Scientific Publishing
terrasig | June 17, 2010Waiting for that coffee to take effect but want it to appear you are doing something scholarly?
Have a look at this pair of highly-read posts at The Chronicle of Higher Education:
We Must Stop the Avalanche of Low-Quality Research
The most-viewed article of the last two days at the online presence of the nation's leading higher ed publication, this team-authored position piece has been a magnet for criticism. The thread of 102 comments (thus far) is as worthy of your time, if not more, and the humorous and insightful payoff by commenter #100 is clever and spot-on, IMHO.
Why 'Female' Science…
pontiff | June 7, 2010Science is dynamic. Sometimes this means that science is wrong, sometimes it means that science is messy. Mostly it is very self-correcting, given the current state of knowledge. At any given time the body of science knows a lot, but could be overturned when new evidence comes in. What we produce through all of this, however, at the end of the day, are polished journal articles. Polished journal articles.
Every time I think about this disparity, I wonder why different versions of a paper, the referee reports, the author responses, and all editorial reviews aren't part of the scientific…
terrasig | May 23, 2010Men. Check.
White. Check.
Grey. Mostly. That dude must use color.
Beards. Only two. Maybe three. Aw, hell, Church's makes up for the rest.
Article here.
Ed Yong (Asian-British, man, young, dark hair, no beard) also lists a great wrap-up of the week's commentary on the work.
revere | April 21, 2010When two of the most loathsome members of the US Senate bring back again a bill that won't die, you'd think I'd be in high dudgeon. But I'm not. I hope the bill isn't killed or is allowed to die -- again -- and we finally get it. I'd much rather that the two right wing whack jobs, Senators Joe Liberman (morally corrupt Independent neé Democrat) and John Cornyn (morally corrupt Republican), spent their time sponsoring this kind of legislation than making their usual mischief that hurts everyone. What is this miracle legislation that brings me together with these usually worthless publicly…
revere | February 10, 2010I'm a scientist and my research is supported by NIH, i.e., by American taxpayers. More importantly, the science I do is for anyone to use. I claim no proprietary rights. That's what science is all about. We make our computer code publicly available, not just by request, but posted on the internet, and it is usable code: commented and documented. We ask the scientists in our program to do the same with the reagents they develop. Reagents are things like genetic probes or antibodies directed against specific targets mentioned in the articles they publish. There is an list of the reagents on the…
terrasig | February 4, 2010Please forgive me for the cranky. I am still confined to bed and am only writing between fits of coughing that still occasionally drive me near unconsciousness due to hypoxia. I'm stuck at home trying to read some research literature across the VPN and proxy servers from my three faculty appointments that give me access to much biomedical research literature.
However, some journals are now no longer granting access if one's IP address does not come directly from the university, even if you are using the university VPN server. And then there's my love-hate relationship with Nature Publishing…
revere | February 3, 2010The Nature blog, The Great Beyond, has an interesting although not surprising report of accusations on BBC that a cabal of researchers has been impeding publication of important stem cell research to help themselves or help their friends:
Truly innovative stem cell research is being suppressed by a clique of peer reviewers for high profile journals, several researchers claimed today.
They told the BBC that the problem lies with those responsible for producing the reviews of research that journals such as Nature use to decide whether to publish the work.
Two scientists told the BBC they…
revere | January 12, 2010[Previous installments: here, here, here, here]
We'd like to continue this series on randomized versus observational studies by discussing randomization, but upon reviewing comments and our previous post we decided to come at it from a slightly different direction. So we want to circle back and discuss counterfactuals a little more, clarifying and adapting some of what we said for the coming randomization discussion.
Let me change the example to a more recent controversy, screening mammography for breast cancer. Should women under 40 get routine screening given that there is said (on the…
revere | January 8, 2010Let me start with an apology. This post is again fairly long (for a blog post). Blog readers don't like long posts (at least I don't). But once I started writing about this I was unable to stop at some intermediary point, although I might have made it more concise and less conversational. I haven't done either. Even worse, I didn't quite finish with the single point I wanted to make, so it will be continued in the next post. Hence the apology. Now to recap a bit and then get down to business.
