Is it really more expensive for a journal to be more selective?

A frequent point raised in the discussion about open access it that it would cost much more per published paper in more selective journals, for example in this Nature News Feature. I’ve never seen this broken down in detail, but the idea seems to be that all these rejections cost a lot, and the costs are then born by the few published paper.

Now as I understand it, Nature and Science reject a lot of papers without peer-review. My experience as a volontary editor at PLOS One is that rejecting without peer review very bad papers is not a lot of work. On the other hand, taking a borderline paper and improving it through rounds of reviewing-edition-revision is a lot of work. This is what a good lowly selective journal like PLOS One should be doing, and which super selective journals don’t even try to do.

Now it’s possible that the mega selective journals have other justified costs. And my evidence is only anectodal. But in my opinion the equivalence selectivity = high costs is not obvious, and should not be accepted without further justification.

What would be reasonably expected to cost more is employing professional editors. So free market, transparent prices, author pays, and let’s see who’s ready to pay for their added value please.

Also, writing News and stuff costs money. Well that’s magazine stuff. Let it stand on its own and people will pay for subscriptions to this if it’s worth it. But bundling the cost of journalism with that of science is not justified and blocks access to science.

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How many paradigm shifts in the history of biology?

Dan Graur, in his usual interesting style, has raised the valid point that the « paradigm shift » terminology popularized by Thomas Kuhn has become way over-used. Every field seems to undergo several a year: Paradigm Shifting and Necrophiliac Fantasies about Thomas Kuhn.

Dan suggests as true paradigm shifters in biology: Mendel, Darwin, Kimura, and Hamilton.

In my opinion, Darwin is the one un-arguable paradigm shift in biology, on par with Newton or Einstein in physics or Lavoisier in chemistry. The questions which could be asked, the frame in which new results are to be understood, were completely changed.

My feeling is that Kimura and Hamilton worked within the Darwinian paradigm, and do not represent true paradigm shifts. They clarified important aspects, true, but they did not change fundamentally the way we look at the study of living organisms. By the way, if you are including these guys, surely Woese belongs in the same list?

For Mendel, I am divided. I would tend to put his work on the same level as Watson & Crick. It was super important work, but we already knew that heritability is important, that offspring look like their parents, and that there must be rules to find. Similarly, for Watson & Crick, we knew that there must be a molecular carrier of heritability.

A more important aspect of the avent of molecular biology as far as I am concerned, although I am not sure that it qualifies as a paradigm shift, is that biologists started thinking in terms of information content rather than in terms of biochemical content. The most important property of a messenger RNA is the genetic code which translates to proteins, not the amount of sugars in it.

And speaking of biochemistry, the only shift which in my mind can be comparable to Darwin’s little book is the rejection of vitalism. This in a way is what led to the question of the structure of DNA being relevant. If life obeys the laws of physics and chemistry, and can be explained by them, then each property of life, including heritability, must have a physical support with the right properties. But I don’t have a clean date and famous name, comparable to Darwin or Einstein (Wikipedia informs me that the synthesis of urea was not the magic bullet I was led to believe). And what is a paradigm shift without a famous old white guy?

So two paradigm shifts in biology for me, and only one with a clear before-and-after date. We do as well as physics as far as I can see. 🙂

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Update: Dan’s post and this one spurred some discussion online.

Nicolas Le Novère has an interesting post defending as paradigm shifts changes such as the avent of molecular biology, or today systems biology. With a very nice analogy to population genetics, so at least go and look at his cool picture of Popper vs Kuhn.

Both Nicolas and Detlef Weigel have defended that Dan and myself have a too narrow view of what constitutes a paradigm shift. So I checked the Stanford Encyclopedia of Philosophy, and apparently it isn’t clear for anyone what exactly is a paradigm shift, and whether it’s relevant, especially in biology.

I also want to quote Rafael Najmanovich: « people confuse technological breakthroughs with paradigm shifts. » This fits a lot of molecular biology thinking in my experience.

All this has made me think a bit more about the question of whether Kimura’s neutral theory of molecular evolution is really a shift in its small corner of science, and the relation to other non adaptive theories. A blogging and twitter exchange which got me thinking; this made my day. 🙂

Publié dans epistemology | 5 commentaires

Predatory #OpenAccess publishers: what’s the worst which can happen?

A recurring theme in discussions about open access is the problem of predatory publishers, illustrated by Beall’s list. Now I agree that it is not nice that these exist (although the threshold for inclusion in the list can be debated), but I am left wondering: if the existence of these predatory publishers is the major problem of open access, how big a problem is it?

So with predatory open access publishers, what is the worst which can happen?

