Category Archives: Science Practice

Join the North Carolina group on Nature Network

Remember a couple of weeks ago, when I complained that Triangle is too narrow a term for a Hub at Nature Network, as there is really no humongous city where everything is centered but the science is distributed all around the state of North Carolina, with people collaborating with each other and traveling back and forth between various regions of the state.
Well, now, to reflect that situation, the Triangle group on Nature Network was renamed the North Carolina group. If it grows in size, it may one day become a proper Hub. So, if you are in any way interested in science and live anywhere in the state of North Carolina, please register and check North Carolina as your geographical location and group.

Let’s meet in New York City next week

I will be on a panel, Open Science: Good For Research, Good For Researchers? next week, February 19th (3:00 to 5:00 pm EST at Columbia University, Morningside Campus, Shapiro CEPSR Building, Davis Auditorium). I am sure my hosts will organize something for us that day before and/or after the event, but Mrs.Coturnix and I will be there a couple of days longer. So, I think we should have a meetup – for Overlords, SciBlings, Nature Networkers, independent bloggers, readers and fans 😉
Is Friday evening a good time for this? Or is Saturday better? Let me know.
You can follow the panel on Twitter or Facebook (I am not sure, but the panel may be recorded in some way and subsequently made available online – will check on that), or, if you can, show up in person. More information can be found here:

Open science refers to information-sharing among researchers, and encompasses a number of initiatives to remove access barriers to data and published papers and to use digital technology to more efficiently disseminate research results. Advocates for this approach argue that openly sharing information among researchers is fundamental to good science, speeds the progress of research, and increases recognition of researchers. The panel will discuss frequently raised questions such as “Can open science practices work for researchers who need to establish priority of publication to advance their careers?” and “Is open science compatible with peer review?”

‘The Art and Politics of Science’ – Harold Varmus on NPR Science Friday

That was last week, but I had no time to listen until now – check out the podcast (in the upper left corner of the page):

In 1989, Dr. Harold Varmus won a Nobel Prize for his cancer research. He was director of the National Institutes of Health during the Clinton administration, and now heads the Memorial Sloan-Kettering Cancer Center. Recently, President Obama named him to co-chair his Council of Advisers on Science and Technology. And he’s written a new book, “The Art and Politics of Science.” In this segment, Ira talks with Harold Varmus about his work, biological research, and the intersection between politics and science.

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.

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.
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.

Of researches and publishability…

Kausik Datta asks:

There may be someone among us who has had this happen to him or her at some point or other: You embark on a new project in uncharted territories with gusto, your goal being gathering preliminary data that would aid generation of a hypothesis. You get data, analyze trends, feel excited, write it up and send it to YFJ (your favorite journal) – and the journal rejects it, saying, variously, “the scope of the study does not suit this journal”, “the data presented are too preliminary”, or the devastating “the research contains no novel finding”.
On another side, you want to work on a problem that you find sufficiently interesting, given, say, your observations in a smaller, restricted cohort. You are scouring through PubMed or Google Scholar for related, descriptive studies that define the problem beyond mere anecdotes. You find zilch, zippo.

Ignorance, arrogance or scientific fraud?

Bob Grant, over on The Scientist’s blog, describes a recent kerfuffle over a Cell paper and what it says about peer-review. The 40 comments on the post are already there with some interesting additional perspectives:

Improper citation, disregard for antecedent research, and shoddy experimentation – those are just a few of the allegations levied against a recent research paper written by a team of Stanford University scientists.
One of the paper’s chief critics, University of Cambridge biologist Peter Lawrence, says that the problems with the publication exemplify a broader problem in scientific publishing.
“There’s a pressure on scientists to publish in these top journals,” Lawrence told The Scientist, “to promote their work as more novel than it really is.”
The paper in question, published in a June issue of Cell, described a model for understanding the genetic and cellular machinery underlying planar cell polarity (PCP), the cell-to-cell communication that epithelial cells use to align and arrange themselves to function as an organized tissue….

Janet discusses the ethics of the whole episode:

Do scientists see themselves, like Isaac Newton, building new knowledge by standing on the shoulders of giants? Or are they most interested in securing their own position in the scientific conversation by stepping on the feet, backs, and heads of other scientists in their community? Indeed, are some of them willfully ignorant about the extent to which their knowledge is build on someone else’s foundations?

Thought-provoking stuff….

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….

Advice on designing scientific posters

This one is good and thorough – by Colin Purrington, Department of Biology, Swarthmore College. Short excerpt from the beginning:

Why a poster is usually better than a talk
Although you could communicate all of the above via a 15-minute talk at the same meeting, presenting a poster allows you to more personally interact with the people who are interested in your research, and can reach people who might not be in your specific field of research. Posters are more efficient than a talk because they can be viewed even while you are off napping, and especially desirable if you are terrible at giving talks. And once you have produced a poster, you can easily take it to other conferences. If you don’t like to travel far, or are broke, many college and university science departments sponsor poster sessions that welcome students from nearby institutions. For all of the above, session organizers typically have a “Best Poster Prize Committee,” which awards fame and often cold hard cash to deserving posters. And when you’re ready to retire your poster from active duty, you can hang it in your dorm room to impress your friends, or display it in your departmental hallway so that faculty can show off your hard work to visitors for years to come. You can also submit your final product to, which promises to keep a PDF version of your poster in perpetuity (for free) and allows people to send you comments about your poster.

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.

Three reasons to distrust microarray results

From Reproducible Ideas:

Even when lab work and statistical analysis carried out perfectly, microarray experiment conclusions have a high probability of being incorrect for probabilistic reasons. Of course lab work and statistical analysis are not carried out perfectly. I went to a talk earlier this week that demonstrated reproducibility problems coming both from the wet lab and from the statistical analysis.

Continue the discussion here….

Impact Factor

Yesterday’s PhD comic strip:
We still have ways to go until we get it right….

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.
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 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.

A Modest Proposal

Tom Levenson has an interesting idea:
A Modest Proposal: A Science Initiative for the Obama Administration

But I’d like to lay down one relatively cheap marker that would, I think, have a significant impact on both the culture and the productivity of American scientific research to a degree disproportionate to the underlying amount of dollars. It’s not a new idea, and hardly original to me -but seeing as it has been completely out of court for almost a decade, I think it bears repeating, even if it is old news to veterans of the business.

More on a Modest Proposal

In this post, I laid out a first marker for what the new administration could do for science, calling for an expansion of support for young scientists and engineers — grad students, post docs and new principal investigators.
For the new PIs, I suggested an increase in the number and shift in the emphasis of what are now called Faculty Early Career Development Program grants, arguing that the availability of no-strings attached discretionary research funds for young scholars would have a disproportionate bang for the buck.

Read both posts (and comments) in their entirety. What do you think?

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?


ScienceWoman gives us a heads-up on a new and interesting organization –

The Feminist Press with IBM have just launched, a new site to involve young women in science and to encourage them to pursue careers in science, technology, engineering and math. The site is part of the Women Writing Science, a project initiated by The Feminist Press at the City University of New York and funded by the National Science Foundation.
The site features personal stories of women scientists, role models, and mentors; tips for parents and teachers; links to related women and science sites; videos; and networking. Some of these features are available now, and others will come later this year as noted in the press release below

On the website they have also started a promising-looking blog.

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….

Ships and Spaceships

Yes, this has been in the works for a long time, and a few hints have been planted here and there over the past months, but now it is official – NASA and The Beagle Project have signed a Space Act Agreement and will work together on a host of projects including scientific research and education. You can read the details on The Beagle Project Blog – space, oceans, biology, science education, history of science, exploration and adventure: all at once. How exciting!
The text of the agreement is under the fold:

