Thank you, Neerja

Neerja Hajela has worked with me for over 22 years as a technician and lab manager. She is extremely skillful, diligent, organized, and dedicated in her work. On top of all that, she is a wonderfully kind and warm person. Now, this is her last week before she retires.

It’s impossible to put into words all that Neerja has done for me, for everyone in the lab, for the LTEE, and for my collaborators. But let me mention a few of the things she has done.

By keeping the lab running in a smooth and orderly fashion, Neerja has enabled me to spend more of my time thinking about science, writing papers, giving talks, etc., etc. We scientists sometimes complain that we have too much to do, and so we joke that we want to clone ourselves. Well, I’ve done better—I’ve had Neerja.

Those of us with labs know that our institutions take laboratory safety very seriously, as well they should. Neerja runs such a tight ship that, on many occasions after inspecting our lab, the safety officers have made comments to the effect that they wish all labs were as neat, clean, organized, and safety-conscious as ours.

One of the challenges of the long-term evolution experiment (LTEE) with E. coli is freezer management. We now have over 30 years of samples, spread over half a dozen freezers, which provide a record of past evolution. Neerja has overseen this ever-growing collection with extraordinary care and dedication. The samples provide critical backups that allow us to restart the LTEE from a recent milestone when mishaps occur, and they provide unique research materials such as when new technologies emerge. A case in point: Michael Desai wrote me a few years ago with a request. In essence, he wanted all of the LTEE samples for metagenomic sequencing. All of them—from each population and every generation with saved samples. Since I started the LTEE in 1988, we’ve always saved duplicate samples, with one of them being a backup to be opened only in an emergency. I could send Michael the backups, perhaps, but that didn’t seem like a good idea. So I decided we should make additional sets by going into the ~1500 key samples spread over several freezers; taking a subsample of each and culturing it to produce a larger sample; splitting the new culture into ten sub-cultures; and freezing those to provide a new set for Michael as well as other sets for collaborators and institutions. It took Neerja many months to accomplish all of this, but as always, she did it with great skill and care. (Oh, and you can read about the results of Michael’s request here.)

Last, but surely not least, Neerja has done more of the daily transfers of the LTEE than anyone else. She performed her first LTEE transfer on February 5, 1996, and since then she has done well over 4,200 daily transfers. (Thanks to Zachary Blount, who went through the LTEE lab notebooks for its 30th birthday.) And when Neerja hasn’t done the transfers herself, she has organized who else is responsible for each and every day’s transfers.

Thank you, Neerja, for all that you have done for me, for everyone in the lab, for the LTEE, and for science. Everyone in the lab joins me in wishing you and Ravindra all the very best in your retirement and new home!

 

Neerja Hajela 13-Mar-2017[Neerja Hajela]

Neerja doing transfers 30-July-2018[Here’s Neerja doing yesterday’s LTEE transfer]

Neerja pointing to entries from 1996 & 2018[Neerja pointing at two of her LTEE entries: her first transfer on February 5, 1996, and the one from yesterday July 30, 2018. The lab notebooks in the background record the daily transfers since she joined the lab.]

Neerja's first LTEE entry from 1996[Close-up of Neerja’s first entry.]

LTEE protocol[Neerja’s protocols for the LTEE, mounted in the lab, so nobody makes a mistake]

Neerja enforcing discipline[And in case that doesn’t work, here’s Neerja enforcing lab discipline]

LTEE transfer board[The LTEE transfer board from earlier this year]

Tanush tower 2017[Horsing around Tanush’s plate tower]

Neerja in lab, May 2017[Neerja making copies of freezer samples]

Neerja and Rich[Neerja and me]

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Ralph Evans

Ralph Evans was an exceptionally talented young scientist and wonderful human being. He joined Bruce Levin’s lab as a doctoral student while I was a postdoc in that lab. Bruce and I met Ralph at the joint meeting of the Genetics Society of America, the Society for the Study of Evolution, and the American Society of Naturalists, which was held in St. Louis in June of 1983. That was an historic conference for anyone who studies microbial evolution because several leaders in that nascent field—including Bruce, Dan Dykhuizen, Dan Hartl, and Barry Hall—arranged a session to discuss the future of the field. Among other things, that session led to the organization of the Gordon Research Conference on Microbial Population Biology; the first of those conferences was held in 1985 and chaired by Bruce.

Among the highlights of that 1983 conference was meeting Ralph Evans. Ralph was from Texas, and he had done his undergraduate studies at Rice University. He was in graduate school at the University of Minnesota working in ecology. But after Ralph heard about this new field, he was determined to join it. I can still recall chatting with Ralph after the discussion session about the exciting things one could do with microbes to understand ecology, evolution, and infectious disease. I forget the exact timing, but Ralph soon joined Bruce’s lab at the University of Massachusetts, Amherst (with the blessing of Peter Abrams, his advisor at Minnesota). Ralph and I talked about science pretty much every day from his arrival in the lab until I left to join the faculty at the University of California, Irvine, in the late summer of 1985.

