5.16.2009

anonymity anomie

There's been a recent renewal of concerns about anonymous science blogging in the wake of DGT's (thankfully) temporary absence. People have been posting their own rules for pseudonymous blogging, and people have been debating taking their own blogs (or some of their more incendiary posts) down. DrugMonkey's appraisal seems, as usual, the wisest:
I have been flabbergasted to read comments suggesting that so many bloggers have not thought these issues through. Really.

For me, at least while I'm untenured, I don't think it makes sense to blog under my own name. I started this because I had been reading and commenting on others' (mostly anonymous) science blogs and I wanted a place to write longer reactions, and to add my $0.02 to the conversation. It's also where I can vent about topics that I might have more difficulty talking about with colleagues face to face, and to think through issues. I hope it is useful to some others and I'm not just writing for myself, but I do appreciate the chance to write something that's not a journal article/book chapter/peer review/grant.

I absolutely feel hemmed in by the prospect of giving away too many identifying details in posts. I've written anonymized posts on amazing, awful anecdotes that I feel I can't publish because I would suffer professional costs if the people/characters in the stories realize who I am. I want to share these because these blogs are how we do communicate to one another what kinds of terrible situations can and do arise in academic science, so we can try to avoid them happening to us. I'd also love to put them up because they are pretty damn entertaining... but for now, they will be reserved for late-night scary science storytelling.

I admire the experimental details posted by some scientists who blog under their real names, but I'm not sure I'd want to put up, in a google-searchable fashion, so many unpublished details of my work. (Good motivation to publish quickly, though... I could use that...) I'm very much looking forward to listening to four perspectives on this topic on Monday at 2:30pm during the "Open Science – The Risks, Rewards and Challenges" session at the American Society for Microbiology general meeting.



I am familiar with microbial evolutionist Rosie Redfield and phylogeneticist/PLoS Biology editor Jon Eisen, and both are proponents of open access publications and open science. I do not know Samuel Kaplan, though he is a former chair of ASM's publications board, or Joseph Deken, who has apparently been working on integrating computing into biology for many years.

For those not going to Philly -- and judging from the hard sell from ASM in recent months, many of us are not going this year -- you can watch this symposium live on Microbe World.

the youngest peer reviewers are often the harshest...

...illustrated by recent articles in the Chronicle and The Onion.

While I can't comment on otter research, the complaints of the humanities scholar about how graduate students read texts ring true for young scientists too.
Why is it that so many graduate students are reflexively critical of what they read? Why are they so eager to dismiss, dislike, and disrespect work that has already been done before they can even hope to begin to contribute?

I think there are some upsides to the arrogance that grad students initially bring to reading the established literature. Grad students, some of them at least, are the future of any field. It's a wonderful thing that they critically evaluate for themselves everything that's become conventional wisdom, because some of that conventional wisdom is wrong. And as we become more entrenched in academic science it's harder to spot the flaws in the conventional wisdom that we've embraced for 10, 20, 30 years...

I remain a very detailed reader and reviewer, but I'm not nearly as acerbic as I was as a graduate student. I also find I have much less time to take on accepted ideas when they are assumed in papers I review... most recently, I lost hours of a week's vacation working on my laptop trying to convince myself (or disprove the author's assertion) of one aspect of one virus' lifestyle. In the end, I now believe there isn't much/any data against the conventional wisdom, but it is crazy that I chose to spend a substantial fraction of my time at a beach house chasing this idea down. I'm too busy now, but I do envy the perspective and time that graduate students have when they read the literature, and when they assist in or write their own peer reviews.

5.13.2009

Failures of Peer Review, Part 2

I've been confronting a few failures of peer review recently, and I think it's time to revive peer reviewing posts. Like most failures of peer review, it may very well be the editors who dropped the ball and not the reviewers -- or a combination of the two.