Continue reading

The Nobel Prize conundrum

I rarely jump on the blogging hype of noting the new Nobel Prize winners every year. Exceptions are cases when I have a different slant on it, e.g., when a Prize goes to someone in my neighborhood or if the winners have published in PLoS ONE and PLoS Pathogens (lots of loud cheering back at the office).
But usually I stay silent. Mainly because I am conflicted about the prizes in science in general, and Nobel in particular.
On one hand, one week every year, science is everywhere – in newspapers, on the radio, on TV, all over the internet. And that is good because it is a push strategy (unwilling consumers getting bombarded with information they did not specifically seek, but find interesting once exposed to) as opposed to the usual pull strategy (when already interested people actively seek information). The journalists usually have a tough job – the Nobels are often awarded for findings that are way beyond 6th grade level and explaining the science which requires quite a lot of background is not easy. Good science journalists prepare very well for the Nobels, though, and usually get the reporting done well. The general population gets to go beyond the basics and learn what’s new and exciting at the present moment. And Nobel winners are celebrities of sorts and people love celebrities. So this is a plus.
But the minuses are many as well.
First, sometimes a prize goes for a technique, not a fundamental discovery. This year’s prize in Chemistry is a case in point – discovery and cloning of the green fluorescent protein (GFP) from the jellyfish, Aequorea victoria. The 1993 prize for Chemistry was similar – it went to Kary Mullis and Michael Smith “for contributions to the developments of methods within DNA-based chemistry”, aka for the polymerase chain reaction (Mullis) and site-directed mutagenesis (Smith) – hmmm, both of these were biology prizes awarded for Chemistry: a pattern?
Like Larry, I think this is a bad idea. First, it reinforces the confusion that many people have – not being able to distinguish between science and technology. Second, I feel that a Nobel should go to discoveries that importantly affect the way we think about nature, rewrite the textbooks and perhaps have big implications for medicine (in the case of the Prize for Medicine). Technique in itself does not do this – it allows thousands of people to chip at nature’s secrets, experiment by experiment, one detail at the time, and perhaps collectively over time bring about fundemantal changes in our thinking about the way the world works. But the prize does not go to those thousands who actually discovered something new, it goes to people who provided the technical tools.
Second, it reinforces the popular notion that science is competitive and that scientists do research in order to gain fame and fortune – you all know the stereotype of the crazy anti-social scientist show spends decades in the basement laboratory dreaming of a Nobel Prize. Where is the usual reason people go into science – natural curiosity?
Third, it messes up with the new incoming scientists – it gives them a skewed idea of what science is all about. So, they do whatever it takes to get into a highfallutin’ school where they can join one of the enormous, faceless, gene-jockey labs with 25 postdocs where all the PI does is write grant proposals, the atmosphere is dog-eat-dog and one is tempted to doctor the data and do other unethical stuff. In that lab, the student is given a little detail to work on, while fostering the dreams of discovering a cure for cancer and getting a Nobel. There is an enormous pressure to produce lots of data quickly and to publish them in GlamourMagz.
What those students are not told is to go check the list of Nobel laureates and see what they got the prizes for. It was not one of the thousands of people working on C.elegans now, it went to the person who was the first to work on C.elegans. It was not one of the thousands of people working on zebrafish now, it went to the person who was the first to work on zebrafish. Likewise, it will not go to one of the thousands of people working on p53, or estrogen receptor, or using transgenic mice, or DNA-arrays, or whatever is the bandwagon now. All of that work needs to be done, but it is not revolutionary (at least not for a Nobel). It is “normal science”, incremental placing of pieces into the puzzle. Nothing wrong with that, but don’t get your hopes too high.
This brings me back to this year’s prize for the Green Fluorescent Protein. You have probably heard the story of Dr.Prasher, the guy who did not win the Nobel although he was the first to clone the GFP gene. He is now a shuttle driver for a garage (interestingly, Kary Mullis, the other guy who got a Nobel for a technique, is also now out of science: a surfer, womanizer and HIV denialist). Why? He could not get funding for the continuation of his work. When did this happen? In the late 1990s, at the time when the science funding started to go down.
So, if this is so revolutionary, why didn’t he get funding? The official notes on his grant proposals are probably official-sounding and diplomatic, but I can imagine what was going on through the reviewer’s head while reading Prasher’s proposal – something along the lines of “What on Earth is this jellyfish, Aequorea victoria? Why would anyone care about such an animal (is it an animal anyway, or what is it?)? Why not do something useful, in humans or mice, or at least in fruitflies? Why waste time and taxpayer money on this Discovery Channel crap?”
Being one of the thousands on a bandwagon is bad. Especially in the time of poor funding. But working on a non-bandwagon question, using non-molecular techniques, in a non-model animal is worse, much worse. At the time of the peak in funding, it was sometimes possible to get funding from NIH, but even then it was not easy for such research. Most biologists, though usually not covered by the media much, do that kind of stuff – just go to the SICB conference one year and see for yourself. Luckily, the research itself is usually not very expensive and a lab can “go on fumes” if needed for a year or so as long as it can keep its animals and rooms. There is alternative way of funding: instead of one large NIH grant, many of these labs have many small grants from NSF, NASA, US Army (or Airforce, or Navy), USDA, private foundations, etc. But at the time of low overall funding, even these sources dry up.
Some years ago, I listened to a very interesting talk by Knut Schmidt-Nielsen. The talk was in an unusual format and initially took some people aback. Instead of starting with a big question, gradually zooming in to the methods and results, then at the end zooming out again to the Big Picture, Knut started with an anecdote. Then, he told another anecdote. Then another. After an hour, we finally ‘got it’ – there was an undelying thread in all of these anecdotes. Each highlighted a piece of strange research by a strange person in a strange organism, marred by lack of funding and appreciation (and sometimes outright derision), yet in the end resulting in a ground-breaking discovery that shook our way of understanding the world, or provided a potent research tool (yes, GFP was one of the examples, tetrodotoxin was another). The take-home message was: do what you are passionate about, look at non-model organisms, let your curiosity take over, do not focus on application, tough out the lean financial times, and who knows, you may deserve a Nobel one day. For doing what you like, not what others told you is “hot”.
Look at that list of Nobel laurates in Physiology and Medicine again. Each one of them was a pioneer, doing something weird that nobody else thought made any sense at the time. They persisted and followed their hunches and finally overcome the resistance of their peers. And many thousands of others who did not win a prize, still retired happy with their career – they did something useful and had fun all along.
Not all of that research even required a lot of money, expensive equipment and large numbers of postdocs. Watson and Crick tinkered with pieces of metal and made a model. My favourite Nobel is the 1973 one: von Frisch used a fine paintbrush to mark the bees and a few dishes with sugar water; Lorenz walked around the yard followed by a flock of ducklings; Tinbergen had some fish in a tank, painted red dots on seagulls’ beaks, and moved some pine-cones around. And each one of them made revolutionary discoveries about the way the brain works. It is better to have a problem to solve and use one’s creativity to solve it in the simplest, cheapest, most decisive way, than to search for a question that you can address with the technique you are good at.
Often those simple, cheap, creative techniques provide more trustowrthy data. I know from my own work – I ran some gels and that’s an art, not science. I do not believe my own data (people around me in the lab did). What I got are hunches, perhaps something that statistics may say is relevant, but I dare you to try to repeat the experiment and get the same results! On the other hand, when I came up with a creative experimental protocol – all I needed to do is count eggs every day – the result I got was an all-or-none uber-conclusive response that does not need no steenkin’ statistics and simply over-rules a few decades of published literature (I really need to publish that stuff). Not all questions require, or could appropriately be addressed by running expensive molecular experiments. Each question is at a particular level of organization and requires the experiment to be done at that level, perhaps higher, not lower (as one can infer the behavior of parts from the behavior of the whole, but not vice versa).
There are many questions at the levels of molecules and cells that are worth asking, but that is not all there is in biology – and that is something that students need to be told. And some people will be really good at designing such experiments and answering important questions. But there are other levels in biology and other approaches, and some people will be better suited for those. And for saving money by designing and building one’s own equipment (my PI always told me if my PhD studies did not get me anywhere, I could always find a job using the skills learned in the lab – as an electrician or carpenter). At least in those other fields, the competitiveness is toned down a notch – no need to ask for millions of dollars every few years, no need to get into a GlamourSchool and publish in GlamorMagz – you can do it anywhere and publish wherever you want. Who can scoop you if you are studying deer in a particular forest? You have a couple of years of data in advance. You see if a competitor comes in – and you offer collaboration instead.
So, it’s up to one’s interests, talents and temperament. I was strongly advised (at the time when a PhD looked likely and such) to do a postdoc in a heavily molecular lab in order to get molecular techniques under my belt because that is “a necessity for getting a job”. So I tried – I went and spent a few weeks in such a lab (they even cleared up some space in the freezer for my samples) and decided that it was not for me. The PI was really nice, but part of that super-competitive atmosphere I detest. The lab consisted of 25 people who seemed really nice – on those rare moments when one could actually talk to them. Most of the time – and that is about 13 hours per day, 7 days a week – they were hunched over their benches, quiet, pale like Eloi. The specter of the Japanese hell-bent on scooping was hanging over everyone’s head. A saw postdoc, a really good, creative, smart guy with several excellent papers to his name, being told, on a Friday afternoon, to re-do his experiments and show the data first thing on Monday morning! WTF!? One thing I most appreciated in my old lab was time – I did my stuff when I wanted to. I did twice as much as asked because I was excited. Those who wasted their time left the lab after a year or less, but I persisted on my own. And nobody ever told me when to get the data or when to do my work. I did a lot of it at nights and over weekends because I am too social – would rather chat with people and attend seminars than work if others are around – but that was my own choice. Nobody tells me what to do.
Back to the topic. In non-bandwagon, non-molecular, non-medical biology, there is no need to rush, or to be secretive about one’s work, or to fudge the data, or not to do Open Notebook Science. No patents or big prizes or big money are at stake. But you have a nice, pleasant career in science suitable to those who are not of the A-type temperament. You have time for family and hobbies. And you enjoy the collegiality and collaborations and the growth in your own respect and authority over the years. That kind of stuff can sometimes even be done by amateurs. Nothing wrong with that.
So, the Nobel Prizes are used, in a way, to lead the students along the wrong paths – to jump on bandwagons. But being on a bandwagon, as history shows, does not result in winning a Nobel – quite the opposite. It is the weirdos, or people who moved from one discipline from another (thus avoiding thinking inside the box of the discipline) – the mavericks – who tend to hit on something really important, sometimes by intent, sometimes by serendipity.
So, go on and study what you are truly excited about in some emerging model system, or something weird like the platypus, or sea cucumbers, or ferns, or Venus flytraps, or silverslippers – who knows where that can end (more likely on science blogs or Discovery Channel where cool animals doing cool things are appreciated, than in Stockholm), but even if it does not, you’ll have fun all the way.

