Category Archives: Open Science

Science 2.0 article quotes four ScienceOnline’09 participants

Science 2.0: New online tools may revolutionize research quotes Michael Nielsen, Eva Amsen, Corie Lok and Jean-Claude Bradley. Article is good but short. If you come to ScienceOnline’09 or participate virtually, you can get the longer story straight from them.

On Peer-Review

Michael Nielsen posted today the first part of his look at peer-review: Three myths about scientific peer review:

What’s the future of scientific peer review? The way science is communicated is currently changing rapidly, leading to speculation that the peer review system itself might change. For example, the wildly successful physics preprint arXiv is only very lightly moderated, which has led many people to wonder if the peer review process might perhaps die out, or otherwise change beyond recognition.
I’m currently finishing up a post on the future of peer review, which I’ll post in the near future. Before I get to that, though, I want to debunk three widely-believed myths about peer review, myths which can derail sensible discussion of the future of peer review.
A brief terminological note before I get to the myths: the term “peer review” can mean many different things in science. In this post, I restrict my focus to the anonymous peer review system scientific journals use to decide whether to accept or reject scientific papers.

The article immediately sparked a fiery debate, which also yielded some good links, e.g., The purpose of peer review and Peer Review: The View from Social Studies of Science (pdf).
What do you think?

The Shock Value of Science Blogs

There was a good reason why the form and format, as well as the rhetoric of the scientific paper were instituted the way they were back in the early days of scientific journals. Science was trying to come on its own and to differentiate itself from philosophy, theology and lay literature about nature. It was essential to develop a style of writing that is impersonal, precise, sharply separating data from speculations, and that lends itself to replication of experiments.
The form and format of a scientific paper has evolved towards a very precise and very universal state that makes scientist-to-scientist communication flawless. And that is how it should be, and at least some elements of style and form (if not format) will remain once the scientific paper breaks down spatially and temporally and becomes a dynamic ongoing communication – clarity and precision will always be important.
But that is strictly technical communication between scientists in the same research field. How about communication between scientists in far-away fields, between scientists and lay audience, or among the educated lay-people? How about communication between scientific colleagues outside of peer-reviewed papers? This is where we are seeing the biggest changes right now and not everyone’s happy. And the debate is reminiscent of the debate in mainstream journalism.
Until pretty recently, the informal communication between scientists was limited to Letters To The Editor of scientific journals, conferences and invited seminars. In all three of those venues, the formal rhetoric of science remained. Fine, but….
Part of training in the academia is training in rhetoric. As you go up the ladder of academic science, you are evaluated not just by the quality of your research (or teaching, in some places), but also in how well you mastered the formalized kabuki dance of the use of Scientese language. The mastery of Scientese makes one part of the Inside club. It makes one identifiable as the Member of this club. The Barbarians at the Gate are recognizable by their lack of such mastery – or by refusal to use it. And it is essential for the Inside Club to make sure that the Barbarians remain at the Gate and are never allowed inside.
Academic science is a very hierarchical structure in which one climbs up the ladder by following some very exact steps. Yes, you can come into it from the outside, class-wise, but you have to start from the bottom and follow those steps “to the T” if you are to succeed. But those formal steps were designed by Victorian gentlemen scientists, thus following those steps turns one into a present-time Victorian gentleman scientist. But not everyone can or wants to do this, yet some people who refuse are just as good as scientists as the folks inside the club. If you refuse to dance the kabuki, you will be forever kept outside the Gate.
The importance of mastery of kabuki in one’s rise through the hierarchy also means that some people get to the top due to their skills at glad-handling the superiors and putting down the competitors with formalized language, not the quality of their research or creativity of their thought. Those who rose to the top due to being good at playing the game know, deep inside, they do not deserve that high position on merit alone. And they will be the loudest defenders of the system as it has historically been – they know if the changes happen, and people get re-evaluated for merit again, they will be the first to fall. This is the case in every area (mainstream journalism, business, politics, etc.), not just academic science.
Insistence on using the formalized kabuki dance in science communication is the way to keep the power relations intact. Saying “don’t be angry” is the code for “use the rhetoric at which I excel so I can destroy you more easily and protect my own spot in the hierarchy”. It is an invitation to the formal turf, where those on the inside have power over those who cannot or will not use the kabuki dance. This has always been the way to keep women, minorities and people from developing countries outside the club, waiting outside the Gate. If, for reasons of your gender, race, nationality or class you are uncomfortable doing the kabuki dance, every time you enter the kabuki contest you will lose and the insider will win. The same applies outside science, e.g., to mainstream journalism and politics.
This is why some people in the academic community rant loudly against science bloggers. If they cannot control the rhetoric, they fear, often rightly, that they will lose. Outside their own turf, they feel vulnerable. And that is a Good Thing.
The debates about “proper” language exist on science blogs themselves. See this and this for recent examples (the very best discussion was on this post which is now mysteriously missing). In response I wrote:

We here at Sb are often accused of being cliquish and insular. But if you look at our 70+ blogs and dig through the archives, you will see that we rarely comment on each other’s blogs – most (99%?) of the comments come from outside readers. Also, most of our links point to outside of Sb. On the other hand, NN [Nature Network] is specifically designed to be a community (not a platform for independent players) and almost all of the comments there are from each other. Thus, it is easy for them to maintain a high level of politeness there (this is not a bad thing – this is how they designed it on purpose). It is much harder to harness the hordes of pharyngulites that spill over to all of our blogs – and I do not mind them at all, I think they make the debate spirited and in a way more honest by bypassing superficial niceness and going straight to the point. This may also have something to do with NN bloggers mainly being in the academia, while a large proportion of SciBlings are ex-academia, journalists, artists, etc. with a different rhetoric. The rhetoric of academia is a very formalized kabuki dance, while the rhetoric of the blogosphere has shed all formalities and is much more reminiscent to the regular everyday oral conversation.

Remember the Roosevelts on Toilets saga? The biggest point of contention was the suggestion by the authors of the paper to the bloggers to move the discussion away from blogs to a more formal arena of letters to the editor. We, the bloggers, fiercely resisted this, for the reasons I spelled above – in the letters to the editor, the Insiders have power over the Outsiders because it is their turf. No, if we want to have a non-kabuki, honest discussion, we will have it out here on the blogs, using our rhetoric, because the honest language of the modern Web places everyone on the even ground – it does not matter who you are, what degrees you have, or how well you’ve learned to dance the kabuki: it is what you say, the substance, that counts. This is why being pseudonymous online works, while academia requires full names and degrees. The Web evaluates you directly, by what you write. The academia uses “tags” – your name and degree – to evaluate you. The academia is in the business of issuing credentials, the stand-ins for quality. The credentials are rough approximations of quality – more often then not they work fine, but they are not 100% foolproof. And if one is insecure about one’s own quality, one would insist on using credentials instead of quality. The use of “proper” rhetoric is, as I said above, a good quick-and-dirty way to recognize credentials.
During the Roosevelt saga, I wrote this post very, very carefully, with a specific purpose in mind. First, I went to great effort to explain the science at length and as simply, clearly and conclusively as possible. This performed several functions for me: first, to establish my own credentials, second, to make my readers understand the science and thus be on “my side” in the comments, and third, to make sure I was as complete about science as possible so as to not have to talk about science at all in the comments. Apart from science, I also included several snarky comments about the authors which served as bait – I wanted them to come and post comments. And they bit. Go read the comment thread there to see what was happening. The author insisted on discussing science. I insisted on refusing to talk about science (to him, I did respond a little bit to some other commenters) and to talk about rhetoric instead.
But first, in a comment I posted even before the authors showed up, in order to set the stage for what I wanted, I wrote this:

In an earlier post, burried deep inside, is this thought of mine:

The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.

What happened on Dr.Isis’ blog is very similar – a clash of two cultures. I think that the picture of the Teddy Bear on the potty was a clever and funny shorthand for your point. If you did it about something I published, I’d laugh my ass off. But I can see how the uptight strain of the scientists would balk at it. It is them, though, who need to get up to speed on the changed rhetoric of science. The straight-laced, uber-formal way of writing in science is on its way out.
The rhetoric, even after it completely modernizes, will still have four concentric circles: the paper itself will always be more formal, especially the Materials/Methods and Results sections due to the need for precision; the letters to the editor will remain pretty formal, but not as formal as they are now; the comments on the paper itself will be still less formal but still polite; the commentary on the trackbacked blogs will be freewheeling, funny and to-the-point, just like yours was, not mealy-mouthing with politeness on the surface and destructive hatred underneath, but honest and straightforward. So, if it is crap, what better way to say it than with a picture of a Teddy Bear on a potty – much more lighthearted and polite than saying it politely, and less devastating for the paper’s authors as it takes their mistake lightly instead of trying to destroy their reputation forever.
The point that both Dr.Isis and I made is that the paper is neat, experimental method sound, data are good, but the interpretation is crap. Now, having a couple of crappy paragraphs in an otherwise good paper is not the end of the world. A paper is not some kind of granite monument with The Truth writ in stone. It is becoming a living document (with comments on the paper and tracbacked blogs), and it has always been a part of a greater living document – the complete literature of a field. That is how science works.
It is hard to know which paper will persist and which one will perish in the future, what sentence will turn out to be a gem of prophetic wisdom, and which one is crap. People publish a lot of stuff, some better than other.
Making a mistake in one paper is not the end of one’s career. But many people perceive criticism as if they are just about to be sent out to join a leper colony. This is, in part, due to the formal rhetoric of science: outwardly polite, but underneath it is an attempt to destroy the person. In comparison, a light-hearted joke with a Teddy Bear acknowledges the failability of humans, allows for everyone to make a mistake and move on (we all shit, don’t we?). It is actually much more normal, and much less dangerous for one’s career to receive such a funny form of criticism than a formal-looking destruction of all our work and our personna.

