They’re back!

They’re back! After a six-month interruption, Devin Lake restarted the long-term evolution experiment and the 12 LTEE lines from the 73,000-generation freezer samples. Now the bacteria are back in their home-sweet-homes: Erlenmeyer flasks with DM25 medium and the shaking incubator set to 37C.

We’re keeping the lab at very low occupancy, and using masks and physical distancing when more than one person is present in a room) until this damn SARS-CoV-2 pandemic is under control.

MSU also has a spit-based surveillence program in place for those entering campus buildings. Each sample is split, and then put into two pools for PCR testing. With each individual’s sample split into two pools, the testing can identify which individual in any reaction that proves to be positive is the source of the virus. That person is then notified and told to isolate and get a definitive diagnostic test.

[Both photos below courtesy of Devin Lake]

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Six Months

It’s been six months since I closed the lab, and temporarily suspended experiments including the LTEE, due to the SARS-CoV-2 pandemic.

The failure to contain this epidemic, especially here in the United States, is truly shocking and sad.

Still, we’ve gotten a lot done. Two superb dissertations completed by Nkrumah Grant and Kyle Card. Several excellent papers submitted, and more on the way. Everyone in the lab remains healthy, and in my own family as well, even as we know that many others have suffered illness and losses.

And please, everyone: Wear your mask and maintain social distancing to protect not only yourself and your own family, but also your community and beyond.

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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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Words of Wisdom for the Next Pandemic?

Almost four months ago, I posted some words of wisdom about the challenges and dilemma of preparing for a pandemic:

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.” — Michael O. Leavitt, 2007 (former Secretary of Health and Human Services)

Given our failure to contain the current pandemic, I’ll offer a corollary:

“It’s not easy to put a pandemic back in the bottle after it’s on the loose. Our early efforts at containment are the least costly and most critical.”

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Celebrating Black in STEM

I have been very fortunate to know and work with outstanding Black scientists throughout my career.  Here are a few of them.

I met Joe Graves when we were undergraduates at Oberlin College.  We took an evolution course together.  I remember discussing with Joe our mutual fascination with evolution and wondering how we might go about studying it.  I met up again with Joe at UC-Irvine, where we were both conducting evolution experiments—Joe using fruit flies, and me with bacteria.  Joe and I reconnected once more when he and I became founding members of the BEACON Center for the Study of Evolution in Action.  Joe now studies bacterial evolution, and we are becoming scientific collaborators as well.

JoAnn White was an ecologist at UNC, studying the life-history and population dynamics of periodical cicadas.  She served on my doctoral advisory committee and was a highly successful faculty member.  Unfortunately, she left academia, even though she had tenure, because it was too frustrating. I was honored that she asked me to write a reference letter when she moved to a new profession.  But it was a terrible loss for academia to lose such an outstanding scientist and role model as JoAnn White.

Paul Turner was one of my first graduate students.  He joined my lab in the Department of Ecology and Evolution at UC-Irvine, and he moved with me to MSU, receiving his Ph.D. in 1995.  Paul has impressed me in many ways, not only as a superb scientist and mentor, but also in his upbeat outlook on life.  Somehow he manages to smile and laugh about the challenges of being a departmental chair and interim dean, even while running a lab that conducts ground-breaking research.

Lynette Ekunwe was my lab manager and technician for seven years after I moved to MSU. She helped to sustain the long-term evolution experiment with E. coli after its move from UC-Irvine, and she helped run my lab group as it grew in size. Lynette moved to Jackson State University when her husband, the late Steve Ekunwe, took a faculty position there. After the move, Lynette earned a doctorate in public health, and she now works in the field of epidemiology.

I first met Scott Edwards when he was a graduate student at UC-Berkeley. I suspected that he was a rising star, and I was right.  Although Scott and I have not collaborated on actual science, we’ve worked together in other ways.  Scott and I served successive terms as Presidents of the Society for the Study of Evolution, and he has been a valued member of the External Advisory Board for the BEACON Center.

Shenandoah Oden was an undergraduate from Detroit when she joined my lab in the 1990s.  She worked with postdoc Santiago Elena on measuring the fitness effects of random insertion mutations in E. coli, leading to a paper in Genetica. What I remember best about Shenandoah is a question she asked me right after Brendan Bohannan presented his dissertation seminar: “How do scientists come up with the questions they ask?” I told her that was the best question that any student had ever asked me.  It reminded me of how Joe Graves and I, when we were undergrads, wondered how we might study evolution. To Shenandoah, I explained the importance of personal curiosity and mentors in finding questions that are both interesting and answerable.

