then in 2000 when he gave a public lecture here. On that second visit, I served as one of his hosts. When I picked Gould up at the airport, I brought along two Lansing Lugnuts caps.  The Lugnuts are a local minor-league baseball team. I explained to Gould that I’d have liked to take him to a Lugnuts game, but the season had ended before his visit. I gave him one of the caps, and I asked if would autograph the other cap as a souvenir for me.

Gould hesitated for a moment. He explained he had been asked to autograph books by Darwin and others. He would sign books that he had authored, but nothing else. When he looked at the Lugnuts cap, however, he realized this was a different kind of request. And so, he signed it: “To the bacterial allstars, Stephen Jay Gould.” Now that’s a souvenir!

Gould and I also had the chance to have a meal together, just the two of us. We discussed our shared interest in the repeatability of evolution, and how our disparate study systems—fossils and flasks—could shed light on that fascinating question.

Sadly, Gould died just two years later. However, he managed to complete a massive volume, The Structure of Evolutionary Theory, shortly before his death. That 1400-page tome included a recounting of the history of evolutionary thought—informed by Gould’s collection of rare old books—as well as a synthesis of modern research in evolutionary biology from his perspective.  I was pleased and honored that he discussed the LTEE at several places in that book.

It’s a Wonderful Life

I’ve sometimes been asked whether the idea of the LTEE was inspired by Stephen Jay Gould’s book, Wonderful Life. In this bestseller, Gould put forward the idea of “replaying” evolution to explore the idea of whether evolution is repeatable. He wrote (page 48): “I call this experiment ‘replaying life’s tape.’ You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past—say, to the seas of the Burgess Shale. Then let the tape run again and see if the repetition looks at all like the original.”  However, Gould then went on to say: “The bad news is we can’t possibly perform the experiment.”

Gould (1941-2002) was a paleontologist as well as an historian of science and prolific author, and he had in mind replaying life’s tape on a planetary scale over millions of years. The Burgess Shale is a geological formation in western Canada that contains fossils from about 500 million years ago. The fossils include exceptionally well-preserved early animals, many of which have body plans that are unlike any modern animals. Building on his thought experiment of replaying life’s tape, Gould pondered the potential outcomes: “If each replay strongly resembles life’s actual pathway, then we must conclude that what really happened pretty much had to occur. But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life? What could we then say about the predictability of self-conscious intelligence? or of mammals?”

Of course, Gould’s experiment is impossible at a paleo-planetary scale. But at a more modest scale, one of the main goals of the LTEE is to study the repeatability of evolution. And so, I often quote from Wonderful Life when I’m giving talks about the experiment. Thus, it’s only natural that someone might wonder if Gould’s book had inspired me to start the LTEE.

In fact, though, Wonderful Life was published in 1989—a year after the LTEE began. I think I first heard about it when Mike Travisano shared some passages with me that were relevant to a paper we were writing on the roles of adaptation, chance, and history in evolution.

So, while Gould and I were thinking about similar issues, we were imagining them at vastly different scales. It’s one of the fascinating aspects of evolution that these broad categories of causality—adaptation by natural selection, chance events from mutations to asteroid impacts, and the effects of past history on future opportunities—play out at these different scales.

I was lucky to meet Gould and discuss these issues with him several years later, as I’ll describe in a future post.

In Other News

Today is the 34th birthday of the LTEE, which I started on February 24, 1988. 

With the invasion of Ukraine, however, it’s not a day to celebrate.

 The LTEE will move to the capable lab and hands of Jeff Barrick this Spring, after all 12 lines have reached 75,000 generations.

Over the decades, several lines fell behind others due to cross-contamination (or concerns about the possibility), which we detected by examining the alternating Arabinose marker and seeing the resulting colony colors on TA plates. Those lines were then restarted from whole-population samples, but they would be 500 generations behind the others (or a multiple of 500 generations behind in some cases).

The picture above shows red and white colonies growing on TA agar in a Petri dish. The red colonies cannot grow on the sugar arabinose that is part of the TA medium, while the white ones can use arabinose. Half of the LTEE lines started from red colonies (Ara–1 to Ara–6), and half started from white colonies (Ara+1 to Ara+6). We alternate the red and white lines each day during their propagation. That way, if cross-contamination occurs, we can detect it by the presence of bacteria that make colonies that are the wrong color. We check colonies before every periodic freeze of the LTEE. These days, with DNA sequencing, we can also use derived mutations that are unique to each lineage to check whether a putative contamination event is real or not. (Indeed, in some populations, especially those that evolved hypermutability, the colony markers don’t work like they did when the LTEE started.) If we confirm that a cross-contamination event has occurred, we restart the affected population from the last frozen sample of that population.

So today, Devin Lake will propagate the last two lagging populations. Our lab will continue to propagate them until they, too, reach 75,000 generations. The last one should reach that goal in late May.

Hat Trick

This past weekend Madeleine and I attended the annual meeting of the American Academy of Arts & Sciences in Cambridge, Massachusetts. The Academy was founded in 1780 by John Adams and several dozen other scholar-patriots “to cultivate every art and science which may tend to advance the interest, honor, dignity, and happiness of a free, independent, and virtuous people.”

It was an especially exciting meeting for us because we got to see three of our dear friends inducted as new members:  Paul Turner and, as International Honorary Members, Valeria Souza and Sebastian Bonhoeffer.  All three of them signed the membership book, putting their “John Hancocks” alongside those of distinguished artists, scientists, scholars, and leaders (including the John Hancock) from the past 239 years, while Madeleine and I celebrated with their spouses and families.

