Tag Archives: academic life

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.

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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]

Paul's family at AAAS 2019

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

Valeria signing, Paul just behind, AAA&S 2019

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

Valeria and family at AAAS 2019

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

bonhoeffers-and-lenski-aaas-2019.jpg

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

AAAS 2019 Mercedes, Paul, Sebastian and me

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

Sebastian, Paul, Valeria, me, Luis AAA&S 2019

[Paul and I compare our biologically themed ties.]

Paul and me at AAA&S 2019

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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.

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A Birthday Sonnet

This past weekend, I celebrated my 60th 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.

 

Ben Kerr's Skakespearean 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.

 

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Another Birthday Haiku

As I said in my last post, I just celebrated my 60th birthday with lots of friends and family. Several folks produced new artistic works, including two lovely haikus that celebrate the E. coli long-term evolution experiment.

Here’s one from Mike Wiser, who did his doctoral research on the long-term lines. A highlight of his work was a paper showing that fitness trajectories in these populations tend to follow a power law, which has no upper bound, rather than an asymptotic rectangular, as I had previously assumed.

Living things adapt.
Evolution keeps going.
No peak yet in sight.

 

Power law prediction, 2013

[The power-law model (blue) predicts future fitness gains much more accurately than does the hyperbolic model (red).  Image modified from Wiser et al. (2013, Science 342: 1364-1367) and shown here under the doctrine of fair use.]

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Birthday Haiku

This past weekend I had my 60th birthday. I was delighted to celebrate it with wonderful colleagues, students, friends, and family.

At a dinner roast and toast, everyone sang When We’re Sixty Four (Thousand), a tribute from the E. coli in the LTEE to the People of the Lab. And several friends came up with new contributions at the intersection of science and culture.

This beauty is from Andy Ellington, a professor in the Center for Systems and Synthetic Biology at the University of Texas and a member of the BEACON Center. As background, Andy coauthored a recent paper that helps to elucidate how one LTEE population evolved the novel ability to use citrate.

Without further ado, here’s his haiku …

Citrate just beyond.

Acetate potentiates.

Glucose is all gone.

 

Citrate

[Image of citrate molecule from Wikimedia Commons]

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Evolving Fun and Games

Science isn’t always fun and games. But sometimes it is!

This guest post is by Terry Soule, a computer scientist, and Barrie Robison, a biologist, both on the faculty at the University of Idaho. The BEACON Center for the Study of Evolution in Action brings together biologists, computer scientists, and engineers to illuminate and harness the power of evolution as an on-going process.

With BEACON’s support, Terry and Barrie have developed a video game, called Darwin’s Demons, where you must fight off enemies that are evolving to defeat your best efforts!

Feel free to comment here.  However, please send any technical queries via email to Terry (tsoule@cs.uidaho.edu) and/or Barrie (brobison@uidaho.edu).

*****

Thanks to BEACON’s support, Polymorphic Games has created the evolutionary video game Darwin’s Demons, and placed it on the Steam website as part of the greenlight process.

Darwin’s Demons adds an evolutionary component and modern flair to an arcade classic.  Darwin’s Demons models biological evolution using enemies with digital genomes. Enemies acquire fitness by being the most aggressive, accurate, and longest lived, and only the most fit enemies pass their genomes to the next generation. The result? The creatures you found hardest to kill have all the babies, making each generation more challenging than the last!

The game includes in-game graphs for tracking evolution, displays the most fit enemies from each wave, and has an experiment mode where you can set parameters like the mutation rate, fitness function, etc.  It also dumps all of the evolutionary data to a file.  So, there are opportunities for experiments on user driven evolution if anyone is interested.  (We are more than happy to share the code and/or make simple modifications for controlled experiments.)

If you get the opportunity please try out the demo (downloadable at either of the sites listed above, with Windows, MAC, and Linux versions), vote for us on Steam, and send us comments, suggestions, or ideas for future directions and collaborations.

Thanks,

— Terry Soule (tsoule@cs.uidaho.edu), Computer Science, UI

— Barrie Robison (brobison@uidaho.edu), Biological Sciences, UI

 

Darwin's Demons

[Darwin’s Demons: image from the Polymorphic Games website]

*****

 

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