Science beyond individual understanding?

Michael Nielsen wrote another long thought-provoking essay (for his book, I guess):

…………Two clarifications are in order. First, when I say that these are examples of scientific facts beyond individual understanding, I’m not saying a single person can’t understand the meaning of the facts. Understanding what the Higgs particle is requires several years hard work, but there are many people in the world who’ve done this work and who have a solid grasp of what the Higgs is. I’m talking about a deeper type of understanding, the understanding that comes from understanding the justification of the facts.
Second, I don’t mean that to understand something you need to have mastered all the rote details. If we require that kind of mastery, then there’s no one person who understands the human genome, for certainly no-one has memorized the entire DNA sequence. But there are people who understand deeply all the techniques used to determine the human genome; all that is missing from their understanding is the rote work identifying all the DNA base pairs. The examples of the LHC and the classification of the finite simple groups go beyond this, for in both cases there are many distinct deep ideas involved, too many to be mastered by any single person. …………..
……………..Such scientific discoveries raise challenging issues. How do we know whether they’re right or wrong? The traditional process of peer review and the criterion of reproducibility work well when experiments are cheap, and one scientist can explain to another what was done. But they don’t work so well as experiments get more expensive, when no one person fully understands how an experiment was done, and when experiments and their analyses involve reams of data or ideas.
Might we one day find ourselves in a situation like in a free market where systematic misunderstandings can infect our collective conclusions? How can we be sure the results of large-scale collaborations or computing projects are reliable? Are there results from this kind of science that are already widely believed, maybe even influencing public policy, but are, in fact, wrong?


Science, Art, Education, Communication

The September 2007 issue of JCOM – Journal of Science Communication – (issue 3, volume 7) is online.: Next issue will be online on the 18th December 2008. There are several articles in this issue that I find interesting and bloggable.

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ScienceOnline’09 – Registration is Open!

First, there was the First NC Science Blogging Conference. Then, there was the Second NC Science Blogging Conference. And yes, we will have the Third one – renamed ScienceOnline’09 to better reflect the scope of the meeting: this time bigger and better than ever.
ScienceOnline’09 will be held Jan. 16-18, 2009 at the Sigma Xi Center in Research Triangle Park, NC.
Please join us for this free three-day event to explore science on the Web. Our goal is to bring together scientists, bloggers, educators, students, journalists, writers, publishers, Web developers and others to discuss, demonstrate and debate online strategies and tools for promoting the public understanding of science.
The conference is organized jointly by BlogTogether, the North Carolina bloggers’ group, and WiSE @ Duke, the Women in Science and Engineering organization at Duke University, with help from Sigma Xi and other sponsors.
The people behind the organization are Anton Zuiker, Abel Pharmboy and myself, with additional generous help by Brian Russell and Paul Jones.
The conference homepage/wiki is now live! Go and explore!
Registration is free and it is now open – go and Register right now!
See who has already registered.
Help us develop the Program.
Perhaps your organization/company would like to be a sponsor? Or you’d like to volunteer?
Just like last two times, we are preparing the publication of the Science Blogging Anthology and, this time, we’ll try to really have it ready and up for sale at the conference itself. This year’s Guest Editor is Jennifer Rohn and you should really start submitting your entries now.
For news and updates about the conference (and anthology), follow the ScienceOnline09 blog or check here, my SO’09 category.
Hope to see many of you in January!

Science in the 21st Century

Everything about the Science in the 21st Century conference at Perimeter Institute can be found here.

Things to avoid when speaking publicly – the video

Coming from this discussion.

Used postdocs

There is a new letter to Nature – Postdoc glut means academic pathway needs an overhaul – which I cannot read as I have no access, but others are discussing it on FriendFeed and there have been recent posts on the topic of endless/hopeless postdoc positions on DrugMonkey and The Alternative Scientist.
Bill sums it up the best graphically:

Post-publication Peer-review in PLoS-ONE, pars premiere

Why is the letter P the most useful for alliterative titles?
But back to the substance. One thing that bugged me for a long time is that I often see on blogs or hear in person a sentiment that “there are no comments on PLoS ONE”. Yet I spend quite some time every week opening and reading all the new comments so I KNOW they are there and that there is quite a bunch of them already. Why the difference in perception? Is it due to the predictable distribution (a few papers get lots of comments, most get one or none, just like blog posts)?
So, when we saw this nice analysis of commenting on BMC journals by Euan Edie, we decided to take a look at our own numbers and see how they compare. We got the data together and sent them to a few people, mostly bloggers, to take a look. As they write their blog posts I will post the links here, especially when they do the nitty-gritty statistical analysis.
But for now, quickly out of the box, two of them have already posted their first impressions they took when they scanned the data.
Deepak Singh writes:

There people post a link and a whole discussion erupts (not always, but often enough). I would throw out this challenge (see the DOI suggestion above). Why should discussion be localized to PLoS One itself. If a paper pubished in PLos One is discussed in 20 other places, it would be considered a success. In other words, we shouldn’t limit our thinking to just on site commenting. Perhaps within the site, we should be focussed on ratings and perhaps tagging and notes.
So what have we learned from this exercise. Quite frankly, I am not sure. Is the commenting on PLoS One at a level that we hoped it would be? Not quite. Is it as bad as some might like to believe? Not quite. What we have is a very very nascent (no pun intended) effort on the part of the scientific community using web publishing platforms as a communication medium. I’d like to ask those same scientists to think about newsgroups. Most scientists are fairly comfortable participating in newsgroups, and here you essentially have one, with very clearly defined thread titles.

Cameron Neylon says:

In that context, I think getting the numbers to around the 10-20% level for either comments or ratings has to be seen as an immense success. I think it shows how difficult it is to get scientists to change their workflows and adopt new services. I also think there will be a lot to learn about how to improve these tools and get more community involvement. I believe strongly that we need to develop better mechanisms for handling peer review and that it will be a very difficult process getting there. But the results will be seen in more efficient dissemination of information and more effective communication of the details of the scientific process. For this PLoS, the PLoS ONE team, as well as other publishers, including BioMedCentral, Nature Publishing Group, and others, that are working on developing new means of communication and improving the ones we have deserve applause. They may not hit on the right answer first off, but the current process of exploring the options is an important one, and not without its risks for any organisation.

There are also two quick responses on Nascent and Genome-Technology.
What is most interesting is that there are no comments on Nascent and Genome-Technology, only a couple on Deepak’s and Cameron’s posts, yet a very nice long discussion on FriendFeed (very much worth reading, and not just for compliments to me)! What can we learn from that fact alone?
Second, the comment (by ‘comment’ I mean Ratings+Notes+Comments) to article ratio on PLoS ONE has risen from 1.1 a year ago to about 1.5 today. For comparison, my own blog has 1.6. And I get lots of comments – on a few posts, while zero or one on most. And I am prolific with quick/short posts like Quotes, so it is a decent comparison: not every paper is exciting or controversial enough (just like most of my posts are not) to motivate people to say anything.
Also, a blog post usually gets comments immediately. After 24 hours it is deemed stale and people move on to the new stuff. A scientific paper will be expected not to get any for the first few months and to only gradually accumulate them over the years as new information comes in that sheds new light on that paper. And I see this every week – older papers get a nice share of comments every week, while papers published this week do not.
See what I wrote last year about this:

One thing to keep in mind is that a PLoS ONE article is not a blog post – the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.
Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology – or in history of science! – and the first assignment is to read all the commentary to that paper. There it is: all laid out – the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!
Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people’s papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn’t that helpful, especially for students?

I hope more of you join in the discussion, and I will post links to other posts as they appear over the next week or two.

The MIST facility

First Line of Defense:

A new facility at North Carolina State University will help provide increased protection to first responders by testing their turnout gear against potentially harmful chemical and biological threats.
The Man-in-Simulant Test (MIST) laboratory, located in NC State’s College of Textiles, will allow researchers to evaluate the capabilities of protective garments against non-toxic vapors that resemble chemical and biological agents. The new facility will give researchers the necessary technological advances to provide test results and analysis faster than similar facilities.
The MIST facility is the only one of its kind located at a university in the United States. The laboratory was funded by a two-year, $2 million grant from the Department of Defense secured by U.S. Rep. Bob Etheridge, who serves on the U.S. Homeland Security Committee.
In the main testing chamber, researchers can test the penetration of chemical vapors through protective clothing on mannequins and human subjects. During testing, subjects can perform the same tasks as a first responder, such as climbing a ladder, crawling, or carrying a victim to safety, in an environment that can be controlled for temperature, wind speed and vapor concentration.

