Archives for posts with tag: science

It’s taken me a little while to be able to write a response to the article “Who’s Afraid of Peer Review?” Every time I sit down to write something, I begin coherently and slowly devolve into angry writing. The article asks, “Who’s Afraid of Peer Review?” and then proceeds to only talk about the peer review, or lack thereof, in open access journals. Because the open access that the article portrays is shoddy and corrupt and seemingly should present no major threat to the vaunted, subscriber-based journals. Somebody should let PLoS ONE know.

The major, fundamental difference is who can access the articles and for how much. The decision about what makes it into which journal is not based on–however much scientists want to believe it is–based on the quality of the science. Nature and Science (where this particular article appeared) have the highest retraction rates of any journal. Knowing that, it’s hard to argue that they publish The Best Science. No, they try to publish good science, but they are also concerned with the sex appeal of the article; they only want the high impact science. So that begs the question: What happens to scientifically solid work that the editors don’t think is sexy enough? Maybe the hypothesis was wrong, or the results were interesting but not game changing, or it’s a less well-known field. Well, in that case, it goes to lower impact journals, maybe along with some stuff that wasn’t as well-done. What if there was an alternative? A journal that only accepts stuff based on scientific merit, publishes it, and then leaves it up to readers to decide whether it gets more or less views. Well it exists: all the PLoS journals.

When I hear people talk about “open access” they’re usually talking about three phenomena–alternatives to subscriber-based journals that seek to remove some of editorializing in paper selection; those subscriber articles that will automatically go open access if they were funded by the US or the UK; and, what this article deals with, a lax, grey market designed to get people publications.

So back to the article itself. It commits some of the same sins that we monitor scientists for:

1) Conflict of interest. Did anyone have a problem with the fact that this was published by a subscriber-based journal with skin in the game (so to speak)?

2) Or, how the article targets potentially notorious open access journals without including a sample set of subscriber journals? (No controls? that’s just bad science.)

Stop with the outrage about author fees–it’s not like publishing in PNAS is free. Servers cost money and current article fees pay to keep all the older articles accessible.

My biggest issue, and perhaps the hardest to explain, are some of the assumptions that the author made. If were were talking about a different field, the term we use would be “microaggression.” A lot of detail was given to the description of the author’s “experimental” set up–how he engineered the names of the authors to look authentically African, how he purposely wrote in poor or grammatically incorrect English, how he included blatantly incorrect data and interpretation, to the point of approaching misconduct. I fully understand wanting to test the limits of whatever review these journals were purporting to offer and how including some factual and grammatical errors would check to see if anybody was reading whatsoever. But why did he, an Oxford-educated white dude feel the need to play up the ‘otherness’ of his fake scientists? Did he think that some of these open access journals would blatantly target scientist from developing nations? What would have happened if he submitted with a different name? I just think it’s really problematic to implicitly tie poor work with scientists from developing nations, even if he wasn’t consciously doing that.

There are plenty of problems in science, but I don’t think open access is one of them. I think the emphasis on “publishable results” (read: positive) and peer review is a much bigger part of the problem. A recent release by Elsevier editors estimated that around 10% of the papers they receive have some evidence of misconduct. That’s a staggering number. So yes, there’s obviously problems in science publication, but I don’t think these open access journals are the cause, although they are perhaps a symptom.

EDIT: A lot of people have been talking about this. One of my favorite responses can be found here, although I hesitate to pile on over the Ar DNA thing:

There are several interesting paradigms in how science is practiced today. I can really only speak to the US, but since international science is based on the American model, we can say that some of these particularities are generally true. There are three main ways that scientific discoveries are reported and all are subject to some level of peer review: articles in journals, conferences, and patents. The first two are far and away are much more important in terms of discoveries and knowledge acquired.

Now, most research is federally funded, especially non-applied research. You just can’t rely on capitalism to fund basic research; the pay off isn’t consistent enough or on a short enough timescale, although the rewards are demonstrable down the road.

So, that being the case, the most prestigious journals are a pay to play sort of thing. A subscription to Science, on of most prestigious (and highest retraction rate–d’oh!) journals costs the individual $146 per year. And that’s if you’re a scientist. If, God forbid, you are an interested civilian, a yearly subscription to Science is $310. To stay abreast of all the federally funded research that gets published, you would have to pay quite a lot of money per year, and yet it’s your tax money that is going into this enterprise. Seem fair? No? You’re right, it’s not. It sucks, actually. I’ve even had collaborators at other universities ask me to send them PDFs of articles because their institution can’t afford the subscription.

Now, there have been various efforts to rectify this. One of the more revolutionary ideas is open access journals, like PLoS and the Frontiers series of journals. They put all the burden to publish on the authors (to be fair, PNAS does this too). Not meaning that there’s no peer review, but rather, the cost of publishing is borne by the authors, not the readers. NPG (Nature Publishing Group) recently acquired the Frontiers journal series, which perhaps lends some more legitimacy to the whole enterprise, or at least an indication that open acces is here to stay. An even greater indication of this is that the Obama administration released a memo via the OSTP, which calls for all agencies that fund more than $100 million in extramural research to make all publications available within a year of publication along with any unclassified, federally-funded research. This is pretty huge, and reflective of greater cultural changes, I think. We have been increasingly insistent on greater transparency in government and science. Obama was practically elected on a platform of greater transparency and then WikiLeaks happened (along with Manning and Snowden), not to mention the plagiarism suspicions/instances that are now rampant in the scientific community (there’s a whole website dedicated to retractions!).

