An Oxford graduate student by day and a scientific activist by night, Nick Anthis isn't letting his Ph.D. research in protein structure get in the way of defending scientific and social progress.
2008 Nobel Prizes
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We're now two weeks into our 2008 ScienceBlogs/DonorsChoose Challenge, which means that the challenge is almost halfway over. So, if you haven't donated yet, please do! Either click on my widget to the left or on this link. The pace of donations has been a little slow this year, which is a shame considering that there are so many worthy proposals in need of funding. Let's step it up!
In case you needed a little bit of extra motivation, though, Seed just announced that it's offering prizes to donors. To maximize your chances of winning, donate as soon as possible, because prize drawings start this Friday! Janet has the details:
I was excited when I saw that The New England Journal of Medicine had today published summaries by Obama and McCain of their health care plans, expecting something quite detailed to appeal to a highly critical expert audience. However, their summaries were still as general and vague as ever. Regardless, these new write-ups are still a nice resource for people interested in the two candidates' plans. You can read Obama's plan here, McCain's here, or see a pdf of both side-by-side here.
On many aspects, both plans--at least as they're presented here--are quite similar. Both stress preventative medicine, modernizing our infrastructure, etc., etc. However, two major differences are apparent. The first is a difference in basic philosophy. Although he doesn't explicitely say it in his NEJM piece, we know that Barack Obama believes that health care in the US is a right, and that comes through in his writing. McCain, however, believes that health care is a "responsibility" (whatever the hell that means), and he includes loaded language throughout his write-up about "government waste" and related conservative talking points.
When I think back to the presidential debate last night, one moment stands out in my mind more than any other. And, no, it wasn't McCain calling Obama "that one". It was the discussion following Tom Brokaw's question "Is health care in America a privilege, a right, or a responsibility?"
Health care came up several times throughout the debate, but here I thought the answers were most telling. This is in spite of the fact that I took issue with the way the question was phrased. Specifically, I felt that the third choice ("responsibility") was unnecessary and just gave the candidates an easy cop out. Guess which one McCain chose:
Earlier today, the Nobel committee announced that the 2008 Nobel Prize in Chemistry has been awarded to Osamu Shimomura, Martin Chalfie, and Roger Y. Tsien "for the discovery and development of the green fluorescent protein, GFP." There's much to be said for how useful a tool GFP has been in cellular biology, but Alex Palazzo has already covered it at The Daily Transcript, so go check out his post for more.
The winners of the 2008 Nobel Prize in Physiology or Medicine have been announced, and the prize has been awarded for early discoveries that have subsequently led to vaccines or treatments of two widespread virus-caused diseases. Half of the prize was awarded to Harald zur Hausen "for his discovery of human papilloma viruses causing cervical cancer" and one-fourth each was awarded to Francoise Barre-Sinoussi and Luc Montagnier "for their discovery of human immunodeficiency virus." For more, check out the official press release or the more detailed description of the prize-winning discoveries from the Nobel Committee.
This is an interesting subject for a Nobel Prize, since a huge number of scientists have contributed to the basic and applied research on HIV and HPV, leading to several significant clinical successes. The committee could have taken this in a few different directions, but they decided in both cases to give the award to just the scientists who made the initial discoveries: the initial descriptions of HIV and the identification of HPV as the predominant cause of cervical cancer. Thanks to the discoveries of Barre-Sinoussi and Montagnier (and an enormous quantity of research by a wide range of scientists that followed them), patients infected with HIV can be treated with a wide array of antiretroviral drugs that can greatly extend their lifespan and improve their quality of life. In the developed world, at least, AIDS is no longer the rapid death sentence it once was in the 1980s. Likewise, thanks to Hausen and the work that followed on his footsteps, we now have two effective vaccines for HPV--which are effectively vaccines for cervical cancer.
Recent polls have shown that voters trust Obama over McCain in addressing the economy by a margin of about 10-15%. But, what do the experts think?
The Economistconducted its own poll of economists (appropriately), and found that they agreed that Obama is the stronger candidate when it comes to the economy--but by a much wider margin. Eighty percent respondents agreed that Obama has a better grasp of economics (versus 8% for McCain), and 81% believed that Obama would pick the better economic team (versus 14% for McCain). On a scale of 1-5, respondents gave Obama's economic plan a 3.3 and McCain's a 2.1.