The Virtual Computing Lab

My old neighbor, while I was living in Raleigh, is making some headlines now: Power to the People:

Within weeks of completing his master’s degree in advanced analytics at North Carolina State University, Arren Fisher scored a job in data analysis at the Laboratory Corporation of America.
“It involves predictive modeling,” Fisher explains. “In layperson’s terms, super duper data mining.”
Despite the tight national economy, Fisher and his classmates are getting lots of job offers because they’re experienced users of the advanced software programs that marketing firms utilize to predict consumer behavior. But they didn’t have to book time in a computer lab to use the software. They had an entire university computer lab – with hundreds of advanced programs – available on their personal computers and laptops at any hour of the day or night.
The system – called the Virtual Computing Lab – is the wave of the future, say the information technology experts at NC State. It’s convenient, free and powerful for the users, and saves the university money by easing the demand placed on traditional computer labs in libraries and academic departments.

Next thing, they outlaw cooking at home: it’s chemistry, after all….

Robert Bruce Thompson is the author of Illustrated Guide to Home Chemistry Experiments, a book I have and like, but cannot really use as it is hard to get the chemicals. Thompson now writes a guest popst on MAKE blog: Home science under attack

The Worcester Telegram & Gazette reports that Victor Deeb, a retired chemist who lives in Marlboro, has finally been allowed to return to his Fremont Street home, after Massachusetts authorities spent three days ransacking his basement lab and making off with its contents.
Deeb is not accused of making methamphetamine or other illegal drugs. He’s not accused of aiding terrorists, synthesizing explosives, nor even of making illegal fireworks. Deeb fell afoul of the Massachusetts authorities for … doing experiments.

So, even if you can find chemicals, you can have the cops coming and confiscating them?!
As NNadir says, It Must Have Been Beautiful to Do Science In Those Days, but not any more. I used to have a decent chemistry kit, and a good little microscope, and bought some additional glassware from a lab store downtown. Can’t get any of that any more:

These days science involves heavy duty – and often expensive – instrumentation, software programs with arcanely programmed guts – LIMS systems, speed, speed, speed, dense arrays of information, and all too narrow focus.
But all this was brought here on the shoulders of giants well after Newton, giants who labored maybe in more obscurity.
Some of what I was looking at today was science from the 50’s and the 70’s, the men and women of the time who first moved beyond this planet’s atmosphere and gravity. And I was struck by the beauty of their jury-rigged lives, where they built stuff from scratch.

Or, as John Wilkins says:

Kids today have emasculated chemistry sets that do precisely nothing interesting. And if Mythbusters has taught us anything, it’s that kids love explosions. That is the route to an educated population of science loving psychopaths. But we didn’t turn out to be psychopaths, we turned out to be lovers of science. We have lost something important. If a frigging chemist, who knows how to work safely, cannot do science at home, the west can pretty well forget about the next few generations of kids ever learning anything useful.

Which now feeds to the entire question of amateur science – can people outside science institutions do science any more (apart from Christmass bird count, I guess)? Janet has written two posts recently that touch, in a way, this question: Peer review and science and Objectivity and other people. Who is a scientist? Who are the peers, and what forms peer-review can take? If you play with a chemistry kit at home, and discover something new, and post it on a blog, and other chemists come by and read your detailed descriptions, and replicate the findings – was that peer-reviewed? How many people would negate this is science because it was not peer-reviewed in a formalized fashion in a scientific journal? How many would understand that peer-review can have many forms? See the comment thread on Chad’s post on this topic.
But if you cannot even do science in the basement, the whole question of peer-review of home-made science gets murky.

Praxis #1 – last call for submissions

PraxisThe new blog carnival, covering the way science is changing (or not changing enough) in the 21st century – Praxis, is about to start. The call for submissions is now open – send them to me at Coturnix AT gmail dot com by August 14th at midnight Eastern so I can post the carnival on the 15th in the morning.
The business of science – from getting into grad school, succeeding in it, getting a postdoc, getting a job, getting funded, getting published, getting tenure and surviving it all with some semblance of sanity – those are kinds of topics that are appropriate for this carnival, more in analytic way than personal, if possible (i.e., not “I will cry as my minipreps did not work today”, but more “let me explain the reasons why I chose to work with advisor X instead of Y” or “how to give a good talk”, or “why publish OA” or “how does an NIH section work?”) and perhaps most importantly how the new technology – mainly the Internet – is changing the world of science. I expect a LOT of entries about Open Access, of course…. 🙂

Paperless Office? Bwahahahaha!

Today, I have everything I need on my computer, and so do most working scientists as well. Papers can be found online because journals are online (and more and more are Open Access). Protocols are online. Books are online. Writing and collaboration tools are online. Communication tools are online. Data collection and data analysis and data graphing and paper-writing tools are all on the computer. No need for having any paper in the office, right? Right.
But remember how new that all is. The pictures (under the fold, the t-shirt is of Acrocanthosaurus at the NC Museum of Natural Science) of my old office are only five years old! You know I am a Web junkie. If I could have survived without paper, I would have ditched it all. But I could not (and the pictures show only half of the office – there were two large file cabinets full of reprints behind the photographer – my brother – and much, much more, plus more in the lab itself):

Continue reading

Praxis #1 – second call for submissions

PraxisThe new blog carnival, covering the way science is changing (or not changing enough) in the 21st century – Praxis, is about to start. The call for submissions is now open – send them to me at Coturnix AT gmail dot com by August 14th at midnight Eastern.
The business of science – from getting into grad school, succeeding in it, getting a postdoc, getting a job, getting funded, getting published, getting tenure and surviving it all with some semblance of sanity – those are kinds of topics that are appropriate for this carnival, more in analytic way than personal, if possible (i.e., not “I will cry as my minipreps did not work today”, but more “let me explain the reasons why I chose to work with advisor X instead of Y” or “how to give a good talk”, or “why publish OA” or “how does an NIH section work?”) and perhaps most importantly how the new technology – mainly the Internet – is changing the world of science.

Well versed in science

Bob read this and sent me some even better stuff:
Completely in verse:
Joseph F. Bunnett and Francis J. Kearley (1971). Comparative mobility of halogens in reactions of dihalobenzenes with potassium amide in ammonia (pdf). Journal of Organic Chemistry 36(1): 184 – 186; DOI: 10.1021/jo00800a036
In verse AND musical notation:
HM ShapiroFluorescent dyes for differential counts by flow cytometry: does histochemistry tell us much more than cell geometry? (pdf). J Histochem Cytochem, 1977 Aug;25(8):976-89.
Now I need to rewrite my old papers in verse…for instance:
There once was a quail flock
That had an eye for a clock.
Those who had eyes
Said “see how time flies?”
And those who had none thought those were lies.

There once was an Editor of FASEB….

….who likes limericks.
His article – Writing Science: The Abstract is Poetry, the Paper is Prose – makes me wish to have something to submit to FASEB just so I could submit the Abstract in the actual form of a limerick. And see what the Editor says.
I actually like it when a paper starts with a short verse. Or a good quote (that’s how I started collecting interesting quotes).
But to include controls in the Abstract? That’s insane! There is no way to even mention all seventeen experiments in the abstract, let alone the details of materials and methods, even less to bother with controls, when the limit is 250 (or in best cases 500) words.
The Abstract gives the basic gist (“in a series of experiments we show that X is Y”) – it is not the place for details. And almost never needs to have any actual numbers in it (especially not stats, e.g., p-values). That is what the paper is for. Abstract is like a mini-press-release, or advertisement, designed to draw you in, not repel. To provoke you to read the rest of the paper in order to see if the exorbitant claim made in the Abstract is actually supported by data. If everything is in the Abstract, why write the rest of the paper just to duplicate all the information?

Web 2.0, Science 2.0, OA, etc.

There is a new study out there – Open access publishing, article downloads, and citations: randomised controlled trial – that some people liked, but Peter Suber and Stephan Harnad describe why the study is flawed (read Harnad’s entire post for more):

To show that the OA advantage is an artefact of self-selection bias (or any other factor), you first have to produce the OA advantage and then show that it is eliminated by eliminating self-selection bias (or any other artefact).
This is not what Davis et al did. They simply showed that they could detect no OA advantage one year after publication in their sample. This is not surprising, since most other studies don’t detect an OA advantage one year after publication either. It is too early.
To draw any conclusions at all from such a 1-year study, the authors would have had to do a control condition, in which they managed to find a sufficient number of self-selected self-archived OA articles (from the same journals, for the same year) that do show the OA advantage, whereas their randomized OA articles do not. In the absence of that control condition, the finding that no OA advantage is detected in the first year for this particular sample of journals and articles is completely uninformative.
The authors did find a download advantage within the first year, as other studies have found. This early download advantage for OA articles has also been found to be correlated with a citation advantage 18 months or more later. The authors try to argue that this correlation would not hold in their case, but they give no evidence (because they hurried to publish their study, originally intended to run four years, three years too early.)

How to do research – special free sample:

Key to doing research is having a discovery network in place to do the grunt work of navigating through the data smog for you. But even more importantly, constructing a discovery network is central to your professional formation, because it makes you ask yourself who you are and what sort of things you want to discover.
In many ways, your discovery network already discovers material out there and then evaluates it for you automatically, filtering through only the material you need. But the machine doesn’t know what you are working on at the moment, and of course is not as finally discriminating as your brain. So you need to filter the stuff your filters have been sending you. This is where the art comes in.

