scientific literature
jstemwedel | March 30, 2010That post about how hard it is to clean up the scientific literature has spawned an interesting conversation in the comments. Perhaps predictably, the big points of contention seem to be how big a problem a few fraudulent papers in the literature really are (given the self-correcting nature of science and all that), and whether there larger (and mistaken) conclusions people might be drawing about science on the basis of a small fraction of the literature.
I will note just in passing that we do not have reliable numbers on what percentage of the papers published in the scientific literature…
jstemwedel | March 27, 2010
Science is supposed to be a project centered on building a body of reliable knowledge about the universe and how various pieces of it work. This means that the researchers contributing to this body of knowledge -- for example, by submitting manuscripts to peer reviewed scientific journals -- are supposed to be honest and accurate in what they report. They are not supposed to make up their data, or adjust it to fit the conclusion they were hoping the data would support. Without this commitment, science turns into creative writing with more graphs and less character development.
Because the…
scientificactivist | October 19, 2009Late last week, I received emails from two journals (The Journal of Biological Chemistry (JBC) and PLoS ONE) indicating that they are now incorporating interactive 3D images of molecular structures in their papers. The atomic coordinates of all published biomolecular structures have been available for some time at the Protein Data Bank. However, making sense of something as complex as a protein structure can require quite a bit of analysis. So, scientists go through great pains to represent important features of their structures in 2D images for publication. Ostensibly, this new functionality…
scientificactivist | April 11, 2009The gold standard for measuring the impact of a scientific paper is counting the number of other papers that cite that paper. However, due to the drawn-out nature of the scientific publication process, there is a lag of at least a year or so after a paper is published before citations to it even begin to appear in the literature, and at least a few years are generally needed to get an accurate measure of how heavily cited an article will actually be. It's reasonable to ask, then, if there exists a mechanism to judge the impact of a paper much earlier in its lifetime.
Several analyses now…
sporte | September 30, 2008One time, I suggested in a list-serve that science teachers make more use of primary scientific literature. Naturally, I learned all the reasons why teachers don't do this-lack of access being one of the biggies- but I also learned something surprising.
One teacher wrote that she re-writes a lot of research articles to make them easier for her students to read. I can understand that notion, in principle. My students struggle with scientific language, too, even those that have bachelor's degrees in biology.
What surprised me was thinking about the amount of time that activity would take!…
scientificactivist | December 31, 2007An individual cell inside the human body is in a dynamic environment: it not only has to anchor itself to its surroundings but also be able to communicate with them and respond as appropriate. One group of proteins--the integrins--play a central role in all of these tasks. The integrins are large (about 200,000 Da) membrane-spanning proteins, and each integrin consists of two subunits (alpha and beta). The vast majority of the integrin is located on the exterior of the cell, where it anchors the cell to the extracellular matrix. Each subunit has a short tail inside of the cell, and the…
scientificactivist | November 29, 2006Anyone who has tried to replicate an experiment based on the description published in a paper knows that this can be difficult, frustrating, and often close to impossible. The protocols in the Methods section can be incomplete, even inaccurate, and sometimes lead the hopeful reader down a trail of never-ending references to previous papers, eventually arriving at a protocol only marginally related to what the reader actually set out to find.
One answer to this problem, in a few cases at least, might be a new video journal spearheaded by Moshe Pritsker, a postdoc at Harvard Medical School/…
scientificactivist | July 11, 2006According to this week's Science magazine, there's some good news and some bad news regarding open access publishing. Which do you want first?
The bad news? OK, here goes.
According to a letter (free access via Sex Drugs & DNA) authored by Michael Stebbins, Erica Davis, Lucas Royland, and Gartrell White (mostly of the Federation of American Scientists), the NIH's voluntary open access project, PubMed Central, has been a massive failure due primarily to lack of compliance:
The NIH public access policy requests that NIH-supported investigators submit final peer-reviewed primary research…
scientificactivist | July 8, 2006On the 29th of June, the Senate finally announced an upcoming vote on HR 810, a bill which would overturn President Bush's current prohibitions on federal funding of embryonic stem cell research. As I reported before, the announcement has been anticipated for some time, and many were disappointed when the one year anniversary of the passage of HR 810 in the House of Representatives (on May 24th) came and went without any progress in the Senate.
The media coverage of this event has mostly been unexceptional, not particularly good or bad, although probably overly optimistic considering the…
scientificactivist | June 22, 2006Today's issue of Nature includes a particularly damning news story about the financial troubles facing the Public Library of Science, a publisher of several prestigious open access journals. In the article, Nature describes PLoS's difficulties and heavily stresses its continued reliance on philanthropic grants.
The Public Library of Science (PLoS), the flagship publisher for the open-access publishing movement, faces a looming financial crisis. An analysis of the company's accounts, obtained by Nature, shows that the company falls far short of its stated goal of quickly breaking even. In an…
scientificactivist | June 21, 2006Nature started it with its recently begun open peer review trial, and PLoS got on board with its own announcement of a new interactive journal, PLoS ONE. Now, The Daily Transcript reports that Cell has also joined the latest trend by allowing reader comments on some of its articles. What's the catch? Comments will only be open on one "highlighted" paper each issue. That's too bad, because I was just reading an older Cell paper today that seemed to raise more questions than it answered....
Interestingly, Alex Palazzo of The Daily Transcript raises an important point at the end of his post…
scientificactivist | June 17, 2006I just found out that the journal impact factors for 2005 were recently released, and as usual, the journals with the highest impact factors are not necessarily the ones that would be considered the most prestigious. Therefore, the following post from the archives, about an alternative rating scheme for scientific journals, seemed relevant. Enjoy!
In regards to my statement below about my old site's PageRank, I did finally get one but apparently the new site hasn't made an impression on Google yet....
(17 February 2006) How do you know how important a website is? You probably already…
scientificactivist | June 14, 2006Via Evolving Thoughts comes news that the Public Library of Science (PLoS) is starting a series of blogs to promote its recently announced interdisciplinary PLoS ONE journal. PLoS publishes several prestigious open access scientific journals and is now taking things a step further with a new journal that will, among other things, "empower the scientific community to engage in a discussion on every paper and provide readers with tools to annotate and comment on papers directly." In the stuffy culture of science publishing, this is a pretty big deal.
Although PLoS ONE won't use open peer…
scientificactivist | June 12, 2006It looks like it's going to be a pretty busy day for me, so here's a post from the archives. I picked this one because it's still very timely (the Federal Research Public Access Act of 2006 is still in committee in the Senate) and it's related to my recent post on open peer review.
(4 May 2006) As society slowly shifts toward more participatory forms of democracy, science policy will increasingly be subject to the will of the general population. The creation of the California Institute for Regenerative Medicine via voter-initiated Proposition 71 in 2004 stands as a significant example of…
scientificactivist | June 8, 2006One of the fundamental principles of modern science, as well as other academic pursuits, is peer review. By subjecting a submitted paper to evaluation by other scientists in the authors' field, the solid science advances at the expense of the not-so-good and the interesting and relevant prevails above the unoriginal. In theory, of course. The effect is a growing body of scientific knowledge that, while still large and unwieldy, is at best authoritative and at the very least trustworthy and accurate. It's a kind of democratization of knowledge, at least in a narrow sense.
But, as in any…