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The next installment of the Nature Network Neuroscience group journal club is now live. The paper proposes a new strategy to track the location of select synapses using split fluorescent proteins.
The contributor discussing this paper for the neuroscience group is Andrew Hires, a postdoctoral fellow at Janelia Farm Research Campus in the lab of Loren Looger. I want to thank Andrew for his participation.
When the community is overburdened by peer review, it's everybody's problem. As of today, Nature Neuroscience has become part of the solution by joining the Neuroscience Peer Review Consortium, a flexible system that allows voluntary participation by authors, referees and editors. Here are more details, from our April editorial:
The NPRC reduces the overall reviewing workload of the community by allowing authors to continue the initial review process when their paper moves from one consortium journal to another, once the paper has been rejected or withdrawn from the first journal. This arrangement is similar to the manuscript transfer system that has been available within the Nature family of journals for almost a decade. So far, more than 30 journals, including the Journal of Neuroscience, have become members of the NPRC, representing a substantial fraction of mainstream journals in the field. The full list of journals can be found on the NPRC website.
Like the Nature journals' transfer system, the NPRC system is completely voluntary for authors. Editors at one journal know that a paper was reviewed elsewhere only if the author chooses to inform them. If the reviews from the first journal do not seem likely to facilitate acceptance at another journal, the authors are welcome to send the paper to the second journal directly and have the paper considered as a fresh submission. However, if the author feels that the reviews may be helpful, transferring them can accelerate the editorial process at the second journal, reducing publication delays. Each journal will transfer reviews only once, to ensure that each transfer includes the paper's full transfer history within the NPRC system. That is, once the paper has been considered by a second journal, only that journal can transfer the reviews to a third journal.
Referees also have the option of whether to participate in the transfer system. When they review a paper, they are asked to state whether the editors may release their names along with the review in the event that the paper is transferred to another journal. If a referee declines, that review is passed along to the next journal anonymously. It is most helpful to the recipient journal if the reviews are accompanied by the identities of the referees, so we strongly encourage our referees to participate in the NPRC system whenever possible. All editors within the consortium are committed to maintaining the confidentiality of transferred reviews, just as they would for their own review process, and do not reveal the referees' identities to the authors.
Finally, editors have full discretion in deciding how to use transferred reviews. The receiving editor may choose to accept or reject a paper based on these reviews, without further consideration; to send the paper to some or all of the previous referees for evaluation of the authors' revisions; or to request a fresh set of reviews from new referees.
Only comments to the authors are transferred to the receiving journal. Confidential comments to the editors are not passed along. Thus, to ensure transparency in the review process, both at Nature Neuroscience and at other journals after the paper has been transferred, we encourage referees to include all their concerns about the paper in comments to the authors. The small amount of extra time required to word the comments diplomatically for the authors should be more than counterbalanced by the resulting improvement in the peer review process. Many members of the community have strong views on the issue of confidential comments, which can be found on our blog, Action Potential.
Referees should use comments to the editors to communicate ethical concerns and for comments that may reveal their identity or other confidential information; for example, to compare the paper to a related paper under consideration that they have also been asked to evaluate. Comments to editors should also be used to indicate whether or not the referee is willing to have his or her name revealed to the receiving editor if the paper is transferred.
We look forward to your comments below.
The next installment of the Nature Network Neuroscience group journal club is now live. The paper explores the in vivo function of neurexins in the coordination of pre- and postsynaptic apposition using Drosophila.
The contributor discussing this paper for the neuroscience group is Margaret Ho, a postdoctoral fellow at the Institute of Molecular Biology, Academia Sinica Taiwan in the lab of Cheng-Ting Chien. I want to thank Margaret for her participation.
[This is the inaugural post for a new feature at Action Potential. Periodically, we will provide insights from a regional correspondent on the interesting news, changes, or issues particularly affecting neuroscience in a particular location. Today's post is from one of our Asian correspondents, Haihong Ye of the Institute for Biophysics in the Chinese Academy of Sciences. She reflects on the dramatic changes that have occurred within Chinese neuroscience during her decade-long absence from this now-flourishing community. We examined these issues in our March editorial, but now invite you to provide your opinion. - N.G.]
Over the past 10 years, especially the last five, the whole world has been amazed by the Chinese economy. To me, however, the improvement in biological science research in China is much more amazing. In the summer of 1998 I left Beijing and went to the US to pursue a Ph.D. in neuroscience. In 2007, after nine years of graduate study and post-doc training abroad, I came back to Beijing, seeking opportunities for further career development. What a difference some strong funding and visionary directives, not to mention a decade, can make.