Marwa AdewaMaia Rowles and Kiyana Weatherspoon were three excellent undergraduate researchers in my lab, all of whom were mentored by Zachary Blount. Maia and Kiyana were coauthors on a paper in the Proceedings of the Royal Society, London B, which reported the results of what we call the “all-hands project”—one in which a generation of lab members performed a set of parallel assays to measure the subtle changes in fitness in late generations of the long-term evolution experiment with E. coli. Marwa now works in the field of veterinary medical research, while Maia and Kiyana are pursuing careers with a biomedical focus.

Judi Brown Clarke was, until very recently, the Diversity Director for our BEACON Center. In that role she generated and managed many successful programs that introduced hundreds of students at all levels to evolution and provided them with opportunities to engage in scientific research. She also was a great listener and valuable source of advice for many of us when we faced personal challenges and setbacks. An Olympic medalist, Judi recently became the Chief Diversity Officer at Stony Brook University.

I met Jay Bundy in 2013, at the Evolution meeting in Snowbird, Utah.  Who was this student who was asking so many thoughtful, insightful questions of the speakers?  I ran into Jay as we rushed between talks, introduced myself, and learned that he was a masters student at Penn State.  He wasn’t sure if he was interested in microbes, but I encouraged him to think about joining BEACON.  Jay came to MSU, first as a BEACON staff member contributing to education and outreach activities, and then as a graduate student in the Department of Integrative Biology.  He also contributed to the all-hands project.  However, he switched from studying bacteria to digital organisms, and he’s now performing and analyzing experiments to quantify how the duration of history in an evolving lineage’s previous environment influences its subsequent evolution in a new environment. Stay tuned for Jay’s findings—he’s working on a huge paper. Jay is as deeply thoughtful about science and life as I imagined when I first heard his questions at the Evolution meeting.

I also met Nkrumah Grant in 2013, when he visited MSU while exploring possible graduate programs.  He immediately impressed me with his personal story of overcoming obstacles.  Nkrumah explained to me his love of science as a child, and how he had gotten discouraged and derailed before undertaking a concerted effort to pursue his dream of science and scholarship.  And pursue it he did … and continues to do.  From a G.E.D. to a Ph.D.  Co-author on the all-hands project, co-first-author on a paper just published in eLife, and three more papers posted to bioRxiv in the last few weeks.  He also just defended his dissertation, giving a beautiful public seminar followed by an engaging, collegial exam.  Nkrumah has done all this and more while being a dedicated father and working tirelessly to promote equity and inclusion in science.

Last but not least, Ali Abdel Magid and Jalin Jordan are two of the current generation of superb undergraduate researchers in the lab. Ali is working with Nkrumah on the evolution of bacterial cell size, while Jalin works with Kyle Card on the evolution of antibiotic resistance.  Both Ali and Jalin are also working toward future careers in medicine. This summer, they are reading work that integrates evolution and medicine including the landmark book, Why We Get Sick, by Nesse and Williams, and the path-breaking paper by Tami Lieberman et al. on the evolution of bacteria in the lungs of CF patients.

My science is better, and my life richer, because of all these people, and many more.  How much better science would be, and how much richer all of our lives would be, if we would open more doors, listen more carefully, and live, learn, and work together.

***

After reading a draft of this essay, Nkrumah Grant, Joe Graves, and Jay Bundy all asked me to say more about this:  How can we achieve the aspirations expressed in my closing sentence above? 

I plan to reflect more on their vital question.  In the meantime, I invite readers who have ideas to put them in the comments below.

EDIT: I should also acknowledge two other influences: A high-school teacher, Mrs. Clayton, who taught a Black History class that I took, and who introduced me to Frederick Douglass, whose autobiography I read with awe and admiration.

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Five More Years

The E. coli long-term evolution experiment (LTEE) began in 1988, and it has run for over 32 years with only occasional interruptions. The latest interruption, of course, reflects the temporary closure of my lab during the ongoing coronavirus pandemic. Fortunately, one of the advantages of working with bacteria is that we can freeze population samples and later revive them, which will allow us to resume their daily propagation when it is prudent to do so.  Indeed, we’ve frozen samples of all 12 populations throughout the LTEE’s history, allowing “time travel” to measure and analyze their fitness trajectories, genome evolution, historical contingencies, and more.