Ralph and I not only shared scientific interests, but Ralph and his wife Barbara (Bard as he called her) became wonderful friends with my wife Madeleine and me. Ralph had a soft Texas drawl, a gentle sense of humor, and a kind and sweet demeanor. He took a special liking to our toddler son Daniel—I still remember all of us walking in a snowy field as Ralph pulled Daniel in a sled. We even shared a washing machine with Ralph and Bard—they owned the machine but had no place to put it, while we had the space and a great need for one!

Tragically, as Ralph was pursuing his doctoral research, he was struck with an aggressive and ultimately lethal brain cancer. He and Bard battled through it together. She joined him in the lab to help with his work, and we sent a then-new-fangled watch that had an alarm setting to help Ralph remember when to do the next step of his experiments. Ralph had a remission, and we all had high hopes when he set off to do a postdoc with Dan Dykhuizen at Stony Brook. Alas, the cancer returned. I gave a talk at Stony Brook and got to say goodbye to Ralph, but not really—for he was in the hospital and non-responsive.

In loving memory of Ralph, and in recognition of the areas of science that most interested him, Madeleine and I have established the Ralph Evans Award. To honor Ralph’s legacy, the award may be given to either a postdoctoral researcher or senior graduate student in the Department of Microbiology and Molecular Genetics here at MSU for important contributions to the understanding of microbial evolution and its underlying ecological and genetic processes.

Thank you, Ralph, for your friendship and inspiration.

[Bruce with three of his UMass graduate students—Lone, Judy, and Ralph—in the late 1980s.]

Bruce, Lone, Judy, and Ralph

[Group photo from the first GRC on Microbial Population Biology: Bruce is front and center, and Ralph is near the back, center-left with a big smile.]

Group photo from 1985 GRC

[Ralph (far left) at a party at Bruce’s home in Amherst in the summer of 1985.]

amherst-goodbye-party-summer-1985[Here Madeleine and I are with Zachary Blount, who received the inaugural Ralph Evans Award.]

Zack, me, Madeleine 2018 Ralph Evans award

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Thirty years is NOT enough

On second thought, let’s get on with the plan for the LTEE to run for at least 50,000-squared generations!

We’re over 1/50,000th of the way there already!

And just a modest donation away! (A few million dollars in an endowment account is all it would take to keep the LTEE going into perpetuity. Contact me if you’d like to fund the experiment when it gets passed along to the next scientist, and the next, and the next, and …)

 

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Thirty years is enough

The LTEE has run for over 30 years and almost 70,000 generations. It’s time to shut it down, as of today.

It’s been a hell of a lot of work, and we have almost nothing to show for it. As some astute commentators have noted around the web, the creatures in the flasks are still just bacteria—creatures, just as they were created.

If you read the first LTEE paper*, you’ll see we predicted the bacteria should become yeast by about 5,000 generations, nematodes at 15,000 generations or so, and fruit flies by 30,000 generations, maybe 35,000 at the outside.

After that, we’d have to stop the experiment anyhow, because we wouldn’t be able to freeze and bring them back alive any longer.

Plus, we’d have to get IRB approval for human experimentation if we ran it much past 50,000 generations.

Well, we’ve given the LTEE all this time, and still … they’re just bacteria. I guess we’ve proven that Charles Darwin was wrong after all.

As an astute reviewer pointed out when we submitted that first paper, “I feel like a professor giving a poor grade to a good student …” I should’ve listened and quit way back then. It would’ve saved everyone a lot of time and effort.

Now it’s going to be a hell of a lot of work next week emptying the freezers and autoclaving all those samples.

*Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C. Tadler. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. American Naturalist 138: 1315-1341.

 

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Ex Laboratorium

The E. coli long-term evolution experiment, or LTEE for short, is approaching its 30th birthday, which will be on February 24th, 2018.

In honor of all the people who have worked on this project, I thought it would be neat to commission a special, but shareable, piece of art. Given the history of science and my own interest in old books, I decided that a bookplate would be appropriate for that.

So the next challenges were deciding what to depict, and who to make the image. I wondered what a smart, curious, but evolutionarily distant organism—like a cephalopod—would think about the LTEE. Who could make an image both interesting and aesthetically pleasing around that idea?

As Stephen Jay Gould wrote in his book Wonderful Life, the evolution of life—like our own individual lives—is often contingent on chance events. And luckily I stumbled via Twitter on TAOJB—The Art Of Jo Brown—during the “Inktober” one-ink-drawing-each-day-of-October event. You can see Jo’s 31 compositions from 2017 here. Looking at her website, I also discovered that she made wonderful images of cephalopods! So I wrote Jo and commissioned a work to celebrate the LTEE’s upcoming birthday!

