Science, meet World
Archive for July, 2011
Get To Know A Scienceblogger: Jonathan Eisen
Jul 28th
Today we have another post in our Get To Know a Scienceblogger series.
Jonathan Eisen is a professor at the Genome Center at the University of California (UC), Davis and holds appointments in the Department of Evolution and Ecology in the College of Biological Sciences and Medical Microbiology and Immunology in the School of Medicine. In addition to his research, Dr. Eisen is also a vocal advocate for “open access” to scientific publications and is the Academic Editor-in-Chief of PLoS Biology. He is also an active and award-winning blogger/microblogger at The Tree of Life and on Twitter. You can learn more about him here. The info in this biography and the picture at left have been taken from Jonathan’s blog, which uses a Creative Commons Attribution License.
What is the topic of your blog?
Many threads woven together
Open science and open access to scientific literature
Microbiology and microbial diversity
Genomics and evolution
What was your primary reason for starting a blog?
Sharing with others fun things I was doing — got sick of sending out lots of email messages and wanted a better way to share …
How often do you post, and roughly how much time goes into each post?
Varies - no system. I post when I have time and have something interesting to post about. Maybe 2-3 x / week. Some posts take five minutes some take 4 hours …
How do you fit in time for social networking?
I view it as a fundamental part of my job as a scientist and an educator. I use social networking to follow the literature, to do outreach, to communicate with colleagues, etc.
Have there been any benefits to blogging, either personally or professionally?
Lots. See http://phylogenomics.
Have there been any downsides to blogging, either personally or professionally?
#1 issue is when I write something that is too obnoxious and regret it later. I have done this maybe 3-4 times and have learned to try and write about ideas without criticizing individual people too much.
What piece of advice would you give other scientists in your situation who are considering moving into social media?
Don’t be afraid. Spend as much time or as little time as you want on this. These systems are tools, no more or no less. You decided how to use them just like you decide how to use a microscope. But like a microscope they can be really useful - so consider experimenting with them.
What have been the most effective ways of promoting your blog?
Twitter …
Were you surprised by anything blog related, either good or bad?
Not really … it’s all pretty straightforward. Main surprise I guess is how many people read my blog …
Any other information that you think people would find useful?
Blogs, twitter, facebook, etc are all just computer programs. They are neither good nor bad. They can be used well or poorly.
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Thanks Jonathan!
Post Publication Peer Review: Blogs vs Letters to the Editor
Jul 25th
There has been a lot of discussion recently about the value of peer review (including this phenomenal post by Joe Pickrell of Genomes Unzipped), and whether other models might be cheaper, faster, and ultimately better than the current system.
Regardless of what these alternative models of publishing look like, I agree with Joe that social media will play an important role in identifying high quality papers. Social media would thus be acting as a form of post publication peer review (henceforth referred to as PPPR), and has actually been doing so for some time (Researchblogging.org being the best example that I can think of, although the PLoS Hubs is aimed at this as well). This is in contrast to Letters to the Editor, which up until a few years ago was the only form of PPPR available to researchers. I have recently had experience with both of these forms of PPPR, and thought it would be fun to compare and contrast the experience with each, focusing on the categories that I considered when deciding whether publish my critique in a blog post or Letter.
Speed
My experience with a Letter to the Editor came about last summer when I felt that the conclusions of this article in the International Journal of Behavioural Nutritional and Physical Activity (IJBNPA) did not match up with their data (actually, I felt that their conclusions were directly contradicted by their data). The article was published on July 29th, 2010, and my colleague Stephanie emailed it to me that same day. I read the paper in detail about a week later, and decided to write a Letter to the Editor with Stephanie and our co-supervisor.
Unfortunately IJBNPA had never published a Letter before, and it took some time for IJBNPA and their publisher (BMC) to decide whether they were willing to publish Letters in the journal, and whether or not they would charge their usual $1670 USD processing fee. Fortunately, by the end of 2010 BMC had told us that IJBNPA would begin accepting Letters, and that they would waive their processing fee.
Thus our Letter was officially submitted to the journal in January of 2011, five months after the initial article had been published. Although it was accepted quite quickly, our Letter couldn’t be published until the authors of the original paper had had a chance to respond. Thus our article was officially published on May 25, nearly ten months after the article we were critiquing. It is worth noting that the original article received BMC’s “Highly Accessed” designation, meaning that it was among the more popular articles in the journal during that time-span (during this time readers had no way to know that anyone felt there was a problem with the paper).
In contrast to a Letter, a blog post about an article can be published as soon as it is written. In this case I wrote a blog post about our critique on June 12, 2011 and published it on June 13, for a total turn-around of 1 day. Rosie Redfield’s famous #arsenicDNA blog post and Letter to the Editor showed similar time differences - her blog post was published on December 4, 2 days after the article she was critiquing. In contrast, her Letter to the Editor wasn’t published online until May 27, a full 5 months after the original article. When it comes to speed, traditional Letters can’t compete with blogs.
