A Change in Plans

Back in February, I wrote about our plan to move the LTEE from here at MSU to Jeff Barrick’s lab at UT-Austin later this year. 

Well, Jeff told me he’s had a change of heart. When he explained to his lab team that the lines required daily transfers that included weekends and holidays, everyone went totally berserk and threatened to resign then and there. And if that happened, Jeff would have to do all the transfers himself, 365 days a year. 

Jeff is a hard worker … or at least he used to be. But he’s a professor now. Like me, I’ll bet he doesn’t even know where the pipette tips and clean flasks are stored in his lab, much less how to make the culture medium from all those jars of chemicals with strange names. 

With that painful possibility in mind, Jeff called me up, and he said we’d have to keep the LTEE going here. I was kind of annoyed because I was in the middle of doing Wordle, and for some reason it wouldn’t accept “ecoli” as a guess. But despite all that, I said ok to Jeff.

So yesterday, when I told the people in my lab that we’d have to keep doing the transfers until I found another sucker lab to take over, everyone here went totally berserk and threatened to resign on the spot. To calm everyone down, I had to promise that today we’d stop the LTEE, empty out the freezers, and autoclave all of the samples.

But that’s no big deal, because we’ve already learned more than any other secular lab in the world about why evolution never does anything interesting. After all, the little buggers are still just bacteria, despite a possible glimpse of something slightly more interesting around this time last year.

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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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New Beginnings

Greetings on this winter solstice!  The winter solstice marks a sort of new beginning, as the days become longer for the next half year, before then becoming shorter until the cycle is repeated. 

Every day, the E. coli populations in the long-term evolution experiment (LTEE) experience a cycle of renewed resources and growth followed by depletion of their food and then waiting for the next transfer event. 

On a much longer timescale, the LTEE also experiences cycles as it is passed from one scientific generation to the next. With that in mind, we’ve made a new website that reflects the beginning of the second scientific generation of the LTEE, as the populations and responsibility for their sustenance will soon pass from my lab to that of the new director, Jeff Barrick.

On this website, you can get an introduction and quick overview of the LTEE including how it works, its goals, some of the key findings, and plans for its future.  You can see a timeline of the experiment with some of the milestones and key events in its history.  You can read, watch, and listen to a few of the news stories about the LTEE.  You can find resources including protocols and links to important datasets.  You can search and find links to the publications that report findings from the LTEE itself as well as descendant experiments that have used the LTEE lines. And last, but not least, you can see the talented people who’ve done and are doing the work behind the LTEE, including propagating the populations, performing analyses, analyzing data, and reporting the findings.

We’ve probably missed some papers, and we know that we’re still missing photos for some participants. We’ve also only scratched the surface of reporting past news.  So please let one of us know if you find someone or something LTEE-related that you’d like to see included on this website.  For now, enjoy the new beginnings as seasons and generations continue onward!

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Vinyl

Who remembers the old LP record albums?  They were made of vinyl, and music was recorded by etching tiny variations along a spiral groove. You put an LP onto a turntable, and you set the stylus with a fine needle into the groove. As the turntable rotated, the needle vibrated according to those tiny variations along the groove. And by amplifying that analog signal, music emanated from your speakers.    

The LP replaced an earlier format that used shellac instead of vinyl. The older format rotated on the turntable at 78 rpm, and a 12-inch diameter record allowed for only about 5 minutes of music per side. The vinyl LP allowed finer etching along a narrower groove, and these albums turned at 33 and 1/3 rpm. This technology allowed over 20 minutes of music to be recorded on each side of the disc. Hence the acronym LP, which stands for “long play.”

Why am I telling you this? I started the LTEE on February 24, 1988. A year on our planet is about 365.25 days, and so a century is 36,525 days. There have been 12,175 days from February 24, 1988, until today. That’s exactly one third of a century.

The LTEE has now revolved around our sun 33 and 1/3 times!  I think that qualifies as an LP.

An old LP album cover …
even older than the LTEE
.

Writing in the lab notebook on the occasion of the LTEE circling the sun 33 and 1/3 times.

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Patience Finally Rewarded in the LTEE

The LTEE has run for over 33 years and more than 74,000 generations. But we had almost nothing to show for all the hard work, until something fantastic happened last night.

Until last night, only one of the 12 lines had done anything even vaguely interesting: It figured out how to consume citrate—lemonade, basically. And it took them years to do even that simple trick.

And as some incredibly astute commentators have pointed out, even those citrate-eaters are still bacteria, just as they were when I started the experiment in 1988.

In fact, they’ve been bacteria for over 6000 years, according to the calculations of James (Jimmy the Bishop) Ussher, who placed the start of the creation at “the entrance of the night preceding the 23rd day of October [in] the year before Christ 4004.”   