The confusion over data rights:

There was a time when I had the naive opinion that academics were all about the open dissemination of science, especially the sharing of basic scientific data. Alas, it turns out that for some the public domain is not exactly that. I suppose that this is a minority opinion, but it is clear that the confusion about scientific data and ownership needs to be resolved and fast. It should be obvious, but it isn’t and even those of us who should know better get confused. In the above case, if there was a paper where the data source had not been cited properly is understandable, but downloading and using sequences; Yowza!!!
There is a distinction between data and content/information. Too many people have trouble making the distinction and as a result there is confusion the ownership rights around the two. Anyway, this issue isn’t going anywhere soon it seems.

Virtual world interoperability:

As the number and variety of virtual worlds increases, so will the demand for interoperability. This will include not only teleporting between worlds, but also interworld communications, interworld asset portability, interworld currency exchange and many other issues. The technological aspects are an important part of this, and the public beta is an important step in the right direction. However, there are many social and business aspects that will also need to be addressed, and these may be even more difficult than the technological ones.

So open it hurts:

Web 2.0 visionaries Tara Hunt and Chris Messina blogged and twittered about their romance to all of geekdom as if it were one of their utopian open-source projects. Sharing their breakup has been a lot harder.

Five Life-Changing Mistakes and How I Moved On:

I’m out meeting with the press right now to promote and I’m getting quite a reaction. Not to the business, but to me. You see, it’s been awhile since I met with them, at least eight years. Many of the people in the press are same ones I met all those years ago. Many I don’t know. No matter if they knew me before or not, they all ask the same question: “What mistakes have you made and what have you learned from them?” And this isn’t a normal “check-the-box” reporter question. This is a loaded question with heavy reference to my past, some would say my infamous past.
First some background, I was the CEO of In case you haven’t heard of it, and its mascot, the Sock Puppet, became the symbol for the dotcom bubble and its subsequent bust. Some have even charged me personally with bringing down the U.S. economy. Pets’ short period of success was fueled by positive press about the company and myself. Pets received even more press when it failed.
As the public CEO, I failed, and it was a very public failure. In fact, I was labeled one of the biggest failures ever. How bad was it? I had people laugh in my face when I introduced myself for years after the company closed. It happened as recently as a year ago. A couple of people asked me what it felt like to be one of the best-known failures in the U.S. Most just walked away from me. One woman told me to my face that I was a loser. I could go on and on, but you get the point: I became a symbol for something greater than myself, and we aren’t talking puppet envy here.
What most people don’t know is that the very same week that failed, my marriage of seven years failed as well. Actually, it had been failing for a long time. It became officially over that week. My husband decided to call it quits the day before I announced to the employees and the public markets that I was shutting down Pets. It was a really bad week…….

A Whole Lotta Thoughts On Blog Network Success (bonus tips included):

First, though, I want to enumerate some reasons why running a blog network, blog ad network or a blog “alliance” is harder than folk realize. But hopefully some of this post can help solve some of the stumbling blocks, as well as highlight the issues so folks go into these projects with eyes wide open.

Cuil: Why I’m trying to get off of the PR bandwagon…:

Journalists thrive off of conflict. That’s why we want a competitor to Google so badly and why we play up every startup that comes along that even attempts to compete with Google.
The problem is that competiting head on with Google is not something that a startup can do.

Carnival of Science/Academia/Publishing?

Martin saw this comment of mine and sprung into action: Name the new ‘Carnival of Scientific Life’!

The two big questions are what to call it, and how often to host it, so I’d like your input in the comments below please. I’ll be making the final decision on August 1st.
What would be a good name for the carnival? (Ideally something without “carnival” in the title.)
Should it be held monthly, or at some other frequency?
The carnival is intended to cover all aspects of life as a scientist, whether it’s the lifestyle, career progress, doing a Ph.D., getting funding, climbing the slippery pole, academic life as a minority, working with colleagues and students, dealing with the peer-review process, publishing, grants, science 2.0, amusing anecdotes, conference experiences, philosophical musings, public engagement, or even historical articles about what life was like in the good (or bad) old days.
In other words, anything related to the experience of living the scientific life. Not blogging about research, but blogging about everything that goes with being a researcher. A sort of “meta-science” carnival if you like.
I’ll be putting together a hosting schedule here in the coming days. If you’re interested, let me know at

This is how he describes it: About the Carnival of Academic Life

The carnival is intended to cover all aspects of life as an academic, whether it’s the lifestyle, career progress, doing a Ph.D., getting funding, climbing the slippery pole, academic life as a minority, working with colleagues and students, dealing with the peer-review process, publishing, grants, science 2.0, amusing anecdotes, conference experiences, philosophical musings, public engagement, or even historical articles about what life was like in the good (or bad) old days.

On the same day, there was a thread on ‘Plausible Accuracy’: Open Science blog carnival – The interest seems to be there, so what about the details?, where I left the following comments:

I’ve seen carnivals come and go, and at this point I do not think there is enough people out there to sustain a carnival on such a narrow topic as OA alone. I would rather have a carnival on all things meta-science, with an OA section in it.
This also means that people who write/read about other aspects of life in science will get to read the OA stuff (people always check out who else is on the carnival they are in, and also link to the carnival), many for the first time, and get introduced to the idea which they can spread to others. Makes the topic less insular when it rubs shoulders with others who write about science but never gave a thought to the business of publishing before. A way to bring in more people to the cause.

I would think that something like this would be OK. Not “I am bummed because my mini-prep did not work today” kinds of posts, but analytic posts about the way science works, the way academia is organized, the internal and external politics of science, discrimination, funding, promotion, careers, the business of publishing, the Science 2.0 and science blogging issues, etc., but with a special emphasis on the way the Web is changing science practice in all of its aspects.
What do you think?

Big Biology

What Alex and commenters say….

In(s) and Out(s) of Academia

Bjoern Brembs is on a roll! Check all of these out:
Incentivizing open scientific discussion:

Apart from the question of whether the perfect scientist is the one who only spends his time writing papers and doing experiments, what incentives can one think of to provide for blogging, commenting, sharing? I think because all of science relies on creativity, information and debate, the overall value of blogging, commenting and sharing can hardly be overestimated, so what incentives can there be for the individual scientist?

Journals – the dinosaurs of scientific communication:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database. It doesn’t take an Einstein to realize that PLoS One is currently the only contender in the race for who will provide this database. For all the involved, it is equally clear what the many advantages of such a database would be. Consequently, traditional publishers are rightfully concerned that their customerbase is slowly dissappearing.

Post-publication paper assessment:

The more variables there are to game, the more difficult it becomes. Now we have one variable (IF) and we all know who is gaming it ad nauseum. In this thread we have 5 measures, add ratings and comments and you have 7. This should be impossible to game for anyone but the hacker who can get thousands to machines on the net to just hype this one paper.
All of these measures are relevant even long after publication. Some papers ignored by the media may later turn out to harbor the most important discovery of the century, while some of those tossed around everywhere turn out to be completely irreproducible. Having these measures in place, if nothing else, would allow us to quantify and study such events.
But again, no matter how many numbers you have, these measures cannot substitute for actually reading the papers! The numbers barely give you a rough idea of where a paper or a scientist can be placed with respect to others in the same field. Yet, these measures would be light-years ahead of any one-dimensional, irreproducible, obviously manipulated and corrupt measure such as the IF.

Building a scientific online reputation:

For me, this basically means that all the expertise and technical prerequisites are there to bring the scientific community into the 21st century. The advantages of the new system need to be succinctly summarized and widely publicized at the same time as the current system’s disadvantages and idiosyncracies need to be pointed out and publicized along with the new proposal. And because criticizing is always easier than advertising, I’ll start by summarizing why Thomson’s Bibliographic Impact Factor (BIF) is dead.

Why Thomson’s Bibliographic Impact Factor (BIF) is dead:

Despite the recent downpour of evidence against the use of Thomson’s BIF, I still get comments from people such as “However, IFs are still the most used way of evaluating a researcher’s career and value. Even if we find this ridiculous, it’s just the way it is.” or “in our institution, every researcher has to publish in journals whose BIF is at least 5.”. In the light of the current state of affairs concerning the BIF, this is just embarrassing. So here are the top three reasons why the BIF is dead:
1. The BIF is negotiable and doesn’t reflect actual citation counts (source)
2. The BIF cannot be reproduced, even if it reflected actual citations (source)
3. The BIF is not statistically sound, even if it were reproducible and reflected actual citations (source)
Now go and spread the information so I don’t have to suffer from these ridiculous statements any more.

Then, on Nature Network blogs and Nature blogs, discussion about the “manners” in the science blogosphere:
Corie Lok: What is fair play in the blogo/commentosphere?:

Now, maybe it’s a generational thing. Those of us who didn’t ‘grow up’ with blogs might be more easily taken aback by what goes on in them. Those of us who did grow up with them perhaps have learned to take the bad with the good.