McCain couldn't even catch a break from Republicans. Although these self-identified Republican economists gave McCain the benefit of the doubt on their assessment of his economic plan and his prospects for picking a better economic team, 46% said that Obama appears to have a better grasp of economics (versus 23% for McCain). This graphic from The Economist gives you an idea of just how stark the results of this survey were:
Yesterday, The New York Timesreported on the latest prominent medical doctor to be outed for not reporting the vast sums of money he was receiving from drug companies:
One of the nation's most influential psychiatrists earned more than $2.8 million in consulting arrangements with drug makers from 2000 to 2007, failed to report at least $1.2 million of that income to his university and violated federal research rules, according to documents provided to Congressional investigators.
The psychiatrist, Dr. Charles B. Nemeroff of Emory University, is the most prominent figure to date in a series of disclosures that is shaking the world of academic medicine and seems likely to force broad changes in the relationships between doctors and drug makers.
Apparently Nemeroff has been at this game for quite a while, and this isn't the first time he's been caught:
For the month of October--and for the third year in a row--ScienceBlogs will be teaming up with the DonorsChoose Bloggers Challenge to raise money for worthy classroom projects. This year, they've added a nifty blog widget, which I've posted at the top of my left sidebar. So, if you're in a generous mood, you can donate directly from my widget, or you can visit my challenge here. DonorsChoose is a website where potential donors can browse through project proposals written by teachers from all across the US, and this year I've personally picked out ten projects that I would like to see funded. Most of my picks involve biology or molecular biology, but there's quite an assortment. You can view the ScienceBlogs leaderboard here, and the leaderboard for all of the categories of participating blogs here. As in previous years, Janet Stemwedel of Adventures in Ethics and Science is coordinating this drive, and you can see her blog entry about it here.
In 2006 my challenge raised $495, and then in 2007 we raised $2,500. As I write this, I have just over $5,000 of unfunded proposals in my challenge. Since some of these projects will also be in other challenges, that's the maximum value we need to raise. I'm optimistic that we can do it, because I know that you ScienceBlogs readers are a generous bunch. In 2006, ScienceBlogs overall raised over $26,000 (including $10,000 is matching funds from Seed). As impressive as that was, in 2007 we managed to raise a whopping $69,000 (including $15,000 from Seed). You've set the bar pretty high, but--total collapse of the American financial system not withstanding--I have a pretty good feeling that we can top that this year.
On Saturday, 20 September, Mo Costandi (Neurophilosophy), Selvakumar Ganesan (The Scientific Indian), Kara Contreary (Pure Pedantry), and I hosted a gathering at the Calthorpe Arms in London to join others in celebrating ScienceBlogs' one millionth reader comment. In addition to footing the bill for the drinks, ScienceBlogs also sent each party a nifty little Flip video recorder. As you can see, we didn't get too crazy with it, but we did manage to capture about half an hour of conversation, and I've divided it up into three separate videos:
Yesterday, the Obama campaign released a letter of endorsement signed by 61 Nobel Laureates (click here for a nicer looking pdf). Michael Stebbins of Scientists and Engineers for America points out that "this is the largest number of Nobel Laureates to ever endorse a candidate for office."
And, why should we be surprised? Obama's answers to a scientific questionnaire released last month were scientifically sound and indicative of good scientific advising. Then, earlier this month, we got to find out who has been behind that solid scientific advising. Wired gave a good rundown of the five-member team (which includes two of the Nobel Laureate signatories of yesterday's letter) made up of Peter Agre, Don Lamb, Sharon Long, Gilbert Omenn, and Harold Varmus.
McCain, on the other hand, has refused to identify his science team.
Update: The Obama campaign also just released a more detailed 11-page science plan.
Yes, these are really the front and back covers of this week's issue of Nature.
Really.
The dog on the left looks so hopeful. The dog on the right... confused.
On a more serious note, Nature does have a full section on the upcoming election, including Obama's answers to some science-related questions (McCain declined to participate). Check it out.
Since our paper on the role of blogs in academia was published earlier this week, we've received quite a bit of feedback from the across blogosphere. Befittingly, the authors of the paper have contributed to this, as Tara gave her thoughts on her blog, I gave mine on my blog (Shelley has been busy traveling for interviews, so she hasn't had a chance to weigh in yet), and we published a list of acknowledgments. (I'd also like to thank our respective universities' press offices for their outreach efforts. I found Oxford particularly pleasant to work with, and they even put up something on their website--although it's a bit overly focused on me, as one might expect coming from my university).