In the next comment I did the one and only hat-tip to science, then moved onto the territory I wanted – rhetoric (many comments, so go and read them all now). As a result, Dr. Janszky grokked it – and we’ll probably see more of him in the blogosphere in the future. The reason he grokked it is because he is confident in his own qualities – he can change the rhetoric and tone and still not lose the debate because he knows what he’s talking about. Those who know they do not have the quality, would just have ranted harder and harder, complaining about the tone. Dr. Janszky adopted the bloggy tone in the comments right then and there. Which was a victory for everybody.
The informal rhetoric of blogs is a form of subversion – breaking the Gate and letting the Barbarians in (while not allowing quacks and Creationist to hitch a ride inside as well – which is why so many science bloggers focus on those potential free-riders and parasites). What we are doing is leveling the playing field, pointing out the inherent dishonesty of the formalized rhetoric, and calling a space a spade. This is a way to make sure that smart, thoughtful people get heard even if they did not have a traditional career trajectory, or refuse to play the Inside club games. If some of the insiders fall down in the process, that’s a good thing – they probably did not deserve to be up in the first place.
Different bloggers do this in different ways. We can use a brilliant, but snarky use of English (PZ Myers), or texting/LOLCat snark (Abbie), or awe and reverence for the great scientists of old (Mo), or sexual innuendo (SciCurious), or shoes (Dr.Isis), or a light-hearted sense of humor (Ed or Darren), or excessive use of profanity (PhysioProf). What we all do is write in unusual, informal ways. We want to shock. We feel there are many people out there who need a jolt, an injection of reality. We do it by using informal language. And this can be very powerful – just see how the dinosaurs squirm when they read some of our posts! But that’s the point. We are testing them: if, like Dr. Janszky, you “get it”, this means that you have the balls, which means you are confident about your own qualities independent from your credentials. If you keep ranting about “dirty, angry bloggers”….what are you so insecure about? Why are you so afraid of being shown a fraud if you are not? Or, are you?
Another point about blogs, which I alluded above already, is the time-frame. This is a very important point that is often forgotten in the scientists vs. bloggers “let’s be polite” debates. In the formal arenas (Letters, conferences, etc.), where formal language is used, the game some people play is to use an outwardly seemingly polite language to write or say something that is designed to destroy a career. Often in multiple places over a stretch of time. On blogs, when we snarkily attack you, our purpose is to teach a lesson (more to our readers than the scientists in question who may not even know the blog post was written). In other words, it is a one-time thing that is designed to correct a single error, not an attempt at destroying a career.
For good recent examples of the way scientists use the formal venues as well as formal language to destroy each other, see this and this (I have seen more on PLoS ONE, but don’t want to draw your attention to those right now, for professional reasons – keeping my job).
I post 8.2 posts per day on this blog, on a large variety of topics. Do you really think I have the time, energy and interest to study in great detail the life-time achievements of everyone who did something wrong on the Internet? Of course not. I see an article that says something stupid and I shoot a post that shows how stupid it is, so the readers, especially if the deconstruction of stupidity requires some expertise I may have and most people don’t, can see why that particular argument is wrong. Then I move on to the next post on some completely different topic. I have forgotten about your existence in about a nanosecond after publishing that post. I have no interest in destroying your career, but I understand that you are touchy – the life in academia, with its poisonous kabuki game, has trained you to defend yourself against every single little criticism because, underneath the veneer of civility is the career-damaging attack by someone powerful who is hell-bent on destroying you. We don’t do that on blogs. We don’t care enough to do that (unless you are a dangerous peddler of pseudoscience or medical quackery). We want to educate the lay audience and have fun doing it. I have no idea if everything else you have written before and after is brilliant and I don’t care – I think that this one stupid paragraph you wrote is good blogging material, amusing, edifying and useful to use to educate the lay audience. You are NOT the target personally. Your stupid argument is. And I don’t care if that was your one-off singular mistake in life, or an unusually bad moment for you. So, don’t take it personally. This is not academia. We are, actually, honest here on the intertubes, and you need to learn to trust us.
The attempts at character assassinations within academia, by using the formalized kabuki language by the powerful and forcing the powerless to adopt the same and thus be brought to slaughter, do not happen only in print. They also happen in person. Read this and this for a recent example of a senior researcher trying to publicly destroy a younger, female colleague at a meeting. And he was wrong. But he was powerful and intimidating. I wish the young woman responded by going outside of formal kabuki dance, shocking the audience in one way or another, giving all the present colleagues a jolt, making them listen and perhaps notice what is happening. Or, if she was shy, I wish some senior male colleague did the same for her and put the old geezer in his place. I wrote a comment:

“Tone it down” and “Why are you so angry?” are typical sleazy tactics used by a person in power over a person not in power. It was used against people of other races, against women, against gays, against atheists – this is the way to make their greivances silent and perpetuate the status quo, the power structure in which they are on the top of the pecking order. The entire formal, convoluted, Victorian-proper discourse one is supposed to use in science is geared towards protecting the current power structure and the system that perpetuates it. Keeping the dissenters down and out. Bur sometimes, anger, or snark, or direct insult, are the jolt that the system needs and it will have to come from the people outside the power structure, and it would have to occur often and intensely until they start paying attention.

And then, there is the area in between scientists and lay audience. The job of translating Scientese into English (or whatever is the local language) has traditionally been done by professional science journalists. Unfortunately, most science journalists (hats off to the rare and excellent exceptions) are absolutely awful about it. They have learned the journalistic tools, but have no background in science. They think they are educated, but they only really know how to use the language to appear they are educated. Fortunately for everyone, the Web is allowing scientists to speak directly to the public, bypassing, marginalizing and pushing into extinction the entire class of science “journalists” because, after all, most scientists are excellent communicators. And those who are, more and more are starting to use blogs as a platform for such communication.
The problem is, the professional science journalists also love to put down the blogs and use the paternalistic “tone it down” argument. But, unlike the political journalists who are incapable of seeing the obvious (stuck too far inside Cheney’s rectum to see what we all could see?), the science journalists have the added problem of not having the expertise for their job in the first place. In politics, everyone with the brain, not just journalists, could see that excuses for going to Iraq were lame. But in science journalism, there exist out there people with real expertise – the scientists themselves – who now have the tools and means to bypass you and make you obsolete because you cannot add any value any more.
To the list that includes MSM “journalists” aka curmudgeouns like Richard Cohen, Sarah Boxer, Andrew Keen, Lee Siegel, Michael Skube, Neil Henry and many others, we can now add curmudgeounly science journalists George Johnson and John Horgan as well – just listen to this!!!!! Yes go an listen before you come back. If you can stand it. But if I suffered through it, you can, too. I am a pretty calm kind of guy, but listening to that “dialogue” filled me with rage – I felt insulted, my intelligence insulted, and my friends insulted. Frankly, I’ve heard smarter science-related conversations from the drunks in rural Serbian bars.
I’ve been in this business (both science and science communication) for a long time, but I have never heard of George Johnson until today. From what I saw in that clip, I have not missed anything. Where does his smugness come from then? As for John Horgan, I’ve heard of him – he earned his infamy when he published – and was instantly skewered and laughed at by anyone with brains – his book “The End of Science”, arguably one of the worst and most misguided books about science (outside of Creationist screeds) ever. Where is his humbleness after such a disaster? Why is he not hiding in the closet, but instead shows up in public and appears – smug. Some people just have no self-awareness how stupid they appear when they behave as if they have authority yet they don’t and it’s obvious. What is it about professional journalists that makes them have illusions they are educated? “No, I am not a scholar but I play one on TV” turns into “Since I can transcribe and read smart stuff I must be really smart myself”.
Luckily, bloggers have no qualms about defending themselves – please read this gorgeous smack-down by Abbie, this older post by Ed in which he explains exactly what he meant, and perhaps this old post of mine which also, in a circuitous way, predicts the extinction of science journalistic dinosaurs.
But perhaps I shouldn’t be that nasty to Johnson and Horgan? After all, my blogging schtick is niceness. This makes it very easy for me to destroy someone – on those rare occasions when someone like me, renowned for endless patience, flies off the handle, people sit up and pay attention. If I use profanity to describe someone, that one probably richly deserves it. I know I have to use this power with prudence. If I attack someone full-blast, people will tend to believe me, as I rarely do that kind of stuff. And if you subsequently Google that name, my blogpost about him/her is likely to be the #1 hit on the search, or in the top ten.
Perhaps Johnson and Horgan are actually nice and smart guys. They may be nice to their wives and kids. Perhaps they wrote, 30 years ago, something really smart. But I have no interest in digging around for that. I want to finish this post and move on. And after watching this movie, I really have no motivation to search for anything else by these two guys as it appears to be a waste of my time. It does not appear to me like a bad-day, one-off mistake that everyone sometimes makes. It is 30 minutes of amazing ignorance and arrogance at display – probably sufficient material to make me doubt I’d ever find anything smart penned by them in the past, so why should I bother with them at all? I can probably evaluate their qualifications quite accurately from these 30 minutes and safely conclude they equal zero. Their “angry bloggers” shtick was the first give-away they know deep inside they are irrelevant and on their way out. Their subsequent chat about science was amateurish at best, no matter how smug their facial expressions at the time.
Perhaps if we remove those middle-men and have scientists and the public start talking to each other directly, then we will have the two groups start talking to each other openly, honestly and in an informal language that is non-threatening (and understood as such) by all. The two sides can engage and learn from each other. The people who write ignorant, over-hyping articles, the kinds we bloggers love to debunk (by being able to compare to the actual papers because we have the background) are just making the entire business of science communication muddled and wrong. Please step aside.
Update: Brian, Greg, Ed, Dr.Isis, Mike Brotherton, Hank and Larry chime in on this discussion as well. More: Alex, Chris Mooney, Mike, Chad, Eric Wolff, Stephanie and Tom Levenson, Sabine and Tom again.

Online submission makes it easier for people in developing countries to submit their scientific manuscripts

Changes in publication statistics when electronic submission was introduced in an international applied science journal:

In a refereed journal in the food and agriculture sector, papers were tracked over a five-year period during the introduction of electronic submissions. Papers originated in the Americas and Pacific region and were processed in Canada. Acceptance times for revised papers were reduced (P < 0.001) to 59% of the original, from 156.5 ± 69.1 days to 92.8 ± 57.5 days. But the start of electronic submission coincided with a change in the geographical origin of papers, with papers from Anglophone countries changing from a 61% majority to a 42% minority. It is possible that submissions from non-Anglophone sources were facilitated, thus creating challenges to the traditional Anglophone reviewer population.

RNA wiki

Publish in Wikipedia or perish:

Wikipedia, meet RNA. Anyone submitting to a section of the journal RNA Biology will, in the future, be required to also submit a Wikipedia page that summarizes the work. The journal will then peer review the page before publishing it in Wikipedia.
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The RNA wiki is a subset of a broader project, the WikiProject Molecular and Cellular Biology, which has marshalled hundreds of scientists to improve the content of biology articles in Wikipedia. It, in turn, is collaborating with the Novartis Research Foundation on GeneWiki 3, an effort to create Wikipedia articles describing every human gene. Beyond Wikipedia itself, scientists are also increasingly using wiki technology to get scientists to help curate other biological databases.