Ten years ago, many of my classmates, having majored in physiology or biophysics, wanted to join neuroscience labs for their graduate studies. At that time, the Chinese neuroscience community was small, with a few labs scattered in the institutes of the Chinese Academy of Sciences (CAS) and the major universities in Beijing and Shanghai. Most of the labs were restricted to electrophysiology, using very traditional animal models. The establishment of the Institute of Neuroscience (ION) by the CAS in Shanghai in November of 1999 marked the beginning of a new era for Chinese neuroscience research. Led by Dr. Mu-Ming Poo, ION is devoted to basic research in all areas of neuroscience, including molecular, cellular and developmental neurobiology, systems and computational neuroscience, as well as cognitive and behavioral neuroscience. Currently there are nineteen labs in ION, with a goal of reaching a steady-state of 30 labs by 2010. In 2005, the State Key Laboratory of Brain and Cognitive Science was formally established in the Institute of Biophysics of the CAS (IBP). They formed a strong team by combining labs utilizing a variety of systems (fly genetics, electrophysiology, fMRI and psychological approaches) to study various topics, including perception, attention, emotion and consciousness. Because of the increasing number of neuroscience labs, many universities have established, or are making plans to set up, centers for neuroscience. Consistent with the expanding neuroscience community, the number and the quality of publications is also increasing exponentially. Ten years ago, graduate students in China struggled to publish papers in Chinese journals. Nowadays, they are publishing in top international journals, making jealous their college classmates studying abroad.
What’s the driving force behind these amazing achievements? I think it’s the convergence of (1) government investment, (2) a backflow of internationally-trained scientists and (3) efforts made by the international science press:
(1) The National Natural Science Foundation of China (NSFC) is a major funding agency for basic science research in China. The budget for the NSFC was 1.85 billion yuan in the FY 1998 and 1999 combined. This number has increased to ~ 6 billion yuan in FY 2008 alone (1.8 billion will go to biology-related research), an average 21% annual increase for the past ten years. A similar, or even greater increase, has happened in other funding agencies, such as the Ministry of Science and Technology. Since 2007, the central government has stressed the importance of science and technology for the continued growth of the Chinese economy. We expect that government funding will continue to rise for a while longer.
(2) Many Chinese scholars, who went abroad in the 1980s or earlier have now established themselves as successful international scientists. Some have reached a stage in their career where they want to do more for Chinese society. China can now provide them with genuine opportunities to play leading roles in shaping the future of Chinese basic research. Some of them (Mu-Ming Poo, Xiaodong Wang, Yi Rao, Yigong Shi, just to name a few) have become the directors of the various institutes, centers and departments in China, implementing the infrastructure of a modern research institute onto the “old” Chinese system. On the other hand, younger scientists, like me, after completing a PhD or post-doctoral training abroad, are attracted by the exciting job opportunities and improved living standards back home.
(3) Another driving force also comes from abroad. In the past few years, major scientific publication groups have started to operate in China. They make efforts to help Chinese scholars publish in English, and provide services to help institutions raise their profile and international awareness of their top research.
The Chinese neuroscience community, like all other basic research communities, is in a fast growing phase and thus still faces a lot of challenges. Despite the increase in government funding, the grant size is generally small. In FY 2008, an average free application grant from the NSFC is ~300,000 yuan for 3 years, only ~US$14,000 a year. Most of the big grants (>1 million yuan) go to only a few institutes and labs in Beijing and Shanghai, a major reason for why these two cities have dominated the neuroscience landscape. One of my friends is a professor in Xiangya Medical School in Hunan province, one of the top five medical schools in China. It’s difficult for her to get grants from the NSFC. These labs live on small grants from local sources, and address questions that are not that “sexy”, very much like the situation in Beijing 10 years ago. As a developing country with a GDP per capita of just over US$2000, and millions of people still struggling to make ends meet, it’s difficult for the Chinese government to match the research budgets of Japan, Europe or the US. To support a large, productive and creative basic research community, we need to think of better ways to attract funding from other sources, such as through international collaboration, interest from pharmaceutical companies, and perhaps even from private donations or philanthropy from the Chinese nouveau-riche.
Another serious challenge for China is still the continuous loss of scientific personnel to the developed world. Although I argued above that this trend is beginning to reverse, each year, many talented and bright blossoming scientists still go to the US or European countries for graduate school or post-doctoral training. Until recently, only a small fraction of these individuals eventually came back. Although there are reasons to be optomistic regarding the reversal, does China need to do more in order to keep them home (e.g. playijng a more active role), or wait for this initial trickle of brain-drain-reversal to continue and (hopefully) broaden?
We must continue to promote the successful policies that have brought us here, while simultaneously establishing new and innovative strategies to nurture future growth. Conducting ground-breaking research, work that is uniquely Chinese, will undoubtedly contribute to the growth of the economy and the well-being of the Chinese people. The future looks bright and it is an exciting time to be a Chinese neuroscientist.
The next installment of the Nature Network Neuroscience group journal club is now live. The paper is on the role of insular cortex in drug craving and the behavioral signs of abstinence-related malaise.
The contributor discussing this paper for the neuroscience group is Ben Saunders, a graduate student at the University of Michigan in the lab of Terry Robinson. I want to thank Ben for his participation.
In the last couple of years, after the recent explosion in the number of resources where scientific discussions can take place rapidly and without boundaries (i.e., using the internet), one could easily have predicted that we were on the cusp of a revolution; the way in which scientists communicated with each other regarding data was about to change forever. Although poster session chatter at your favorite scientific meeting was never going to be replaced, now researchers could interact, trade ideas and get feedback from anyone, anywhere, at any time. Sounds pretty good, right? Unfortunately, it doesn't seem like neuroscientists are taking advantage of these cool new offerings. I could extrapolate to biology in general, but for more simplicity (and other obvious reasons), let's stick to what we know best.