  1. Articles which have not been properly peer-reviewed are available online. Which is already the case in ArXiv, which is widely regarded as a useful service.
  2. The publisher might disappear. Since the papers should be published under creative commons, they can be stored and redistributed from any other service on the web. So if any paper was of interest to anyone, or if any author had some iniative, then the paper should not be lost.
  3. Authors who were not careful about their choice of journal, or who are more vain than rigorous, will have lost a small sum of money.
  4. The authors CVs might be inflated by less than rigorous publications. Since most committees for hiring, funding, etc, will not recognize these journals, the risk seems low.
  5. Science consumers outside academia (MDs, politicians, journalists…) might be fooled into thinking that this was peer-reviewed and handled by a competent editor, whereas it was not. A real risk.

Most of these risks do not seem to be real to me. I would like to compare risks 2 and 5 to the classical subscription-based publication system.

For risk 2, any publisher can go backrupt or otherwise disapear or change its business model, and in closed access publishing the papers are potentially all lost. Predatory open access actually wins over the status quo in this case.

For risk 5, the creation of pseudo-peer reviewed journals for Big Pharma, creationists, or other interest groups, predates open access and will certainly continue. At least if the pseudo-science is open access, everyone can see what’s inside and maybe notice the problem. At worst, predatory open access does not seem worse than the status quo.

So can we stop discussing what seems to be mostly a non issue, and concentrate on the reality of high quality publicly funded science locked up by commercial publishers and unavailable?

Publié dans open access | Un commentaire

Why did I refuse a challenge sponsored by Philip Morris International?

This is a translation of a post on my French blog, Tout se passe comme si, following a suggestion by Nicolas Robine.

I was recently contacted to take part in a challenge which was interesting and relevant to my research, in the framework of the Systems Biology Verification (SBV) IMPROVER project. The problem is that it is organized and supported by Philip Morris International, a small tobacco company which you might of heard about.

I refused.

Which raises the question: why did I refuse, whereas I might have accepted if it were financed by a different industry?

In a normal industry, R&D can have legitimate aims. In fact, if there were no R&D, it would be a problem. We can debate the implementation, and think that some things could be better done, but we something should be done. For example junk food is a bad thing, but we need to eat, thus there is place for legitimate and useful R&D in agro-food business. Big SUVs are bad, but we need to move, and there is place for legitimate and useful R&D on efficient less polluting motors, etc.

But what can be the aim of R&D in tobacco industry? Making tobacco slightly less dangerous? There’s a simpler solution: don’t smoke. It is not a legitimate need. And research supported by tobacco industry has another point: spread doubt and obscur research which shows clearly and unambiguously that tobacco is a horrible poison. It can be subtle, often supporting research on real issues which move the spotlight elsewhere.

In the case of this « Challenge », the theme is « Species translation », and it seems to focus on the problems with transferring experimental results between species. For example, problems in transferring to human toxicology results from mouse or rat. It’s a real question, but you cannot help but feel that it is to the advantage of the producer of toxic substances to put this forward.

Publié dans ethics, translation from French | Un commentaire

Another thought on publishing reviews: a resource for data mining

Following my previous post about the relevance of publishing reviews and reviewer names as discussed at PLOS One, here is another contribution of mine to the discussion:

If all reviews were made publicly available, that would allow for some interesting data mining which might uncover trends about the reviewing process, which could in turn help us improve the process. How often are reviewers completely inconsistent? (see http://dynamicecology.wordpress.com/2012/11/25/how-random-are-referee-decisions/) Are reviewers more stringeant or less detailed for authors from specific backgrounds (gender, country, etc.)? What is the overall balance in reviews between correcting style and correcting substance? Which proportion of reviewer recommendations are accompagnied by a specific reference? Etc.

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What is the actual work of a PI? Lots of stuff.

Recently Michael Eisen (lab, blog, twitter) tweeted:

are there any studies of how PIs apportion time between grants, teaching, papers, writing recs, meetings and actual work?

To which I reacted:

.@mbeisen With due respect, I think you are mistaken about what your « real job » is. Teaching major responsability. & planning advising etc.

A small dialogue ensued:

@marc_rr and you know what my real job is because…?
@mbeisen let’s say the job of a PI who’s a university prof. 140 char lack nuance but excluding teaching from real work seems shocking to me
@marc_rr i am paid to do research, my teaching is voluntary
@marc_rr and that is not me disrespecting teaching – into which i put a shit-ton of time – just a fact of where my money comes from
@mbeisen OK I see. The original tweet said « PI » not « Mike Eisen ». I understand your position now. Still not 100% clear about « real work ».
@mbeisen and meetings are often an important real work of a PI IMO: share info, make decisions etc

So first a clarification: Michael Eisen is an HHMI investigator. Which as I understand it, means that he doesn’t need to teach. So super cool that he does!

Second, I still take issue with the exclusion of « grants, teaching, papers, writing recs, meetings » from « actual work« .

The question is, what is the actual work of a PI? Situations can varry widely, so I’ll take a common case for now of a Professor who’s also a PI, has a lab with grad students (known in Europe as PhD students) and postdocs. Presumably, if you’re a Professor you are supposed to teach (but see above), and presumably if you have a lab with students and postdocs you have soft money grants. So what should you be doing?