PLoS ONE Second Birthday Synchroblogging Competition – entries so far

The entries for the PLoS ONE Second Birthday Synchroblogging Competition have been coming in all day. Here are the posts I found so far. If you have posted and your post is not on this list, let me know by e-mail. I will keep updating this post and moving it to the top until the competition closes at dawn tomorrow:
Ed Yong of Not Exactly Rocket Science: Predatory slime mould freezes prey in large groups about the article: Exploitation of Other Social Amoebae by Dictyostelium caveatum
Scicurious of Neurotopia (version 2.0): Why Did the Dolphin Carry a Sponge? about the article: Why Do Dolphins Carry Sponges?
Scicurious of Neurotopia (version 2.0): Einstein was smart, but Could He Play the Violin? about the article: Practicing a Musical Instrument in Childhood is Associated with Enhanced Verbal Ability and Nonverbal Reasoning
Allyson of Systems Biology & Bioinformatics (Semantically Speaking) on One way for RDF to help a bioinformatician build a database: S3DB (also cross-posted on The mind wobbles: One way for RDF to help a bioinformatician build a database: S3DB) about the article: A Semantic Web Management Model for Integrative Biomedical Informatics
Simon Cockell of Fuzzier Logic: Contextual Specificity in Peptide-Mediated Protein Interactions about the article: Contextual Specificity in Peptide-Mediated Protein Interactions
Mike Haubrich of Tangled Up in Blue Guy : Small-Bodied Humans on Palau – A Disagreement about the articles: Small-Bodied Humans from Palau, Micronesia and Small Scattered Fragments Do Not a Dwarf Make: Biological and Archaeological Data Indicate that Prehistoric Inhabitants of Palau Were Normal Sized
Martin of The Lay Scientist : Catching Snowflakes: The Media and Public Perceptions of Disease about the article: Medicine in the Popular Press: The Influence of the Media on Perceptions of Disease
Nir London of Macromolecular Modeling Blog: Model for the Peptide-Free Conformation of Class II MHC Proteins about the article: Model for the Peptide-Free Conformation of Class II MHC Proteins
Greg Laden of Greg Laden’s blog: How to make an elephant turn invisible about the articles: Risk and Ethical Concerns of Hunting Male Elephant: Behavioural and Physiological Assays of the Remaining Elephants, Roadless Wilderness Area Determines Forest Elephant Movements in the Congo Basin, Elephant (Loxodonta africana) Home Ranges in Sabi Sand Reserve and Kruger National Park: A Five-Year Satellite Tracking Study and Population and Individual Elephant Response to a Catastrophic Fire in Pilanesberg National Park.
The Neurocritic of The Neurocritic blog: Can You Reread My Mind? about the article: Using fMRI Brain Activation to Identify Cognitive States Associated with Perception of Tools and Dwellings
Moneduloides of Moneduloides blog: A trypanosome and a tsetse walk into a bar… about the article: Factors Affecting Trypanosome Maturation in Tsetse Flies
El-Ho of Pas d’il y’on que nous: The Etiology of Fear about the article: Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations
Ian of Further thoughts: Evolution and conservation in Mexican dry forests about the article: Sources and Sinks of Diversification and Conservation Priorities for the Mexican Tropical Dry Forest
Alun Salt of Archaeoastronomy: If you put a snail shell to your ear can you hear the sound of your thoughts? about the article: Climate Change, Genetics or Human Choice: Why Were the Shells of Mankind’s Earliest Ornament Larger in the Pleistocene Than in the Holocene?
Michael Tobis of Only In It For The Gold: The Singularity about the article: Ecosystem Overfishing in the Ocean
PodBlack Cat of PodBlack blog: Pet Ownership – Maybe Not For Better Health, Perhaps Sense Of Humour? about the article: To Have or Not To Have a Pet for Better Health?
Juan Nunez-Iglesias of I Love Symposia!: Randomise your samples! about the article: Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

The U.S. Commitment to Global Health

Listen here to the The December 16, 2008 David E. Barmes Global Health Lecture given by Dr.Harold Varmus:

Harold Varmus, former Director of the National Institutes of Health and co-recipient of a Nobel Prize for studies of the genetic basis of cancer, is President of Memorial Sloan-Kettering Cancer Center in New York City. Dr. Varmus chairs the Scientific Board of the Bill & Melinda Gates Foundation’s Grand Challenges in Global Health program and leads the Advisory Committee for the Global Health Division. He was a member of the World Health Organization (WHO) Commission on Macroeconomics and Health, and is a co-founder of the Public Library of Science, a leading publisher of open access journals. In addition, he serves as co-chair of the Institute of Medicine’s committee on The U.S. Commitment to Global Health. The committee will issue its interim report on the day preceding the lecture.

Scientific Red Cards: a good idea or opening a hornet’s nest?

From The Scientist: Flagging fraud:

A team of French life sciences grad students has launched an online repository of fraudulent scientific papers, and is calling on researchers to report studies tainted by misconduct.
The website — called Scientific Red Cards — is still in a beta version, but once it’s fully operational it should help the scientific community police the literature even when problems slip past journal editors, the students claim.
The database might also prevent researchers from citing papers that they don’t even realize are fraudulent, said Claire Ribrault, a PhD student in neurobiology at the Ecole Normale Superieure in Paris, who unveiled the new website last month at a workshop in Madrid, Spain, organized by the European Science Foundation’s Research Integrity Forum.
After misconduct is detected in a published paper, “sometimes the paper is not retracted, depending on the policy of the journal, and even if the paper is retracted sometimes it’s still cited after the retraction,” Ribrault said in a press release.
The website color-codes misconduct into three categories: red for data-related misconduct, including fabrication, falsification, and plagiarism; blue for publication-related misconduct, such as when editorial policies are not followed; and green for research practice misconduct, including problems with consent forms.
Each problematic paper in the register includes a full bibliographic reference, a link to published accounts of the misconduct, and a discussion board for users to leave their comments. So far, only around 30 papers have been listed.
Scientific Red Cards received a cautious thumbs-up from the meetings’ attendees, although some voiced concerns over legal problems and the site being used for scientific smear campaigns. Other countered that it provides a transparent way to patrol the literature.

Olivia Judson needs a primer on Science Online

Oh-oh, Olivia Judson is not up-to-speed on Open Access, Open Science and Science 2.0 stuff – though the article is interesting and thought-provoking:

As a system, it was a little clumsy — photocopying was a bore, and if I wanted to spend a couple of months writing somewhere other than my office, I had to take boxes of papers with me — but it worked. I knew what I had and where it was.
Then the scientific journals went digital. And my system collapsed.
On the good side, instead of hauling dusty volumes off shelves and standing over the photocopier, I sit comfortably in my office, downloading papers from journal Web sites.
On the bad side, this has produced informational bedlam.
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One caveat. I say “access to information is easier and faster than ever before.” With respect to scientific information, this is true for people within universities, but not for those without them. One of the consequences of the scientific journals going digital is that it has become harder for members of the public to get access to original scientific information. It used to be the case, for example, that anyone could get permission to spend a day at the library at Imperial College; once there, they could read any of the journals on the library shelves. Now, subscriptions to the paper editions of many journals have been stopped — the journals are no longer physically there — and only members of the university are allowed access to the online versions. Some journals give free access, at least to back-issues; but many do not. Then, if you are not a member of a university and you want to read some articles, they may cost you as much as $30 each. I think this is a pity. Perhaps not many people want to read original scientific research; but somehow, it seems against the spirit of the enterprise.

Readers (and there are over 200 comments there) mostly give advice on how to use Zotero and similar tech stuff, but there is not enough about OA and how much has happened about it over the past few years. It is unfortunate she cannot make it to ScienceOnline09 in January, to hear the cutting edge thinking on all of the topics she touched on in this essay.

Co-Researching spaces for Freelance Scientists?

Pawel tried, for a year, to be a freelance scientist. While the experiment did not work, in a sense that it had to end, he has learned a lot from the experience. And all of us following his experience also learned a lot about the current state of the world. And I do not think this has anything to do with Pawel living in Poland – I doubt this would have been any different if he was in the USA or elsewhere.
You all know that I am a big fan of telecommuting and coworking and one of the doomsayers about the future existence of the institution of ‘The Office’. And you also know that I am a scientist, so it is no surprise that I have been also thinking how to connect these two – is there a way to have a coworking (or co-researching) facility for freelance scientists?
If you work 9-5 for The Man, it is understandable that you should strive mightily to sharply delineate work from the rest of your life, and to measure your worth in dollars (or place of employment, e.g., Harvard). But if you are lucky (and work to make it happen), you will do what you like to do, what you’d do for free anyway. Thus, you express your person through your work, you are what you do and your job is you, and it is perfectly fine to completely blur that distinction. If that is the case, your worth is not measured in dollars – you can say you “made it” if you can live wherever you want on the planet (or even off of it if you are adventurous), surrounded by people you like, doing what you like, and having lots of friends. You will be measured by the size of your network – who is your (mutual – it has to be mutual!) friend.
Sure, you can make many mutual friends online, through blogs, Facebook, LinkedIn, Twitter, FriendFeed, etc. But, as a human being, you also need physical proximity to some of the people you really like a lot. What are blogs but means to find each other in order to organize a Blogger Meetup or BloggerCon?
So, if you have that luck and freedom, you will choose where on Earth to live both by the criterion of climate and natural beauty and by unusual concentration of people you really like and want to be surrounded with.
But what about your work – how can you transport your work wherever you want to live? This depends, of course, on the nature of your work. If your job is to think, read, write, communicate, publish or do stuff with computers, you can do that everywhere as long as there is electricity and internet access. You can work at home, or a corner cafe, or a nice local coworking space.
But what if you are a scientist? How can you do that?
Remember World 2.0 at Rainbows End? In that plausible world, which will cease to be Science Fiction in mere years, some scientists obviously work at universities or at institutes that may or may not be associated with universities. They are presumably hired to teach and train the new generations of scientists there. But most of scientific research is apparently happening elsewhere – in the virtual world, on the “boards”.
When I read about those “boards”, I was reminded of sites like Innocentive, Innovation Exchange, Nine Sigma or even 2collab – places where funders and researchers find each other and exchange money for discoveries – a free-market type of funding. As an alternative, it sound pretty good, though big basic science would probably still have to be funded by the government agencies.
But, Vinge never tells where those scientists live and where they actually do their research. They may pick up jobs online, but they still have to do wet work in some lab somewhere. Where? Some may be at universities, supplementing their income in this way. But many are likely freelancers (many of those perhaps without any formal degrees in science, just talented people who learned by themselves and through their thoughts, words and actual discoveries, built their reputations in the scientific community). Where do those freelancers do their research?
Perhaps in a scientific equivalent of a coworking place – perhaps something like a Science Hostel. I have been thinking about this for quite a while, but I did not know that Garret Lisi also came up with this concept. Apart from being on the cutting edge of science publishing, he is also apparently thinking innovatively about the way science in the future will be done. In his interview on Backreaction, Garett says:

I’ve been thinking about what the ideal scientific work environment would be, and the best thing I’ve been able to come up with is a Science Hostel. I envision a large house where theorists could live and work on their stuff alone or in groups while having their meals and living space provided. The idea is to give researchers time, with an easily accessible but undemanding social atmosphere, and as little responsibility as possible. And, of course, it would have to be somewhere beautiful — with good hiking and other things to do outside. For the past year I’ve been living near Lake Tahoe — a great environment for thinking and playing. Anywhere in the mountains would probably be good for a Science Hostel — even better if it’s next to a good ski hill. 🙂

Now that is all very nice if you are a theorist – all you need is an armchair. Or if your only scientific tool is a computer, you can do it there. But what if you need more?
A coworking space has three important components: the physical space, the technological infrastructure, and the people. A Science Hostel that accommodates people who need more than armchairs and wifi, would need to be topical – rooms designed as labs of a particular kind, common equipment that will be used by most people there, all the people being in roughly the same field who use roughly the same tools.
But this is not such a new idea. Remember Entwicklungsmechanik from the late 19th and early 20th century? The winters in Germany are cold, so the developmental biologists spent a lot of their time at Stazione Zoologica in Naples, where they made their discoveries by studying eggs and embryos of sea urchins. That was a Science Hostel. How about Woods Hole? Cold Spring Harbor? Perimeter Institute? Those are all Science Hostels.
But in the modern world, there can be more of those. There will be vast differences in size, type and economics. Some will be built and funded by large, rich institutions. Others will be cooperative projects. Some will be free, but by invitation only. Others will be open, but charging for space and use of the facilities. While most of the past and existing institutes of this sort only cater to people who are already associated with other academic institutions, some of the new hostels will cater to freelancers as well (needless to say, Open Access to literature is essential to development of such spaces).
And people will choose to live where the appropriate Science Hostel is located because this is where they can do their work and live their lives surrounded by like-minded people. There will be a lot of physicists living in the village that has a Physics Hostel. A lot of molecular biologists surrounding a Hostel equipped for them. Perhaps there will be a Hostel specifically geared towards research on whole animals with its own IACUC, facilities and staff.
We’ll wait and see….

