 |
|
|
Coturnix alerts me to the fact that I'm late for a party yet again (as usual). Apparently, Nature is feeling the PLoS competition breathing down its neck. This can be seen in a Nature news article entitled "PLoS stays afloat with bulk publishing" by Declan Butler. In it, Butler describes with little attempt to conceal his arrogance and disdain that PLoS is very successful. According to the article, the means by which PLoS is generating income is mainly by philanthropic subsidies and authors' fees from PLoS One. Butler specifically refers to the ~2500 papers published in PLoS One when he says that Public Library of Science (PLoS), the poster child of the open-access publishing movement, is following an haute couture model of science publishing — relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals. [...] PLoS One uses a system of 'light' peer-review to publish any article considered methodologically sound.
I only have a few sentences to add to the sizzeling hot discussion all over the place. The article in particular and the discussion in general again raises the old question:
Why, with today's technology, do we still have about 20,000 different 19th century journals around?
Butler's "non-light" peer-review is just a popularity contest anyway, Nature Neuroscience editor Noah Gray (among other colleagues there) admits freely that the toughest obstacle is getting past the editors: Nature Neuroscience aims to send 30-35% of papers out to review, so getting past that stage is the biggest hurdle. It needs to be pointed out here that publishing in these "non-light" journals decides over grants, tenure, promotions and thus peoples' careers and livelyhoods. So one could paraphrase the current system of publishing in science in the following way: If the scientific community were a large corporation, it would be out-sourcing it's hiring and firing to a group of ex-employees who either left the corporation because they didn't like it or were fired themselves. Now how many managers would implement such a system in their company?
Instead, we should have one single, decentralized, publicly accessible database where the current assessment by editors (i.e., the "non-light" component of peer review in e.g. Nature) comes after publication as one of many measures of post-publication review and assessment. The first review should be done by scientists on the science - whatever happens to the paper afterwards is open to debate. I, for one, value the input of professional editors and their expert judgement of scientific newsworthyiness and would not want to miss it.
Conflict of interest statement: I have published in Science and PLoS One; I volunteer as academic editor for PLoS One.
|
|
|
|
|
|
2008 is only about half way over and it's already been a devastating year for monopolist Thomson Scientific, formerly Institute for Scientific Information, ISI. First, the company's impact factor flunks a scientific test twice (ok, that was December 07, but still). In January, Thomson tries to fight back but with little impact. In March, PLoS One published a paper which presents a new way of calculating journal impact. In May, The journal Epidemiology presented several articles arguing eloquently for getting rid of the bibliometric impact factor (BIF - or brain irritability factor). Earlier this month, a special issue of the journal Ethics in Science and Environmental Politics in which authors hammered the use of the impact factor left right and center.
And now there's a new hole in the IF bucket. How mcuh longer will it be able to stay afloat? This time, the mathematicians have had a closer look at bibliometrics in general and the impact factor specifically. The International Mathematical Union (IMU) has published a report on citation statistics (PDF). The summary contains some nice information which I would like to quote here:- Relying on statistics is not more accurate when the statistics are improperly used. Indeed, statistics can mislead when they are misapplied or misunderstood. Much of modern bibliometrics seems to rely on experience and intuition about the interpretation and validity of citation statistics.
- While numbers appear to be "objective", their objectivity can be illusory. The meaning of a citation can be even more subjective than peer review. Because this subjectivity is less obvious for citations, those who use citation data are less likely to understand their limitations.
- The sole reliance on citation data provides at best an incomplete and often shallow understanding of research-an understanding that is valid only when reinforced by other judgments. Numbers are not inherently superior to sound judgments.
Using citation data to assess research ultimately means using citation‐based statistics to rank things-journals, papers, people, programs, and disciplines. The statistical tools used to rank these things are often misunderstood and misused. - For journals, the impact factor is most often used for ranking. This is a simple average derived from the distribution of citations for a collection of articles in the journal. The average captures only a small amount of information about that distribution, and it is a rather crude statistic. In addition, there are many confounding factors when judging journals by citations, and any comparison of journals requires caution when using impact factors. Using the impact factor alone to judge a journal is like using weight alone to judge a person's health.