Policy changes like this are part of a greater shift towards transparency that was, in part, brought about by the internet and all the data that anybody can access. There are a group of scientists that are dedicated to opening up science in general–making lab notebooks available, encouraging citizen scientists, and overall increasing transparency. I actually think this is a great idea. I know that in highly competitive fields, this level of transparency is anathema to getting to be the first one to publish something, but nobody says you can’t delay publicizing your lab notebooks. Maybe if more of the day to day grind of science were made available, we wouldn’t have so many drugs getting pulled off the market, and people might appreciate how difficult doing science actually is. Or I’m a total idealist and opening up data will just result in a kerfuffle like publication of some of the climate science data did. If you’re interested in this idea of opening up lab notebooks, the folks over at are hosting a free online course/discussion group to get this going.

So is there a happy ending with the OSTP memo? Actually, yes. The American Association of Publishers has announced CHORUS, which stands for ClearingHouse for Open Research of the United States. It basically takes advantage of existing infrastructure via CrossRef and puts all of those publications that are federally funded under a 1 year embargo, after which the article goes open access. This is the publisher’s solution the the memo, but doesn’t necessarily reflect its final form, which will require some changes in the federal agencies themselves (especially after some recent debate in Congress). Overall, I think it’s a revolutionary step forward. What remains to be seen is also what happens with publishers (like NPG) who have not signed on to CHORUS and are not US-based.

As a trainee on the NIH’s Chemistry Biology Interface Training Grant, I recently had the opportunity to attend the 1st Annual Career Development conference, which was held in Urbana-Champaigne, Illinois, and featured representation from all the Midwestern CBI programs. Given the changing scientific environment, (training) programs in general need to focus more on the post-graduation outcomes of their students. To this end, conference organizers arranged for five panels focusing on  entrepreneurial, industrial, academic, post-doctoral, and non-traditional careers. Additionally, there were two keynote speakers, Laura Kiessling and Peter Senter, and two poster sessions. 

Probably the most important lesson I learned from the conference was not networking, but rather, that it’s never too early to start planning your career. For most post-docs and many jobs you need to start thinking as early as two years ahead, but more like a year and a half for most positions and places. And that’s where networking comes in. If you’re a graduate student–get yourself to conferences! Start meeting people and making connections. And if you’re an advisor of graduate students–get them to conferences! It’s hard for many of us to ask to go to conferences, but it’s the second-best thing you can do to help your students succeed (making sure they finish their Ph.D. being the first). 

But more on this conference: to put it bluntly, the conference was fantastic. I would consider myself to be relatively well-informed about the post-doc job search process. That being said there were a lot of things that I had no idea about, like industrial post-docs. However, for me the most informative and striking career panel was the non-traditional careers panel. I’ve always planned on a post-doc, but have been a bit agnostic about my career prospects after that. Or rather, not so much agnostic as closeted. I love science; it’s been a huge part of my childhood, adolescence, and adulthood. I read journals for fun and popular science magazines for light reading. But what I’m most passionate about is sharing that love–communicating science to non-scientists, advocating for more money for research, thinking about the best structure for our education and research systems, and encouraging as much diversity in science as possible. So I’m coming out of the closet: I want a non-traditional science career. Or at least to have these aspects be a large part of my professional life in the future. 

In part, this has spurred my participation in blogging. I spend a lot of time thinking about these issues, but I need more practice actually writing them. Almost all of the writing I do these days is personal or scientific, and finding the sweet spot in between personal communication and scientific communication is a skill that most scientists (including myself) need to develop. I’m planning on using this medium to keep up to date with current events in these fields, do some background reading, and writing about it. Hopefully, I can learn a lot about myself in the process and make some good connections that will aid me in the future. 

Working on some more elaborated thoughts on the conference, but for now a few quick thoughts/highlights:

  • Anything Laura Kiessling has ever said. Seriously. She’s hilarious. And while she didn’t explicitly talk about it, she has an amazing story of being a high-powered woman in science at a time when there weren’t many. She went into an interview and actually said that she wanted a group of about 20 people and didn’t listen when people were incredulous.
  • Getting to be creative with my TED talk. A note on the student TED talks…they’re a fantastic idea. We put such a premium on being the MOST accurate, MOST precise, and MOST data-filled, but in an interdisciplinary conference this gets you almost nowhere. While we scientists should get familiar with other fields, we also need to take on the challenge of making our ideas more communicable. Forcing scientists, especially students, to think outside the box and focus on how to communicate their ideas is important and this idea of a TED talk is a way of doing that.
  • All the meals. And not just for the food, which was significantly above average, but also for the interesting conversations at the table. 
  • Non-traditional careers panel. Fantastic.
  • Miles Fabian. What a character.
  • Jeff Peng. If you are at Notre Dame, you should make an effort to get to know this guy. Totally irreverent for a professor (I have a soft spot for irreverent professors), which is refreshing, and with an interesting range of experience.
  • Peter Senter and pharmaco-economic distress.
  • Industrial post-docs are a thing. Yup. And you’re pre-cleared for publication.