The long view
A conversation with George O'Toole on publishing, peer review, and the unwritten rules of a scientific life
George O’Toole has spent a career at the workbench of microbiology and, increasingly, at its editorial machinery. A professor at the Geisel School of Medicine at Dartmouth and Editor-in-Chief of the Journal of Bacteriology, he is known both for the science that bears his name – the crystal-violet biofilm assay that thousands of labs now run and that has been instrumental in many advances in the study of surface colonisation by microbes – and for a plainspoken willingness to say how the profession actually works. The conversation that follows is by no means specific to microbiology. It ranges across the terrain most early-career scientists navigate by instinct and rumour: what a society journal is for, whether a career should hang on a masthead, what peer review still does that preprints cannot, and the unwritten rules that decide who thrives. George answers the way he edits, with candour, a long memory, a desire to make things better, and a refusal to pretend the system is either broken beyond repair or fine as it is.
PBR: Can you persuade me that society journals still matter?
Prestige now flows to a few high-impact venues while society journals are often treated as fallbacks. What’s the argument that a journal like the Journal of Bacteriology is an instrument of renewal rather than a relic — and what can it actually offer an early-career author that the glamour journals can’t?
GO’T: I think that society journals play a number of positive roles in the modern publishing environment vs. “flash” journals (as an aside, while I am the EiC of JB, I believe what I am saying is true for any American Society for Microbiology (ASM) or other society journals).
First and foremost, the editors at society journals are practicing scientists whose primary goal is helping members of the society publish high-quality science. The “editors” at these flash journals typically have never been an anchor author on a paper, and their incentives are somewhat perverse and not so different from the idea of “if it bleeds it leads”, that is, to get clicks. Perhaps it is not so surprising that there is a positive correlation between journal impact factor and paper retractions (P < 0.0001 by Spearman rank correlation; PMID: 21825063) with society journals having markedly lower retraction index. While I stopped publishing in these other journals years ago, it seems as if the editors have two modes - pass along any absurd review to the author and/or ignore the reviewers and publish something because it is “exciting”.
Second, my experience (15+ years as an editor and editor in chief) is that the reviewers at ASM journals are trying to HELP authors – they often provide detailed and helpful reviews. They are particularly supportive of junior faculty (despite what the narratives on social media seem to say). Third, how many of you have sent a paper to a flash journal, have had it sent out to review, were asked to do a 12-18 months’ worth of experiments, none of which change the core conclusions of the paper, resubmitted the paper, then are told “never mind, but maybe our B level journal would work for you”. You have just more or less wasted a year of some postdoc or student’s time: most of us don’t have this kind of funding to waste. [BTW, if I am at a table at a meeting and someone starts complaining about the horrible experience they just had at one of these flash journals, I just get up and walk away. Might as well say “well, I cut off my own arm and boy it hurt”]. Fourth, the page charges for society journals are typically lower, and any “profit” is ploughed back into the society activities like travel awards, mentoring programs, etc. For many non-society journals, profits from public funds go into the pocket of investors (you’ve written about this process on this blog). Hey folks, if publishing was not making lots of money, we would not have paper mills and predatory journals! Finally, and my personal bone to pick, is that I am a busy person (we all are) - why am I spending my time, for free, to enrich a private publisher? It makes no sense! [If you have that kind of free time, I have some work around my house - painting, weeding - that needs to get done!] Are society journals perfect? Of course not! Do they screw things up from time-to-time? Yes! But I would say by-in-large, the people working at society journals (from scientists to staff) are motivated by helping authors publish their terrific science, not making a buck or getting clicks.
PBR: Is it possible to decouple careers from journal names?
Young scientists are told their future hinges on the masthead. From the editor’s chair, what do you watch authors do to survive that system, and what would it take to break the link between career survival and journal prestige?
GO’T: You’ve put your finger on an important problem, but one I think is quite solvable. Turns out that Proceedings of the National Academy of Sciences, USA (PNAS) is a society journal. A pretty good journal too. High profile, nice IF for those that are excited about such things. I would argue there are plenty of excellent and successful scientists that can build an outstanding career living in the world of society journals. This is an issue that no one else can fix but practicing scientists voting with their feet. There are (and always will be) folks that love the prestige of a flash paper - good for them. Honestly, most people outside their immediate field still won’t know who they are, and a vast majority of those papers will soon be forgotten (the high IF at flash journals are typically driven by just a couple of papers). Building a legacy over a career of solid (i.e. rigorous, repeatable) science should be the goal. I do see that the quest for the flash paper usually goes hand in hand with ignoring related literature (gotta be novel) or overstating the work (gotta be exciting) - the incentives here do not lead to the best work.
