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.”


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

Diversity in STEM: it matters

Diversity in the sciences is a recurrent topic on this blog (and – well – basically everywhere). Scientific American has an excellent overview on what “diversity” is and why it matters to the STEM fields. So whether you think about these issues a lot or a little, I highly recommend reading “Diversity in STEM: What it is and why it matters“.

When we consider scientific research as group problem-solving, instead of the unveiling of individual brilliance, diversity becomes key to excellence. In his book,The Difference, Professor Scott Page lays out a mathematical rationale and logic for diversity. He shows that, when trying to solve complex problems (i.e., the sort of thing scientists are paid to do), progress often results from diverse perspectives. That is, the ability to see the problem differently, not simply “being smart,” often is the key to a breakthrough. As a result, when groups of intelligent individuals are working to solve hard problems, the diversity of the problem solvers matters more than their individual ability. Thus, diversity is not distinct from enhancing overall quality—it is integral to achieving it.


“Biodiversity” is a little different from “diversity in bio” – but still a nice photo, eh?

A science-y tweet makes my heart skip a beat

When I first heard about Twitter (several years before I actually understood what it was) – I remember thinking it sounded silly. Who cares what celebrities are thinking (Figure 1)? I dismissed everything Twitter-related as irrelevant and continued on my merry way. I think it was during Evolution 2011 that Jeremy (from this blog) suggested I join Twitter because you can follow interesting talks and remain engaged throughout conferences. It took a little while for me to work up a real affection for Twitter but the longer I’ve been a member (and perhaps the longer Science and scientists have had to assimilate it into our work world), the more useful I find it (Figure 2).

Figure 1: An example of the "Why bother?" side of Twitter. Why 103,000 people thought this was worth repeating via "retweeting" is beyond me because it gets dumber each time I read it...

Figure 1: An example of the “Why bother?” side of Twitter. And why 103,000 people bothered repeating this via “retweeting” is beyond me. It gets dumber each time I read it.

Figure 2: Why you actually should bother. Devin's posts include (top to bottom) - passing along a job opportunity, interesting publication, a professional interaction about science spam, a second paper and link to our blog!

Figure 2: Why you actually should bother. Devin’s posts include (top to bottom) – passing along a job opportunity, interesting publication, a professional interaction about science spam, a second paper and link to our blog!

Regarding social media and scientists in general, Bik & Goldstein have written a great introduction. They discuss the pros and cons of several platforms (i.e., blogs, Facebook, Twitter) and how to choose amongst these depending on your interests. For example – are you most interested in communicating science to the “general public”? TO THE FLOW CHART! Perhaps creating your own content in the form of a blog is for you. Alternatively, are you more interested in compiling cool stuff you’ve found from across the world wide web? Consider Facebook.

Despite the ubiquity of social media in our world, many scientists are reluctant to embrace it. That’s somewhat understandable – “Why bother?” is an easy question to ask and get no answer to if you’re “unplugged”. Bik & Goldstein outline four major “research benefits from an online presence”.

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Should scientists be more subjective?

Peer-Review-Nick-Kim-cartoon3-resizeThough the goal of scientific research is to objectively follow evidence to advance our knowledge of the world we live in, it has become increasing apparent that there are some substantial road blocks in our way.  For example, a number of recent articles have argued that (A) we get the wrong answer – a lot, (B) the hotter the area of research, the more likely we are to get it wrong, and (C) the higher the profile of the journal we published in, the more likely we are to have got it wrong (Ioannidis 2005, Pfeiffer & Hoffmann 2009, Brembs et al. 2013).  Ideally, science is self-correcting process, allowing us to reach the correct answer over time, in spite of such misleading results.  However, the authors of a recent Nature article argue that a phenomena they refer to as “herding” can prevent or severely delay the process of self-correction and their proposed solution is quite surprising: add more subjectivity to the peer review process (Park et al. 2013).

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Batesian and aggressive mimicry in academic publishing: A proposal for escalation of the coevolutionary arms-race

The following is a guest post from friend of the blog and Assistant Professor of Biology at Willamette University Chris Smith.


Figure 1. Kingsnakes and milksnakes are Batesian mimics of the deadly coral snake. 1A: An eastern coral snake. Photo by Norman Benton, via Wikimedia Commons. 1B: A Mexican milk snake. Photo by Dawson, via Wikimedia Commons.

Mimicry is a common phenomenon in the natural world, where one organism evolves to resemble another. Familiar examples include (harmless) king snakes that have banding patterns remarkably similar to the (extremely venomous) coral snake (Figure 1), or (palatable) Viceroy butterflies that resemble (toxic) monarchs. These so-called ‘Batesian’ mimics enjoy the benefits of appearing to be dangerous while paying no costs. That is, they escape being eaten by predators without having to produce toxins themselves.

A second, less familiar, form of mimicry is ‘aggressive’ mimicry, in which predators use deception to more effectively attack their prey. For example, some fireflies mimic the sequence of flashes emitted by females of other species, and then attack and eat the unsuspecting male fireflies that come to court them. Similarly, some butterflies in the genus Maculinea are social parasites of ants, and produce chemicals on their exoskeleton that resembles the scent of ant larvae. Foraging ants discover these seemingly helpless babies that appear to have wandered away nest and carry them back to the brood chamber, where the butterfly larvae proceed to devour the ant larvae.

The world of academic publishing has recently seen the convergent evolution of mimicry in ways that remarkably mirror the strategies seen in the natural world. As has been carefully researched and documented by Jeffrey Beall, a reference librarian at the University of Colorado, Denver, the Open-Acces movement has inadvertently given rise to a legion of ‘predatory publishers’. The publishers offer (for a hefty fee) to publish research papers without the process of rigorous peer review that would normally precede the publication of scholarly work. (NIB contributor Sarah Hird described her experience with a predatory publisher here).

Most of the papers published by such ‘predatory publishers’ are Batesian mimics. They enjoy the imprimatur of academic legitimacy without having to pay the cost of rigor, but like the king snake they are otherwise ‘harmless’. These are typically papers of low importance and low impact, sometimes with shoddy experimental designs, that would not pass muster in more rigorous journals. But rarely, if ever, is the work truly fraudulent.

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