About JournalFire

February 16th, 2010

This blog has been up for quite some time, but so far none of the posts are actually about JournalFire.  Here is a brief intro.

JournalFire is about discussing journal articles.  As graduate students, we love reading and discussing the latest scientific articles with our friends and colleagues. We wanted to find a way to keep the discussion going outside of lab, and to include scientists from around the globe in the conversation.  JournalFire does just that, by making it easy to start discussing any article and to see what articles your friends and colleagues are reading and discussing.

The best way to understand JournalFire is to experience it for yourself.   Start sharing and discussing at http://journalfire.com

When research papers have a comment section

May 29th, 2009

Even if the comments aren’t always insightful, at least they’ll be entertaining.

Science Commons video

April 18th, 2009

It’s a few months old, but I just came across a great little video describing Science Commons directed by Jesse Dylan.  Dylan is known for his Emmy Award winning music video Yes We Can.  It’s great to see someone of his notoriety working on a project to help science.

Busting myths about Peer Review

January 9th, 2009

Michael Nielsen had a great post yesterday in which he attempts to debunk a few common myths about peer review.

Myth 1: Scientists have always used peer review
Myth 2: Peer review is reliable
Myth 3: Peer review is the way we determine what’s right and wrong in science

In his post, Michael presents some interesting anecdotes demonstrating just how bad peer review can screw up.  For instance, between 2000 and 2001, one author was able to slip 21 fraudulent papers past the editors and peer reviewers at Science, Nature, and the Physical Review.  The papers were retracted only after the broader scientific community weighed in.  Equally shocking were the papers that were initially rejected by top-tier journals.  Michael cites several high impact papers, including two that led to Nobel Prizes, which at first did not make the peer review cut.  Any peer review system will have its flaws, and Michael reminds us once again that our current system has plenty of its own.

BioBarCamp

September 10th, 2008

A few weeks ago I had the good fortune of being able to attend BioBarCamp in Palo Alto.  It was first BarCamp I was able to attend in its entirety and I am still impressed with just how well an unconference actually works.  The sessions ranged from strictly bio (biology of aging and DIYbio) to more general issues in science (open science, online communities for scientists, and scientific intellectual property) to the rather unique (science as a religion).  The one downside of a BarCamp is that you can’t attend every session.

One of the more interesting sessions I was able to attend was “Dealing with Noise in Science / How should scientific articles be measured?” lead by Pedro Beltrao and Peter Binfield of PLoS ONE.  The session discussed how impact in science is currently measured and explored what some better alternatives might be (right up our alley!).

Photo by Easternblot

For those who couldn’t make it, there was plenty live blogging coverage in the BioBarCamp room on FriendFeed.  I hope to see more unconferences for scientists pop up in the future.  I might just have to organize one here in Southern California.

Science and the Social Web

November 20th, 2007

John Wilbanks, Executive Director at Science Commons, has a nice post about the challenges of applying Web 2.0 (Social Web) technologies to science. He lists 3 major barriers:

The first [barrier] is the lack of a crowd – not only is the total number of scientists in any one field pretty low in terms of internet numbers, but it’s even lower in reality with specialization. Before you disagree, riddle me this. Would you fund a company with a total potential customer base of 60,000? That’s neuroscience, all of it, globally, and it’s a generous number.

That’s just a small number for Social Web. There’s a lot more college students for facebook than there are neuroscientists for neurobook. And the scary thing is that leading authorities have recommended the best way to deal with the life sciences PhD glut is to lower the number of life scientists!

While he may be right, I am not yet convinced that the current size of the crowd is a limiting factor. To write a Wikipedia, you need a crowd of millions, since for any one topic most people are non-experts. However, if the focus is solving problems in neuroscience, a crowd of 60,000 neuroscientists may be just enough.

Second problem is that scientific communication is a different beast than normal human communication. Scientists talk to their friends, but when talking to people they don’t know, it’s much more formal. They use communication to spec theories and to claim ground as theirs.

Zoom in. The people in one subdiscipline (let’s say brain function) probably have a lot in common with another (brain pathology) – same genes, proteins, pathways, areas of the brain. But they don’t do a lot of talking. They’re outside each other’s social micro-circles. They don’t knock back pina coladas together at SfN, look at the same poster sessions, attend the same lunchtime roundtables. They sure don’t read the same papers. Who has time to do that? And there’s a good chance that a scientist would draw a tighter boundary around her communications outside that micro-circle – you might engage in wild-ass guesses with your friends, but if you did that in front of a stranger scientist, you could look stupid. Worse, you could be right and get scooped.

[...]

Put simply, if a scientist isn’t going to say it to her colleagues at a conference, she probably isn’t going to blog it.

Although subdivisions certainly exists on paper, in practice, neuroscience is increasingly interdisciplinary. For instance, in my lab of about a dozen, we focus on insect olfaction, and have people working on genetics, behavior, electrophysiology, imaging, and computational modeling. So in addition to staying current in the insect olfaction literature, individuals in the lab need to stay connected to researchers in other disciplines who use similar tools or perform similar analyses. I imagine if you linked all these people together you would end up with a crowd that was larger and more diverse than one may initially expect.