Some thoughts about Science2.0

This is pretty long and not easy to read, but it puts together a lot of thoughts about blogs, wikis and the stability of the Web as a science publishing platform. Post your comments there, or here.

Open Science – post-mortem analysis of H.M.’s brain

As you know, H.M. died last week.
Listen to this brief (9 minutes) NPR Science Friday podcast – you will be able to hear Henry Gustav Molaison’s voice. But most importantly, he has donated his brain to further scientific study. His brain will be sliced and stained and studied at The Brain Observatory at the University of California, San Diego.
But the way they are going to do it will be in a very Open Science manner. Dr. Jacopo Annese, who is leading the project said, in this interview, that the entire process will be open – there will be a forum or a blog where researchers from around the word can make suggestions and discuss the procedure and the results. This will include, especially, people who have worked with Molaison when he was alive and may, thus, have the most insight into what would be most important to study, e.g., exactly what dyes to use to trace which brain circuits, etc. It will be interesting to watch.

The structure of scientific collaboration networks

On arXiv, by M. E. J. Newman (Santa Fe Institute):

We investigate the structure of scientific collaboration networks. We consider two scientists to be connected if they have authored a paper together, and construct explicit networks of such connections using data drawn from a number of databases, including MEDLINE (biomedical research), the Los Alamos e-Print Archive (physics), and NCSTRL (computer science). We show that these collaboration networks form “small worlds” in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances. We further give results for mean and distribution of numbers of collaborators of authors, demonstrate the presence of clustering in the networks, and highlight a number of apparent differences in the patterns of collaboration between the fields studied.

Dr. Exotica

Tending to recent immigrants and other travelers, Carlos Franco-Paredes diagnoses diseases that few other physicians in North America have ever seen:

Q: What’s the most important diagnostic tool you use?
A: The Internet. We rely on it heavily, probably more than other specialists do. Online, we access recent medical journals from all over the world, including PLoS Neglected Tropical Diseases and the Journal of Infectious Diseases in Developing Countries. They have really good articles written by people on the local level. But beyond that, we use the Internet to keep up on what’s happening in various cultures. I read international newspapers and the Websites of the U.S. State Department and refugee organizations.

New journal: Ideas in Ecology and Evolution

Ideas in Ecology and Evolution is a new Open Access journals which is also experimenting with the review process.
Bob O’Hara and commenters go into details. I hope it does not end like Medical Hypotheses: a great source of blog-fodder for snarky bloggers and not much else. We’ll keep an eye….

SciAm Podcast

Scott Derrickson, director of the new version of The Day the Earth Stood Still, talks about his take on the iconic sci-fi movie. And Nobel laureate, Richard Roberts, discusses the importance of open-access science publishing. Plus, we’ll test your knowledge about some recent science in the news.

Listen here.

Interview with Michael Nielsen

Sam Dupuis (yes, the son of John) contacted Michael Nielsen and posted a nice, smart, long blog interview. Check it out.

Jesse Dylan video on Science Commons

News from Science Commons:

Today, we are proud to announce the release of Science Commons’ first informational video. The video was directed by renowned director Jesse Dylan, the director of the Emmy- award winning “Yes We Can” Barack Obama campaign video with musical artist will.i.am from the Black Eyed Peas. The video can also be seen on the front of sciencecommons.org.
“I believe Science Commons represents the true aspiration of the web, and I wanted to tell their story,” Dylan said. “They’ve changed the way we think about exploration and discovery; the important and innovative ideas need to be shared. I believe it’s vital to revolutionizing science in the future. I hope this is just the beginning of our collaboration.”
This video is launched in conjunction with a letter of support from Richard Bookman, the Vice Provost for Research and Executive Dean for Research and Research Training at the University of Miami. Bookman joins a group of esteemed Commons supporters featured in this year’s “Commoner Letter” series, including this year: Eben Moglen of the Software Freedom Law Center and Columbia University, Renata Avila – CC Guatemala Project Lead, and singer/songwriter Jonathan Coulton. More information and an archive of past letters can be found at http://support.creativecommons.org/letters.

If you are a University, Open Access is cheaper

Philip Johnson makes some back-of-the-envelope calculations, very conservatively assuming that all OA journals are author-pay (not true) and all author fees for publishing are born by the Universities (not true) and concludes that even with such harsh handicapping, universities that switched to OA-only policies would immediately save substantial amounts of money (also check the excellent comments on that post):

Subscription costs would obviously be nil for an open access journal: we are all free to access the content of an open access journal via the internet, with no restrictions on who can read the content. In contrast, the author would pay to publish the article. This is perhaps the biggest resistance from scientists (and I’m sure the situation would be similar in the arts, or law, or what have you) to the open access movement, many feeling they don’t have enough funding for students or experimental equipment as is, and couldn’t possibly afford to pay to publish as well. I can appreciate this argument, though some progress is being made as you can specifically request funding to cover open access publication charges from some of the granting agencies.
(Also, let’s be honest, the current situation of paying for page charges and to have colour figures means the author is already paying to publish, and sometimes non-trivial amounts.)
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Let’s further assume that the economies of scale would kick in if universities around the world decided to embrace this philosophy. This should lead to an overall lowering of the publication costs, all the while bringing access to academic literature to everyone with an internet connection. It is also easy to imagine the costs being even lower, as the collaborative nature of academic work means many papers now have authors from multiple institutions, all of whom could share in the cost of publishing. (Determining the rules for who-pays-what would be tricky, but should be doable.)
There are probably some key issues I’m missing here (the most obvious one which I’ve even mentioned is that we need open access journals to publish in!), and my idea is prefaced on the assumption that universities are the significant driving force in the academic literature game, but I think the take-home message is reasonably clear, at least using the University of Toronto numbers: we could already afford going entirely open access.
I certainly wouldn’t feel bad if Elsevier and their ilk went out of business given the exorbitant increase in subscription costs and the non-obvious reasoning why, and I’m sure the societies could come to embrace the open access movement, which would bring the majority of high quality journals into the fold.

Peter Suber adds some useful links and calculations, including:

# Since November 2006 several studies have give us newer data on the the ratio of no-fee OA journals to fee-based OA journals. The best current estimates are that 67% of the journals listed in the DOAJ charge no publication fees, and 83% of OA journals from society publishers charge no publication fees. Clearly if Johnson zeroed out the publication fees for two-thirds of the articles published by Toronto faculty, the projected saving would rise significantly.
# The bargain would be even more compelling if we could subtract the publication fees paid by funding agencies rather than universities. Unfortunately there are no studies yet estimating that number.

Why does Impact Factor persist most strongly in smaller countries

The other night, at the meeting of the Science Communicators of North Carolina, the highlight of the event was a Skype conversation with Chris Brodie who is currently in Norway on a Fulbright, trying to help the scientists and science journalists there become more effective in communicating Norwegian science to their constituents and internationally.
Some of the things Chris said were surprising, others not as much. In my mind, I was comparing what he said to what I learned back in April when I went back to Serbia and talked to some scientists there. It is interesting how cultural differences and historical contingencies shape both the science and the science communication in a country (apparently, science is much better in Norway, science journalism much better in Serbia).
But one thing that struck me most and got my gears working was when Chris mentioned the population size of Norway. It is 4.644.457 (2008 estimate). Serbia is a little bigger, but not importantly so, with 7.365.507 (2008 estimate – the first one without Kosovo – earlier estimates of around 10 million include Kosovo). Compare this to the state of North Carolina with 9,061,032 (2007 estimate).
Now think – what proportion of the population of any country are active research scientists? While North Carolina, being part of a larger entity, the USA, can afford not to do some stuff and do more of other stuff, small countries like Norway and Serbia have to do everything they can themselves, if nothing else for security reasons, e.g., agriculture, various kinds of industry, tourism, defense, etc. Thus, North Carolina probably has a much larger percentage of the population being scientists (due to RTP, several large research universities, and a lot of biotech, electronics and pharmaceutical industry) than an independent small country can afford (neither Norway nor Serbia are members of the EU).
So, let’s say that each of these smaller countries has a few thousand active research scientists. They can potentially all know each other. Those in the same field certainly all know each other. Furthermore, they more than just know each other – they are all each other’s mentors, students, lab-buddies, classmates, etc., as such a country is likely to have only one major university in the capital and a few small universities in other large cities. It is all very….incestual.
With such a small number of scientists, they are going to be a weak lobby. Thus, chances of founding new universities and institutes, expanding existing departments and opening up new research/teaching positions in the academia are close to zero. This means that the only way to become a professor is to wait for your mentor to retire and try to take his/her place. This may take decades! In the meantime, you are forever a postdoc or some kind of associate researcher etc.
If each professor, over the course of the career, produces about 18 PhDs (more or less, depending on the discipline) who are indoctrinated in the idea that the academic path is the only True Path for a scientist, the competition for those few, rare positions will be immense. And they all know each other – they are all either best friends or bitterest enemies.
This means that, once there is a job opening, no matter who gets the job in the end, the others are going to complain about nepotism – after all, the person who got the job (as well as each candidate who did not) personally knows all the committee members who made the final decision.
In such an environment, there is absolutely no way that the decision-making can be even the tiniest bit subjective. If there is a little loophole that allows the committee to evaluate the candidate on subjective measures (a kick-ass recommendation letter, a kick-ass research proposal, a kick-ass teaching philosophy statement, kick-ass student evaluations, prizes, contributions to popularization of science, stardom of some kind, being a member of the minority group, etc.), all the hell will break loose at the end!
So, in small scientific communities, it is imperative that job and promotion decisions be made using “objective” (or seemingly objective) measures – some set of numbers which can be used to rank the candidates so the candidate with the Rank #1 automatically gets the job and nobody can complain. The decision can be (and probably sometimes is) done by a computer. This is why small countries have stiflingly formalized criteria for advancement through the ranks. And all of those are based on the numbers of papers published in journals with – you guessed it – particular ranges of Impact Factors!
Now, of course, there are still many universities and departments in the USA in which, due to bureacratic leanings of the administration, Impact Factor is still used as a relevant piece of information in hiring and promotion practices. But in general, it is so much easier in the USA, with its enormous number of scientists who do not know each other, to switch to subjective measures, or to combine them with experiments with new methods of objective (or seemingly objective) measures. From what I have seen, most job committees are much more interested in getting a person who will, both temperamentally and due to research interests, fit well with the department than in their IFs. The publication record is just a small first hurdle to pass – something that probably 200 candidates for the position would easily pass anyway.
So, I expect that the situation will change pretty quickly in the USA. Once Harvard made Open Access their rule, everyone followed. Once Harvard prohibits the use of IF in hiring decisions, the others will follow suit as well.
But this puts small countries in a difficult situation. They need to use the hard numbers in order to prevent bloody tribal feuds within the small and incestuous scientific communities. A number of new formulae have been proposed and others are in development. I doubt that there will be one winning measure that will replace the horrendously flawed Impact Factor, but I expect that a set of numbers will be used – some numbers derived from citations of one’s individual papers, others from numbers of online visits or downloads, others from media/blog coverage, others from quantified student teaching evalutions, etc. The hiring committees will have to look at a series of numbers instead of just one. And experiments with these new numbers will probably first be done in the USA and, only once shown to be better than IF, transported to smaller countries.
Related:
h-index
Nature article on the H-index
Achievement index climbs the ranks
The ‘h-index’: An Objective Mismeasure?
Why the h-index is little use
Is g-index better than h-index? An exploratory study at the individual level
Calculating the H-Index – Quadsearch & H-View Visual
The use and misuse of bibliometric indices in evaluating scholarly performance
Citation counting, citation ranking, and h-index of human-computer interaction researchers: A comparison of Scopus and Web of Science
H-Index Analysis
The EigenfactorTM Metrics
Pubmed, impact factors, sorting and FriendFeed
Publish or Perish
Articles by Latin American Authors in Prestigious Journals Have Fewer Citations
Promise and Pitfalls of Extending Google’s PageRank Algorithm to Citation Networks
Neutralizing the Impact Factor Culture
The Misused Impact Factor
Paper — How Do We Measure Use of Scientific Journals? A Note on Research Methodologies
Escape from the impact factor
Comparison of SCImago journal rank indicator with journal impact factor
Emerging Alternatives to the Impact Factor
Why are open access supporters defending the impact factor?
Differences in impact factor across fields and over time
A possible way out of the impact-factor game
Comparison of Journal Citation Reports and Scopus Impact Factors for Ecology and Environmental Sciences Journals
Watching the Wrong Things?
Impact factor receives yet another blow
Having an impact (factor)
In(s) and Out(s) of Academia
The Impact Factor Folly
The Impact Factor Revolution: A Manifesto
Is Impact Factor An Accurate Measure Of Research Quality?
Another Impact Factor Metric – W-index
Bibliometrics as a research assessment tool : impact beyond the impact factor
Turning web traffic into citations
Effectiveness of Journal Ranking Schemes as a Tool for Locating Information
Characteristics Associated with Citation Rate of the Medical Literature
Relationship between Quality and Editorial Leadership of Biomedical Research Journals: A Comparative Study of Italian and UK Journals
Inflated Impact Factors? The True Impact of Evolutionary Papers in Non-Evolutionary Journals
Sharing Detailed Research Data Is Associated with Increased Citation Rate
Measures of Impact