  • Advising and managing your students and postdocs. Depending on their number and degree of autonomy, this can take quite a bit of your time. In my opinion, a very legitimate part of your work.
  • Often related to the above, writing and correcting papers, managing the review process (what revisions do you do? which ones do you try to argue away? where do you (re)submit?). Also legitimate.
  • Since the students and postdocs are paid, you need to get grants, which means that you need to write them. The legitimacy of this taking up your time is for me a question of degree. I don’t think that we would be justified giving grants without asking for a project and reviewing it, and actually thinking about your plans for the next years, how they relate to the competition, how feasible they are, and how they make for not-too-bad PhD projects is important and useful. On the other hand, I can understand the frustration of my US colleagues who need to write an awful number of grants to get a few funded. Moreover, various agencies from the NIH to the EU FP programs ask for all kind of non scientific stuff which is mostly bureaucratic and of dubious use. So I’d say that in principle writing grants is a legitimate part of a PI’s work, but that if it takes too much of our time the system is broken (success rate too low and/or too many useless requirements).
  • Writing recommendation letters and generally following up on people who worked with you. Seems legit to me.
  • Keep up with the literature. Obviously.
  • Also obviously (I hope) reviewing other peoples papers and grants.
  • Teaching. If you’re a Professor at a University, it seems quite legitimate to spend some time on what you’re paid for. But further than that, I think that teaching, from undergraduate (Bachelor) to summer schools for PhD students, is a very important responsability, and that we should try to do it well. Which means spending more time preparing classes and interacting with students, and can also mean reading up or going to lectures about pedagogy. Very legitimate.
  • Meetings. Ah-ha, no one likes meetings, right? Yet every meeting was called by someone, and others agreed to come. Fact is, meetings can be quite useful and frankly indispensable. You want to coordinate the teaching between Professors to provide a consistent learning experience which meets your goals? You want to decide on the future directions of your department? You want to launch a new interdisciplinary effort? You want to organize a conference? All these things need meetings. So it’s true that a mis-managed or mis-called meeting is a waste of time, but so is debugging code. You don’t get to do it 100% right. Like grant writing, a question of degree then.
  • If you have time, as a Professor you can even do some hands-on research yourself! But in my experience, it would be unrealistic to expect this to be more than 5-20% of your time, unless you’ve decided on a very small group strategy (i.e., you and one student).
  • OK, there’s one thing which I have to do and which would not be part of my job in an ideal world: dealing with the ever changing rules of my central administration concerning refunds of expenses and human resources. For this, you need a full time competent admin (disclaimer: I have a competent admin whom I share with 7 or 8 other group leaders).

In summary, I think that there are many aspects to a Professor / PI / group leader’s job, and that most of these can be considered « actual work ».

We are no longer postdocs (see also this interesting discussion)…

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My 2 cents on open peer review

There’s a discussion about the relevance of publishing reviews and reviewer names on the restricted discussion forum of PLOS One editors. I’m miroring my own contribution here:

My 2 cents:

  • I would really like to see the reviews published next to the paper. This way the work done by the reviewers would not be lost to the community, the readers would be able to see which points were contentious or not, the reader could also see whether a given methodological point (dear to the readers heart let’s assume) was covered, everyone could see how much the review process improves many papers submitted to PLOS One (in some cases I feel the reviewers contributed more than some authors). I fail to see any drawbacks whatsover.
  • BUT I don’t believe in publishing the reviewers’ names, at least in the present state of things. Too many possibilities of pressure, retaliation, etc.
  • I am also favorable to double-blind. I’ve read that in quite a few cases the reviewer can guess the authors. I fail to see how it’s a problem. Similar to publishing the reviews, I don’t see any potential drawbacks.
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How open is #openaccess? A few comments

Major actors of open access publishing have taken an excellent initiative, namely establishing a grid detailing how open different publishers are.

They took into account different aspects of open access, and also asks for comments. So here are my suggestions of additional criteria to take into account for publication openess:

  • Are the peer reviews publicly available next to the article, anonymously or not?
  • Is it possible to freely comment on the publisher’s website, next to the article (as in PLOS and BMC)?
  • Does the publisher have a systematic policy of embargo towards the press, conference presentations, etc?
  • When relevant, must authors provide Open Source source code? (for PLOS Computational Biology you have to, but not for OUP Bioinformatics.)
  • When relevant, must authors deposit raw data in independent reliable databanks à la GenBank?

Did I miss anything? Will they really take into account such annoying suggestions? Time will tell.

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And now for something completely the same

Those who know me, might know that I have an active blog in French. This allows me to reach out to people who are interested in science, but would not necessarily read about it in English.

But for some topics, I would like to reach out to my colleagues, irrespective of language. I.e., in English. Hence this other blog, where I will post from time to time on topics of interest to other scientists.

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