To which I commented:

A lot depends on one’s prior experiences. If one comes to science blogging out of academia with its highly formalized and ritualized kabuki dance of language-use, extremely polite on the surface, yet often very vicious in the subtext, then one sees blogs as very uncourteous and unpleasant – the things that are supposed to be hidden between the lines and now said openly.
Many of the most popular science bloggers have a different history – many years of battling Creationist and other pseudoscience crusaders on Usenet groups in the early 1990s, people who, if they can use language at all, use it in a very vicious way, sometimes with threats of bodily harm. I spent the early 90s on Balkans usenet groups, battling heatedly nationalist Serbs, Croats and Bosnians who do not just voice empty threats but would, if they could find you, really kill you. Others cut their teeth on political blogs or feminist blogs, which are very blunt and heated. Just try not supporting Howard Dean in the 04 primaries or Obama in 08 – you get your fill of human nastiness. And that is nothing compared to what Republicans say once the general election starts!
My first blog was political – I wrote highly opinionated and strongly-worded posts. And of course, I got, let’s put it diplomatically, some highly opinionated commenters. I never deleted. Sometimes I responded (politely at first – that is unusual and disarming – I turned some trolls into friendly and polite commenters that way), sometimes I ignored, sometimes my other commenters took care of trolls.
Then, after the move to Sb, I gradually reduced writing about politics and religion and my threads are now quite nice and polite most of the times. Various heated debates about “framing” or the latest “Nature vs. PLoS” kerffufle are sweet lullabies compared to most of the stuff I saw and suffered over the years online. One grows a thick skin, understands that people behave strangely online, laughs at the most egregious examples, and moves on.
There is no single definition of a “science blog”. Blog is a piece of software. You do what you want with it. If you are a scientist with a blog, or if you write more-or-less regularly about science (or meta-stuff, e.g., life in the lab, women in academia, politics of science funding….), then you can claim that your blog is a science blog. And your blog is going to be different from all other science blogs out there, as it is what you want it to be, reflecting your own interests, goals and personality. Nobody can tell you how to do it. There is no, and there should be no “template” or “definition” of a science blog – that is the beauty of the beast.
Thus, some blogs are serious, others not. Some are nice, some are inflammatory. Some focus 100% on latest peer-reviewed research. Others are a smorgasbord of everything the blogger feels like posting at any given time (like my blog, for instance). There is no recipe, no straightjacket, no “one right way” to do it. And that is what makes the science blogosphere so exciting and vibrant – so many cool voices, interesting personalities! Who says that scientists are socially-inept or bad communicators?!

The discussion there continues:
Noah Gray: Getting into and out of character:

We seem to be at a critical juncture concerning the intersection of blogs and other Web 2.0 technologies with science. This is no time to poison the atmosphere and turn away the more “relaxed” or “casual” participants. Polarized communities refusing to tolerate rival positions, or unwilling to engage in a civil debate over any topic, from publication business models to the role of Ca2+-permeable AMPARs in LTP, will shut out many would-be contributors and stunt the growth or slow the adoption of blogs, commenting, and other web-based technologies dedicated to the pursuit of scientific collaboration. If such technologies are ever really going to work for science, it will be because of inclusivity, not exclusivity.

Maxine Clarke: Manners in the blogosphere:

The anonymity of cyberspace provides protection to both share honest opinions and participate in mud-slinging without repercussion, he notes. Yet interaction on the Internet is more personal. “So why should some choose to check their manners at the door before logging on?” He argues that intolerant online communities unwilling to engage in a civil debate — whether on publication business models or the role of glutamate receptors in long-term potentiation of neurons — will turn off would-be contributors and stunt the growth of online scientific collaboration. Web-based collaborative technologies will not work for science if they become dominated by exclusive, aggressive types. Gray isn’t calling for “communal singing of Kum Ba Yah during scientific debates”, but simply a certain level of restraint and professionalism online.

This is an interesting segue to Michael Nielsen’s latest instalment of his future book about the future of science: Shirky’s Law and why (most) social software fails:

Shirky’s Law states that the social software most likely to succeed has “a brutally simple mental model … that’s shared by all users”.
If you use social software like Flickr or Digg, you know what this means. You can give friends a simple and compelling explanation of these sites in seconds: “it’s a website that lets you upload photos so your friends can also see them”; “it’s a community website that lets you suggest interesting sites; the users vote on submissions to determine what’s most interesting”. Of course, for each Flickr or Digg there are hundreds of failed social sites. The great majority either fail to obey Shirky’s Law, or else are knockoffs that do little not already done by an existing site.
To understand why Shirky’s Law is important, let’s look at a site where it’s violated. The site is Nature Network, one of the dozens of social networking sites aspiring to be “Facebook for scientists”. Like other social networks, Nature Network lets you connect to other users. When you make a connection, you’re asked whether you would like to connect as a “friend” or a “colleague”. Sometimes the choice is easy. But sometimes it’s not so easy. Furthermore, if someone else connects to you, you’re automatically asked to connect to them, but given no immediate clue whether they connected as a friend or as a colleague. The only thing shared in the users’ mental model at this point is acute awkwardness, and possibly a desire to never connect to anyone on Nature Network again.
I don’t mean to pick on Nature Network. It’s the most useful of the social networks for scientists. But it and most other social websites (apart from the knockoffs) don’t even come close to obeying Shirky’s Law.
Why is Shirky’s Law so hard for developers to obey? I’ll give three reasons.

Interesting…. 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 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 reminiscient to the regular everyday oral conversation.
Moving on to other, related topics…
Jocalyn Clark: Is the NIH open access policy regressive?:

Panellists noted that the recent NIH public access policy emphasises free not open access. That is, the policy may lead to freely accessible publications (for which publishers or organisations may reap profits from charging authors a fee to deposit their manuscripts), but these will remain under restrictive licenses (thus limiting text-mining).
This, Cockerill argued, makes the NIH policy regressive.

NASA to launch OA image collection:

Nasa is to make its huge collection of historic photographs, film and video available to the public for the first time.

Rhea Miller: Vow to never become Jaded…:

But I do NOT understand why it is socially accepted to be a Jaded student…to be completely negative about the research he/she does, to avoid showing up to journal clubs/seminars, or to never participate in scientific discussions. What does being burnt out do for you in becoming the best you can be?? How does it help your science, your field, or your coworkers??
I really only notice these attributes in young scientists, i.e. graduate students and post-docs. Does this mean that the Jaded ones eventually give-up, get use to it, change their prospectives, or do they hide that inner Jaded color as they progress?? Or maybe it’s just that grad students/postdocs can’t seem to see the light at the end of the tunnel until they get there??

Panthera studentessa: Letting fear take over:

As time goes on, I’m becoming more and more concerned that I don’t have what it takes to hack it in graduate school. In every community, every blog, every forum that I read, people always talk about how stressful and all-consuming grad school is. To be perfectly honest, my mental health isn’t exactly the best it’s ever been. I just worry that I won’t be able to handle the mental and physical stress.
I suppose there’s always the option of just not going to graduate school, but that really throws a wrench in my career plans. I don’t even know what kind of jobs a person can get with a bachelor’s in zoology. And anyway, I don’t want to let my fear determine what I do with my life. I just wish I knew how to begin to get over it.

Maddox2: Advice on Freelance Science Writing:

Caveat: I am writing this advice from the perspective of an editor who regularly works with freelance science writers. However, the market in which I work may not be the same as some of you out there work in, or want to work in. Therefore, I can guarantee that following the advice below will endear you to K-12 educational publishers (and to companies like mine who work for educational publishers). I can’t speak to journals, newspapers, etc…but I can’t imagine they’d mind if you follow this advice! And given that a lot of people here have expressed an interest in freelance writing, I thought I might be able to provide a bit of a different perspective on things.

Mad Hatter: Networking Nuts And Bolts:

I think the most important thing to keep in mind when networking is that your contacts are much more likely to help you if they like you. My personal philosophy on networking is this: when my networking contact turns on her computer and sees an email from me, I want her to click on the email thinking, “Hey, I remember Mad Hatter. I liked talking to her. I wonder what she’s been up to?” What I don’t want her to do is groan and think, “Oh, no…it’s Mad Hatter again. What does she want now?” So with that in mind, here are some tips on networking that have worked for me.

John Hawks has posted first two of a 4-piece series on Blogging And Tenure: How to blog, get tenure and prosper: Starting the blog:

Last month, the University of Wisconsin officially granted me tenure. So, I can say without any doubt (if other examples had not been sufficient), it is absolutely possible to write a daily, high-profile blog and still be recognized by your colleagues as a scholar. In fact, it is possible to blog, do good research, and earn tenure at a Research I university.
That seems like progress, compared to the situation four years ago when I began blogging. A few high-profile tenure denials in late 2005, including physicist Sean Carroll and political scientist Daniel Drezner, made it seem like a blog might be the kiss of death for a research reputation. Inside Higher Education ran a story on the subject, as did Slate, with the melodramatic title, “Attack of the Career-killing Blogs”. Since I was interviewed in that article, I suppose I should have been a little nervous (I wrote about it here).
Happily things have changed.

