Science magazine section - "Scientific Communication" - October 4, 2013

Just in time for Open Access Week later this month (October 21-25), Science has published a section on scientific publishing, a topic regarding which they surely are not unbiased. 

I love the infographic,  The Rise of Open Access, by Randall Monroe of xkcd fame which claims that new scientific papers are published at an accelerating rate, currently about one every 20 seconds, and that since 2011, half of new papers are open access. That part of the article comes from an article by Jocelyn Kaiser in another issue of Science (DOI: 10.1126/science.341.6148.830).

There are other worthy pieces in this section, but the one that got my goat was a piece by John Bohannon, "Who's Afraid of Peer Review", an account of his sting operation, sending a scam article to a large number of open access journals to see which of them would catch its problems in their peer review systems. He made some valid points, but overall, I think the project was flawed by not including non-open access journals. The inferences drawn by him and others (see/hear the report on NPR) make it seem like the problems arise from open access rather than from poor peer review. Other bloggers  have written more articulate posts about the shortcomings (see Peter Suber's or Michael Eisen's). 

Science is hosting a live chat session on this issue with the article's author and several others including Eisen, on Thursday, Oct 10, 2013 at 3pm EDT.

Academy Rankings Tell You a Lot, But Not Who's No. 1 in Any Field

Jeffrey Mervis
Science 1 October 2010: 18-19. 

This week's release of the long-awaited assessment of the quality of U.S. research doctoral programs by the National Academies' National Research Council will disappoint those who simply want to know who's No. 1 in any particular field, because the NRC assessment can look quite different depending on your definition of "best." 

 This National Academies' NRC study was discussed in a recent meeting I attended of the UMass Amherst Faculty Senate's council which is the liaison to the University's Development Office.  Rankings of this kind are always of interest to University administrations, naturally. Everyone speaking about it acknowledged that the 'rankings' are problematic in a number of ways.  One member commented that the people doing the ranking wouldn't have first-hand knowledge of the  departments they were judging among - it's a matter of reputation, apparently, rather than anything based on real data. That said, people will make use of the numbers in whatever way will benefit their agenda.  From the article in Science:

To be sure, NRC does rank programs—but oh so carefully. Instead of assigning a single score to each program in a particular field, the assessment ranks the program on five different scales. Each score is also presented as a range of rankings reflecting the 5th and 95th percentiles of the scores it received. The scales themselves are based on 20 characteristics (see table, p. 19) that the NRC panel deemed appropriate for a quantitative assessment. Two are supposed to portray the overall quality of the program—one derived from a reputational survey (the R scale), the other from a quantitative analysis (the S scale). Three others rely on subsets that address important dimensions of quality: research activity, student support and outcomes, and diversity. The report itself highlights the uncertainties generated by such an exercise by calling the results "illustrative rankings [that] are neither endorsed nor recommended by the NRC as an authoritative conclusion about the relative quality of doctoral programs."

 The report's Excel spreadsheets are available at www.PhDs.org or www.nap.edu/rdp.

Science paper on glycosylation retracted

News from The Scientist by Jef Akst:

Researchers are retracting a highly-cited 2004 Science paper describing a new way of adding sugars to proteins -- a longstanding challenge in molecular biology -- citing their inability to repeat the results and the absence of the original lab notebooks with the experiment details, they announced in Science last Thursday (November 26).

It's a little curious - that absence of the original notebooks. Here's the retraction:

Science 27 November 2009: Vol. 326. no. 5957, p. 1187 DOI: 10.1126/science.326.5957.1187-a

Letters

Retraction

We wish to retract our Report (1) in which we report that β–N-acetylglucosamine-serine can be biosynthetically incorporated at a defined site in myoglobin in Escherichia coli. Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions, and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand. We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.

Zhiwen Zhang,¹ Jeff Gildersleeve,² Yu-Ying Yang,³ Ran Xu,⁴ Joseph A. Loo,⁵ Sean Uryu,⁶ Chi-Huey Wong,⁷ Peter G. Schultz^7,*

"Regrettably, through no fault of the authors..." is a curious way to report this - absolving themselves, but not giving any other explanation. In an email to The Scientist, Schultz says again, "There are clearly complexities associated with suppression and cellular bioavailablity of these and other glycosylated amino acids that we did/do not understand, and, regrettably, we no longer have the notebooks to help resolve these issues (through no fault of any coauthors)." One wonders what happened.

"Scientists Decry Isotope, DNA Testing of ‘Nationality"

In the special issue of Science out today, a news item describes a dismaying misuse of science and technology. As one of its tests, the Borders Agency in Britain is piloting use of DNA analysis and isotope testing of soft tissues to verify (or not) whether a person applying for asylum in the U.K. comes from the country they claim to have come from.

"My first reaction is this is wildly premature, even ignoring the moral and ethical aspects," says Alec Jeffreys of the University of Leicester, who pioneered human DNA fingerprinting. ...

After reviewing the Border Agency's plans, Jeffreys [wrote] in an e-mail to Science: "The Borders Agency is clearly making huge and unwarranted assumptions about population structure in Africa; the extensive research needed to determine population structure and the ability or otherwise of DNA to pinpoint ethnic origin in this region simply has not been done. Even if it did work (which I doubt), assigning a person to a population does not establish nationality - people move! The whole proposal is naive and scientifically flawed."

Because the hue and cry over this is so widespread in the scientific community, I wondered if this might be a case of those in power trying to use science to intimidate rather than actually expecting to get at the truth. Questionable asylum-seekers might be threatened with the use of "scientific tests" in hopes that they will admit to falsifying their country of origin. This might be deemed reasonable if the tests would actually produce relevant information, but, instead, what is questionable is the attempt to assign country of origin by these means.

Ardipithecus ramidus - special issue of Science magazine

Science 2 October 2009:
Vol. 326. no. 5949, pp. 60 - 61
DOI: 10.1126/science.326_60a

from Introduction to the Special Issue, by Brooks Hanson, "Light on the Origin of Man"
...

This issue presents 11 papers authored by a diverse international team (see following pages) describing an early hominid species, Ardipithecus ramidus, and its environment. The hominid fossils are 4.4 million years old, within this critical early part of human evolution, and represent 36 or more individuals, including much of the skull, pelvis, lower arms, and feet from one female. The papers represent three broad themes. Five focus on different parts of the anatomy that are revealing for human evolution. These show that Ardipithecus was at home both moving along trees on its palms and walking upright on the ground. Three characterize Ardipithecus's habitat in detail, through analysis of the hosting rocks and thousands of fossils of small and large animals and plants. These show that Ardipithecus lived and ate in woodlands, not grasslands. The first paper presents an overview, and it and the last two papers trace early human evolution and synthesize a new view of our last common ancestor with chimps. One conclusion is that chimps have specialized greatly since then and thus are poor models for that ancestor and for understanding human innovations such as our ability to walk.