Even as the experiment is on ice, the lab team continues to analyze recently collected data, prepare papers that report their findings, and make plans for future work. Their analyses use data collected from the LTEE itself, as well as from various experiments spun off from the LTEE.  Nkrumah Grant is writing up analyses of genomic and phenotypic aspects of metabolic evolution in the LTEE populations.  Kyle Card is examining genome sequences for evidence of historical contingencies that influence the evolution of antibiotic resistance. Zachary Blount is comparing the evolution of new populations propagated in citrate-only versus citrate + glucose media. Minako Izutsu is examining the effects of population size on the genetic targets of selection, while Devin Lake is performing numerical simulations to understand the effects of population size on the dynamics of adaptive evolution.  So everyone remains busy and engaged in science, even with the lab temporarily closed.

Today, I’m excited to announce two new developments.  First, the National Science Foundation (NSF) has renewed the grant that supports the LTEE for the next 5 years. This grant enables the continued propagation of the LTEE lines, the storage of frozen samples, and some core analyses of the evolving populations. The grant is funded through the NSF’s Long Term Research in Environmental Biology (LTREB) Program, which “supports the generation of extended time series of data to address important questions in evolutionary biology, ecology, and ecosystem science.” Thank you to the reviewers and program officers for their endorsement of our research, and to the American public and policy-makers for supporting the NSF’s mission “to promote the progress of science.”

Second, Jeff Barrick joins me as co-PI on this grant for the next 5 years, and I expect he will be the lead PI after that period.  In fact, Jeff and his team will take over the daily propagation of the LTEE populations and storage of the sample collection even before then. I’m not planning to retire during the coming grant period. Instead, this transfer of responsibility is intended to ensure that the LTEE remains in good hands for decades to come. In the meantime, Jeff’s group will conduct some analyses of the LTEE lines even before they take over the daily responsibilities, while my team will continue working on the lines after the handoff occurs.

Several years ago I wrote about the qualifications of scientists who would lead the LTEE into the future: “My thinking is that each successive scientist responsible for the LTEE would, ideally, be young enough that he or she could direct the project for 25 years or so, but senior enough to have been promoted and tenured based on his or her independent achievements in a relevant field (evolutionary biology, genomics, microbiology, etc.). Thus, the LTEE would continue in parallel with that person’s other research, rather than requiring his or her full effort, just like my team has conducted other research in addition to the LTEE.”

Jeff is an outstanding young scientist with all of these attributes. Two years ago he was promoted to Associate Professor with tenure in the Department of Molecular Biosciences at the University of Texas at Austin.  He has expertise in multiple areas relevant to the LTEE including evolution, microbiology, genomics, bioinformatics, biochemistry, molecular biology, and synthetic biology. He directs a substantial team of technicians, postdocs, and graduate students, which will provide ample coverage for the daily LTEE transfers (including weekends and holidays). Last but not least, Jeff has participated in the LTEE and made many contributions to it including:

  • Participated in propagating the LTEE lines and related activities while he was a postdoc in my lab from 2006 to 2010.
  • Authored many papers using samples from the LTEE, including almost all of them that have analyzed genome sequences as well as several recent papers examining the genetic underpinnings of the ability to use citrate that evolved in one lineage.
  • Developed the open-source breseq computational pipeline for comprehensively identifying mutations that distinguish ancestral and evolved genomes.

Someone might reasonably ask if the LTEE will work in the same way when it is moved to another site. The answer is yes: the environment is simple and defined, so it is readily reproduced. Indeed, I moved the LTEE from UC-Irvine to MSU many years ago, the lab has moved between buildings here at MSU, and we’ve shared strains with scientists at many other institutions, where measurements and inferences have been satisfactorily reproducible. As an additional check, Jeff’s team at UT-Austin ran a set of the competition assays that we use to measure the relative fitness of evolved and ancestral bacteria, and we compared the new data to data that we had previously obtained here at MSU. The two datasets agreed well, in line with the inherent measurement noise in assessing relative fitness. Fitness is the most integrative measure of performance of the LTEE populations, and it is potentially sensitive to subtle differences in conditions. These results provide further evidence that, when the time comes, the LTEE can continue its journey of adaptation and innovation in its new home.

Evolve, LTEE, evolve!

LTEE flasks repeating

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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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