Of course, we already knew what we thought, so let's see what others had to say. I'll start with some of the more favorable posts. In particular, Brian Switek of Laelaps, John Dennehy of The Evilutionary Biologist, and Dave Munger of ResearchBlogging all gave positive reviews, each from a different perspective. Munger focused on the role of ResearchBlogging, Dennehy draws on his own experiences, saying "blogging has been one of the best academic decisions I have ever made" and addressing those not convinced by pointing out that "back in 1994, hardly any labs had a web page, but now it seems obligatory". Switek gave his own case for the value of blogs in academia, one that runs parallel to the arguments we make in our paper. In particularly, I'd like to quote the following paragraph from Switek, because it is relevant to addressing some of the criticisms discussed below:
Earlier today, Elias Zerhouni--who has been the director of the NIH since 2002--announced that he will resign at the end of this October. According to the NIH press release, he is stepping down "to pursue writing projects and explore other professional opportunities." The Hill has more from Zerhouni about his resignation:
"I felt it would be in the best interests of the NIH for me to leave before the election," Zerhouni said. With a vacancy in the directorship, he explained, when Sen. John McCain (R-Ariz.) or Sen. Barack Obama (D-Ill.) wins the presidential election in November, he would be more inclined to name a replacement, he said.
"I would want people to focus on NIH as early and as soon as possible after the election," Zerhouni said, rather than assume the agency is in good hands already. Zerhouni said he has no interest in remaining in office under the next administration.
Zerhouni stated that "there's no precipitating event" that led to his decision to vacate his position and rejected characterizing his departure as a resignation. "It's just basically stepping down at the right time," he said. "I've always said I would end my tenure at this time."
Eliot Zerhouni has overseen the NIH at difficult time, when its budget has been stagnant, leading to a precipitous decline in grant success rates. Two decent accomplishments, however, that occurred during his tenure were ethics reform and the NIH's new policy on open access to publications funded by its research dollars. The legacy of what's more commonly touted (at least by Zerhouni) as his major achievement--the NIH Roadmap--remains more dubious, as it is often blamed for siphoning funding away from more basic and higher-risk research.
Yesterday, I blogged about the paper that Shelley Batts, Tara Smith, and I just published in PLoS Biology on integrating blogging into academia. As promised, we have a very long list of people we would like to acknowledge for their contributions to this work. As I noted yesterday, this paper was built upon the anecdotes, suggestions, and other feedback we collected from across the science blogosphere. In addition to the people listed below, we also gained insight from a variety of discussions that took place within the internal ScienceBlogs forums, and we owe a big thanks to all of our fellow ScienceBloggers who participated in those.
I should note that these conversations took place over the course of a year and involved three different authors talking to different subsets of bloggers, making the compiling of such a list of acknowledgments difficult and the risk of leaving someone out more than we would like. If we left you out, please accept our apologies, and realize that it's nothing personal (and please contact me if you were left out so that we can include you).
So, without further ado, we owe a very big thanks to the following contributors:
Just over a year ago, I joined fellow science bloggers Shelley Batts (Of Two Minds) and Tara Smith (Aetiology) in setting out to catalogue the accomplishments--and pitfalls--of the scientific blogosphere and to explain why people should pay attention. In a sense, we wanted to say "We are the science bloggers; hear us roar!" And, in order to make our case, we drew from the collective experience of our fellow science bloggers, far and wide, asking how blogging had affected their work, their careers, and their lives--both positively and negatively.
The results were astounding. Across the blogosphere, scientists had started new collaborations, enhanced their scientific work, advanced their careers, been able to communicate science as never before, and had been offered a whole array of new and unique experiences and opportunities in part or in full due to their blogs. In fact, the stories we heard were so compelling that instead of just communicating them we asked ourselves another question: why has this phenomenon gone so underreported and unappreciated within academic circles? And, more pointedly, how can we most effectively communicate this potential to an academic audience--in hopes of catalyzing even more of these wonderful successes?