Winner: Blogging.
Impact
Academic career versus fulfilling personal life: are they mutually exclusive?
Jul 13th
Travis’ Note: Earlier this year Nature held a Career Columnist Competition looking for Post Docs and PhD Students who were interested in writing about the ups and downs of being a trainee. They received over 300 submissions, and the 6 who were chosen look fantastic. Unfortunately for me I was in the 294+ who did not get selected, but the good news is that I can now repost my submission here! It doesn’t relate specifically to science communication, but I’m hoping it may still be of interest.
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I am currently in the second year of a four-year PhD program. I enjoy the work that I am doing, and frankly I love the lab that I am working in. But as I inch towards the completion of my degree, I can already feel myself becoming increasingly anxious about what comes next. I have many friends who have gone down this road before me, and they have taken a number of routes, both traditional and otherwise. Some have gone on to post-docs, and several are in tenure-track positions at research or teaching universities. Still others have gone to work with industry or government, and a few have even decided to focus on science writing or other “non-academic” pursuits.
But when it comes to deciding what I want to do next, I really have no idea. The one thing I do know is that in addition to a job, I also want a life. And this is something that I have noticed many, if not most, of my graduate student peers are also looking for. While they still love research, they don’t want the typical tenured professor’s life of previous generations - those professors who spent 16-hour days in the lab, whose entire life revolved around their work with little time for family or other interests. In the limited number of conferences that I have attended, I have already heard multiple professors begin a Lifetime Achievement Award acceptance speech by thanking their family for “putting up with the fact that I was never home”. That doesn’t strike me as a fond way to look back at a lifetime of research.
It seems at times that having a life outside of research – spending any waking hours away from work and the lab – can be viewed by some as a form of academic infidelity. Take, for example, Kathy Weston’s recent article in Science Careers which details the way in which she fell out of love with her research career at a well-respected institution, largely because she fell in love with the rest of her life. At times it seems that there really is no happy medium – we can either give up our lives for a successful career, or give up our career for a successful life. And yet I would expect that any rational person (which I hope would include most scientists) would realize that allowing some semblance of work-life balance would not only make life as a professional researcher more pleasant, but also more alluring to students like myself. As Dr. Weston explains in her recent article, she would likely not have become as disillusioned with her career as a scientist if it had been possible to accommodate her additional roles as a mother, wife, and daughter.
And so it is not surprising that when I speak with my graduate students colleagues, they describe long-term career goals that are likely more modest than those of previous generations – a fulfilling job with a modest income, and the ability to do good science and/or teaching. But most are quick to add that they are not interested in being that professor - the world-travelling superstar – because most of us do not feel capable of being that type of scientist without giving up everything else in our lives.
So when I finish my PhD, I really don’t know where I will go next. But I hope that there will be an option that allows me to be fulfilled both professionally and personally, rather than having to choose one over the other.
Travis
Scienceblogging Roundup: July 3-9
Jul 9th
While we post lengthy discussions here on Science of Blogging, there are many research updates, news stories, videos, etc. related to science communication that we come across on a daily basis that never grace the pages of the blog. Most of these mini-stories we share with our followers on Twitter, and we encourage those of you with active Twitter accounts to communicate with us there to get real-time updates of all the stuff we are discussing (Follow Peter and/or Follow Travis). For those of you who shy away from Twitter, enjoy below the best mini-stories that we came across during the prior week along with links to the original source so that you can follow the full story.
- The effects of churnalism on healthcare news and the public (PLoS Guest Blog)
- At a recent conference Rebecca Watson was propositioned in an elevator. She told people, and all hell broke loose. John Rennie examines the inhuman treatment Rebecca Watson has received this week, and makes the obvious but excellent point that it is wrong to make people pointlessly uncomfortable (Gleaming Retort)
- Researchers at Johns Hopkins claim they can track public health trends using twitter (Johns Hopkins University)
- Is it beneficial for obesity researchers to build trust with industry? (Obesity Panacea)
- Scientific American has unveiled their new blog network, which has an absolutely amazing lineup (including the only lineup of the major science blogging networks that is more than 50% female). Congrats to former Scibling and Plogster Bora Zivkovic for assembling such a terrific crew, and to all of the bloggers who have joined the network! (Scientific American)
Can we trust scientists who give TED talks?
Jul 7th
I came across an interesting article this morning in Slate questioning recent papers on the “contagiousness” of factors ranging from obesity to divorce. The papers were published in top journals like the New England Journal of Medicine (I wrote this enthusiastic blog post about the findings back in 2008) and have generated a wide range of media attention, including the TED talk which I’ve embedded below.
