I don’t usually blog about my actual research, but this week one of my last papers was published, a characterisation of the protein TbSmee1 in the unicellular eukaryotic parasite Trypanosoma brucei (here). “Mr Smee” has had a long and painful genesis, and in many ways the story of this paper is the story of my own research group, and one I definitely plan on telling at a later date. 

For now though, the paper is worth highlighting because I think it illustrates a number of features of contemporary publishing dynamics, peer review, and the importance of frontline research to undergraduates.

The paper was based on my identification of the protein (then Tb927.10.8820) in a paper using proximity labelling when I was still a postdoc in Vienna. We found that it was essential for the viability of T. brucei before I left for Würzburg to start my own group, and so it was earmarked for more detailed analysis. 

Incredibly, the characterisation of this protein first began back in 2015 when Daja Schichler, one of my first rotation students, joined the lab. It then inched along for a long time, was paused while we completed a structural studies paper on a different protein, and resumed in earnest in 2019 when Eva-Maria Spath, Antonia, Konle, and Sina Riegler (amongst many others) sequentially joined the project.

It was still not ready for publication when my group’s funding was cut at the end of 2021, but was finally ready for publication in early 2022, when we sent it to the preprint server bioRxiv.

Peer review was coordinated by EMBO Press’ wonderful Review Commons platform, and the three reviews (including one toxic one – more on that below) arrived in April 2022. Some requested experiments that sounded turned out to be far from trivial, and then the revision process also got caught up in the fallout from my resignation and departure from the Department of Cell & Developmental Biology. 

Revisions were finally completed in August 2023, by which time I was so heartily fed up with the story that I was having to force myself to work on it in small bursts in the evenings. Three days after completing the revisions, it was accepted for publication. 

So what are some of the things this story tells us? 

1. Preprints really do accelerate dissemination into the public domain

Obviously Mr Smee had a highly unusual route to final publication, and an abnormally long interval between first “submission” (upload to bioRxiv in this case) and final publication. This though only goes to highlight how fantastic preprints are for accelerating the dissemination of research results – without the preprint, the gap between completion of the “submission version” of the paper and it actually going public would have been more than 1.5 years! Instead, even though progress was glacially slow, the story itself was still out and available for the community.

The revised preprint (v2) certainly benefitted from peer review but as is usually the case, the main conclusions of the first submission were not materially altered by the review process. There’s a fantastic analysis paper form Johnny Coates & coworkers (here) that shows this is the norm so you don’t have to take my word for it. It’s still surprisingly common to hear people criticise preprints because “anybody can publish anything”. Errrr, no – actually, scientists who strive to do good work will publish good-quality preprints, just as they publish good-quality papers. 

2. Preprints can be a director’s cut

Another plus of preprints became apparent during the post-acceptance process of Mr Smee.  Version1 of this preprint (here) was the original submission to Review Commons; version 2 (here) is the revised preprint which incorporates changes made as a result of peer review. 

Version2 then underwent post-acceptance edits at the Journal of Cell Science in order to conform to their figure/word limits, however: Fig S2 was cut, and Fig2 moved into the supplementals. Around 1000 words of text were also cut, mostly from the Discussion. The accepted article at JCS is non-identical to version2 at biorXiv.

As such, the version2 preprint is a kind of “director’s” cut of the paper. This is another advantage of preprints! They let you tell a longer story in your own words. Of course, there are some journals that don’t have word/figure limits, but I can also see the advantage of having two versions of a paper simultaneously available online. The more succinct Journal of Cell Science version has all the essentials; the real aficianados of this topic (I think there’s at least one or two others besides me!) can consume the long-form preprint version that has a bit more Discussion of the findings.

 

3. Published peer reviewer reports can highlight bad practice

Third point: do please take the time to read the reviews that we got for the original submission, because to me, Reviewer 1 is a perfect example of how NOT to do peer review. 

In fact, Reviewer 1 neatly illustrates the misuse of anonymous peer review – the weaponisation of feedback under cover of anonymity in order to disparage and denigrate work, instead of providing constructive criticism to help the authors improve it. Peer reviewers (as I noted in an earlier posting) are like midwives – their job is to assist delivery of a paper, not try to prevent its birth.

Obviously it’s hard for me to be completely impartial, but I find it hard to see what scientific purpose Reviewer1’s feedback serves. They seem to be doing their very best to ruin the paper’s chances of publication, and even go on to attack Reviewer 2 in the cross-commenting discussion.

It shows too how malicious peer review is written with the editor in mind as the audience, rather than the authors. Reviewer 1 quite plainly misunderstood the whole philosophy of Review Commons – namely to provide journal-independent research assessment so that the quality of the science can be the focus rather than subjective estimations of paper value and journal status. I don’t know if they didn’t like the work, or don’t like me, but either way, their nasty little diatribe is now online for everyone to see. Please read this, and don’t ever do the same.

4, Undergraduates can and should be involved in frontline research

Lastly, you may have noticed that the author list of this paper is rather long.

As regular readers of the blog will know, in the 8 years I spent as a group leader I did not have even a single PhD student to supervise, as the Department was not able to financially support me. My “Eigene Stelle” grant from the DFG, which paid 100% of my salary from 2018-2021, also did not come with a PhD student but the rules of the Eigene Stelle meant I was not allowed to apply for other sources of third-party funding. 

Thus, in research terms I had to make do with undergraduates, and it was enormous fun doing so although for obvious reasons, this slowed research progress to a crawl – nobody was in the group for longer than around 9 months at a time. There are 23 authors on this paper in all, and 19 were at the Department of Cell & Developmental Biology (including me).

Of these 19 authors, 16 were undergraduates at the time of working on this project. The topic is undoubtedly niche (my interests have always tended towards the esoteric), but the data are absolutely of publication-grade. Undergraduates are 100% capable of participating in frontline research.

One of the biggest challenges we face is ensuring that undergraduates get appropriate and sufficient exposure to frontline research as part of their studies. This is something where Germany excels – I did my undergraduate studies at the University of Cambridge, but all of my lab experience came from volunteering to work at labs on my summer holidays. 

German undergraduates rotate through multiple labs as part of their Bachelor and Master’s studies, in addition to receiving weeks-long practical courses. The University of Cambridge ranks dizzyingly higher than the University of Würzburg in the global university league tables, but in terms of practical training there is no comparison: the German university wins hands-down.