I have been thinking about these issues for a long time, ever since I commented on the introduction of Nature Precedings last June (which was my first post on this blog, for those of you keeping score). I was skeptical about the speed with which scientists would give up their unpublished data, and at 57 neuroscience papers currently in the archive, this was even a bit slower than I expected (but other subject areas are doing quite well, with Bioinformatics boasting 110 submissions, for example). Shortly thereafter, I discussed commenting forums in general, and felt again that although adoption may be slow, that this medium would eventually become fundamental to the scientific process and discussion. In my opinion, we have a long way to go before we reach that lofty prediction.
My hand was forced by two excellent and recent commentaries (here and here) that provide many of the theories for why scientists do not widely use these new technologies. I would like to focus mainly on the concept of commenting on papers and data, the style embraced by PLoS, PLoS ONE, Neuron, Nature Precedings, and more recently, in the neuroscience journal club started at Nature Network.
So why are neuroscientists not taking advantage of this seemingly golden opportunity to communicate with one another? Granted, some papers are comment magnets (e.g. this or this, but consider the subject matter and/or implications). But most of the time, papers sit with a "Comments" link beside them that links to nothing. What about telling the author your alternative hypothesis? How about suggesting a future experiment? Why not simply ask a very innocuous question about which buffer worked best for the biochemistry experiments? I can't put actual numbers on it without some painstakingly-boring grunt work, but I spent quite a bit of time clicking on paper "Comments" links at all of these sites that offer such a luxury, and found very few random hits where any comments had been made. I've attended enough journal clubs to know that somebody always has an opinion about most papers, so where are those people now? This should be their critical dream-come-true!
For those few publications that did receive comments, it was even rarer for the authors to respond. I took the liberty of commenting on some papers at Precedings within the categories of environmental sciences or evolution, and on only 1 occasion out of 5 did I receive a response. So why do these authors even post their papers if they are not interested in feedback? It is an obvious question for pre-prints, but even for published work, researchers put their efforts out in the public domain to be scrutinized. The authors should then be obliged to answer such scrutiny if and when it does arise. Can you imagine the oddity of a speaker staring out into space without responding during a question-answer session at a meeting? Well, the cyber-equivalent was going on at most places that I looked.
As Anna Kushnir and David Crotty pointed out in their blog commentaries (see above links), one of the main reasons for a lack of initiating comments is the fear of placing one's name with a criticism. That criticism may be wrong, too abrasive, not well-written, and now it is associated with the submitting party for all of cyber-eternity (or at least until server failure). At a meeting, after asking a really stupid question, we have plausible deniability. Unless somebody was taping the session, there is no hard evidence revealing our misguided thoughts (saying to our friends: "Well, the speaker didn't understand my question and blah, blah, blah..."). Not the case with these forums. But even that can be circumvented. Although anonymous comments are not really allowed in these forums, what's to stop people from simply making up a name and providing a Gmail account address like "sciencegeek@gmail.com" to establish legitimacy for the servers (or moderators, for that matter) accepting the comments? Although I disagree with anonymous commenting, I understand that some prefer this incognito approach. But despite the ability to use this cover of darkness, we still haven't seen a massive adoption of commenting practices!! So perhaps the age-old beast, lack of time, again wins out and should take most of the credit. Although probably true, I find this to be a lame and sad excuse.
During graduate school, we are taught that we learn the most when we present our data to the community, whether it is at a conference or even at lab meeting. We can learn just as much, if not more, from participating in online forums to discuss data, hypotheses, and interpretations. I still firmly believe that commenting forums will indeed become fundamental to practicing and publishing neuroscience in the future, and not just a fad, as it currently looks. So I say to you, readers of Action Potential, let's not miss out on an excellent chance to be early-adopters, with neuroscientists taking the lead on internet-based dialogue and collaborative thought amongst the biological science disciplines. With so many branches of neuroscience having deep roots in physics, computational methodology, programming and bioinformatics (all fields that are seemingly well-stitched into the fabric of Web 2.0 technology), it is an opportunity that would be shameful to miss.
Nobel prize-winning neuroscientist Linda Buck has retracted a 2001 Nature paper. In the retraction in this week's Nature, the authors report difficulty replicating the data and 'inconsistencies' between the original data and figures and data printed in the paper. Buck told Nature reporter Heidi Ledford that the figures and data in question were contributed by the first author, Zhihua Zou, who was unavailable for comment.
This is the highest profile retraction that I can recall in neuroscience, but so far, there has been little fallout. Perhaps that's because the original findings were notable only in the neuroscience community rather than in the general public. Regardless, it indicates that neuroscience and its well known labs are not immune from fraudulent data. Although I admire Buck's swift and direct action, it concerns me that the first author has been assigned the lion's share of the blame. This seems like a familiar refrain, and I find it troubling.