I'm not sure if this is the answer, but our best effort at addressing this gulf between academia and the blogosphere was published today in PLoS Biology. In our paper, we address various instances of efforts to bring academia and blogging closer together, and we offer a series of suggestions for how academic institutions--and bloggers--might carry this forward to the next level. We believe that when bloggers and academic institutions work together, the result can be mutually beneficial for both parties, and can be carried out in a way that advances the institution's mission without destroying the independence that makes the blogosphere so powerful. By no means are we saying that all science bloggers would want to be more closely associated with an academic institution--far from it, actually--but we give suggestions for how this might be accomplished when deemed desirable. I won't say much more here--instead encouraging you to take a look at the paper yourself--except for offering you the take-home message of the paper in the form of its final paragraph:
As ScienceBlogs prepares to receive its one millionth reader comment, ScienceBloggers are planning parties around the globe in celebration of the event. For our readers in London, Mo Costandi (Neurophilosophy), Ed Yong (Not Exactly Rocket Science), Selvakumar Ganesan (The Scientific Indian), Kara Contreary (Pure Pedantry), and I have planned a party on Saturday, 20 September. So, if you are in the area, please come and join us at the Calthorpe Arms, a pub near Russell Square and King's Cross (see details here,) from 7:00 pm until close. ScienceBlogs has given us $100 per blogger ($500 total), and we're going to use that money to provide food for everyone and then pay for drinks until the money runs out. So, if you want to drink for free, try to show up early!
It is by no means necessary to RSVP, but if you do think you're coming, let me know by email or in the comments section to help us plan how much food we should order. Also, if you haven't already, make sure you enter the Millionth Comment Contest for your chance to win a very sciencey trip for two to NYC.
Update: Ed Yong can no longer make it to the London party, but the rest of us will still be there.
If so, you should check out EcoliWiki, which you might find a useful resource, and you might even find yourself compelled to contribute some of your knowledge to it.
Since I'm already blogging about E. coli today, I thought I would also bring up an interesting project I found out about earlier this week. I'm currently wrapping up a short visit to my alma mater, Texas A&M University, and while there, I've met up with two local science bloggers that I know of: Matt Springer of Built on Facts (a fellow blogger here on ScienceBlogs.com) and Jim Hu of Blogs for Industry. Hu is an associate professor of biochemistry and biophysics, and earlier this week he told me about EcoliWiki, which is one of his latest projects. The goal of EcoliWiki, which functions under the larger umbrella of the NIH-funded EcoliHub project, is to use open-source/wiki methods to fully annotate the E. coli genome.
As more and more genomes become fully sequenced, annotating each by traditional means, relying solely on in-house curators, becomes increasingly expensive and impractical. The goal of EcoliWiki, on the other hand, is to instead distribute this task among the scientific community at large, making the task more time- and cost-effective--and hopefully serving as an example for other genomes as they go online as well. To prevent spam and to provide some quality control, annotators have to be registered in order to contribute. The project already has many contributors, but many more are needed for it to reach its full potential, so if you're interested in contributing, you can email Hu or myself. For more on the use of wikis in science, check out this article in Nature or this letter in Science.
Microcosm: E. Coli and the New Science of Life by Carl Zimmer
Pantheon: 2008, 256 pages. Buy now! (Amazon)
I come face-to-face with Escherichia coli every day. In a sense, we all do--as billions of E. coli inhabit every individual's intestines. But for me, E. coli is a protein factory. I'm a structural biologist, and my work depends on being able to produce large amounts of specific proteins--generally proteins found in humans or mice. However, purifying large amounts of these proteins from humans or mice would be virtually impossible, and manipulating these proteins in the manner I need for my studies would be literally impossible. Instead, all I have to do is introduce a small piece of engineered DNA into a single E. coli bacterium--just one cell--and in less than 24 hours, I'll have billions of E. coli bending to my will and producing milligrams of my protein of interest on demand.
If you've gone to ResearchBlogging.org lately, you may have noticed that it's been given a face-lift. Actually, it's more than just a face-lift, as cofounder and president Dave Munger points out, including these new features:
Multiple language support (and 30 new German-language bloggers!)
Topic-specific RSS feeds
Post-by-post tagging with topics and subtopics
"Recover password" feature
Email alerts when there is a problem with posts
Users can flag posts that don't meet our guidelines
Customized user home pages with bios and blog descriptions
Blogger photos/other images displayed with each post
On Saturday, ScienceDebate 2008 and Scientists and Engineers for America (SEA) announced that Barack Obama answered a fourteen-part questionnaire that they put together along with several other scientifically oriented organizations. Major props to ScienceDebate, SEA, and these other organizations for making this happen and to Barack Obama for thoroughly answering these fourteen questions.
