I guess that as a CAFA organizer, I should really contribute to the second page. And I will. But I really don’t mind if someone else jump-starts it.

http://en.wikipedia.org/wiki/Protein_function_prediction

http://en.wikipedia.org/wiki/Critical_Assessment_of_Function_Annotation

“We seek to download from the amazing successes of the computer industry two principles: that of open source, and that of crowdsourcing; to quickly, responsibly accelerate the delivery of targeted therapeutics to cancer patients. Our business model involves all of you. This research is funded by the public.”

1. Men don’t tell the truth about their penis. No kidding? But this is somewhat more serious. It has been accepted for some time that male circumcision dramatically reduces the rate of HIV infection. But recently, some reports have shown that high rates of infection prevail among circumcised men as well. But since circumcision is usually self-reported, could there be a problem there? This study shows that in a cross-sectional (sorry…) study among recruits to the Lesotho Defense Force, 50% of the men that reported they were circumcised were, in fact, partially (27%) or completely (23%) not circumcised. The researchers conclude that biases in the self-reporting of male circumcision may lead to erroneous reports that show high HIV infection rates among circumcised men.

Concluding quote:

…until further research can document improved methods for obtaining accurate self-reported MC [male circumcision I.F.] data, all assessments of MC and HIV prevalence, as well as projections for VMMC [voluntary male medical circumcision I.F.] interventions, should be informed by physical-exam-based data [as opposed toself reporting, I.F.].

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027561

Can sharing data help prevent errors and fraud?

From the abstract:

Background: The widespread reluctance to share published research data is often hypothesized to be due to the authors’ fear that reanalysis may expose errors in their work or may produce conclusions that contradict their own. However, these hypotheses have not previously been studied systematically

So Jelte Wicherts and his colleagues from the University of Amsterdam wanted to see whether sharing data was related to the number of statistical analysis errors in a paper. So, to phrase this as a null and alternative hypothesis:

H0:There is no difference in the number of statistical errors in those papers where the authors are willing to share data, and those where the authors are unwilling to do so.

H1: (one sided): the number of weaker evidence and statistical errors in papers where the authors are unwilling to share data is larger than those in which the authors are willing to share data.

Wicherts and colleagues contacted authors of 141 papers published in five journals of the American Psychological Association, requesting their data. Trouble is, they could not get enough authors to share data to make their own study significant: in a previous study, some 73% of the authors contacted were unwilling to share data. Wow.

However, authors publishing in two of these journals, Journal of Personality and Social Psychology (JPSP) and Journal of Experimental Psychology: Learning, Memory, and Cognition (JEP:LMC), were somewhat more forthcoming.  Wicherts and colleagues therefore limited their analysis to a subset of 49 papers published in those journals. (Note that sometimes lack of data sharing is due to legitimate considerations, such as being part of an ongoing study, or third-party proprietary rights. However, those were not considerations in 49 papers analyzed here.)

Wicherts  then checked for specific types of statistical errors in these papers, and compared the number of errors in papers from authors willing to share data to those who did not. Here are some of the findings:

Distribution of the number of errors in the reporting of p-values for 28 papers from which the data were not shared (left column) and 21 from which the data were shared (right column) for all misreporting errors (upper row), larger misreporting errors at the 2nd decimal (middle row), and misreporting errors that concerned statistical significance (p<.05; bottom row). doi:10.1371/journal.pone.0026828.g001

Pretty clear picture: those papers where the authors authors were willing to share data were less prone to statistical errors.

Concluding quote:

In this sample of psychology papers, the authors’ reluctance to share data was associated with more errors in reporting of statistical results and with relatively weaker evidence (against the null hypothesis). The documented errors are arguably the tip of the iceberg of potential errors and biases in statistical analyses and the reporting of statistical results. It is rather disconcerting that roughly 50% of published papers in psychology contain reporting errors [33] and that the unwillingness to share data was most pronounced when the errors concerned statistical significance.

Although note that Wicherts is very careful about drawing conclusions:

Although our results are consistent with the notion that the reluctance to share data is generated by the author’s fear that reanalysis will expose errors and lead to opposing views on the results, our results are correlational in nature and so they are open to alternative interpretations. Although the two groups of papers are similar in terms of research fields and designs, it is possible that they differ in other regards. Notably, statistically rigorous researchers may archive their data better and may be more attentive towards statistical power than less statistically rigorous researchers. If so, more statistically rigorous researchers will more promptly share their data, conduct more powerful tests, and so report lower p-values. However, a check of the cell sizes in both categories of papers (see Text S2) did not suggest that statistical power was systematically higher in studies from which data were shared.