I agree that breaking away from the current model of scientific communication is not a trivial task. It may take some time before scientists are comfortable will making less formal scientific discourse public. However I do think there is plenty of valuable and insightful discourse that takes place at conferences, lectures, and in journal clubs, and we are only now starting to see some of that information appear online in places like PLoS ONE, Nature Precedings, and science blogs.

Third problem is that there are no rewards for participating in these new forms of communication. Thus the title of the post. Has anyone gotten tenure for a well-linked blog in the life sciences? I’ve asked at every university and I’ve yet to hear of even one place where there’s an entry on the tenure review form. And again, if you blogged a novel theory and someone else won the Nobel for proving it to be true, well..that’d be bad. There’s no way to reward you, even if you’d timestamped it on your blog.

There is however an extended space for your citations on every last one of those review forms. Because citations aren’t like blog posts, where you lay out a wild theory (see for reference: this very post) for the world. Citations are a place in science where you have demonstrated something to be true (or at least an approximation of truth). They’re a formal style of communication that says, not only is this a fact of nature, but I – ME - am the one who proved it to be so.

This isn’t the kind of communication one blogs, because there’s no reward for it. That’s a fundamental disconnect that isn’t yet addressed.

The current reward and tenure system is certainly problematic, especially for young non-tenured researchers who may be more willing to adopt the Web as a new form of communication. While it seems certain that the Web will drive a culture shift science, I wouldn’t expect the shift to start with the reward and tenure system. Expect it to start like all things on the Web, from the bottom up.

So far, the science 2.0 revolution has been off to a slow start, but it may just be that we’re still missing that key disruptive technology. More than likely, that technology is being developed right now. It can’t get here soon enough, because when it does, that’s when the fun starts.

Victory for Open Access Bill

October 29th, 2007

The Senate on October 23 approved a bill containing the provision to require all NIH funded research to be made publicly available within 12 months of publication. In addition, Senator Inhofe (R-OK) withdrew his two amendments which would have rendered the provision ineffective. Thank you to all those who contacted their representatives during the eleventh hour. While this a great victory for Open Access, the struggle will likely continue since all indications are that the White House will veto the bill.

The Library Journal Academic Newswire provided a brief summary of the outcome and the three year history of the proposed NIH legislation (Thanks to Peter Suber). Excerpt:

Despite heavy lobbying from publishers against the public access provision, as well as White House opposition and the threat of two last-second amendments to gut it, the legislative battle culminated yesterday with overwhelming approval of the Labor, Health and Human Services appropriations bill (75-19). If enacted with the NIH language fully intact, the law would require NIH researchers to deposit their papers in the NIH’s PubMed Central database to be publicly available within a year after publication.

The legislative process, however, is far from over. The bill must now be reconciled with the House Appropriations Bill, which contains a similar public access provision. Negotiators from the House and Senate are expected to meet this fall. The final, consolidated bill will then have to pass the House and the Senate before being delivered to the President, where it is expected to be vetoed. Although the public access provision enjoys broad support, and the LHHS appropriations bill passed with hefty margins, the House bill passed with 279 votes, 11 short of the number needed to override a presidential veto.

Nevertheless, SPARC executive director Heather Joseph said even with many hurdles remaining, passage by Congress was “a milestone.”

Indeed, getting a public access policy at NIH through Congress has been a three-year odyssey for SPARC, an early and integral champion of the policy. The initially proposed NIH policy was introduced in 2004 as a mandatory policy with a six-month embargo. In a bitter setback, it was gutted at the eleventh hour, and implemented in 2005 as a voluntary measure. Lawmakers and advocates, however, vowed they would monitor the policy’s effectiveness. By 2006, the policy was failing so spectacularly (less than five percent of individual investigators deposited papers) that it no doubt helped marshal the heavy bipartisan support for the revised NIH policy passed on Tuesday.

[...]

Publishers, meanwhile, remain opposed to the NIH policy, contending it could undermine scholarly publishing, and they will likely have more opportunities to fight the public access mandate, either during reconciliation and/or if the LHHS appropriations bill is vetoed. They have also laid the groundwork for a legal challenge to the suit centered on copyright. While copyright experts doubt that claim could ultimately prevail, it could nevertheless delay implementation, giving publishers another chance to organize opposition in 2009.

Urgent: Take one minute to save Open Access

October 22nd, 2007

The U.S. Senate is currently considering a bill to require all National Institutes of Health (NIH) funded research to be made publicly available via PubMed Central within 12 months of publication. The bill has already been approved by the House and by the Senate Appropriations Committee. However on Friday, Senator Inhofe (R-OK) slipped in two amendments aimed at either removing the policy or adding language such that the policy is made ineffective. U.S. citizens can take action by contacting their representatives online by using the American Library Association’s online action center and providing a zip code.