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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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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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How to Write a Response to Reviewers in Ten Easy Steps

This post is intended for early-career scientists who have just received the reviews for one of their first journal submissions.  It’s probably most relevant for papers that received generally positive reviews, and which require only minor or moderate revisions.*

  1. Copy all of the reviewers’ comments into a new document.  If the editor has substantive comments—especially ones that guide you to which reviewer comments are most important—then copy those, too.
  2. Write a short note of thanks to the reviewers and the editor at the top, above all of their comments.  See, you’re already making progress!
  3. Use a different font (bold or color) for your responses, to make them easy for the editor (and reviewers, if the paper is returned to them for re-review) to find.
  4. Draft a quick response to each comment.  Some responses will be easy, while others will take more time.  I suggest tackling the easy ones first, because it helps you see that you can make good progress even when there are several pages of single-spaced comments (as there often are).  You can polish your responses or change them later, as needed.  Each quick response is a way of recording your initial reaction and the difficulty (small or large) of addressing a specific comment or suggestion.  However, do NOT start editing the actual paper. That should wait until you have got a complete draft of your response letter, which will serve as a “road map” for revising the paper.
  5. Reviewers often begin by providing a synopsis of your paper. Thank the reviewers (again, after the synopsis) for their summary and kind remarks, when appropriate. There’s no need to write anything more after the synopsis, unless there’s a substantive misunderstanding of an important point that comes up again in a later comment.  In that case, you might say something like “Thank you for this summary of my/our paper. However, you may have misunderstood one point, about such and such, that I/we address in response to your comment below.”
  6. Try to view every comment as constructive. Reviewers may well be mistaken on some points, but rarely (in my own experience) do they say things that are clearly inappropriate. (However, it does occasionally happen.)  That means that you should accept their suggestions, if they improve the paper.  At the same time, you can push back (gently) against a suggestion that you don’t accept, because either (a) it’s not feasible and/or beyond the scope of your study to address it, or (b) you have a different opinion on the issue at hand.  In any case, your response should explain why you don’t accept a particular suggestion.  If (a), then that probably only needs to be said in the response, rather than requiring a change to your paper. Or perhaps you could add something to the paper about the value of future work to examine that issue. If (b), use your response to explain why you disagree and add something like this: “In the revised text on page NN, we have clarified our reasoning on this point.”  Of course, that means you really do need to clarify the issue in the text — but not yet (see point 4 above).
  7. Pay special attention to comments where two (or more) reviewers comment on the same issue.  If they both agree (for example, they tell you to clarify or delete some passage), then that is almost certainly something you should do. You should cross-reference the reviewers’ comments when appropriate. You can simplify your responses by saying, for example, “Reviewer #2 made a similar point …” and “We addressed this point in our response to the related comment from Reviewer #1.” If two reviewers made opposing suggestions, then you should also state that fact. Explain how and why you’ve followed one recommendation or the other; if possible, find a way to strike an appropriate balance. For example: “While Reviewer #1 thought we should delete this passage entirely, Reviewer #2 suggested we emphasize the point and provide more context from the literature. After considering both possibilities, we made the following changes: First, we added a sentence with historical context and several references. We then clarify that the relevance of this earlier work to our own study is speculative, and that it is therefore an issue worth exploring in future work.”
  8. Once you’ve got a draft response, share it with your co-authors (if any) to see whether they are on board with your resonses or have other suggestions.  Once everyone is in agreement, then use your response letter as a “road map” to edit your paper.  Track your edits, so your co-authors (and the editor and reviewers, if requested in the editor’s instructions) can focus their attention on the relevant sections.
  9. You’ll probably find that some text is trickier to edit than you thought in your draft response.  For example, new sentences to address a reviewer’s concern might disrupt the existing flow.  That’s the scholarly life: careful working and reworking are needed at every stage. Also, be cognizant that changes in one section might require (or at least suggest) changes elsewhere to maintain consistency.  For example, if your paper’s Introduction says there are two scenarios (or models or hypotheses or possible outcomes), and a reviewer then suggests adding a third scenario to the Discussion, then maybe you need to edit the Introduction as well. Or perhaps you decide to leave the Introduction as it is, but then clarify in the Discussion that, while you presented two alternatives in the Introduction, your new results (or whatever) raise a third possibility. The point is that changes to one part of a paper may require additional changes elsewhere. Here’s one obvious, and simple, case: If you delete a passage that cites references, you may need to remove them from the Literature Cited (unless you cite them elsewhere) and/or renumber other references, depending on the journal format.
  10. Once you and coauthors are satisfied with the revised text, then go back and edit your responses to reviewers. Clarify the changes that you actually made (as opposed to those you initially imagined you would make). When appropriate, add page numbers (from the revised paper) so the reviewer and/or editor can see how you rewrote important passages.
  11. Bonus advice! Check out the journal’s instructions for authors.  Make sure all of your paper’s formatting, references, figures, and such conform to those instructions before submitting the revised version.  This will save you from having to submit a re-revised version.