In fact, Wicherts also wrote a piece in Nature where he argued that sharing data can help avoid fraud, such as in the recent infamous case of Diederik Stapel, a highly regarded psychologist at Tilburg University in the Netherlands.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026828

3. Toilet paper. A study of surfaces of public restrooms has shown that they are covered with bacteria, mainly the kind that is known to live on and in humans. So now we have a somewhat broader view of the species living in restrooms, including the uncultured ones.

Two interesting quotes from the paper:

Although many of the source-tracking results evident from the restroom surfaces sampled here are somewhat obvious, this may not always be the case in other environments or locations.

Not sure about this bit: if the sources here are obvious, then is this paper a proof-of concept?

Also:

Unfortunately, previous studies have documented that college students (who are likely the most frequent users of the studied restrooms) are not always the most diligent of hand-washers.

No shit! (Pun intended).

Concluding quote:

Although the methods used here did not provide the degree of phylogenetic resolution to directly identify likely pathogens, the prevalence of gut and skin-associated bacteria throughout the restrooms we surveyed is concerning since enteropathogens or pathogens commonly found on skin (e.g. Staphylococcus aureus) could readily be transmitted between individuals by the touching of restroom surfaces.

Translation:

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0028132

Thomas, A., Tran, B., Cranston, M., Brown, M., Kumar, R., & Tlelai, M. (2011). Voluntary Medical Male Circumcision: A Cross-Sectional Study Comparing Circumcision Self-Report and Physical Examination Findings in Lesotho PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0027561

Wicherts, J., Bakker, M., & Molenaar, D. (2011). Willingness to Share Research Data Is Related to the Strength of the Evidence and the Quality of Reporting of Statistical Results PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0026828

Flores, G., Bates, S., Knights, D., Lauber, C., Stombaugh, J., Knight, R., & Fierer, N. (2011). Microbial Biogeography of Public Restroom Surfaces PLoS ONE, 6 (11) DOI: 10.1371/journal.pone.0028132

The Scientist is one of my favorite go-to destinations for keeping up with current biomedical research. That’s why I was rather sad when it was recently announced that The Scientist will be closing down. However, it seems like The Scientist will continue to be published after all:

NEW YORK, NY–(Marketwire – Oct 14, 2011) – Sciencenow Inc., a member of The Science Navigation Group, and LabX Media Group are pleased to announce that they have signed a nonbinding Letter of Intent specifying terms for the acquisition of The Scientist by LabX Media Group. The parties hope to close a transaction by the end of October.

Sande Giaccone, Sales and Marketing Director of The Scientist, said, “We are delighted that, following the decision to cease publication of The Scientist, LabX Media Group has stepped in to save The Scientist and keep the majority of its existing team together. We hope to return to our normal high service level for all our readers, contributors, and advertisers in the next few weeks. We sincerely appreciate the support of our advertisers in the past and hope to regain their confidence going forward. The Scientist is complementary to LabX Media’s existing stable of products and, subject to closing of a transaction, we look forward to working with them in the future.”

Mary Beth Aberlin, Editor in Chief of The Scientist, said, “Naturally, we were all saddened by the decision to cease publication of The Scientist, and grateful to our readers and contributors for all their kind words concerning the magazine. The editorial team and I are delighted that LabX Media Group has been able to agree on terms with Sciencenow, Inc. with such dispatch. Our dedicated editorial team will remain intact and continue to produce a magazine that maintains our editorial standards.

Bob Kafato, President of LabX Media Group, said, “The quality life science content that The Scientist produces is second to none and we are happy to be adding this to our portfolio of media products for lab professionals.”

Kudos to LabX. You have rescued a fine journal. Thanks to Linda Kosta for calling my attention to this fortunate turn of events.

The journal will employ an open and transparent peer review process in which papers will be accepted or rejected as rapidly as possible, generally with only one round of revisions, and with limited need for modifications or additional experiments. For transparency, reviewers’ comments will be published anonymously.

Nice. The journal will be online-only and open access too, and they promise  ”an opportunity to create a journal and article format that will exploit the potential of new technologies to allow for improved data presentation.” I especially like the “limited need for modifications or additional experiments”, especially since even Nature has recently published a scathing opinion piece about reviewers’ almost reflexive demands for additional experiments.

With these three giants behind the journal, it’s a safe bet this journal will be up there with PLoS Biology, Nature and Science.

For now, Byte Size Biology readers are welcome to suggest a name for this new journal. Maybe you can strike a deal with the yet-to-be-named editor-in-chief: a lifetime  publication fee waiver if your name gets chosen.

Of course, I have no affiliation with this new journal, so don’t bet on it happening.

The National Academies Press are offering all their books in PDF format for free. The announcement yesterday created a serious traffic surge on their site. But the books are still there, and are still free. Got to buy that new 5Tb external disk now….