…and: Graduate students and blogging:

As far as I know, there are no data concerning blogging and career success — or, for that matter, between any kind of public outreach and success in research careers (as opposed to teaching or industry careers that directly involve outreach). Anecdotally, there are some people who spend a lot of effort on outreach who have very well-respected research careers, and others who don’t. I’d say it’s up to the individual to chart her own course.
I’d like to advocate for a model of blogging that many graduate students might find useful. If I were starting out today, I’d blog my dissertation. Why not? Is there really anything so secret in your history and literature review that it couldn’t be read by the few hundred people who will find your blog?

New issue of the Journal of Science Communication

New issue of the Italian Journal of Science Communication is out with some excellent articles (some translated or abstracted from Italian, all in English):
Cultural determinants in the perception of science:

Those studying the public understanding of science and risk perception have held it clear for long: the relation between information and judgment elaboration is not a linear one at all. Among the reasons behind it, on the one hand, data never are totally “bare” and culturally neutral; on the other hand, in formulating a judgment having some value, the analytic component intertwines – sometimes unpredictably – with the cultural history and the personal elaboration of anyone of us.

Collaborative Web between open and closed science:

‘Web 2.0’ is the mantra enthusiastically repeated in the past few years on anything concerning the production of culture, dialogue and online communication. Even science is changing, along with the processes involving the communication, collaboration and cooperation created through the web, yet rooted in some of its historical features of openness. For this issue, JCOM has asked some experts on the most recent changes in science to analyse the potential and the contradictions lying in online collaborative science. The new open science feeds on the opportunity to freely contribute to knowledge production, sharing not only data, but also software and hardware. But it is open also to the outside, where citizens use Web 2.0 instruments to discuss about science in a horizontal way.

The future of the scientific paper:

Will the use of the Web change the way we produce scientific papers? Science goes through cycles, and the development of communication of science reflects the development of science itself. So, new technologies and new social norms are altering the formality of the scientific communication, including the format of the scientific paper. In the future, as PLoS One is experimenting right now, journals will be online hosts for all styles of scientific contributions and ways to link them together, with different people contributing to a body of work and making science more interdisciplinary and interconnected.

Public domain, copyright licenses and the freedom to integrate science:

From the life sciences to the physical sciences, chemistry to archaeology, the last 25 years have brought an unprecedented shift in the way research happens day to day, and the average scientist is now simply awash in data. This comment focuses on the integration and federation of an exponentially increasing pool of data on the global digital network. Furthermore, it explores the question of the legal regimes available for use on this pool of data, with particular attention to the application of “Free/Libre/Open” copyright licenses on data and databases. In fact, the application of such licenses has the potential to severely restrict the integration and federation of scientific data. The public domain for science should be the first choice if integration is our goal, and there are other strategies that show potential to achieve the social goals embodied in many common-use licensing systems without the negative consequences of a copyright-based approach.

To blog or not to blog, not a real choice there…:

Science blogging is a very useful system for scientists to improve their work, to keep in touch with other colleagues, to access unfamiliar science developed in other fields, to open new collaborations, to gain visibility, to discuss with the public. To favour the building of blog communities, some media have set up networks hosting scientists’ blogs, like or Nature Network. With some interesting features and many potential uses.

The other books – A journey through science books:

On March 2007 JCOM issue, Bruce Lewenstein made this question: why should we care about science books? Next he analyzed some fundamental roles of science books. As a continuation for that enquiry, this text wants to be a dialogue about science, readers, and books, just a quick look at many of the other books, science books, those that do not find easily their place in bookstores and libraries; these books situated beyond labels like fiction or romance but equally memorable, necessaries and desirables.

….and several other articles, all worth checking out (you need to save and download PDFs of each, though).

An alarming picture of scientific misconduct in the USA

Repairing research integrity:

Misconduct jeopardizes the good name of any institution. Inevitably, the way in which research misconduct is policed and corrected reflects the integrity of the whole enterprise of science. The US National Academy of Sciences has asserted that scientists share an ‘obligation to act’ when suspected research misconduct is observed1. But it has been unclear how well scientists are meeting that obligation. In the United States, the Office of Research Integrity (ORI) evaluates all the investigation records submitted by institutions and plays an oversight role in determining whether there has been misconduct at institutions that receive support from the Department of Health and Human Services (DHHS). The reported number of investigations submitted to ORI has remained low: on average 24 institutional investigation reports per year2.
ORI focuses resources, not only on evaluating institutional reports of research misconduct but also on preventing misconduct and promoting research integrity through deterrence and education. To evaluate these initiatives, we investigated whether the low number of misconduct cases reported to ORI is an accurate reflection of misconduct incidence, or the tip of a much larger iceberg. The latter seems to be the case.
The 2,212 researchers we surveyed observed 201 instances of likely misconduct over a three-year period. That’s 3 incidents per 100 researchers per year. A conservative extrapolation from our findings to all DHHS-funded researchers predicts that more than 2,300 observations of potential misconduct are made every year. Not all are being reported to universities and few of these are being reported to the ORI.

Read the rest

Impact Factors 2007

If anyone is interested, Thompson has just released the new Impact Factors for scientific journals. Mark Patterson takes a look at IFs for PLoS journals and puts them in cool-headed perspective.
One day, hopefully very soon, this will not be news. What I mean by it is that there soon will be better metrics – ways to evaluate individual articles and individual people in way that is transparent and useful and, hopefully, helps treat the “CNS Disease”. Journals will probably have their own metrics based on the value they add, but those metrics will not affect individual researchers’ careers the way they do now.

3D visualization

Another SCONC event:
RENCI to Show the Power of Visual Communications at Lunchtime Bistro:

The Renaissance Computing Institute (RENCI) invites the public to a Renaissance Bistro lunchtime demonstration and lecture from noon to 1 p.m. Thursday, June 26 in the Showcase Dome room at the RENCI engagement center at UNC Chapel Hill.
The Bistro is free and includes lunch on a first-come, first-served basis.
RENCI experts, Eric Knisley, 3D visualization researcher, and Josh Coyle, new media specialist, will demonstrate three-dimensional visualizations and interactive touch screen displays. Attendees will observe a brief demonstration of the Showcase Dome, a research environment equipped with a 15-foot tilted multi-projector dome display for interacting with data in an immersive 180-degree field of view.
RENCI at UNC Chapel Hill is located in the ITS Manning Building on UNC Chapel Hill campus, 121 Manning Drive. Parking is available in the UNC Hospitals lot on Manning Drive. For directions, see
RSVP by June 23 to

Historical OA

More and more societies are compiling their ‘classical’ papers.
Here is another one.
And here I wrote, among else:

“In discussions of Open Access, we always focus on brand new papers and how to make them freely available for readers around the world as well as for people who want to mine and reanalyse the data using robots. But we almost never discuss the need to make the old stuff available. Yet we often lament that nobody reads or cites anything older than five years. Spending several years reading everything published in the field in the 20th century up until about 1995 (as well as some 19th century stuff) helped me greatly in my own research. It would help others, I’m sure, especially those who are now revisiting old questions with new techniques. How are the classical papers going to be made available for today’s students?
SRBR is working on it now, and I assume that this will be done piece-meal, with each society doing their own work on making old literature available. What I saw (not yet available for public) is a development of a ChronoHistory website. Yes, people will send in pictures and anecdotes and old posters and stuff (and I hope once that material is online that SRBR will get a professional historian of science to make sense of it all), but the most important part of the site will be a repository of the old papers. Services of a real science librarian have been secured to deal with everything from copyright to technical problems in order to provide copies of many old papers on the site. Probably some of the papers will be available to everyone for free while others, due to copyright, may be available only to SRBR members with a password.”

I discussed this with Peter Suber and he says that we tend to focus on new literature because it’s the low-hanging fruit. Yet he agrees that ‘OA to past literature is highly desirable and that we should start thinking about ways to make it happen’. He wrote an article describing a *partial* solution to this problem: Unbinding Knowledge: A proposal for providing open access to past research articles, starting with the most important.
Peter says: “Ultimately we need all peer-reviewed journals to digitize their backfiles for OA. Some are already doing it. Some are digitizing their backfiles but charging for access. Some can’t afford to digitize their backfiles at all.”
Google is willing to digitize the backfile of any journal. Peter blogged about it in December 2006, although Google still doesn’t have a web page for the program. The Google deal isn’t very good. But for journals that can’t find any other funds to digitize their backfile, Peter thinks it’s better than nothing. Google does not have a website for this, but see this interview (this August 2007 interview – via):

Representing another effort to reach currently inaccessible content, Google Scholar now has its own digitization program. “It’s a small program,” said Acharya. “We mainly look for journals that would otherwise never get digitized. Under our proposal, we will digitize and host journal articles with the provision that they must be openly reachable in collaboration with publishers, fully downloadable, and fully readable. Once you get out of the U.S. and Western European space into the rest of the world, the opportunities to get and digitize research are very limited. They are often grateful for the help. It gives us the opportunity to get that country’s material or make that scholarly society more visible.”

Peter also said (personal communication): “As far as I know, the Open Content Alliance doesn’t (yet) digitize journals, but I hope it will start. However, when Google digitizes print literature it pays all the costs (and slightly restricts use of the results); but when OCA digitizes print lit, it requires the possessor or a donor to pay the costs (and provides full OA to the results).”
What do you all think? What is your Society doing about this, you favourite Journals?