PBR: What are your thoughts on peer review versus preprints.
You sit at the machinery of peer review while the field increasingly routes around it. Is peer review reformable, or is it being quietly replaced — and what should an early-career researcher actually trust?
GO’T: I might be old fashioned (or perhaps just old), but I think classic peer review works pretty darned well, especially in the context of society journals as I detailed above. And especially with editors who edit and who don’t just forward the reviews to an author. This is the strength of society journals with experienced scientists as editors - they can process and synthesize reviews to understand what is “need to know” versus “nice to know”. These editors should be giving clear guidance - you need to do X, doing Y is nice, doing Z is for the next paper.
In terms of preprints, they are useful - I put all our papers on BioRxiv to get the info out sooner. But these of course are unreviewed manuscripts. But honestly, when you read a peer reviewed paper, aren’t you always reviewing it in your head anyway? The same should happen with a preprint. I would say that while the preprint is generally a good thing, in my experience, beyond a few retweets, I have seen no real engagement from readers. No one has pointed out another experiment I should do or a control I missed. Probably because their name will be on the comment and they are afraid the authors will get cranky. This point gets to another new idea - should we sign our reviews? I say “no” - I would bet the ranch that most of the signed reviews are positive, resulting perhaps in an implied quid pro quo? The system we have now is robust! We have 2-3 reviewers with independent comments on a manuscript (that in my experience almost always align), we have an editor as another layer to make sure the process does not go off the rails. We also have an appeal process (I’ve had several appeals over the years - some of which altered or reversed decisions). I say this with the utmost respect possible, but authors need to consider that if their paper is rejected, perhaps it is not the reviewers but the manuscript you wrote. In my experience, as many papers get rejected because 3 reviewers find the text extremely difficult to read versus because there is a scientific flaw in the paper. Most campuses have writing centres or faculty have senior mentors – use those resources if you are struggling to get your work published. Publishing is hard - and that is OK. We want a rigorous system of review before something is thought of as “fact”.
PBR: Are there hidden secrets that we need to know?
You’ve put a lot of effort into teaching the unwritten rules. Why does so much of what determines a young scientist’s success stay informal – and therefore unevenly distributed – and what would it mean to make it a shared resource rather than a matter of whose lab you landed in?
GO’T: This is a great question! Part of my answer can be posed as a fictitious scenario: I sometimes feel like the call for mentoring is akin to bringing a new-born home from the hospital on Monday, then attending a “How to apply to college” seminar on Tuesday. Hey - I’m barely keeping this kid alive, I don’t have time for a college seminar. What I mean to say is: we learn the stuff we need to learn when we need to learn it. And this is a perfectly fine strategy. Maybe think about this as the difference between a Materials and Methods section and a protocol - the M&M gives you a gist of what you need to do, but it is the protocol that gets into the nitty gritty. A faculty workshop does the former, a conversation with a colleague (or a couple of colleagues) does the latter. A conversation with a colleague on how to become a Full Professor does not make a lot of sense for a first year prof! You know that the promotion is coming someday (it’s in the M&M), but the details of the protocol can wait until you’re an Associate Professor for a few years! As an aside - if you are not getting the mentoring you need from your professor, go find it somewhere else. Be proactive - a collaborator at another school, a senior faculty member in another department - whatever!
In terms of practical advice, I think the single most important word to learn as an Assistant Professor is “NO!”. I tell people - be proactive about the one thing you want to do as an Assistant Professor (serving on the grad committee is a good one) and use it as a shield to protect yourself from all other service. If you volunteer for 12 committees to make your chair happy and you don’t publish or get a grant, well you are not going to get tenure. If you have a great lab group, are doing great science and say “no” to your chair a couple of times - well, you’ll be fine! [As an aside, a well-kept secret that is perhaps not surprising – chairs will tend to ask people to do things if they think those people will get the task done! Of course - they’ll keep asking the competent first. It is OK to say “no” – the chair is getting paid the big bucks to get the incompetent to get stuff done].
Related to the point above - if all goes well you’ll have a 25-35 year career in academia – spend your time as an Assistant Professor building a great lab (the selfish phase), during your time as an Associate Professor you can think about making an impact at the department or institutional level (the short view phase), and as a Full Professor you can change the world (the altruism phase)! You have time to change the world.
PBR: Intensive summer courses are tough, rewarding – what’s your take?
For many years you ran the summer Microbial Diversity course at Woods Hole — weeks of immersive, hands-on training away from the home lab. What did that format give young scientists that a PhD program can’t, and is that kind of apprenticeship something science is quietly losing?
