Opening up open access

At a conference a few years ago I spoke with a friend who said “when I talk to people who say “I’m going to publish 5 papers this year, even though I haven’t submitted any” and it’s July I smile inside. It takes so long to publish papers there is no way they will be able to publish 5 by December”. It’s true, it takes forever to publish (after the writing and submitting part, which for me takes awhile too).

But some scientist, even Nobel Prize laureates, are publishing things online before even submitting it for review in an “official” publication. Not only does this cut out the journals who are arguably making a ton of profit off our free labor (see here and here), but it gets your work out to the scientific community faster.

Read about it over at the New York Times! 



The insignificance of the significant pvalue



We’re told early and often that this means that your data is significant. But statisticians and biologists that are statistically inclined, while tell you (and have been telling us for awhile) that this is a completely arbitrary figure. Like most tools, in statistics if you use the pvalue incorrectly you’re doing yourself and your science a disservice.

And the American Statistics Association agreed, and disagreed. Last week they released an AWESOME statement on p-values.

Read the original, or the equally excellent synopsis over at the Molecular Ecologist (I can’t give that blog enough love…)

xkcd comics

xkcd comics

Reflections on getting your first publication out the door

I know friends who celebrate every paper they submit. I think that is awesome.

But by the time I get a paper submitted, back for revisions, revised, submitted again, accepted and final edited, I hate that paper. I have seen it so many times, and written each sentence with exacting intention that I never want to see it again.

Which is why a post over at the blog “Ecology B1ts” entitled Reflections on my first first-author pub (and the seven years it took to get there) was so interesting to me. Margret Kosmala talks about how life, mentorship and rejection can all influence getting a paper published.

Well worth the read!




The authors would like to thank…

I’m abysmally bad at acknowledgments sections of papers. I just want to write a quick “thanks guys!”

But over at Scientist Sees Squirrel there is a really good post by Stephen Heard about how to acknowledge criticism.

“For critical suggestions and discussion I thank [names]. Not everyone agreed with everything but even that helped (West-Eberhard 2014).”

The post goes on to discuss how, feedback on a manuscript helps the most when it comes from people who don’t agree with you. It makes your paper and your argument stronger.

Also, for those of you who don’t get to the footnote, it also mentions how “constructive criticism” is important, but being a jerk is just that… being a huge jerk:

“*^It’s true that some reviewers don’t understand this. I once submitted a manuscript reporting some limited but (I think) interesting natural-history data. One reviewer wrote, anonymously, that they wouldn’t have given my manuscript a passing grade in their undergraduate Introduction to Ecology course. Nothing more – they didn’t explain what they thought was wrong, or how they thought it might be improved! The editor should never even have passed this “review” on to me; but fortunately, I was too stubborn to give up, and I sent the manuscript to another (better) journal. It was accepted with a few minor revisions, and now I have a funny story to put in a footnote.”


Reasons academia is NOT the worst

There are plenty of reasons to be frustrated by academia (anyone on the job hunt knows this all too well). I’ve spoken extensively about my hesitations about joining the academic workforce.

So it’s pleasant to find a post that does exactly the opposite, and lists the reasons being in academia is not only not so bad, but really pretty good.

Read about it over at the Guardian!introduction-h2


Citing retracted papers

Over the holidays I stumbled onto this blog post (from Retraction Watch), which has kindly calculated how many times retracted papers have been cited.

Both before retraction (forgivable, you didn’t know it was going to be retracted) and after retraction. How are these papers still being cited?

I’m taking a unkind view of this, and blaming everyone. I blame the authors for citing a paper that shouldn’t be citable. I blame reviewers of that paper for not realizing that their discussion or research is built on faulty evidence. I’m blaming publishers for not doing a better job conveying that something should not be common knowledge.

But I’m in my post holiday sugar slump. It’s possible I’m taking too harsh a view. Anyone else? Am I missing something?