Doing science publicly: Interview with Jean-Claude Bradley

Jean-Claude Bradley and I first met at the First Science Blogging Conference where he led a session on Open Science. We then met at SciFoo and later joined forces on a panel at the ASIS&T meeting and finally met again at the second Science Blogging Conference back in January where Jean-Claude co-moderated a session on Making Data Public. Jean-Claude is famous for being the pioneer of the Open Notebook Science movement. He started posting his daily lab activity and results on his blog Useful Chemistry. Soon, he attracted a lot of feedback and subsequently some excellent collaborators. As the work became more complex, Jean-Claude added more blogs, e.g., UsefulChem Molecules and UsefulChem Experiments, but in the end realized that wiki was a better format for this and started the UsefulChem Wiki where you can see, among else, how one of his students is writing a Masters thesis in real time.
Welcome to A Blog Around The Clock. Would you, please, tell my readers a little bit more about yourself? Who are you? What is your scientific background? What is your Real Life job?
I am an associate professor of chemistry at Drexel university. I’ve been there since 1996. My Ph.D. is in organic chemistry and I have done postdoctoral work on DNA chips and gene therapy. At Drexel I worked on nanotechnology and scientific knowledge management until 2005 when I started the UsefulChem project, centered on synthesizing new anti-malarial compounds using Open Notebook Science.
What do you want to do/be when (and if ever) you grow up?
I’ve worn many hats in my career and part of the fun is not really being able to predict what makes sense doing several years down the road. I try to concentrate on working on projects that I think will have an important impact and where I am in a unique position to contribute.
When and how did you discover science blogs? What are some of your favourites? Have you discovered any new cool science blogs while at the Conference?
I discovered science blogs just through using various social networking sites and finding like-minded people. Some of the blogs I follow most closely: Cameron Neylon’s Science in the Open, Deepak Singh’s BBGM, Antony William’s ChemSpider, Bill Hooker’s Open Reading Frame, Shirley Wu’s One Big Lab and Peter Murray-Rust’s blog. I don’t like answering these types of questions because I don’t want to leave people out:) There are many others in my blog reader but these are probably my main focus right now because they deal with Open Science issues.
bradleypic.JPGYou are one of the pioneers of Open Notebook Science. Could you, please, explain to my readers what this is?
Open Notebook Science is simply the practice of making one’s laboratory notebook completely public in as close to real time as possible. In organic chemistry this is pretty straightforward – researchers must keep a notebook where they record what they do and observe in an experiment, generally with the intent of making a specific compound. In other fields, records may be kept in different formats but the idea is that the research group doing ONS should strive to do research transparently with as little “insider information” as is reasonable. In organic chemistry this means providing access to all raw data files (spectra for example) so that another researcher can independently verify all observations and conclusions made.
You started your Open Notebook on a blog, but then later moved it to a wiki. Why? What are the advantages and disadvantages of the two platforms?
Yes, initially I started with a blog but realized fairly quickly that it was not sufficient to function as a lab notebook because there is no record of changes made. A wiki is really close to a perfect tool for the actual notebook since all page versions are time-stamped. We use Wikispaces as our hosting service, which has the advantage of providing third-party timestamps on everything recorded or changed.
Doing science is like focusing a lens. At first you have few data points and make some tentative observations. As more data get added and more thinking and talking get done, things become clearer and the notebook is updated accordingly. Sometimes that means errors get fixed and that entire process is tracked by the wiki. I still use the blog as a means of reporting on big picture issues and milestones. I can then link from the blog to the wiki to back up any claims I make.
Very few scientists are doing Open Notebook Science right now – do you see the practice exploding in the near future, with almost everyone doing it? Will this be a generational thing? Or dependent on the scientific discipline?
I don’t see the practice of full ONS becoming used by the majority of researchers very soon, although I do think many more scientist will become more open in some way. For example they may blog more about their current work or make more raw data available after their papers come out. I don’t think the practice should be mandated. Those who choose to do will most likely find it rewarding, if only in meeting new colleagues and collaborators. There may be something to the generational effect – the YouTube generation probably does expect information to be free to consume and share. There is certainly a discipline dependence – where intellectual property is a concern there will be an additional barrier.
When we talk about Science 2.0 and science blogging, we usually discuss science communication, publishing, networking, political action and teaching. But you have performed experiments in Second Life, i.e., Internet is also a tool for actually doing science. Do you see this happening more – people using the Web as a tool in scientific research in the open view of everyone who cares to come by and watch you?
Yes I do see researchers using the web to share their primary research – Gus Rosania and Cameron Neylon are probably the best recent examples. As far as Second Life, it is another tool – with Andrew Lang we are now able to interact with spectra (NMR, IR, etc) simply by “talking” to the display. We can display proteins and molecules in 3D with realistic shapes. Right now, for my work, I view Second Life to be like a website or blog – I can provide basic information about my research and link to the lab notebook on the wiki if people want more information. I have areas on Drexel Island and the American Chemical Society Island to share my lab’s work. My organic chemistry students also do projects for class in Second Life. I think the most useful outcome of using Second Life is meeting new smart people with similar interests. I have met a few wonderful collaborators that way.
Is there anything that happened at this Conference – a session, something someone said or did or wrote – that will change the way you think about science communication, or something that you will take with you to your job, blog-reading and blog-writing?
The most memorable event at the conference was probably meeting Moshe Pritsker from the Journal of Visualized Experiments. He offered to send someone over to my lab to record a protocol – I still have to arrange that….
It was so nice to see you again and thank you for the interview. I hope to see you again in January.
Check out all the interviews in this series.

What makes a memorable poster, or, when should you water your flowers?

What makes a memorable poster, or, when should you water your flowers?Being out of the lab, out of science, and out of funding for a while also means that I have not been at a scientific conference for a few years now, not even my favourite meeting of the Society for Research on Biological Rhythms. I have missed the last two meetings (and I really miss them – they are a blast!).
But it is funny how, many years later, one still remembers some posters from poster sessions. What makes a poster so memorable?

Continue reading

The Scientific Paper: past, present and probable future

From the ArchivesA post from December 5, 2007:
Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.
Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.

Continue reading

NIH public access law is now being implemented

As many of you may be aware, yesterday was the first day of the implementation of the new NIH law which requires all articles describing research funded by NIH to be deposited into PubMed Central within 12 months of publication. Folks at SPARC have put together a list of resources one can consult when looking for answers about the implementation of the access policy.
Bloggers on Nature Network as well as here on will write posts about the NIH bill and its implementation throughout the week (the ‘OA week’), informing their readers about the implementation, the next steps to be worked on in the future, and related topics. NIH is collecting public comments on the policy until May 1 so feel free to chime in yourself.
This law is not something that just appeared out of thin air a couple of months ago. As Liz Allen explains:

It’s been a long and winding road to get to this point and PLoS has been closely involved from the very beginning. Inspired by the desire to harness the potential of the internet to foster faster, freer exchange of biomedical knowledge, Harold Varmus, then director of the National Institutes of Health, proposed an electronic publishing site called E-biomed that would provide barrier-free access to the peer-reviewed and pre peer-reviewed scientific literature. After a period of public review (during which E-biomed met with fierce opposition from established publishers, sound familiar?), Dr. Varmus announced the creation of PubMed Central. Launched in February 2000, PMC is the NIH’s free digital archive of biomedical and life sciences journal literature and is the repository into which all NIH funded research articles must be deposited from today.

Of course, if you publish with PLoS, you do not have to worry about any of this – we know what to do and we do it for you automatically. The moment your paper is published, it is immediatelly deposited in PubMed Central, so you can go on with your work without worrying about the new law. In today’s issue of PLoS Biology, Harold Varmus exlains:

In contrast, open-access journals, like those published by PLoS or BioMed Central, make their articles immediately and freely available in PMC, eliminating any extra work by the authors and any delay before the articles are fully accessible. Furthermore, these journals permit far greater use of their articles, by allowing readers to explore and reuse the texts under the terms of a Creative Commons license. These degrees of freedom are possible because access and use do not diminish revenues: open-access publishers recover their costs upfront, frequently by charging a publication fee that is paid from research expenses, rather than with subscription charges to libraries and readers. Thus the distribution and reuse of open-access content can be without limit, just as scientists and the public would wish.

Science in the 21st Century

Bee and Michael and Chad and Eva and Timo and Cameron will be there. And so will I. And many other interesting people. Where? At the Science in the 21st Century conference at the Perimeter Institute (Waterloo, Ontario) on Sep. 8th-12th 2008. And it will be fun. This is the blurb of the meeting:

Times are changing. In the earlier days, we used to go to the library, today we search and archive our papers online. We have collaborations per email, hold telephone seminars, organize virtual networks, write blogs, and make our seminars available on the internet. Without any doubt, these technological developments influence the way science is done, and they also redefine our relation to the society we live in. Information exchange and management, the scientific community, and the society as a whole can be thought of as a triangle of relationships, the mutual interactions in which are becoming increasingly important.

So, register now while there is still space!