Credit: mcwetboy on Flickr http://www.flickr.com/photos/mcwetboy/3394518027/

Click for larger image

The next email in my inbox was this:

OK, that’s taking things a bit too far. Random solicitation of editors (did I mention that was not my field?) does not lend credibility to the publisher.

Which brings us to a nice post by Kevin Karplus about the not-so-savory side of open access publishing, or the “author-pays” model. First, a clarification of terms:  Open Access means access to research publications by the general public without needing to pay for access through a personal or institutional subscription. Author-pays would mean that publication fees are covered by the author. The two are not necessarily cojoined. There are plenty of closed-access publications whose page and figure charges run as high or even higher than Open Access publications. But in the case of Open Access, the revenue does not come from subscriptions. The only other sources are advertisements and author fees. Since many Open access publications are web-only and are quite specialized, advertisements are not a practical source of revenue. This leaves us with author fees. So to publish open access you pretty much need to have money. If you happen to fall on hard times and you lose some funding, or need to skimp for a while, author-pays publishing is becomes less of an option, despite supposed hardship fee waivers. Since more journals are adopting the Open-Access model,  many publications venues are being closed off to poorly funded researchers.

But I would like to address a point that was minor in Kevin’s post, yet is quite important: the wrongly perceived association of Open-Access with the cheapening of scientific publication. And by “cheapening” I do not mean the lowering of costs, although publication costs for web-only publications are considerably lower than those for print. I meant cheapening in the figurative sense: the attrition of scientific quality. Since the barrier for getting a scientific publication up & running is  not lower: you still need staff, good editorial board, good editors, etc, etc. This all costs money, even if you do away withe  the substantial expense of paper printing.  But the barrier is considerably lower if you are willing to do away with credibility, and just set up what is essentially a web-based manuscript clearinghouse. Since many of those journals (like the one above) profess to be Open Access, some misinformed souls may associate Open Access ~= Bad Science. Especially if they are inundated by these emails like I am. From several publishers at that.

I worry that widespread adoption of the new policy could result in dominance of author-pays models for publication, which would squeeze out unfunded researchers from publication, and lead to a further dilution of peer review, as the journal publishers would no longer care as much about quality (no subscribers to please) as about quantity (maximizing author fees).

– Gas station without pumps, December 15, 2010

Now, bad journals, bad papers and fraud have been around for ever. In early 2009 it was revealed that Elsevier published a journal that was almost entirely ghost-written by Merck to promote Vioxx. The Elsevier fake journal and  ghost writing scandal had nothing to do with Open Access. Other examples of marginal or even fraudulent publications in closed-access forums are not hard to find. Especially funny is the 2005 case of  SCIgen, a program that generates random Computer Science research papers, including graphs, figures, and citations. One randomly generated paper was accepted to WMSCI 2005. (See the whole story on the scigen blog, you’ll need to page back to the beginning. This makes for a fascinating, surreal and somewhat disturbing read.)

But emails such as those above (and I get them weekly from many sources despite –or maybe because– repeated requests to unsubscribe), do show that some publishers all but say that they will publish for cash, and they obviously couldn’t care less who provides editorial and review services as long as they go through the motions of supposed peer-review. They justify the author-pays publication costs by providing Open Access — the icing on top a rather rancid cake. Unfortunately, spam such as this may cause some people to associate anything Open Access with the publication of marginal and low quality research.

Well, but if my Thunderbird email client can tell the difference between good and bad science, maybe we can educate humans about the non-association of Open Access with bad science. I jut hope that the term Open Access is not one of the parameters in my Thunderbird’s spam filter. Does anyone know how to check that?

Any views represented in this hype cycle diagram are my own, and in no way represent the  views of my employers, family, friends, neighbors, greengrocer, auto mechanic, my skin microbiome or my internet provider who just slapped me with a 30% fee increase.

Click for full size. Template (without writing) taken from Wikimedia Commons, under GFDL. Credit for template: Jeremy Kemp.

If you are reading this, and you are in Boston on those dates, consider showing up, it is a great experience. There will also be a codefest on the two days before the meeting. This year’s topic is cloud computing for bioinformatics. If you like using AWS for bioinformatics or if you want to learn more, this is your chance. Amazon have provided a grant towards this codefest. (Thanks!) Biopython, Bioperl, Biojava and Bioruby developers will all be there, tailoring code to the cloud.

Which brings me to the latest poll: if you are a bioinformatics programmer, which of the Bio* packages  are you using in your programming, if any? If more than one, check the one you use most frequently. Poll answers on the right. As with all Internet polls, you must be crazy if you take it at all seriously.