Article Year of retraction Cites before retraction Cites after retraction Total cites
1. Visfatin: A protein secreted by visceral fat that mimics the effects of insulin. SCIENCE, JAN 21 2005Fukuhara A, Matsuda M, Nishizawa M, Segawa K, Tanaka M, Kishimoto K, Matsuki Y, Murakami M, Ichisaka T, Murakami H, Watanabe E, Takagi T, Akiyoshi M, Ohtsubo T, Kihara S, Yamashita S, Makishima M, Funahashi T, Yamanaka S, Hiramatsu R, Matsuzawa Y, Shimomura I.


   2007 247 776 1023
2. Purification and ex vivo expansion of postnatal human marrow mesodermal progenitor cells. BLOOD,  NOV 1 2001Reyes M, Lund T, Lenvik T, Aguiar D, Koodie L, Verfaillie CM.


2009 655 214 869
3. Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. LANCET, FEB 28 1998Wakefield AJ, Murch SH, Anthony A, Linnell J, Casson DM, Malik M, Berelowitz M, Dhillon AP, Thomson MA, Harvey P, Valentine A, Davies SE, Walker-Smith JA.


2010 675 308 983
4. An enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. PLANT JOURNAL, MAR 2003Voinnet O, Rivas S, Mestre P, Baulcombe D.


2015 897 N/A 897
5. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO JOURNAL, NOV 16 1998Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC.


2015 792 N/A 792
6. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC EVOLUTIONARY BIOLOGY, JUN 28 2004Jobb G, von Haeseler A, Strimmer K.


2015 748 N/A 748
7. Spontaneous human adult stem cell transformation. CANCER RESEARCH, APR 15 2005Rubio D, Garcia-Castro J, Martín MC, de la Fuente R, Cigudosa JC, Lloyd AC, Bernad A.


2010 371 269 640
8. Combination treatment of angiotensin-II receptor blocker and angiotensin-converting-enzyme inhibitor in non-diabetic renal disease (COOPERATE): a randomised controlled trial. LANCET, JAN 11 2003Nakao N, Yoshimura A, Morita H, Takada M, Kayano T, Ideura T.


2009 572 101 673
9. A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis. CELL, JUN 12 2009Valastyan S, Reinhardt F, Benaich N, Calogrias D, Szász AM, Wang ZC, Brock JE, Richardson AL, Weinberg RA.


2015 530 N/A 530
10. Regression of human metastatic renal cell carcinoma after vaccination with tumor cell-dendritic cell hybrids. NATURE MEDICINE, MAR 2000Kugler A, Stuhler G, Walden P, Zöller G, Zobywalski A, Brossart P, Trefzer U, Ullrich S, Müller CA, Becker V, Gross AJ, Hemmerlein B, Kanz L, Müller GA, Ringert RH.


2003 348 166 514

Academic publishing companies make how much?!

Academic publishing is a 25.2 billion dollar a year industry. I’m not kidding.

Long ago in a land far far away, Forbes predicted that the academic publisher Elsevier’s relevance and lifespan in the digital age was going to be short. “Cost-cutting librarians and computer-literate professors are bypassing academic journals- bad news for Elsevier” the article proclaimed.

But here’s the thing. Elsevier hasn’t been run out of town. In fact, it’s thriving. So are Springer, Taylor & Francis, and Wiley. In fact, Elsevier in 2013 had a higher profit margin than Apple Inc.

Why is this? Brian Nosek, a professor at the University of Virginia and director of the Center for Open Science, has an idea:

“Academic publishing is the perfect business model to make a lot of money. You have the producer and consumer as the same person: the researcher. And the researcher has no idea how much anything costs. I, as the researcher, produce the scholarship and I want it to have the biggest impact possible and so what I care about is the prestige of the journal and how many people read it. Once it is finally accepted, since it is so hard to get acceptances, I am so delighted that I will sign anything — send me a form and I will sign it. I have no idea I have signed over my copyright or what implications that has — nor do I care, because it has no impact on me. The reward is the publication.”

Read more about it over at SAS Confidential.