- For papers, instead of relying on the actual count of citations to compare individual papers, people frequently substitute the impact factor of the journals in which the papers appear. They believe that higher impact factors must mean higher citation counts. But this is often not the case! This is a pervasive misuse of statistics that needs to be challenged whenever and wherever it occurs.
- For individual scientists, complete citation records can be difficult to compare. As a consequence, there have been attempts to find simple statistics that capture the full complexity of a scientist's citation record with a single number. The most notable of these is the h‐index, which seems to be gaining in popularity. But even a casual inspection of the h‐index and its variants shows that these are naïve attempts to understand complicated citation records. While they capture a small amount of information about the distribution of a scientist's citations, they lose crucial information that is essential for the assessment of research.
Is there anything I could add to that? The IF's dead, baby, the IF's dead.
|
|
|
|
|
|
As usual, I'm way late to the party. PZ alerts us all to a fantastic e-mail conversation. Required reading for this week, if not this month! Best I've seen in a long time - here's the scoop:
- Richard Lenksi publishes PNAS paper on how E. coli evolved the ability to use citrate as energy source.
- Conservapædia's Andrew Schlafly, a lawyer with a bachelor's degree who teaches history and economics to homeschoolers, asks to see the raw data of the paper.
- Lenski offers to send anyone the bacteria, if s/he can make sure they're treated properly and promises not to scoop him!
Just to emphasize how funny this is: I have studied biology from 1991-1996 (major in neurobiology and genetics), worked on my PhD until 2000 and am currenty a full-time research scientist in neurobiology. Even with such a fairly advanced education in biology, I would not accept Lenski's paper for peer-review and instead refer the manuscript to more suited colleagues, if I ever had been asked. And there comes a lawyer and asks for the raw data! It just cracked me up! But it doesn't stop there: Schlafly then admitted he had never even read the paper! I almost fell from my chair! Not that I'd expect him to understand any of the paper anyway - which probably is the reason he only "skimmed" over it.
Anyway, go and read it for yourself! The language in the e-mails is just hilarious! Lenski so pwn3d Schlafly, I couldn't stop reading. That a guy like Schlafly would so willingly embarrass himself like that is beyond my understanding.
I think I have now finally understood what "irreducibly complex" really means: a statement, fact or event so simple it cannot be simplified any further, but still too complex to be grasped by a creationist.
And no, it's not polite to make fun of Andy's name if you're German! 
Sigh - and I only got into this fun because I was procrastinating trying to track down every single one of my co-authors ever to be on a paper with me. I need a signature on the "authors' contribution" from every one of them for every one of my papers to add to my "habilitation"... 
|
|
|
|
|
|
Up until last year, I was applying for faculty jobs in the US. With the news about the NIH funding being cut yet again, I ceased applying for the few advertised jobs.
This morning I was alerted to a 2007 paper by DrugMonkey. The paper is Heinig SJ, Krakower JY, Dickler HB, Korn D. Sustaining the engine of U.S. biomedical discovery. N Engl J Med. 2007 Sep 6;357(10):1042-7. [Publisher Link]
In it, you can find the following graph displaying the amount of NIH funding over the years. It shows in a graphic (duh!) way, why I stopped applying in the US:
The graph makes clear in what a serious crisis the US biomedical sciences are. There will be many more labs closing as funding is getting tighter and tenure will be denied because of lack of grants. The doubling of the NIH budget at the end of the nineties produced a huge surplus in biomedical researchers looking for permanent jobs now. At this crucial time for many scientific careers, the funding is dropping back to the level before the doubling. Obviously, this will have a huge impact on the entire biomedical research infrastructure. Funding has always been cyclical, but this time around the cuts are bad. Real bad.
Looking at this graph, why would anybody want to work in the US biomedical sciences today?
|
|
|
|
|
|
As reported earlier, I received an invitation to publish two video articles with JoVE. The first one just appeared today and I think it turned out really well:
The only problem I just realized is that I made a mistake and said Karl Götz was in Göttingen, when indeed he was in Tübingen of course!
|
|
|
|
|
|
This one comes via Pharyngula. PZ Myers managed to write the entire syllabus for a course that involved creationism/intelligent design:
A magic man done it.