I'd encourage you to check out his answers for yourself, at either of the links above. My own analysis is that his answers overall are quite satisfactory. He says all of the right things for the most part, although not always in enough detail to indicate how his ideas would actually come to fruition. (To be fair, he does provide more detail than I would expect from a politician.) Of course, I don't expect him to have all of the answers--especially not this early in the process--so the most important thing he can do is continue to build a body of reliable, outspoken, and diverse scientific advisors that can formulate ambitious but workable plans to tackle the various difficult issues his administration will face--issues that have largely languished under the current administration.
...apparently involves reposting others' blog posts without permission or proper attribution.
I'm being facetious here, of course, but it is quite ironic that Mike Dunford of The Questionable Authority just caught anti-open-access warrior Elsevier copying the majority of one of his blog posts and posting it on a freely available site without attribution to him (although there is a link to his original post) or his permission. Click here to see his original post and here to see Elsevier's reposting (Mike also saved it as a pdf).
Although it is common practice within the blogosphere to quote liberally from other sources, we do this with the understanding that others may quote liberally from us. In fact, we hope that they will--as long as they give proper attribution. While we do this, our own material is made freely available, with running costs being paid for by advertisers (i.e., a pretty standard open access model) or just being footed by the blogger. Elsevier, on the other hand, not only reserves most of its material for paid subscribers, but actively fights the open access movement with insidious initiatives like PRISM.
In case the irony here is somehow lost on you, Mike eloquently explains:
You may have noticed a link on the right sidebar advertising the ScienceBlogs/Seed reader survey. Either way, I'd encourage you to spend a few minutes of your time to give some feedback. The powers that be certainly take your comments into consideration--and you could even win an iPhone 3G, a MacBook Air, and a 40 GB Apple TV. Based on current turnout, you might even have a decent chance of winning. Click here to take the survey. (The survey closes at 11 pm EDT, this Friday, August 15th.)
Because they've let in another Aggie. Matt Springer, who writes ScienceBlogs' newest blog, Built on Facts, is a graduate student in physics at Texas A&M University, my alma mater. His blog is live now, so go check it out.
Below is the second part of my interview with planetary geologist Bethany Ehlmann. In the first part, she discussed two of her recent papers on Martian geology (see citations below). In this segment, she discusses water on Mars more generally.
Bethany Ehlmann
Nick Anthis: Would it be possible to briefly take our readers through the history of the discovery of water (or traces of past water) on Mars? I know that this is an important area, but it seems like there's so much work on it coming out now that it's hard for someone not in the field to put it all into context. Maybe you could just tell us what the key discoveries were.
Bethany Ehlmann: Part of being a graduate student is that I'm still learning what's been done before. So with that caveat...
NA: I understand. I'm writing my PhD thesis now, and I'm certainly discovering things now in the literature that I wish I had known about before I started my work!
BE: I really think it goes all the way back to Percival Lowell's canali: artificial straight channels that he thought he saw in his telescope. It really captured the public and scientific imagination even though later scientists couldn't replicate his find.
Planetary geology is a fascinating area--particularly when it pertains to the search for extraterrestrial life. I wrote about it once during my brief stint as a student science writer, but it's not an area that I've really covered on my blog. However, a former colleague of mine from Oxford, Bethany Ehlmann, was recently involved with a couple of papers on geological formations left by ancient Martian water, so I thought that this would be a perfect opportunity. Ehlmann is currently a PhD student in the geological sciences at Brown University and part of the CRISM (Compact Reconnaissance Imaging Spectrometer for Mars) team . Before that, she was a Rhodes Scholar at Oxford, where she completed two MSc degrees. She was recently the fourth author on a paper in Nature and just before that the first author on a paper in Nature Geoscience, both on Martian geology (see references below).
I've broken our interview into two parts. In the first part, published here, Ehlmann discusses her two recent papers. In the second part--which is published in a separate post--she discusses water on Mars more generally.
For those of my readers in the UK (or anywhere else where you have access to Sky News), I'll be appearing live on Sky News at about 10:30 11:30 BST this Friday to talk about Barack Obama's visit to the UK and his support among Americans living abroad. I'm not sure if the video will be posted online afterward, but if it is, I'll post a link to it here.
If I like what I see, I'll receive 5 more issues (6 in all) for just $14.95. That's 50% off the cover price! If I'm not completely satisfied, I'll simply write "cancel" on the invoice and owe nothing. The free issue is mine to keep.
An Oxford graduate student by day and a scientific activist by night, Nick Anthis isn't letting his Ph.D. research in protein structure get in the way of defending scientific and social progress.
