On Being a Scientific Zebra

I got a phone call today from someone asking permission to suggest me as a reviewer of a manuscript this person was about to submit. For future reference, if it's similar to anything I've blogged about, I'd be happy to be a referee. I generally get my reviews in on time (though near deadline), a practice I have gotten much better about since getting a "your review is late" note from a Nobelist -- not the sort of person you want to get on the wrong side of.

I end up reviewing a half dozen or so papers a year, from a handful of journals. NAR has used me a few times & I have some former colleagues who are editors are a few of the PLoS journals. There's also one journal of which I'm on the Editorial Board, Briefings in Bioinformatics (anyone who wishes to write a review is welcome to leave contact info in a comment here which I won't pass through). I'll confess that until recently I hadn't done much for that journal, but now I'm actually trying to put together a special issue on second generation sequencing (and if anyone wants to submit a review on the subject by the end of next month, contact me).

I generally like reviewing. Good writing was always valued in my family, and my parents were always happy to proof my writings when I was at home. This space doesn't see that level of attention -- it is deliberately a bit of fire-and-forget. A review I'm currently writing is now undergoing nearly daily revision; some parts are quite stable but others undergo major revision each time I look at them. Eventually it will stabilize or I'll just hit my deadline.

There's two times when I'm not satisfied with my reviews. The worst is when I realize near the deadline that I've agreed to review a paper where I'm uncomfortable with my expertise for a lot of the material. Of course, if I'd actually read the whole thing on first receipt I'd save myself from this. You generally agree to review these after seeing only the abstract, so I suppose I could put in my report "The abstract is poorly written, as on reading it I thought I'd understand the material but on reading the material I find I don't", but I'm not quite that crazy.

The other unsatisifying case is when I'm uneasy with the paper but can't put my finger on why. Typically, I end up writing a bunch of comments which nibble around the edges of the paper, but that isn't really helpful to anyone.

I also tend to be a little unsatisfied when I get to review very good papers, because there isn't much to say. I generally end up wishing for some further extension (and commenting that it is unfair to ask for it), but beyond that what can you say? If the paper is truly good, you really don't have much to do. A good paper once inflicted a most cruel case of writer's block on me -- it was an early paper reporting a large (in those days) human DNA sequence, I we were invited to write a News & Views on it -- and I couldn't come up with anything satisfying and missed the opportunity.

That leaves the most satisfying reviews -- when a paper is quite bad. This isn't meant to be cruel, but these are the papers you can really dig into. In most cases, there is a core of something interesting, but often either the paper is horridly organized and/or there are gaping holes in it. It can be fun to take someone's manuscript, figure out how you would rearrange & re-plan it, and then write out a description of that. I try to avoid going into copy editor mode, but some manuscripts are so error-ridden it's impossible to resist. Would it really be helpful to the author if I didn't? One subject I do try to be sensitive to is the issue of authors being stuck writing in English when it is not their first language -- given that I can hardly read any other language (a fact plain and simple; I'm not proud of it) it would be unfair of me to demand Strunk&White prose. But, it is critical that the paper actually be understandable. One recent paper used a word repeatedly in a manner that made no sense to me -- presumably this was a regionalism of the authors'.

I once reviewed a complete mess of a paper and ended up writing a manuscript-length review of it. In my mind, I constructed a scenario of a very junior student, perhaps even an undergraduate, who had eagerly done a lot of work with very little (or very poor) supervision from a faculty member. The paper was poorly organized as it was, and many of the key analyses had either been badly done or not done at all. Still, I didn't want to squash that enthusiasm and so I wrote that long report. I don't know if they ever rewrote it.

I can get very focused on the details. Visualization is important to me, so I will hammer on graphs that don't fit my Tufte-ean tastes or poorly written figure legends. Missing supplemental material (or non-functioning websites, for the NAR website issue) send my blood pressure skyrocketing.

I wouldn't want to edit manuscripts full time, but I wouldn't mind a slightly heavier load. So if you are an author or an editor, I reiterate that I'm willing to review papers on computational biology, synthetic biology, genomics and similar. I'd love to review more papers on the sorts of topics I work on now -- such as cancer genomics -- than the overhang from my distant past -- a lot of review requests are based on my Ph.D. thesis work!

What's in a title?

Boston has two major daily papers, The Boston Globe and The Boston Herald. The Globe is the more stately broadsheet, whereas the Herald revels in being the sensational tabloid. My tastes tend strongly towards the Globe, though it sometimes seems more like The Boston Glob, but I do browse the Herald -- when I can get it for free. Yes, I'm a bit of a newspaper snob -- though nothing like James D. Watson, who would apparently put down the Herald (and by extension readers of that paper) on a daily basis when he was at Harvard (I got this first hand from his glasswasher -- who read a Herald daily).