‘….the potential future of an open, transparent peer review process. …’

Garrett Lisi’s Exceptional Approach to Everything:

When Lisi published his physics paper, “An Exceptionally Simple Theory of Everything,” to an online archive last year, it created a media buzz about his lifestyle and an onslaught of support and skepticism about his model. Although the verdict is still out on whether Lisi’s theory will prove predicatively accurate, the means by which he released and vetted his research point to a larger trend in the scientific community.
Barriers to data are falling, a cross-disciplinary community of commenters is replacing journal-selected peer reviewers, and “information to the people!” is becoming the raison d’être of the science information superhighway. The movement, combined with an evolving image of the contemporary scientist, is redefining how society interacts with science.
—————-snip—————-
Why did you choose not to submit your paper to a traditional peer-reviewed journal?
I think peer review is important, but the journal-operated system is severely broken. I suspected this paper would get some attention, and I chose not to support any academic journal by submitting it. Under the current system, authors (who aren’t paid) give ownership of their papers to journals that have reviewers (who aren’t paid) approve them before publishing the papers and charging exorbitant fees to view them. These reviewers don’t always do a great job, and the journals aren’t providing much value in exchange for their fees. This old system persists because academic career advancement often depends on which journals scientists can get their papers into, and it comes at a high cost – in money, time, and stress. I think a better peer-review system could evolve from reviewers with good reputations picking the papers they find interesting out of an open pool, such as the physics arXiv, and commenting on them. This is essentially what happened with my paper, which received a lot of attention from physics bloggers – it’s been an example of open, collaborative peer review.
What is the alternative to the way problems in physics are typically approached?
I don’t think there is a typical way physics is being done; there’s a great deal of variation. But there does seem to be more pressure on young researchers than there should be, especially on post-docs and new professors. Science shouldn’t be a grind to publish more papers and advance a career – we’re supposed to be doing this because we love it and find it fascinating. High-quality work and interesting projects should be valued, not just a lengthy publication record. And since science helps society, I think society should be better to scientists and support them in doing the research they want, rather than requiring them to jump through so many hoops.
—————–snip——————–
How will “open science” and other new ways of sharing information transform science?
I think we’re in the midst of a gradual revolution, following the rise of the Internet. The success of the physics arXiv – where physicists post freely available versions of their papers – has made it possible for anyone to access the literature from anywhere. This let me move to Maui 10 years ago and stay in touch with the field. Now an NIH mandate, requiring that publicly funded papers be posted to PubMed, will produce the same liberating effect in other fields. The net is also affecting the way scientists work directly, with wikis and blogs used for discussions, collaborations, and individual note keeping. These new tools, along with online social networks, allow geographically independent researchers to keep in perpetual, productive contact. Since theoretical researchers are no longer anchored to one location, I’ve been working on creating Science Hostels – micro-institutes in beautiful places where scientists could live and work, while having a bit of fun, and keeping more of a balance in their lives.

Read the whole thing….

The promise of peer review

An interesting and insightful article by Vivian Siegel:

It is ironic that, in an era known for the great speed and availability of information – where we could choose to blog our results rather than submit them to journals – publishing papers seems slower and more painful than ever before.
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I believe our best hope for fair and constructive decisions is to relieve reviewers of the responsibility to make recommendations for or against publication and to maintain a separate, much smaller pool of editors who can be dedicated to the journal and to its standards, and who can discuss the decision with full knowledge of other papers being considered by the journal. This would of course require editors to take responsibility for their decisions and not to hide behind the recommendations of anonymous reviewers.
If we ask reviewers to concentrate on the research, I think it will make the review itself more constructive. When we launched PLoS Biology, I noticed that reviewers often wrote that they were unable to make recommendations because they didn’t know what we wanted to publish, so they had to stick to the strengths and weaknesses of the paper, leaving the editors to decide whether to accept it. Interestingly, authors told us that the reviews from PLoS Biology were among the most constructive they had ever received, even if we decided against publishing the paper. I’ve heard this phenomenon echoed by editors at other new journals, leading me to imagine a day when peer review is uncoupled from journal selection, making the process essentially ‘journal blind’.

Science 2.0: You Say You Want a Revolution?

A nice article in the HHMI Bulletin:

Slowly, however, the culture is changing, not only through blogs but also by means of open notebooks, open publishing, and other interactive models. Those involved call it Science 2.0, an effort to harness the capabilities of the Internet to help scientists communicate better among themselves as well as to the public at large.

Science by press release – you are doing it wrong

And, while on the topic of “Science by press release“, it struck me that announcing intentions of future research is a Good Thing. Isn’t that what we are all talking about – Open Science?
If you signal in advance that you are working on something, you allow others to either move on to something else so as not to duplicate the effort, or to speed up their work in order to scoop you, or to give you a call and offer to collaborate. The second option is likely to be rare and localized in a few research fields that are hugely competitive (e.g., cancer research). The first and the third options are much more likely.
I think the problem is that the researchers are doing it wrong. They are placing those announcements in wrong places using the wrong mechanism. When you go to a press release page of a University, or to Eurekalert or ScienceDaily, you expect to find press releases about the stuff that has been already done and published. The meaning of the word “published” may be completely different in 50 years, but it is not today. So, when you browse press release you expect to find only reports on published work. Seeing that a press release is about work yet to be done in the future is, of course, going to be jarring. Not because it is not nice to know what people are up to, but because they are using a wrong venue to do this – an article about an intention is masquerading as an article about a done deal.
I think researchers and their press officers need to figure out a different method and venue for publishing intentions. A blog?

Reviewing Peer-Review

On the Seed Magazine site…:

ScienceBloggers discuss the advantages of open science and debate the necessity of the current peer-review system.

Nice! But of course I’d say that. Just to emphasize, in case the article does not make it clear enough, Open Access and changes in peer-review will both be a result of the Age of the Web, but the two are not necessarily tied to each other in each individual instance of a publishing venue. Different journals, pre-print sites, etc., are experimenting with OA and with changes in peer-review in different ways and at different rates, the two processes being independent from each other at this stage in history.

Tell Obama administration about Open Access

ObamaCTO (independent of the Obama transition team) is a site for recommending ideas to Obama’s new Chief Technology Officer. You can go and suggest ideas or vote on ideas already there.
I just voted for this suggestion – “Require open access for publicly-funded research”. You should vote for it as well and add a comment if you care about this issue (and I bet most of my readers do).
See also Moving Toward a 21st Century Right-to-Know Agenda: Recommendations to President-elect Obama and Congress, report (pdf)
(via)

RSS Feed aggregators as sources of information and knowledge in medical sciences

RSS Feed aggregators as sources of information and knowledge in medical sciences (in Serbian – PDF) is an excellent article by Vedran Vucic geared towards medical professionals in Serbia. He will talk about this at the Belgrade’s Medical School this Saturday as a part of a symposium on electronic libraries, biomedical information, and Open Access.

John Wilbanks – a Game Changer

My SciBling, John Wilbanks has been interviewed for Seed Magazine’s Game Changers series. Watch the movie:

Seedmagazine.com Revolutionary Minds
John will be at ScienceOnline09, leading a session on Semantic web in science: how to build it, how to use it.
Hat – tip: Kaitlin Thaney (who can also be seen in the movie in the background, sitting at her desk at Science Commons and typing something while John is talking).

The usefulness of commenting on scientific papers

Here is a great example by Cameron Neylon:
It’s a little embarrassing…

…but being straightforward is always the best approach. Since we published our paper in PLoS ONE a few months back I haven’t been as happy as I was about the activity of our Sortase. What this means is that we are now using a higher concentration of the enzyme to do our ligation reactions. They seem to be working well and with high yields, but we need to put in more enzyme. If you don’t understand that don’t worry – just imagine you posted a carefully thought out recipe and then discovered you couldn’t get that same taste again unless you added ten times as much saffron.
None of this prevents the method being useful and doesn’t change the fundamental point of our paper, but if people are following our methods, particularly if they only go to the paper and don’t get in contact, they may run into trouble. Traditionally this would be a problem, and would probably lead to our results being regarded as unreliable. However in our case we can do a simple fix. Because the paper is in PLoS ONE which has some good commenting features, I can add a note to the paper itself, right where we give the concentration of enzyme (scroll down to note 3 in results) that we used. I can also add a note to direct people to where we have put more of our methodology online, at OpenWetWare. As we get more of this work into our online lab notebooks we will also be able to point directly back to example experiments to show how the reaction rate varies, and hopefully in the longer term sort it out. All easily done on the web, but impossible on paper, and in an awful lot (but not all!) of the other journals around.
Or we could just let people find out for themselves…

Yes. If you find out after publication that you need to tweak your experimental protocol, the only place where other people interested in using your technique are guaranteed to find the new information is if it is attached to the paper itself.