There, you’re done!  Congratulations and good luck!!

*If your paper was rejected, I’m sorry for that.  If it’s any comfort, it happens to everyone.  And yes, it’s often upsetting, even to senior scientists, though many of us have gotten pretty used to it.  Take some time to “blow off steam” by going for a long walk or whatever works for you. Then step away from the paper and reviews for a few days. When you return, you might wonder whether it’s worth appealing the decision to the journal. My general advice would be that it’s rarely worth appealing. I’ve tried it only once or twice, without success. I realize now there are so many fine journals, and so many ways to share papers (preprints, Twitter announcements, etc.), that it’s better to move on and try somewhere else. Of course, you may well want to revise your paper based on the reviews that led to its rejection. Even those reviewers who recommend rejection often have useful comments and advice.

 

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Time to restart the LTEE, this virus be damned

The LTEE ran for over 32 years and more than 73,000 generations, without missing a beat. Then this stupid coronavirus came along and made me shut down the lab and stop the experiment. Well, I think it’s high time for everyone to return to the lab and get back to work.

We’ve wasted a hell of a lot of time here.  The LTEE lines were frozen on March 9th.  That’s 23 days ago, for crying out loud.  Do you know how many generations have been lost?  With 100-fold daily dilution and regrowth, that’s ~6.7 generations per day.  So we’ve already lost over 150 generations. And with 12 populations that’s a net loss of more than 1,800 generations.

Another way of looking at it is that each population produces around half a billion new cells each day.  So that’s 23 x 12 x 500,000,000 cells that went missing. You get the picture, that’s a sh*t-load (a technical term for those of us who study E. coli) of baby bacteria that never got born!

I’ve gotten in enough trouble already with a certain crowd for our claim to have observed evolution. If they find out we’ve denied these adorable baby bacteria their existence, there’s no telling what letters they might send me.

Plus, speaking as a scientist, I have this premonition that something really big would have happened during those missing generations. I’ve been expecting them to evolve the ability to produce palladium from citrate. They could then use the palladium for cold fusion, which would surely get some attention. Stupid virus!

Heigh-ho, heigh-ho, it’s back to work I go.  I sure hope you have a nice day at home.

Calendar April

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Revisiting Telliamed

I started this blog, Telliamed Revisited, back in August of 2013, after attending a conference at which a colleague emphasized the value of social media in science.

I recall being questioned on Twitter by someone who expressed skepticism whether my blog would last or quickly be dropped. (Hey, I had already been running the LTEE for a quarter of a century at that point, so you’d think I’d get a little slack.) Anyhow, I said I didn’t really know, and that this blog was a personal experiment in communication.  In any case, I’ve now kept it up for six years, but with only occasional posts … about 100 in total so far.

If you want to follow a regular blog that is focused on science and related issues, I highly recommend Dynamic Ecology.  Jeremy Fox, Meg Duffy, and Brian McGill discuss interesting issues multiple times almost every week.  Impressive!

Anyhow, reflecting on my blog experiment as we head into a new decade, I was interested to see which of my posts had been viewed most often.  Here are the top 10:

Here are five more that are among my own favorites, but which didn’t make the top 10:

Also, if you’re wondering about the name of this blog, see the following post:

Last but not least, Happy New Year—and New Decade—to one and all!

Telliamed

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