My "challenge" from 10 days ago has drawn quite a response: over 40 quite substantive comments on the…
revere | December 10, 2009The other day the British Medical Journal (BMJ) published a clutch of articles about whether Tamiflu was as useful a drug as some have touted. I read the main article, another one of the Cochrane Collaborative meta-analyses of the studies they deem useful about any particular subject, and it didn't seem to make much news. It confirmed what their previous review had said about the neuriminidase inhibitor antivirals for influenza (Tamiflu and Relenza): these drugs work but their effect is modest. We've been saying the same thing for years here, not because we did a fancy meta-analysis, but…
revere | December 5, 2009If you are a publishing scientist this will hit home. It's making the rounds of the science community, so you may have seen it, but if you haven't, it's hilarious. In fact it's still hilarious after the third and fourth times through. Warning: If you are sensitive about Hitler associated parodies, don't watch it; I take my cue from Mel Brooks on that subject [added: in light of a comment from a German speaker, please take this warning seriously. While the German dialog is irrelevant and it is the English subtitles that are funny, if hearing and understanding the German in this already much…
revere | October 29, 2009One of the by-products of the brouhaha (here, here) over The Atlantic article on vaccines was some interesting issues raised by the way the Knight Science Journalism Tracker handled it (here, here). If you aren't familiar with KSJ Tracker, it's a site that does "peer review" of science journalism. It's goal "is to provide a broad sampling of the past day’s science news and, where possible, of news releases or other news tips related to publication of science news in the general circulation news media, mainly of the U.S." I don't get a chance to read it as often as I'd like, but when I do I…
awild | October 24, 2009Last week was Open Access Week. At the risk of sounding like a stick-in-the-mud, let me play devil's advocate to the blogosphere's near-universal celebration of Open Access (abbreviated, OA). Thus: I don't think most OA advocates have thought deeply enough about long-term implications.
First, though, what is Open Access?Â
OA is a publication model where scholars (or their subsidizers) foot the bill and readers enjoy studies free of charge. Anyone can log on and read an OA article with nary a registration or fee. OA marks a radical change from the traditional model, where most costs are…
revere | October 9, 2009Skeptical, but Hope Springs Eternal.
The heaviest of the heavy-hitter science journals in the US is Science Magazine, a publication of the American Association for the Advancement of Science (AAAS). It publishes in all aspects of science. Its main competitor is the venerable Nature magazine in the UK. I subscribe to both. They come every week. Since I am overwhelmed by work and scientific papers in general and have a journal of my own to edit (full disclosure), these weekly news and science sources more likely than not pile up unread. But because I subscribe I can easily get the latest hot…
revere | October 6, 2009Vaccines is a topic I don't like writing about so much for many reasons. Vaccination programs are important to public health but we (all the Reveres, including this one) have always interested either in basic science or programs that are applied to the whole population at once, such as clean water, air or food or safe products in the marketplace. But vaccines keep coming up so we talk about them. Since this blog has spent a lot of time on flu, most of it has related to influenza vaccine, but not always. This is a "not always" post, and it is partially about the latest news that US Army and…
revere | August 13, 2009Science Based Medicine is a site we highly recommend with experienced scientists and practitioners in charge. In other words, it's run by adults. But scientists often disagree about things. This is apparently a secret to non-scientists and many reporters who assume that when two scientists disagree, one is lying or wrong. But it's true nonetheless. Whatever the subdiscipline, there are disagreements. If you pick up almost any issue of Science or Nature you will find plenty of them, usually (but not always) couched in polite language in the Introduction or Discussion section of a paper or in…
pontiff | July 16, 2009A friend sent me a link to Detextify2:
What is this?
Anyone who works with LaTeX knows how time-consuming it can be to find a symbol in symbols-a4.pdf that you just can't memorize. Detexify is an attempt to simplify this search.
How does it work?
Just draw the symbol you are looking for into the square area above and look what happens!
My symbol isn't found!
The symbol may not be trained enough or it is not yet in the list of supported symbols. In the first case you can do the training yourself. In the second case just drop me a line (danishkirel[[[at]]]gmail.com)!
I like this. How can I help…
terrasig | June 18, 2009My apologies to readers who have been looking for novel content the last few days. I am swamped with all variety of personal and professional issues but when I finally had a moment to write about something of value, I needed a copy of a short review article from a European cancer journal published by Elsevier to which my institution does not subscribe. I patiently went through their process to register for their site, told them who I was, where I worked, what subdiscipline, etc.
So, I logged in clicked on the PDF link for this two-page article and was told it would be $31.50, thank-you-very-…
sciencewoman | June 12, 2009The following email appeared in my inbox yesterday, and I thought some of you might have some more thoughts to share.
Dear ScienceWoman,
I recently discovered your blog, and have a question regarding academic publishing. I am just now entering a PhD. program, and plan to get married in about 2 years. Given the nature of my particular field, it is expected I will have at least co-authored one paper before the wedding. After marriage, I plan to take his name, for a number of reasons, including the commonality of my last name compared to his name. My question is this: should I start…
revere | June 12, 2009However this pandemic evolves, we are going to learn a lot about how pandemics evolve -- or maybe even start. A paper just published online in Nature sets out a bit more of what we know about this pandemic strain (yes, we can officially refer to it that way now) and makes some observations about its prehistory (its history before it became known and documented by we mortals). Maryn McKenna has an excellent run-down over at CIDRAP News, which you should read. Here's our take on it.
First, we'd like to make a "meta-science" observation. This paper is unusual in several ways. The least…