Heather Joseph: Getting the message across

There is a very nice interview with Heather Joseph, the Executive Director of the Scholarly Publishing and Academic Resources Coalition (SPARC) about Open Access:

We find that the more policy makers delve into the issue and understand the benefits of the mandate for advancing science and improving public health, the more committed and supportive they become. The roadblocks we’ve run into have been largely the result of misinformation–members of Congress have been told everything from, “the policy will encourage government censorship of science,” to, “the policy will destroy peer review,” to, “the policy will encourage bioterrorism.”
The latest area of confusion has been copyright. Opponents of the policy have long argued that the NIH public access policy conflicts with current U.S. copyright law. However, as leading legal experts have attested, the policy is a contract issue, and does not present a conflict in any way with copyright law (2).
As this became clear, the latest attempt to derail the policy took a new tack–the introduction of proposed legislation to amend current copyright law to make policies such as the NIH’s illegal. The “Fair Copyright in Research Works Act” (HR 6845) would change U.S. Copyright law to forbid agencies like the NIH from conditioning their grants to require public access to the published results of its research. The bill would essentially forbid all government agencies from seeking any rights to the research that they fund, and continue to limit the reach of results to only those who can afford to pay for them.
As with all of the previous attempts to block or reverse the NIH policy, the most effective countermeasure is accurate information. Members of Congress need to understand that researchers want greater access to the work of other researchers, and that they want other researchers to be able to access their results seamlessly as well. They need to know that journals such as the JCB thrive with access policies that do even more than what the NIH policy calls for, and in doing so effectively serve the interests of the scientific community and the public.

Read the whole thing.

Why silence?

Because I spent the day here having great fun.

Genome Technology – Open Access Special

Today’s issue of Genome Technology contains six nice articles about Open Access:
Ready or Not, Here Comes Open Access:

Here’s the central conundrum of the open access debate: you can’t find anyone who’s actually opposed to it. Really. For all the grandstanding and arguing, the fiercest opponents and supporters alike tend to support the underlying principle — that freely accessible data would be a boon to the greater scientific enterprise. In an ideal world, most everyone agrees, there would be no restrictions on scientific results. It’s the real-world practical concerns that provide the point of contention.

Open Access: What Does It All Mean?:

The pure form of open access is considered research that’s made freely available for reuse in any way another scientist might dream up. In general, as long as the original author is credited for what’s his, any other scientist can add to the work with no strings attached.

Many Flavors of Open Access:

When people refer to open access journals, there are actually a number of different models that they have in mind. Nick Fowler, head of strategy at Elsevier, breaks them down into the four main flavors.

An Acquisition, an Association, and a Celebration:

In the past month alone, the movement for open access saw a number of milestones. For starters, the group celebrated its first holiday — Open Access Day was held on October 14, with a number of organizations taking note of the occasion. Community bloggers made a special effort to raise awareness for the concept, releasing essays, videos, and other materials to introduce unfamiliar scientists to it.

PubMed Central: The ‘Mildly Destabilizing’ Compromise:

PubMed Central has become a critical component of the scientific research landscape, but 10 years ago it was just a gleam in Harold Varmus’s eye. Originally conceived as E-Biomed, the vision was far more broad-reaching than what eventually became PubMed. “The original idea for PubMed Central was probably too radical,” Varmus says. “I probably went too far initially.”

Reluctant Publishers and the Birth of PLoS:

Pat Brown, Michael Eisen, and Harold Varmus have become the face of the Public Library of Science, but none of them ever set out to be a publisher.

[Hat-tip: Michael Eisen]

Roosevelts on Toilets

Poop%20on%20the%20Potty.jpg
If you are wondering why I posted this picture and what it all (including the title of this post) means, you need to read the comment threads on these posts:
The Transition to Daylight Savings Time and the Risk of Myocardial Infarction
The Response from Janszky and Ljung — Dr. Isis Defends the Blogosphere
What is ‘the normal way to debate and discuss scientific findings’ anyway?
Spring Forward, Fall Back – should you watch out tomorrow morning?
Notes of importance
Bora is the Most Brilliant Man Ever and I Love Him
Pseudonimity, scientific criticism and respect on the blogs…
Discourse give me hives
The Pseudonymity Laboratory: When Authors and Bloggers Collide
Letter to the Editor as a mechanism of post-publication scientific discussion
Cadres vertueux
Update – there’s more:
On Caricature
Getting the roles of blogs and journals straight
Bring in da light, bring in da snark
On the Need for Women to Defend Women in Science…

Low-Hanging Fruit

Low-Hanging Fruit is a website which collects data about drug/compound screens against parasitic organisms.
Michelle Arkin and James McKerrow explain:

The apples on the tree at the website represent links to data for the parasites indicated. In some cases, this data is a simple list of hits to be viewed by those individuals and agencies interested in rapid follow-up. In other instances, a more complete database can be accessed under “protocols and statistics” as compiled by Pipeline Pilot (Accelrys) software.

Are you still struggling with EndNote? How quaint….

Duncan Hull and colleagues just published an excellent, must-read article – Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web:

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

The paper goes through each of the services, one by one, explains the pros and cons of each, and makes suggestions for the future development, as well as pointing out barriers and possible ways to overcome those. A couple of listed services are almost there – but are you using them? If so, why? If not, why not?

In today’s ‘Guardian’

Web journals ‘narrowing study’ by Linda Nordling:

Online publishing has sparked an explosion in the number of places where academics can showcase their work. Today, no field of study is too obscure to have its own dedicated title. But have platforms such as the Journal of Happiness Studies or Archaeoastronomy and Ethnoastronomy News made academic publishing more democratic?
Far from it, says Alex Bentley, an anthropologist at Durham University. “We’re just producing so much wordage that nobody has time to read anything. It makes academic publishing, and even science itself, a bit like trying to get hits on blogs or try to make yourself the Britney of science.”
Although the internet puts information at our fingertips, we have no time to trawl it. As a result, we trust sites like Digg.com to guide us through the information jungle. This phenomenon is called “herding” by economists, who use it to explain, say, fashion trends and stockmarket bubbles.
————snip—————–
SEO can, however, make articles tedious to read. A headline that once read “Of mice and men” for a study that discussed the suitability of mice when testing drugs for humans might now say “Suitability of mice for in vivo drug testing” or something even more jargon-laden.
But those who fear an end to eloquence in research articles should stop worrying, says Bora Zivkovic, community manager at open access publisher PLoS One and author of the blog Around the Clock (http://scienceblogs.com/clock). According to him, today’s dull SEO writing is a passing phase. The open access movement will tear down the walls between academic publishing and the rest of the internet, making eye-catching titles not only optional but downright necessary.
Better searching
“Titles that go ‘the effect of x and y is z’ are perfect for machines right now, but the machines are getting better and advances in technology will mean that search engines are going to find the important keywords in the text,” he says. But catchy titles and readable writing will be necessary to draw in lay people, journalists and bloggers, who will have a much bigger role in determining what research is read. “Google loves blogs, so if your work is being blogged about, it will generate interest in your paper.”
“Google Scholar initially wasn’t very good, but now it is,” he adds. “It covers more of the literature than Web of Science [another, older academic search engine].” However, the big difference about Google Scholar is that you don’t have to be a rocket scientist to use it, he says. It is intuitive and will lead you to a free version of an article if one exists.
As search engines get more sophisticated, the technology will hopefully result in better ways of measuring research quality, says Bentley. “Citations have always been important. But they have never been as ridiculously important as they are now,” he says. “I think that people are recognising this and that we will see more evaluation mechanisms that are based on actually reading the articles.”

Lawrence Lessig for Copyright Czar!

Peter Suber, James Love and Glyn Moody have already blogged about this, but we need to make sure this spreads far and wide:

The AAP and Copyright Alliance want to prod the next President of the US to tilt the unbalanced US copyright law further toward publishers. According to a letter the AAP sent to its members (thanks to James Love and Glyn Moody), the two organizations are trying to identify the positions “that will influence intellectual property policy”, and will then “offer suggestions regarding appropriate candidates for these positions to both presidential campaigns.”
But first they want to blackball one potential nominee:
…AAP is concerned, for example, that based on their past academic relationship, Senator Obama might choose among his appointments a divisive figure such as Larry Lessig – a law professor and leading proponent of diminished copyright rights….

Yup, those are the PRISM arguments – black is white, up is down, and Lessig is anti-copyright!@#$%^&*
So, how can we help push Lessig to get appointed Copyright Czar in the Obama administration? After all, nobody in the world knows more about it than him and he would be a perfect person for the job.

Publishing and Communicating Science

The W. M. Keck Center for Behavioral Biology at North Carolina State University (which includes students, faculty and staff from Departments of Biology (formerly Zoology, my own Department), Genetics and Entomology) is a group I called home for a large chunk of my own graduate experience. Every year, on top of monthly discussion meetings for members, they organize other interesting events, including this one, coming up in two weeks:

The W. M. Keck Center for Behavioral Biology at North Carolina State University announces its 2008 Professional Development Workshop:
Publishing and Communicating Science
Orli Bahcall, Senior Editor of Nature Genetics: The Nature of Scientific Publishing
Peter Binfield, Managing Editor of PLoS ONE: PLoS ONE-Leading a Transformation in Academic Publishing?
John Rennie, Editor-in-Chief of Scientific American: How and Why Scientists Should Talk to the Public
Joe Palca, Science Correspondent for National Public Radio: How Much Can You Say in Three Minutes?
Saturday, November 8, 2008
8:30 am – 3:00 pm
Sigma Xi Conference Center, RTP
****registration required****
A registration fee of $20 is required. Registration after the deadline is $40. Payment by check only, made out to “NC Agricultural Foundation”.
The registration fee includes breakfast, served at 8:30 am, and a box lunch, and is non-refundable.

For more information, check the flyer. I’ll be there….

Clay Shirky: It’s Not Information Overload. It’s Filter Failure.