Yup, that's it. You can close your mouths and start clapping now. Apparently, PZ has the line from this video:
I think it's absolutely hilarious and should be THE tagline for anyone arguing with someone promoting ID/creationism as a science subject in school.
|
|
|
|
|
|
Originally, it was planned to release our latest video on the Drosophila flight simulator with an article I wrote for the website of BBC radio show "The Naked Scientists". However, I now was invited to contribute to the neuroscience carnival "Encephalon" and the article is not quite ready for publication, yet (but very soon, check here). So I decided to go ahead and load the video onto YouTube for the carnival and for your viewing pleasure:
|
|
|
|
|
|
 I had the priviledge to meet Randolph Nesse ("Why we get sick", his blog) here in Berlin at a dinner with visiting blogger Bora. He now sent me one of his articles on Evolutionary Medicine: "The great opportunity: Evolutionary applications to medicine and public health" It's open access so you can go and download it without subscription. What is evolutionary medicine? From the article: "At the core of evolutionary medicine is recognition that diseases need both proximate explanations of bodily mechanisms and evolutionary explanations of why natural selection has left the body vulnerable to disease." The article is about how much medical research and education would have to gain from a more evolutionary perspective in their approach to disease. Here are some more quotes from the text:
An evolutionary perspective fundamentally challenges the prevalent but fundamentally incorrect metaphor of the body as a machine designed by an engineer. Bodies are vulnerable to disease – and remarkably resilient – precisely because they are not machines built from a plan. They are, instead, bundles of compromises shaped by natural selection in small increments to maximize reproduction, not health. Understanding the body as a product of natural selection, not design, offers new research questions and a framework for making medical education more coherent. I also liked this one:
Universities talk a lot about promoting interdisciplinary work precisely because their structures so efficiently prevent it. However, disciplines exist for good reasons. There is too much to know. Trying to synthesize work from diverse areas is frustrating, especially if the goal is general understanding, not some fine point. Also, going beyond your specialty means you will inevitably get some things wrong. It is easier to maintain quality by keeping to a narrow focus. The authors argue, and I think successfully, that without the evolutionary perspective, medicine is only using half of biology. Obviously, one important aspect is genetics. The authors reinforce the notion that many if not most genes which are associated with a certain disease are not defective in any way:Many physicians think of genes that cause disease as abnormalities in an otherwise ‘normal’ genome. This is a nonevolutionary view on two counts. First, it tacitly views the genome as a product of design with a blueprint that defines ‘normal.’ The genome is, instead, a collection of those genes that have tended to increase reproductive success (or hitchhiked on the success of other genes) while interacting with each other and the environment to construct a functional organism. Second, while some DNA sequences can be accurately described as ‘damaged’, it is increasingly clear that many medically relevant genetic variations are helpful or harmful only in interaction with particular aspects of environments. I really like this argument and I also think that it constitutes a very profound insight which changes the way in which diseases are perceived. There is one really small instance where I would argue differently, though:
Taking out [...] a gene and looking to see what goes wrong can generate hypotheses about how an organ or gene is useful. Often, no abnormality is observed. Of course, this does not mean that the gene is useless, only that its effects are covered by redundant systems, that its benefits are manifest only in special situations, or that the benefit is just too small to be observed in a laboratory setting. Redundancy is something that is very hard to achieve in evolution. If one gene is functional, the redundant gene is not needed and will accumulate mutations. I would argue that degeneracy is a much better explanation for many failures to find a phenotype associated with a specific gene knock-out.
Besides the interesting and important insights into evolutionary medicine in general, the article also offers a few fascinating factoids such as:
Nearly 10% of Staphylococcus aureus are now resistant even to methicillin; infections
caused by this resistant organism now cause 18 650 deaths per year, more than the 12 500 caused by AIDS (Klevens et al. 2007). The economic burden of antibiotic resistance is estimated at about $80 billion annually in the USA.
In all, I found it to be a very interesting and enlightening article which will help me explain why what I'm doing is not only fun, interesting and beautiful, but may also one day be useful. 
| | |
Friday 04 July 2008 - 08:12:32
-----