In addition to an image, bookplates often say “from the library” or “ex libris” (Latin for “from the books”) followed by the owner’s name. I also decided that, instead of ex libris, mine would say “ex laboratorium” with my name.

But that presented another problem, because I want to give some of the bookplates to people who might like them with their own names. So I’ve asked Jo to make a second version that says ex libris along with a blank area for the recipient to write his or her name.

After Jo’s art is complete, I’ll have a printer use her drawings to make bookplates. I’ll give a few to anyone who has ever done an LTEE transfer and/or coauthored a paper based on the LTEE with me! Please let me know if you read this and are one of those folks.

I’ll also eventually post the images here, but for now you can watch Jo’s twitter feed as she shows her progress on executing the design!

ADDED on Nov. 29:  Here are links to Jo’s work in progress including one that shows steps along the way toward the first version and time-lapse videos of her drawing the second version. And the final one shows the two versions completed! Wow & wow!!

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Time fleas, with apologies to Jonathan Swift

Over on twitter, Kyle Card posted a photo of Halloween in the Lenski lab. That prompted Morgan Feeney to reply: “You mean you don’t all dress up as different generations of the LTEE? I am SHOCKED.”

 

And that got me thinking about Jonathan Swift’s rhapsody on fleas:

So nat’ralists observe, a flea

Has smaller fleas that on him prey;

And these have smaller fleas to bite ’em.

And so proceeds ad infinitum.

 

With apologies to Swift, here’s my rhapsody to the LTEE:

So ‘lutionists observe, a cell

Had older cells from which it came;

And these had older cells beget ’em.

So life proceeds and don’t forget em.

 

LTEE flasks repeating

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The Philosophers’ Way

Sometimes we forget … forget to take a break, forget to go outside, and forget to reflect on our individual and collective pasts.

After an intense three days of talks at EMBO—hearing about exciting work by diverse and superb biologists in 13-minute chunks (plus Q&A); seeing dear friends Santiago Elena, Sebastian Bonhoeffer, and Roy Kishony; and making new friends, too—I’ve got the weekend to work quietly and explore Heidelberg.

Yesterday I took the beautiful hike known as Philosophenweg, or the Philosophers’ Way. After crossing the river Neckar, a quick right on Ladenberger Strasse, then the walk up past the grand houses and physics buildings before the gardens that overlook the river, old city, and castle perched in the hills across the way. There were also intriguing and enticing paths into the woods above, but I didn’t take them yesterday.

I returned this morning, despite the chill and overcast sky. The Philosophers’ Way was as scenic as yesterday, but I hardly lingered and hustled up the path to do some exploring in the woods today, hopefully before the rain began.

Off the main path, it soon became very quiet and beautiful in a different way—no longer the dramatic views across the river, and instead the smells, sounds, and colors of autumn in a beautiful forest. The sights and sounds of leaves falling and crunching under foot, and the smells of leaves, branches, and trees returning to the soil.

The slopes and colors and smells reminded me—not exactly, but close enough—of days long past when I hiked and worked in the forests of the Nantahala mountains in North Carolina. I’d be willing to bet there are a lot of carabid beetles in the woods above the Philosophers’ Way. And they have been walking through these woods far longer than the philosophers.

As I walked up and up, there were lots of paths, and at many of the intersections old stones with names, all unfamiliar to me. In particular, this one—Thingstätte—caught my attention. It seemed kind of funny, but maybe in a dark way. I wondered what it meant, and so I took a picture to remind me to look it up when I returned to the city.

Thingstatte

My mind also wandered to these woods, and to history. There weren’t any markers of battles or massacres, but what did happen here in the 1930s and 1940s? With friends and family about 20 years ago, I went on a peaceful walk in the lovely forests near Krakow, where we came upon markers for sites of executions during the Second World War. And the violence of man (and it’s almost always men) against humanity continues—from crazed gunmen shooting on happy crowds to suicide bombers, genocidal wars, and even the threat of nuclear war.

In The Better Angels of Our Nature, Steven Pinker tells us the world is becoming less violent. But Peter Turchin warns us that history is nonlinear—it can come in waves, sometimes constructive but other times violent and destructive. I sure hope Pinker is right.

About that Thingstätte above Philosophenweg. It’s a large amphitheater in the woods, built by and for the Nazis. It was opened in 1935 with a speech by Joseph Goebbels, who called it “National Socialism in stone.” I’m glad that I turned around before I got there …

Can we all turn around now? Let’s take The Philosophers’ Way back from the brink, and get on with studying the amazing world that we all share.

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