OADay winner: My Father the Anthropologist; or, What I Offer Open Access and Why

Here is the other one of the two winning posts in the Open Access Day blogging competition: My Father the Anthropologist; or, What I Offer Open Access and Why by Dorothea Salo:
In 1980 or thereabouts–I was eight or nine–my father the anthropologist started yet another rant about serials cancellations at his university’s library while he drove the family somewhere in the family car. He thought the problem an artifact of library underfunding, I remember. I don’t recall that he ever did anything about it save rail bitterly on the subject to us, his captive, powerless, and resentful audience.
At the inaugural meeting of the Open eBook Forum in 2000, David Ornstein and Janina Sajka explained what they hoped electronic books would accomplish. Amid the faux-visionary fluff and the crass dollar signs, one hope they expressed made me vibrate: that for the first time, a visually-impaired person would be able to walk into Borders or Barnes & Noble and buy a book off the shelf just like anyone else.
Access to human knowledge and creativity. Access for the wrongly disenfranchised. Access. I loved markup, I loved text, I loved design, I loved standards work–but then and afterward, it was the access argument that kept me engaged with electronic books. My father the anthropologist, his own eyes not what they had been, understood and endorsed that argument at once.
I certainly know how reassuring accurate, authoritative medical information can be. When my father the anthropologist went to the hospital for bypass surgery, I looked for every scrap of reliable information I could find about what he’d have to go through, what his chances were, what would happen afterwards. Information is hope for helpless bystanders.
I know what information gaps mean to the efficacy of medical care, too. I started my quest to treat my repetitive stress injury when my hands and wrists hurt so badly I couldn’t sleep some nights, nor survive a day’s work without severe pain. The open web, obvious misinformation aside, contained little more than nonsensical and insulting condemnations of RSI sufferers as malingerers, as well as blatant advertising of invasive surgery on the websites of orthopedic surgeons.
My primary-care physician insisted on old-fashioned treatment modalities before she would refer me anywhere. I paid for and endured weeks of wrist braces that I knew would not relieve my pain because I had tried them, as well as a tennis-elbow strap that left me in such agony that I refused to put up with it longer than a day. I did achieve a referral at last, and physical therapy turned out to be the right treatment. As I healed, the new search skills I was acquiring in library school, along with the access that being a student entitled me to, helped me discover that the medical literature understood why my doctor’s initial recommendations had been wrong. Why did I waste time, money, and pain over my inability to produce reliable information to assist my medical provider in treating me appropriately?
I can only be glad I wasn’t suffering from anything life-threatening, like artery blockage.
I was slotted into an online course in “Virtual Collection Development,” taught with patient lucidity by Jane Pearlmutter, my first semester in library school. Among the readings was “The Librarians’ Dilemma: Contemplating the Costs of the ‘Big Deal’‘” by the University of Wisconsin’s own Ken Frazier. There it was again, this problem of serials cancellations, framed in terms so transparently sensible that I could only exult.
Later in the semester came a unit on open access. It would be nice to say that lightning struck and I knew that was what I wanted to do with my professional life, but it didn’t and I didn’t. Of course I was intrigued; I knew several for-profit journal publishers from the worm’s-eye view of an erstwhile lowly data-conversion peasant. I wove the complaints I remembered from my father the anthropologist, my own experience in scholarly publishing, and what I learned in class into a rich, detailed mental tapestry, and I felt real hope that open access was an answer I could take back to him that he would understand and appreciate. Discovering that I would shortly join the profession backing open access only confirmed that library school was the right choice for me, even should I not work in the open-access niche myself.
When I landed my first library position just after graduating, I called my father the anthropologist. His first question was “How much will you be paid?” I declined answering. His second question was “What’s your title?”
“Digital Repository Services Librarian,” I said, with pride and no little amusement.
On the other end of the line, a lengthy silence.
My father the anthropologist used to buy lab equipment out of his own pocket, rather than struggle with byzantine university purchasing procedures and skeptical departmental scrutiny. Rightly or wrongly, he was convinced no one would understand or support him and his work, but he refused to knuckle under. He would do what it took, spend what he had to, to further the research he fervently believed in.
I have bought quite a bit out of my own pocket too, rather than charge it to the libraries that have employed me. I have bought color inkjet printers, various sorts of expensive paper for brochures and bookmarks and whatnot, and poster printing. I have bought software that I use for work-related purposes. Once I bought an expensive print run of a color brochure because an opportunity came up to distribute a lot at once so suddenly that I didn’t have time to print and fold them myself as I usually did. I bought a cross-country trip to an important repository conference when I was de facto between jobs. I bought a laptop on which I do repository-related work when the occasion warrants. I have bought buttons with images of Mars on them, because when you’re handed a golden acronym you might as well make the most of it. Like as not the libraries I have worked in would have paid for some or all of this–I never asked.
I have read, written, rewritten, commented, and debugged code in Java, Python, and XSLT. I have tweaked JSPs, murdered unnecessary HTML tables, and rewritten CSS designs from the ground up, swearing sulfurously at various versions of Internet Explorer. I have edited metadata in XML by hand. I have translated Endnote records into Dublin Core. I have screenscraped ugly HTML and cudgeled it into legible metadata. I have screenscraped yet more ugly HTML for transformation into preservation-worthy markup. I have built convoluted SQL queries slowly and carefully from the inside out, run them on production databases with fear and trepidation, and once or twice cleaned up after them when I’ve gotten them wrong. I have typed cargo-cult incantations at command lines to keep server software running and upgraded, and raked Google for answers when some incantations didn’t work as promised.
I have stared at lengthy CVs with a sigh, and then waded resolutely in to clear rights on as many of the publications as I could. I have searched SHERPA/RoMEO and Bowker’s Books in Print. I have hunted down agreements from publisher websites. I have asked faculty for their copyright-transfer-agreement files, and tried not to let my smile grow too pained when they told me they don’t keep such things. I have explained the difference between preprints, postprints, and publisher PDFs to politely incredulous auditors. I have read scads of legalese, and interpreted it as best I could. I have read and pondered the words of librarians and lawyers who understand the legal fine points much better than I. I have made some risky calls, likely some wrong ones. I haven’t been called on the carpet for them… yet.
I have held one-on-one meetings and demo sessions with faculty and librarians. I have designed and produced brochures, flyers, slideshows, posters, web pages, wiki pages, and one mini-movie. I have presented at innumerable campus expos, showcases, lectures, symposia, conferences, and workshops. I have called and written my elected representatives. I have blogged. I have written articles and self-archived them, sometimes after polite and fruitful discussions with publishers. I have run any number of failed efforts toward building a community of practice among repository managers, each new attempt the triumph of hope over experience. I have cold-called librarians, faculty, department chairs, deans, and administrators. I have been to more meetings than ought to fit in the three years I’ve been doing this.
You needn’t be obsessed like my father the anthropologist and me. Believe me, that’s the last thing I’d recommend to anyone. If you cannot find even one thing you can do in the above list, though, I wonder about you.
I once explained to a pleasant elderly faculty member that the repository didn’t easily allow changes. “It’s like a roach motel,” I said. “Files go in, but they don’t go out. Once they’re there, they’re stuck.” Suppressed chuckles from librarians in nearby cubicles greeted that statement, and I returned from ushering the faculty member out to find that my colleagues had good-humoredly dubbed me the Innkeeper at the Roach Motel.
I loved the sobriquet, despite the unhappy truth of its depiction of institutional repositories. I have never liked telling faculty members that my services couldn’t do what they needed, and I’ve had to tell them that often and often. Worst of all, I couldn’t envision my services as anything my father the anthropologist would find useful, compelling, or even comprehensible; the promise of green open access was fading fast in the unforgiving floodlights of faculty diffidence. I looked around the open-access community for understanding and a path forward, but I found little to help or reassure me.
My father the anthropologist and I are alike in one way at least: we don’t suffer fruitless systems in silence. In one way at least, we are different: I cannot content myself with complaining to the powerless and uninvolved.
I don’t think there’s a community I operate in that my gadfly ways haven’t irked or even alienated. My library school. My librarian colleagues. DSpace developers. Green open access. Library bloggers. The DSpace Foundation. Library coders. Repository managers. The open-access community in general. While I accept all this as the price gadflies pay for being pests, it is no source of pride, nor is it pleasant. I have feared for my job, and like as not I deserve to. I have feared that the career I find myself in will not exist in five years’ time, and I have wondered uneasily whether my own behavior has hastened rather than forestalled that eventuality. I have been cautioned, questioned, belittled, berated, cut down to size in public, stepped cautiously away from, set up as homo stramineus, misquoted, deliberately or carelessly ignored–and much of it I have richly earned.
I have also been heeded. I have also made change. Not much, perhaps; certainly not all the change I wanted to make, wanted to show my father the anthropologist, wanted to offer the world. Even so, change is my gift to them and to you: my gift I offer in my much-abused hands on this Open Access Day.

OADay winner: A poem for Open Access Day

Here is one of the two winning posts in the Open Access Day blogging competition. A poem by Greg Laden:
A poem for Open Access Day
Open Access Day

They said:

“if you publish
in an open forum
your paper’d be rubbish
and clearly hokum”

“pub’s commercial know
how to review with the peerage,
how to make data flow
and hurdles clearage”

“limited space on the page
with every new edition
so few make the passage,
it’s editorial selection!”

“we have always done
and it’s never been changed
the readers we dunn
and the paper’s in chains”

“what is ought to be
why change it now
it is so plain to see
must limit the flow”

But in, PLoS chimed,
and challenged that dragon
everyone joined
and the boycott was on

“The authors we’ll dunn
when funding provides
we’ll have much more fun
when all readers can chide”

“the new Open Access
to everyone’s work
can be the new praxis
and everyone’s perk”

“with the previous method
the work was all gratis
publishers prod
to maintain their status”

“the cash it did flow
to the publishers coffers
we were covered with snow
from ingenuous offers”

“It’s all in the model
be it business or open
pub’s whine and they yodel
but their way is broken”

“Open Access is true
for me and for you
the pub’s they be blue
but it’s now, and it’s new”

“they can keep their closed access
and journals galore
but we’ve a new process
that we’ll use ever more. “

*
Open access matters to me because it is one of the pillars of the new world of the 21st century. It is the democratization of information. I’ve been aware of Open Access since before it existed, as I’ve always thought this is how it should be done. Research should be provided in an Open Access format (with no or only very minimal delays) because we expect society to support, through government, private funding, and free-riding on corporate profits, this research. It is not our research. To support Open Access, I blog about it, and my next paper will be submitted to an Open Access journal.
Gotta go …. need to work on paper…

And the Winner is…..!

The Open Access Day blogging competition is now over. We received over 40 excellent entries that took quite a nice chunk of last night to read – they are all good so go and read them all.
In the end, we decided that one prize is not enough and are awarding the First Place to two bloggers:
Dorothea Salo, for her post: My Father the Anthropologist; or, What I Offer Open Access and Why (already cross-posted on the PloS Blog and soon will be posted here and a couple of other places). Dorothea is the Digital Repository Librarian at the University of Wisconsin, where she serves the state university system’s consortial institutional repository, MINDS@UW.
Greg Laden for A poem for Open Access Day. Also, the cross-posts will happen very soon (the first one, on the PLoS Blog is here). Greg is a SciBling, an archaeologist and anthropologist, and a part time independent scholar and part time adviser with the Program for Individualized Learning, University of Minnesota.
Congratulations to the winners, and congratulations to all the contestants for a great day of synchroblogging!

Open Access Day – the videos 4

Voices of Open Access from Open Access Videos on Vimeo.

Open Access Day – the blog posts

As you know, blog posts about Open Access – What It Means To Me? are in competition today! I will be posting and updating the links of entries throughout the day (until midnight Eastern) for all to see – if I miss yours, send me the URL of your entry.
Caveat Lector: My Father the Anthropologist; or, What I Offer Open Access and Why
Greg Laden’s blog: A poem for Open Access Day
A k8, a cat, a mission: Open Access Day
Laelaps: Happy Open Access Day!
Moneduloides: Why Does Open Access Matter To You?
Stuff: Open Access Day – How are we sharing our knowledge?
The Parachute: Open Access Day
RepositoryMan: A Present for Open Access Day!
Plausible Accuracy: What Open Access Means to Me
Science in the open: Where does Open Access stop and ‘just doing good science’ begin?
Open Access, Freedom Space: Open Access, from form to content
McBlawg: Why I am an OA Advocate
What You’re Doing Is Rather Desperate: Open Access Day
Humans in Science: Open access day – redux
O’Really? at Duncan.Hull.name: Open Access Day: Why It Matters
Library Lines Online: Open Access Day
bbgm: Open Access and me
The Sciphu Weblog: The Likes of Blog Publishing (Open Access Day 08 entry)
Digital Serendipities: The first international Open Access day
Freelancing science: Open Access Day
Glyn Moody: Celebrating Open Access (Day)
I was lost but now I live here: Happy Open Access Day!
Semantic Library: Happy Open Access Day!
WAYS | Science, Remixed: Open Access is an important step on the way towards open science
Publishing Archaeology: Open Access Day
NY Adventure Blog: Open Access Day
Science Librarian Notes: Open Access Day
Walt at Random: Open access: A quick post
DarkRepository: What Open Access means to me
Just Browsing: Open Access Day
The RePEc blog: October 14, 2008, Open Access Day
Common Knowledge: Happy Open Access Day…
The Imaginary Journal of Poetic Economics: Why Open Access Matters to Me (Open Access Day Synchroblogging)
Confessions of a Science Librarian: Open Access Day: OA & me
Gobbledygook: Open Access – what’s in it for me?
Fuzzier Logic: Open Access Day
Uncommon Ground: Open Access Day
Ouroboros: Open Access Day
Pimm – Partial immortalization: For your free information (FYFI): it’s Open Access Day!
Isayev.info: October 14: Open Access Day
Stuff To Do In NC: Learn about open access
Social Life of Information: Open Access Day
Filipino librarian: Open Access Day 2008

Open Access Day – the videos 3

Diane Graves, Librarian from Open Access Videos on Vimeo.