1. I came across a 2008 paper with an incredibly low resolution figure that prevented me from reading the labels of the data points (and there were >100 labels). This wasn't a problem of my computer (the pdf looked just as bad -- even more pixelated and harder to resolve at higher magnifications -- with several viewers), didn't get better on the print out, wasn't available at a better resolution in the html version), I asked others to try their hand at reading it with no success, etc. Now, this wasn't a very important figure to read to get the conclusions of the paper, I admit... it's more that the figure had to exist to get the paper published. But it was important to me for a study I'm trying to start, and I had to spend several hours deciphering the figure. I know that the reviewers could not have been able to evaluate the data in the published version of the figure, so either the journal published a lower resolution version than they gave the reviewers or neither/none of the reviewers actually read/checked this figure.

2. Twice in the last month I've been asked by senior scientists what I think of a recent paper in our field. I happen to know the paper well, since I reviewed it and recommended rejection on a number of solid grounds. Even though I still think the study is flawed, I must have been in the minority, since the paper was accepted with only a few changes. However few people will read the paper thoroughly enough to see the newly introduced hedging statements; in this busy day and age, all most people will read or remember are the title, the abstract and the quality of the journal it was published in.

So I gave these senior scientists my detailed rationale for why one shouldn't trust the paper's conclusions, it was easy to convince them, and I doubt either one will be citing it anytime soon. But I can't shake the feeling of being a failure myself as a reviewer, since the paper did get into the literature virtually unchanged. Rereading the review, I was constructive in my criticism, but I clearly challenged the premises of the paper, and backed up my argument with references. I reiterated the cause for rejection in more frank language in the confidential comments to the editor. And maybe, with another editor, my comments would have caused the paper to be rejected... but the next time I feel strongly about a rejection I will be tempted to use more emphatic language.

5.11.2009

two cultures, two deadlines.

While many are talking and blogging about the two cultures these days, I want to highlight the gulf between our academic disciplines with an article from the Chronicle of Higher Education on the attempts to speed up publication in the humanities. While peer reviewers in science are being pushed for one or two week turnarounds from an increasing number of journals, the humanities are trying to move the average time from eliciting a book review to publication from year(s) to months.

The article says one of the reasons for the long turnaround is that "reviewing tends to be a rather thankless task, so it gets pushed to the bottom of a reviewer's agenda." Certainly, it's a similar situation in the sciences... but there seems to be a stronger system of reciprocal altruism in the sciences, where we all need to get our papers published, we all want them published quickly, and we do (largely) comply with the deadlines we're given. The article also highlighted the low number of reviews that can be published in each monthly/quarterly issue of a journal, and it could be that online-only journals will spur faster publication times in the humanities just as they have in the sciences.

It's not an apples-to-apples comparison between the fields: the publications being discussed are the peer review themselves.

I appreciate how quickly biology progresses these days, but it can be overwhelming. Having to keep up with online-early publications, the myriad table of contents emails, the automatic search emails, the increasingly short review times for journals... at times the slower publishing pace of other parts of academia could be very appealing.

4.20.2009

join academia, see the world

While many others, apparently, are at Experimental Biology this week, I'm off to a small meeting in Europe. And while there are many reasons I am now a scientist, the amount of travel required by the job is absolutely one of them.

My family didn't travel much when I was growing up, and my traveling for science also started slowly and unglamorously... my first conference was in scenic Detroit. But since then, I've gone to meetings on four continents and have gathered a couple of truly unique passport stamps along the way. Most international places I've visited have been far off the tourist track, and I love the mix of work and vacation that foreign visits entail.

I even appreciate the domestic travel. One of the downsides of academia is how frequently we have to move, but one of the upsides is that we tend to move among a relatively small number of cities/regions. I almost always reconnect with a friend or a former labmate when I'm visiting someplace to give a seminar. And you can exploit this further -- I'm cultivating a collaboration that will require me to travel at least once a year to a part of the country where a good friend of mine is doing her PhD.