GO’T: I’ll be brief here because I can do a whole post on these sorts of training courses. The Microbial Diversity course at the Marine Biological Lab in Woods Hole is ~100 hrs of lecture and ~300 hrs of lab over 6 weeks - a full 18 credit semester load in half a semester and focused on microbiology! Intense, but fun. I think it is the whole atmosphere - the intensity of information delivered, the diversity of approaches people use in the science, the many seminars. And the ability to absorb it all and think without the distraction of day-to-day business back at home. These courses are expensive and hard to fund - it is a challenge to keep them alive. But people can do versions of these courses at home - use parts of the summer, times when the undergrads are on break, and/or engage students/postdocs who are excited about teaching. It is a great mechanism to educate. But I would say these courses work best when the PhD students have a 3-4 year foundation of classes, reading, and lab experience. So I see them as complementing PhD programs - not an alternative.
PBR: Do we train too many PhD students?
We train far more PhDs than the system can absorb. Is that a training failure, a funding failure, or a values failure – and what does a good scientific life look like for someone doing excellent work with no permanent position in sight?
GO’T: I think the failure here is that we have overgrown the system. I remember in the 90’s when I was a postdoc at Harvard. There was an influx of NIH funds and Harvard (and lots of other schools) slapped up new buildings, hired a bunch of new faculty and grew their graduate programs. But this could not go on forever. There is a trend now to unionize grad programs, which was not generally popular among faculty, but in the end I think it was the right thing to do (but not for the reason most students think). I think students felt that if their salaries went up, schools and the NIH would sprinkle new money around and all would be well. Turns out, that is not the case! We have the same amount of money (sometimes less), so we ended up accepting fewer students and this process has propagated through the whole system. As a consequence, we will have fewer PhDs in the coming years. The “problem” of too many PhDs will self-correct. Having said that, from my point of view, I don’t know of many of the PhDs from Dartmouth that are unemployed and a vast majority have stayed in science. So the academic system can’t absorb all PhDs but other job markets (with high quality and challenging jobs) can.
PBR: Is there a place for the workhorse in science?
The crystal-violet assay you popularised spread in part because you wrote it down clearly. Careful, reusable methodology is exactly the kind of work early-career researchers do – and it’s undervalued next to novelty. How does the reward system need to change to credit it?
GO’T: For workhorse science, one does have to take the long view I think. So the impact factor scheme doesn’t really work in this context. I would also say that it is hard to have one paper figure out a whole biological process; it’s usually a series of papers. For the crystal violet assay, it is a tool originally used to identify genes important for biofilm formation - that was the easy part! Figuring out what those genes and their products do is hard. Having said that, when we looked over the most cited papers in the Journal of Bacteriology in its first 100 years, almost all of those papers were methods papers - so they will get their due if useful. I would say that a method that moves the needle in a field can help earn a young scientist a great niche – this is a good thing! So I think what you are saying is really context dependent. For example, as a junior faculty I was on a paper with Matt Parsek and Dan Wozniak in PNAS that reported a negative result – it showed that alginate was not important for in vitro biofilms despite “accepted knowledge” in the field. I think this is a negative result that helped launch the extracellular polysaccharide (EPS) field in Pseudomonas aeruginosa and motivated the discovery of Pel and Psl polysaccharides. So publish those methods and those negative data!
PBR: How about a final word?
If you could change one thing about how we fund, publish, or evaluate science to improve the next generation’s lot, what would it be?
GO’T: I think one of the most impactful moves has been the development of the Maximizing Investigators’ Research Award (MIRA) award as a mechanism for more consistent and equitable distribution of funding. The NIH should consider adopting this program across institutes. Steady funding, I believe, allows more risk-taking, as long as groups stay productive. There are many issues in publishing but one thing remains true – our work needs to be published to be impactful. And you did not ask this, but it is important to try to have fun. With the day-to-day demands of a faculty position we sometimes forget why we got into science in the first place!
George, I couldn’t agree more with your final comment – and in fact with much that you have written. The process of discovery, which is where one catches the bug, is absorbing and excruciatingly fun! No matter one’s career stage, there is nothing so wonderful as to actually acquire / analyse data, see something no one else has ever seen; to have that new knowledge become the germ of an idea that is then realised in some concrete way.
So, George, thank you for being such a willing participant; many thanks for your time, frankness, and for treating these questions as the practical matters they are rather than occasions for platitude. Much of what you have offered here is the kind of counsel usually passed quietly from one bench to the next, but is so valuable to have set down in the open, where anyone starting out can find it. And again, to your final comment: work has to be published to matter, and somewhere in the middle of all the demands, it helps to remember why we started.