While I have no love for the Herald's style & quality of journalism (e.g.: when the Globe fired a populist columnist for plagiarism, the Herald gleefully scooped him up), I do enjoy their screaming headlines. Short, pithy & fun -- though accuracy and fairness clearly aren't strong selection criteria.

The headlines in scientific journals and newswires tend to be long on long and short on punchy. Perhaps some is an urge to cram as many keywords as possible into the title, and perhaps some is a deliberate desire for dryness. While these titles often fit the purpose, it isn't uncommon to be able to rewrite one for more zazz, especially if you are emailing abstracts to a colleague rather than editing a journal.

Of course, one advantage of long and ponderous is a single possible meaning -- spell it out in detail, and nobody can misinterpret it accidentally -- or deliberately. Rarely can a scientific paper title or newsfeed item become a candidate for Jay Leno's headlines schtick, but it does happen. GenomeWeb is usually a good provider of useful news, but the other week I got a grin out of a headline that could be seen as a politically incorrect description of enlisting patients in their own cause

Sick Kids to Use GenoLogics' Geneus Software in Multi-Lab Stem Cell Research

. Of course, the item really refers to The Hospital for Sick Kids in Toronto.

Other times, someone does put together a clever headline that grabs the eye -- usually with a clever name for a hypothesis

Retaliatory mafia behavior by a parasitic cowbird favors host acceptance of parasitic eggs

-- now there's a memorable piece of jargon!

However, I do not like titles to mislead.

The calorically restricted ketogenic diet, an effective alternative therapy for malignant brain cancer.

If you skip to the bottom of the abstract, it's even worse

This preclinical study indicates that restricted KetoCal(R) is a safe and effective diet therapy and should be considered as an alternative therapeutic option for malignant brain cancer.

It's an interesting idea (with precedent in the literature), but 'safe & effective'? The key term left out of the title is 'xenograft mice'. Only proven so if you are a xenografted mouse, a population for which a huge variety of 'cures' already exist. The abstract as a whole isn't bad, but I'll hardly be shocked if I start seeing ads touting the final sentence without qualification.

Feed Frenzy

In response to a previous posting about journal tables of contents, I received the helpful suggestion of trying our an RSS feed reader. I soon installed the Sage reader for Firefox, and have had found it a very useful way to keep up. It is interesting to note the wide diversity of what various journals provide as far as RSS feeds.

The first frustration is those things I'd like as RSS feeds but aren't available (ah! the zeal of the newly converted). Science Magazine's advance publication spot, Science Express being at the top of the list. The ASBMB follows a similar line: Molecular & Cellular Proteomics and Journal of Biological Chemistry also fail to provide feeds for their advance articles.

The key point of variance is in what is provided. Oncogene opts for the most terse: just the title of each article. Many journals, including most Nature family journals (which Oncogene is in), give titles and complete abstracts. Journal of Proteome Research (an ACS journal) has titles, author lists, and an iconic graphic from the paper. PNAS picks a strange mix: the title, the author list, and then the timeline of submission, review, acceptance, etc. That's some administrivia I really don't see high in my list of things I need to keep on top of. PNAS also includes a short bit of the first sentence, but never enough.

I'm sure there are other permutations out there -- I'm opting to accrete RSS feeds slowly. Overall, I think I prefer the title+abstract format or the title+graphic format. This is what whets my appetite for a paper. Titles alone are nice and terse, but perhaps too terse.

Graphical table-of-contents

I am a serious journal junkie, and have been for some time. As an undergraduate I discovered where the new issues of each key journal (Cell, Science, Nature, PNAS) could be first found. In grad school, several of us had a healthy competition to first pluck the new issue from our advisor's mailbox -- and the number of key journals kept going up. Eventually, of course, all the journals went on-line and it became a new ritual of hitting the preprint sites at the appropriate time -- for example, just after 12 noon on Thursdays for the Cell journals. A good chunk of my week is organized around the rituals.

Most pre-print sites, indeed most on-line tables-of-contents, are barebones text affairs. That's fine and dandy with me -- quick & easy to skim. But, I do appreciate a few that have gone colorful. Some now feature a key figure from each article, or perhaps a figure collage specifically created for display (much like a cover image, but one for each paper).

Journal of Proteome Research is at the forefront of this trend. Of course, since it is a pre-print site the particular images will change over time. As I write this, I can see a schematic human fetus in utero, flow charts, Venn diagrams, spectra, a dartboard (!), bananas, 1D & 2D gels, a grossly overdone pie chart, and much more.

Nature Chemical Biology is the other journal I am aware of with this practice. The current view isn't quite such a riot, because NCB doesn't have the large set of pre-prints that JPR has, but both a fly and a worm are gracing the page.

The graphical views do provide another hint of what might be in the paper beyond the title. In particular, they give some feel for what the tone of the paper might be (that dartboard must indicate a bit of humor!). They certainly add some color to the day.