I know many scientists, including those without kids, who dislike the traveling science involves. But I'm enjoying getting my carry-on packed for the first conference of the "summer," and I've got my phrasebook ready...

4.18.2009

Gossip Girl, PhD

I read an interesting first person over at the Chronicle of Higher Education. An assistant professor recounts a rumor that was spread about her in graduate school (that she was having an affair with an administrator, and that's why she got a plum teaching assignment), and how it was perceived from many different angles.

It was a good reminder of the painful downsides to academic gossiping. It's juicy to know -- and retell -- which scientists are hooking up with one another. We've all passed on gossip that later turned out to be untrue or was outdated... and we should hold our tongues more often for fear of hurting both the innocent and guilty.

But a case can be made that a certain amount of "gossiping" is necessary for social interactions in science... for instance, knowing two scientists are romantically involved can prevent awkward conversations/situations at conferences. Having heard through the grapevine that a professor is on the job market would prevent you from approaching her for a postdoc just because her lab is geographically convenient. I think that many forms of gossip serve as the way we pass on essential knowledge of the social aspects of academia more than we might like to admit.

The author of the Chronicle article wasn't sleeping with her superior, but there are many pairs of romantic partners we encounter in science, and it's not uncommon for one of the pair to be the boss of the other. Usually this is out in the open, for instance, one person is the PI of the lab and the partner is the lab manager. A non-trivial number of grad students marry their advisors... and the first part of the relationship is clandestine, if just for the fact that most universities consider such a relationship unethical. It's good politics to know that you can't behave the same way with that lab manager, that grad student, as you can with someone who isn't relating their whole day's events to a member of the faculty over dinner. And if the superior is giving advantages and plum assignments to their romantic partner underling... it's good to have advance knowledge so you might not get as upset, and to know the minefield you'd be negotiating if you complained about the unfair treatment.

Couples, if they share a lab, open their relationship up to some level of scrutiny as their relationship impacts lab interactions. I have known several people who got along great with their PIs, but not with the PI's wives, who were the lab managers. In all of these cases, the PIs slowly became converted to their wives' perspective, and a few of these students were outright asked to leave those labs. This could mean that the lab managers had more detailed knowledge of the students and were faster at seeing that the students weren't up to snuff... but that certainly isn't how the students perceive their situations. In the case of partner PIs who jointly head a lab, the same dynamics can occur. And as dual hires have become a regular occurrence, scientific divorces are also becoming more common, and these splits can have devastating effects on the career of their trainees. Even if a trainee stays with the same major advisor, they lose the benefits of the joint lab, which might have been one of the more attractive parts of taking their position, and they often lose time to switching institutions -- one, if not both, of the divorcees usually moves to a new position.

It's prudent for any prospective graduate student to try and discern lab dynamics. We hope that we get honest information from the existing lab members and, hopefully, all parties exercise discretion and not pass anything on further. When romantic partners work together, a prospective student really does have to guess at the nature and health of the partnership in order to determine how stable their six-year educational experience might be... and trying to find out information on the romantic relationships of people in a department is something that's hard not to call "gossip."

Beyond workplace romances, one person's gossip is another person's cautionary tale of unethical behavior, or how a university/professional society/journal really works. One of the most memorable things from my graduate career was the hair-raising tales of breaches of ethics that the oldest member of the department had personally witnessed in his 50 years at the university. One of the stories ended up with an unfairly blackballed postdoc killing herself, another ended up with a person graduating with a PhD even though s/he had acknowledged, in writing, that they had faked their data. All of his anecdotes were anonymized... is that the difference between gossip and sage stories passed on to younger scientists? That would certainly cover all the science bloggers who change names, create untraceable abbreviations for locations and remove details so they can relate what's been happening without as much fallout in their professional lives. I find this sharing very useful -- it's good to know I'm not alone, it's good to know what other indignities others are suffering (and if I can preemptively protect myself from them), it's good to have a place to vent about the confusing and unfair aspects of academia. Such posts may very well qualify as gossip but they also are a key aspect of professional development in 21st century academic science.