It’s too bad that Ussher didn’t just make it Saint Patrick’s Day. That way, we would at least all remember to celebrate that pretty special day. After all, Ussher was an Irish Primate.

Well, speaking of primates, guess what Devin discovered in one of the LTEE flasks when he went to do the transfers this morning?  Monkeys!  Yes, monkeys!!

Not quite the primate sort of monkeys, though.  No, these were Sea-Monkeys!

With hindsight, I should have realized that with a liquid culture medium, we would evolve aquatic animals, not terrestrial ones. Maybe if we put some of those little plastic trees inside the flasks we could evolve real monkeys. 

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The Next Time

As we continue to fight the current covid pandemic caused by the SARS-CoV-2 virus, it’s not too early to begin thinking about the next pandemic.  I’ve been mulling this over for a while, and I was prompted to write this post by a twitter thread from Michael Baym.

Michael wrote about some work that he and Kaylee Mueller started, early in the pandemic, to develop a rapid colorimetric assay for covid.  They decided to curtail their work, however, when the personal risk of continuing to work in the lab seemed too great. But Michael is now wisely looking ahead, thinking about what science can do to respond even more quickly to the next pandemic.

Last February, as most of the world was just waking up to the threat posed by covid, I wrote a post with words of wisdom for pandemic preparedness. The words were written by a former Secretary of the US Department of Health and Human Services, Michael O. Leavitt, in 2007, who at that time was especially concerned about the potential for an influenza pandemic. He said: “Everything we do before a pandemic will seem alarmist. Everything we do after a pandemic will seem inadequate. This is the dilemma we face, but it should not stop us from doing what we can to prepare.”

So congratulations, and thanks, to Michael and all the others who are looking ahead. But really, all of us need to look and think ahead, using our hearts as well as our minds

Almost exactly a year ago, I was very worried about how hard this country would be hit by the pandemic.  I wrote:  “I think it is entirely possible, maybe even likely, that Europe will get hit harder by the coronavirus than China has been hit, and the US may get hit even harder than Europe.” 

I suggested that a number of epidemiological and sociopolitical issues would contribute to the United States being especially hard hit by the pandemic.  Among the former, “China’s outbreak started from a single point source in Wuhan … The US, meanwhile, has gotten many independent seeds both from China and from Europe … hundreds or even thousands of smoldering embers at first, most growing unseen and uncontained …”  Among the latter, “here in the US, we have deep social divisions, widespread skepticism of expertise (often fed by those divisions), an extremely complex political landscape with federal, state, & municipal layers of government … and many independent-minded people who are inclined to disregard advice and instructions—a wonderful attitude some of the time, but an exceptionally dangerous attitude during a pandemic.”

My worries about the next pandemic have been leaning to the problems of social division and disregard for evidence.  As terrible as this pandemic has been, the next one could be worse … even much worse.  How will people react if the next pandemic is 10 times more deadly than covid?  What if the next outbreak causes disproportionate mortality in kids or young adults?  Would the (mostly) right-wing denialists still refuse masks? Would anti-vaxxers (on the left & right) still oppose vaccination?

So, Michael Baym is right to be thinking ahead, as was Michael O. Leavitt. As a nation, we need to commit resources to support science (including the basic sciences that lead to breakthroughs in medicine) as well as our often neglected public-health system.  But we also need to find ways to come together as people, to overcome the sometimes willful ignorance, and to discuss things in a meaningful, non-conspiratorial way. 

Science and public-health workers can only do so much. The rest is up to all of us to protect ourselves, our families, and our communities from covid … and from the next pandemic … and from ourselves.

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How NOT to Write a Response to Reviewers

Last year I outlined my strategy for writing a response to reviewers.  It was intended primarily for early-career scientists, and the strategy I outlined was most relevant for a paper that had generally positive reviews.

One piece of my advice was to try to view every comment as constructive, even if you disagree with it. Reviewers are often mistaken on some points; indeed, one of the major benefits of the review process is that it calls attention to where we, as authors, have not explained ourselves clearly to the reader.

In my experience as an author and editor, it is pretty rare for a reviewer to say things that are truly hostile or otherwise inappropriate. However, it does occasionally happen that reviewers are unfair. 

I’ve blogged previously about one particularly aggressive and unconstructive review that my coauthors and I received. It was a harsh critique of the very first paper on the long-term evolution experiment with E. coli.  Fortunately, the other reviewer was very positive, and the editor requested a revision.

For some time I’ve thought about posting my response to that negative review. However, I thought the response was perhaps somewhat ill-tempered and overly long. Now, more than 30 years later, if I were advising a young scientist facing a similar review, I’d probably say: “Forget revising it for that journal. Just move on and try again elsewhere.”  But I didn’t do that myself, and I guess it worked out alright in the end.

Without further ado, here’s the response to that reviewer. (You can click on the image for each of the 4 pages to enlarge it.)


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