I’ve known Paul, Valeria, and Sebastian for decades.  Paul was a graduate student in my group at UC-Irvine, and then he moved with me to MSU, receiving his PhD in 1995. For his dissertation, Paul studied issues related to vertical and horizontal transmission in bacteria, including the roles of density- and frequency-dependent selection. Paul is a professor at Yale University, where he and his team study the evolution and ecology of viruses, including some that can specifically target antibiotic-resistant bacteria and have been used to cure life-threatening infections.

Valeria was a postdoc in my group, also first at UCI and then again at MSU. She worked with Paul on a fascinating, but challenging, experiment to investigate the effects of horizontal gene transfer on the speed of adaptive evolution in bacteria. Valeria is a professor at Universidad Nacional Autonoma de Mexico, where she and her group conduct research and work with the local community, governmental agencies, and nonprofits to conserve the Cuatro Cienegas basin, a biologically unique and fragile system of oases in the Chihuahuan Desert.

Sebastian and I met at Oxford University in 1993, where he was a graduate student and I was on sabbatical. We collaborated on a theory project that examined the hypothesis that pathogens with long-lived propagules would evolve to be more virulent. More recently we’ve taught together in the Guarda (Switzerland) summer course on evolutionary biology. Sebastian is a professor at ETH Zurich, where he and his team construct and analyze mathematical models of population dynamics to understand, for example, the pathogenesis and spread of HIV and other viruses.

Besides being creative and talented scientists, Paul, Valeria, and Sebastian are three of the nicest people around. I’ve been incredibly fortunate not only to work with them, but also to know them as close friends.

And there were so many other outstanding inductees, some of whom I’ve also known for many years including microbial ecologist Jo Handelsman (University of Wisconsin), theoretical ecologist Mercedes Pascual (University of Chicago), evolutionary biologist Mark Rausher (Duke University), plant biologist Detlef Weigel (MPI Tubingen), and evolutionary biologist Kelly Zamudio (Cornell University).

Each of the 5 “classes” had a speaker give a short talk to all the inductees and their families. Representing the Biological Sciences, Jo Handelsman gave an impassioned talk “On the importance of soil.” It’s something almost everyone takes for granted, and yet fertile topsoil is incredibly valuable, it’s disappearing in many areas, but it can be preserved and even enhanced with improved agricultural practices. Representing Public Affairs, Business, and Administration, Sherrilyn Ifill (NAACP Legal Defense Fund) gave a clarion call to fix American democracy.

The evening before the induction ceremony there were artistic performances and presentations by several new members including jazz pianist, composer, and singer Patricia Barber.  The morning after the induction included a performance by, and discussion with, the incredible playwright, filmmaker, and actress Anna Deavere Smith, who performed and described how she constructs her amazing one-woman shows.

Throughout all the events, the staff of the American Academy of Arts & Sciences were superbly organized and warmly welcoming.

[Paul Turner’s family in the theater just before he signs his name into the book of members of the American Academy of Arts & Sciences]

[Valeria Souza signing the book, with Paul Turner just behind her and waiting his turn]

[With Valeria Souza and her family following the induction ceremony]

[Sebastian Bonhoeffer and his wife Hanna (next to me) with Madeleine (next to Sebastian) and me the evening before the induction ceremony]

[Yours truly along with Mercedes Pascual, Paul Turner, and Sebastian Bonhoeffer]

[Sebastian, Paul, Valeria, me, and Luis Eguiarte (Valeria’s husband, and also a superb evolutionary plant biologist]

[Paul and I compare our biologically themed ties.]

Privilege

At my 60th birthday party this summer, I made a few remarks about how fortunate I have been in my life:

Born to parents who nurtured me.

Born into a nation that values life, liberty, and the pursuit of happiness.

Born at a time and in a part of the world where science and public health greatly improved my chances of survival and good health. (Living to age 60 was once a rarity, and it still is in much of the world.)

Fortunate to have had a superb education, and to have met so many wonderful people along the way, including my wife.

Lucky to have three talented, interesting, and kind children, two loving and good sons-in-law, and now two healthy grandkids.

Fortunate to have a career where I get to study how the world works, and where I get to work with incredibly talented and motivated students and colleagues.

Today I was reminded of another aspect of privilege:

Privilege is getting to vote with no long lines and without intimidation. I was privileged today. I wish all Americans had that privilege.

It’s something we should all embrace.  Working to deny citizens their right to vote is wrong. It also threatens all of us today and future generations, and the freedoms and privileges that we sometimes take for granted.

A Birthday Sonnet

This past weekend, I celebrated my 60^th birthday with friends and family from all over. One of the roasters was Ben “The Bard” Kerr, a professor at the University of Washington and colleague in the BEACON Center for the Study of Evolution in Action.

Borrowing from another bard, Ben waxed poetic about one of the lineages in the long-term evolution experiment and raised a toast with this Shakespearean flask.

 

ODE TO AN LTEE LINEAGE

Shall I compare Ara-3 to a summer’s day?

Thou start more humbly, but sure potentiate.

Rough spins do shake the darling bugs of Rich’s gaze,

And latecomer’s “fleece” hath all to port citrate.

One line’s long-shot passed by eleven lines,

And how was its controlled complex “skin” pinned?

Promoter capture, over some time refined.

By chance, with nature’s arranging force, trimmed.

But thy Cit-minus partner shall not fade

Nor gain possession of the flair of most

C₄ shall Cit^– snag, now spawned by carbon trade

Then on it turns ‘til lines will species now boast

     So long these cells can achieve, so wise to see,

     So long lives this work- and awe is rife, Lenski.