We pass on informal critiques on the quality of fellow scientists and their work to colleagues all the time. I have sometimes considered that a professional responsibility -- if you know that the conclusions of a paper are incorrect because of subsequent work the group conducted, but they neither published the new work nor retracted the paper, shouldn't you tell people how to correctly interpret that paper when it comes up in conversation? It doesn't seem like gossip to offer inside knowledge on one of the many papers that received less than perfect peer review... but is it gossip if you preface it with "well, you know they'll never correct this, but..." and roll your eyes?

I think the style of delivery is part of what we consider gossip. For instance, it's a dry and unembellished fact about some labs that they are slow to publish -- sometimes they are years behind on publications. However, that same information can be more dramatically related in a story about a frustrated student who didn't get any papers out until they were done with their first postdoc and the choice words he had for the PI... It's more entertaining to tell a fable than a fact.

I'd say some gossip is a necessary part of a researcher's apprenticeship. I imagine that discerning social relationships and passing on information about past events is part of the training for every kind of career (except for a reclusive novelist?). We need to learn what the informal hierarchies are, what's the best way to approach that dean, the de facto way things work. The problem seems to lie more in the propagation of lies than in gossip per se, and maybe in what areas of a scientist's life are up for public consumption. But we probably can't create any blocks that prevent false rumors from being spread around, not while personal candor bordering on gossip is such an important part of the social fabric of science. However, I'm not in any way suggesting we start gossiping more...

4.03.2009

being okay with being #2...

DrJ&H has a recent post titled "It turns out I'm ok with being 2nd", but just like my last post, the title isn't what I thought it would be. DrJ&H was talking about the difficulty accepting she's THE expert in a sub-sub-field, and how she's okay being the second most expert person...

Whereas I want to post about what it's like to actually know you're the #2 young professor in my sub-sub-(sub-)field. I'm not sure how that sets me up for tenure -- is #2 good enough? -- and I'm having trouble navigating how much I should help the seeming #1 in my area when he asks for my opinions.

We are both young PIs and interested in ridiculously similar questions. Now, there isn't 100% overlap in our interests and expertise, but it's substantial, and we both have multiyear research plans that will keep bumping up against each other. We know that collaboration is one way out of this, but this has begun without great communication of what areas we're going to share, what we'll both conduct parallel work in, etc. And we have no joint funding.

While the thought of giving any competitor/colleague the ammunition with which they could scoop you would drives one to extensive email editing, it's worse with this particular frival. He's *much* faster at publishing than I am, he publishes in higher impact journals than I do (those two facts are not independent), and, for the last five years, I've had the concrete sense he's smarter than I am. This opinion isn't just based on having been blown away by him since the first time we met, it's based on the fact that several of my mentors have used the word "genius" to describe him. My postdoctoral advisor, for example, decided to decline an invitation to write a book chapter and recommended my frival -- someone who had never been associated with my mentor's lab -- instead of one of his own postdocs.

I should mention somewhere in here that my frival is also an amazingly nice and kind person. This isn't a personal, or personality conflict, in the slightest.

But having regular email contact with the frival is helping me see some cracks in the pedestal that I have put him on. We are having some intellectual disagreements, and I don't just think I'm right: his data support my side... leading to conclusions he didn't see on his own. In another instance, I was able to come up with the critical literature citations that radically changed the conclusions of another paper of his... I still don't know how much to reveal/hold back in any given conversation (the frival is a man of fewer words than I, and he never volunteers what his next steps will be), but having a peek under the hood of his gleaming, cherry red corvette of a research program has humanized him, and made me confront another iteration of impostor syndrome. He may be #1, but I'm not all that far behind at #2.

I have been trying to imagine whether there are things about me that might intimidate my frival. But of course, my frival is so perfect that he might just be the one young scientist without impostor syndrome himself...