Open Access Day – the videos 2

Sharon Terry, Patient Advocate from Open Access Videos on Vimeo.

Open Access Day – the videos

Tomorrow is the Open Access Day and today you can watch the videos, like this one, for example:

Barbara Stebbins, Middle School Science Teacher from Open Access Videos on Vimeo.

Why does Open Access matter to you? A blogging contest

Open Access Day is on October 14th (don’t tell me I did not warn you in advance!). The day will be marked with lots of events, online and offline (if you are local, you may choose to go to Duke, for instance) so watch my blog for more information on Tuesday.
What you as a blogger will probably be most interested in is the Blogging Contest!
How does it work? Well, you are all supposed to synchroblog on Tuesday (but NOT before) on the topic:”Why does Open Access matter to me?”
Write a post and publish it on October 14th, and you will be entered in the competition and you can win a bag of swag, e.g., a one-year print subscription to Seed magazine, a PLoS travel mug, a couple of cool PLoS t-shirts and other items, plus your post will be cross-posted to the blogs where the judges blog.
And the judges will be:
Liz Allen – Head of PLoS Communications
Aaron Rowe – blogger on Wired Science
and, well, yours truly… 😉
As Liz says:

On October 14, 2008, wherever in the world you live, we want you to tell everyone why Open Access Matters to you in celebration of the first ever Open Access Day. We want the cumulative effect of all these posts to show the blogosphere how Open Access touches the lives of many many people. Apparently, experts tell me that this activity is known as synchroblogging.

So, what are the rules of engagement? Not that it is easy to get bloggers to follow any kind of rulz, but here they are, try to follow them the best you can:

There are 4 key points that we would like you to address in your post (these are the same questions that we asked the stars of the Voices of Open Access Video Series that we will also release on that day):
* Why does Open Access matter to you?
* How did you first become aware of it?
* Why should scientific and medical research be an open-access resource for the world?
* What do you do to support Open Access, and what can others do?
To enter the competition, all you have to do is blog on this topic on October 14, 2008. We’ll use Google News/Technorati to track entries – to make this easier please use the phrase “Open Access Day” in your post. We’ve assembled a small team of judges who will review all these posts and vote on a winner. The winning post will have their entry cross posted on some or all of the sites where the judges blog on October 14h or thereabouts depending on space and other deadlines.

If your blog is very new, or on an unusual platform, so you are not sure that either Google Blogsearch or Technorati will pick up your post with the keywords “open access day”, please e-mail me the Permalink of your October 14th entry, or just drop it in the comments of this post.

Springer buys BMC

Open access publisher BioMed Central sold to Springer:

Those in the open access movement had watched BioMed Central with keen interest. Founded in 2000, it was the first for-profit open access publisher and advocates feared that when the company was sold, its approach might change. But Cockerill assured editors that a BMC board of trustees “will continue to safeguard BioMed Central’s open access policy in the future.” Springer “has been notable…for its willingness to experiment with open access publishing,” Cockerill said in a release circulated with the email to editors.

Wikipedia, just like an Organism: clock genes wiki pages

ResearchBlogging.orgThe October issue of the Journal of Biological Rhythms came in late last week – the only scientific journal I get in hard-copy these days. Along with several other interesting articles, one that immediately drew my attention was Clock Gene Wikis Available: Join the ‘Long Tail’ by John B. Hogenesch and Andrew I. Su (J Biol Rhythms 2008 23: 456-457.), especially since John Hogenesh and I talked about it in May at the SRBR meeting.
Now some of you may be quick to make a connection between this article and its author Andrew Su and A Gene Wiki for Community Annotation of Gene Function, published in PLoS Biology back in July, where one of the authors is also Andrew Su. And you would be right – it’s the same person and the two articles are quite related.
In the PLoS Biology article, they write:

A loose organization of Wikipedia editors has spearheaded the creation and expansion of several thousand articles related to molecular and cellular biology (the “MCB Wikiproject”), including many gene-specific pages. These articles vary widely in quality, format, and completeness, ranging from relatively complete encyclopedic entries (e.g., “enzyme,” “oxidative phosphorylation,” and “RNA interference”) to very short collections of information called “stubs” (e.g., “amphinase” and “glomus cell”). As an example of the collaborative writing process, the article on RNAi has been edited 708 times by 232 unique editors since its initial creation in October 2002. On the subject of human genes, generally only the most well-characterized of genes and proteins have highly developed entries (e.g., “HSP90” and “NF- B”).
In principle, a comprehensive gene wiki could have naturally evolved out of the existing Wikipedia framework, and as described above, the beginnings of this process were already underway. However, we hypothesized that growth could be greatly accelerated by systematic creation of gene page stubs, each of which would contain a basal level of gene annotation harvested from authoritative sources. Here we describe an effort to automatically create such a foundation for a comprehensive gene wiki. Moreover, we demonstrate that this effort has begun the positive-feedback loop between readers, contributors, and page utility, which will promote its long-term success.

In the JBR paper, the authors focus on the development of Wikipedia pages describing genes involved in circadian rhythms, probably the first genes to be done comprehensively there, as an example for others as to how to do this kind of thing:

Why use Wikipedia for this? First, Google and Wikipedia have already become scientific research tools. When you Google an unfamiliar gene you usually end up at common sites of gene annotation such as the National Center for Biotechnology Information. Though these sites have expert curators who do the best they can, they are usually not domain experts and are so overloaded that they frequently fall behind in accurately summarizing the literature. (It’s actually amazing what they accomplish given available resources.) For confirmation, research your favorite gene. Using Wikipedia will allow our community to build and evolve living, up-to-date summaries on the function of important genes in the circadian network. Check out the pages on Arntl (http://en.wikipedia.org/wiki/ARNTL) and Rev-erb-alpha (http://en.wikipedia.org/wiki/Rev-ErbA_alpha). Second, in part due to Wikipedia’s past success, its pages appear near the top of search engine lists such as Google, and consequently attract viewers. Finally, our field competes with other disciplines for the best and the brightest young scientists. These people use Wikipedia. High quality pages on annotated clock genes will attract their attention, and attract them to our field.

Importantly, the gene pages need not be extremely long. What is much more important is that they be well referenced. See, for instance Wikipedia pages they mention, those for ARNTL gene (also known as Bmal1 or Mop3), or Rev-ErbA alpha (I have written about some of these genes before, e.g., Lithium, Circadian Clocks and Bipolar Disorder, Tau Mutation in Context and The Lark-Mouse and the Prometheus-Mouse if you want more background). That is all that is needed – if I wanted to be silly, I could say that since genes are small, their wiki pages need to be small as well. But that is only half-silly, really.
This is just like in the real world. Genes don’t really do anything. They are coded descriptions of parts in a catalog. To explain a biological function, one needs to go from genes to their mRNAs to proteins, then to look at protein modifications and how multiple proteins interact with each other. Then see how such protein interactions affect the behavior of a cell. Then see how the altered behavior of a cell affects the entire tissue and how the changes in that tissue affect distant organs. Finally, one gets to explain the function once one understands how a collection of organs, interacting with the external environment, results in changes in biochemistry, development, physiology or behavior of the organism, and how this function evolved.
In the same way, gene pages on Wikipedia are not supposed to be stand-alone. Knowing everything about a clock gene does not mean one knows anything about circadian rhythm generation and modulation (not to mention its evolution). The value is in links – to all the other clock genes, to genes that do similar things (e.g., other transcription factors or nuclear receptors), to primary literature on the proteins coded by these genes and their interactions, and to higher-level functions, e.g., the Circadian Rhythms page and links within.
Some would ask – Why Wikipedia (I know, there are still some people out there who don’t like it):

What’s the downside? The major criticism is poor annotation. Actually, we argue that no annotation is worse than poor annotation, as the latter tends towards self-correction by provoking experts to intervene. In fact, a recent study concluded that Wikipedia was as accurate as Encyclopedia Britannica, and unlike Britannica, growing at a rate of 1500 articles per day (Giles, 2006). Another potential downside is non-consensual or controversial entries. We would argue that these are better addressed in real time via Wikipedia than in journal articles, where they remain fixed for years. Wikipedia even has tools to deal with controversial topics (for examples, see entries on “Intelligent Design,” evolution, “Swift-boating,” or climate change).

And, I’d argue, clock gene pages are not as contentious as those on climate change or creationism. Very few Wikipedia pages are so controversial as to be continuously suspect. Almost all of the pages are on non-controversial subjects, written and edited by experts on the topic, and are as reliable, or better, as anything else one can find out there, not to mention the fastest to get updated once new information comes in.
The effort is starting with the focus on mammalian genes, for obvious reasons of medical relevance and the existence of a wealth of information. But there is just as much, if not more, information on Drosophila clock genes. And comparative analysis of clock-genes in a variety of organisms is the key to understanding the circadian function and its evolution, so if your strength is in other old or emerging model organisms (did you see Japanese quail on that list?!), don’t hesitate to add the pages and information on those.
Finally, I’d like to urge you to contribute – I know that many chronobiologists read this blog (though most are silent types who never comment). It will take 30-60 minutes of your time to make or edit a page on the gene (or a higher-level process) in circadian biology and this effort will have much bigger audience and much broader impact than all of your peer-reviewed papers put together. It’s worth your time even if probably will have no effect on your getting tenure. But the tenure committee is not your only audience – there are researchers around the world (many in developing countries), teachers and students and lay audience, who will be affected by your contribution in a much more lasting and important ways than the inner circle of your department. Isn’t this why you are doing science in the first place?
If you want to discuss this more, come to ScienceOnline09, where John Hogenesh, one of the authors of the JBR article, will demonstrate Wiki Genes, answer questions, and deeply internalize your suggestions 😉
References:
John B. Hogenesch and Andrew I. Su, Clock Gene Wikis Available: Join the ‘Long Tail’, J Biol Rhythms 2008 23: 456-457.
Jon W. Huss, Camilo Orozco, James Goodale, Chunlei Wu, Serge Batalov, Tim J. Vickers, Faramarz Valafar, Andrew I. Su (2008). A Gene Wiki for Community Annotation of Gene Function PLoS Biology, 6 (7) DOI: 10.1371/journal.pbio.0060175