As far as I know the questions surrounding these papers have been entirely statistical (as opposed to ethical) in nature. Below is the abstract of a critique published in the journal of Statistics, Politics, and Policy earlier this year which nicely outlines the problem of having a high profile paper with a poor stats section:
The chronic widespread misuse of statistics is usually inadvertent, not intentional. We find cautionary examples in a series of recent papers by Christakis and Fowler that advance statistical arguments for the transmission via social networks of various personal characteristics, including obesity, smoking cessation, happiness, and loneliness. Those papers also assert that such influence extends to three degrees of separation in social networks. We shall show that these conclusions do not follow from Christakis and Fowler’s statistical analyses. In fact, their studies even provide some evidence against the existence of such transmission. The errors that we expose arose, in part, because the assumptions behind the statistical procedures used were insufficiently examined, not only by the authors, but also by the reviewers. Our examples are instructive because the practitioners are highly reputed, their results have received enormous popular attention, and the journals that published their studies are among the most respected in the world. An educational bonus emerges from the difficulty we report in getting our critique published. We discuss the relevance of this episode to understanding statistical literacy and the role of scientific review, as well as to reforming statistics education.
I should mention that frankly this stats discussion is well over my head, and it may be that these critiques are thoroughly off base - it took the authors a long time and multiple attempts to get this article published, which could be a sign that there is little weight to the arguments, although it could also be a sign that it’s just hard to get this sort of thing published (our friend Yoni Freedhoff detailed the whole process a few weeks ago, which is where I first heard about these new issues). The point being that these papers are among the most high-profile studies published in my field of research in the past few years, and yet people are now saying things like this:
“[Christakis and Fowler’s] errors are in some places so egregious that a critique of their work cannot exist without also calling into question the rigor of review process,”
When I was reading the Slate piece this morning it got me thinking about other recent scientific findings which have been presented in “big idea” forums like TED only to have important questions raised about their veracity.
For example, earlier this year Felisa Wolfe-Simon and other NASA researchers published a paper in Science claiming to have found bacteria which could use arsenic rather than phosphorous as the backbone of its DNA. Shortly thereafter Rosie Redfield wrote a scathing review of the paper on her blog, spawning a massive backlash against the paper in the field as a whole. This backlash prompted Dr Wolfe-Simon and her co-authors to retreat from the media and argue that:
Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated.
And yet just a few months later David Dobbs reported that Dr Wolfe-Simon had not only presented her findings at TED, but had also reiterated her paper’s highly disputed conclusions. Here is what David had to say in March:
Apparently the peer-reviewed realm now includes the high-profile TED conference, where on Wednesday Wolfe-Simon talked about her paper. Neither video nor transcript is released as yet [Travis’ Note: I still haven’t seen them online, but please let me know if someone else has seen them], but accounts suggest she discussed her controversial discovery outside the realm of peer review — in fact, in the most public venue imaginable —and one anonymous source I spoke to today said she repeated the paper’s explicit and disputed claims about arsenic incorporating DNA.
And then there is the case of Marc Hauser, popular author and Harvard researcher who has been under investigation for academic misconduct for the the past year, and whose ultimate fate (as well as his guilt or innocence) remains very unclear. In fairness, he hasn’t presented at TED (although Slate called it “TED-level stuff“), but his popular book Moral Minds certainly places him into the “big idea” category of scientist.
The fact that these eminent “big idea” researchers seem to keep making questionable moral/ethical/academic misjudgments is distressing for a few reasons. First and foremost, it’s because these “big idea” scientists are really the stewards for all of us. TED talks, popular books - these are the way that many non-scientists find out about what is that we do, and why it matters. If the people doing those talks and writing those books turn out to be sketchy then it makes all of us look bad.
But it is also worries me because this is not good for science. I had to stop myself from writing this is not the way that science is done, because that just seems like a cliche in a blog-post mentioning Rosie Redfield and #arsenicDNA. But for science to be done there has to be room for genuine debate, and TED talks don’t seem to have much of that… they seem more like a monologue where you present your ideas as fact. If Dr Wolfe-Simon’s talk had been a debate between herself and one of her critics then I think it would have been far more useful to the advancement of science. And while I realize that advancing science per se is not the purpose of a TED talk, I can’t help but feel that there is something fundamentally wrong about presenting your shiny new finding as fact to a large and very influential audience when it is still eminently unclear whether the finding is legitimate or not. Not that TED talks are wrong, but that it’s dangerous to get too far ahead of the science, or present something as fact when there remain unresolved questions. I have been unable to find a video or transcript of Dr Wolfe-Simon’s talk so I could be off base here, but it certainly seems distressing on the face of it.
The final thing that I find personally distressing about these issues is that I love listening to TED talks and reading books about big ideas. And to be honest I would love to be one of those people who gives those sorts of compelling talks that so clearly demonstrate why an idea or piece or research has meaning outside of the lab. It worries me that other people who share that goal seem to be spreading a message which may not actually represent the “truth”… it makes me nervous about knowledge translation in general if those who are among the most successful are also those pushing the most questionable findings.
Travis



