New NN papers

Of course I forgot to put up last week’s papers during the maelstrom that is SfN — sorry. Here they are. Published online on 15 October:

Hahn et al., Phase-locking of hippocampal interneurons’ membrane potential to neocortical up-down states

Hansen et al., Memory modulates color appearance

Garriga-Canut et al., 2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBP–dependent metabolic regulation of chromatin structure

Rust et al., How MT cells analyze the motion of visual patterns

Veruki et al., Activation of a presynaptic glutamate transporter regulates synaptic transmission through electrical signaling

And here is this week’s set of papers, published online on 22 October:

Chen et al., Optimal decoding of correlated neural population responses in the primate visual cortex

Ma et al., Bayesian inference with probabilistic population codes

Özdinler & Macklis, IGF-I specifically enhances axon outgrowth of corticospinal motor neurons

Enjoy, and feel free to comment if any of the papers inspire you to. Next week and through the end of the year I’ll follow a suggestion from our executive editor Linda Miller and give each new paper its own blog entry, in an attempt to make the blog more attractive as a feedback forum.

I still owe y’all a few notes on the last two days of SfN. Yes, I did venture into the faraway QQ section! More about that, and other impressions — tomorrow…

Tuesday thoughts

Today was the fourth day of SFN 2006, and I find myself seriously frustrated with the setup of the meeting this year – there seems to have been little to no thought put into where to schedule the various concurrent sessions. Usually there are multiple slide sessions each morning or afternoon that are of interest. The natural thing to do is to skip back and forth between sessions to catch the most interesting talks, but here in Atlanta this is all but impossible given the distance separating even closely related sessions. The Atlanta convention center consists of three connected buildings, each of which has multiple levels connected with escalators. It takes a good 10 minutes to walk from Building B to Building C, and yet sessions that are fairly similar in focus are routinely allocated to different buildings. On Sunday the session on objects and faces (mostly fMRI of the ventral pathway) was in B and one on extrastriate visual cortex was in C, as was a session on attention. No doubt most of the people interested in one of these sessions would have been interested in the others, and yet it was all but impossible to go back and forth. This has happened to me every day thusfar. Many of the scientists here have expressed a similar frustration. The problem would be easy to remedy – someone just needs to put related sessions in nearby rooms. The room assignments, as far as I can tell, are totally random, which has detracted from the meeting.

This afternoon featured a well attended talk on the current funding woes, given by the heads of the various agencies of the NIH (the NIH director was supposed to give it, but his flight was delayed). The talk focused on explaining why we are currently experiencing a funding crunch in the US, and attempted to highlight what the NIH folks say are widespread misconceptions about NIH funding. The increased competition for funds has apparently been mostly driven by an increase in grant applications (rather than a funneling of resources to more clinically oriented research), fuled in part by a boom investments in the biomedical sciences by universities. New facilities have brought with them new jobs, and there are now many more people applying for grants. NIH funding doubled between 1998 and 2002, but has leveled off since then, so supply has not kept pace with demand. Tom Insel stressed that they are still committed to basic research; apparently the proportion of directly translational research they fund has not increased. He did not address the issue that most of the scientists I know are interested in – whether basic research grants need to explain how the research might ultimately benefit human health in some way. There was a Q&A session at the end that I had to skip out on, so perhaps someone queried him about this. They did offer some encouragement, citing previous periods when funding dried up and funding rates were as low as 10%, and explaining how grants that are ending now will free up uncommitted funds for new grants. They also concluded by stating the need to better explain the importance of the NIH to the public (apparently only 10% even know what the NIH is).

SfN, Day 3

Some interesting sessions yesterday. First, the panel discussion on the future of scientific publishing that Sandra already described (below). I was impressed with several of the panelists, particularly Heather Joseph from a consortium of academic libraries dubbed SPARC. She made numerous valuable points. Access barriers are not the only problem users of scientific information face these days. There is also the explosion of biomedical literature, leading to colossal information overload for everyone. So SPARC encourages the development of better semantic search and indexing applications, to allow users to get a grip on what’s even out there. More polemically but in the same vein, Michael Keller from Highwire Press said that he’d be thrilled if the number of scientific publications could be reduced by half – as 50% of papers never get cited even once!

Heather Joseph also mentioned science blogs as a new medium that’s changing science communication, and she wasn’t talking about the popular ones such as The Loom or Pharyngula, but about specialized ones that serve as informal hallway discussions or minisymposia. (I’ll look into those some other time, and put a few links on the blog if I can find any.) An audience member suggested a blog-like format for readers to provide feedback on published articles. Well, that’s exactly the idea that prompted us to start Action Potential almost a year ago! It’s not working too well, though (yet??)… (A short internet walkabout reveals that the ‘audience member’ was blogging grad student Jake Young, whose take on the SfN meeting you can read here!) Michael Keller mentioned that the British Medical Journal had run an article feedback option a while ago but stopped it for lack of actual feedback. And Gary Westbrook announced that the Journal for Neuroscience has just launched eLetters for exactly the same purpose! W’ell be getting there some day; to the ongoing exchange of neuroscience ideas over the internet that is… (Annette the optimist speaking!)

Then Donald Kennedy, chief editor of Science and overall grand old man in the field, declared that he avoids blogs like the plague. Oh my! But apparently Dr. Kennedy relishes setting himself up for target practice — he also said that the Open Access movement should stop claiming the moral high ground, and that Science magazine was open access ‘for all practical purposes’. I cannot hold a candle to Dr. Kennedy, but I do respectfully disagree. Nature and Nature Neuroscience are easily available to anyone associated with a big research institution, but they are not open access by any means. Neither is Science.

I also want to mention a lady from the University of South Carolina who told the panel and audience about an undergraduate science journal she advises. I apologize for not getting her name, and I hope to walk by her poster “in the QQ section where nobody goes” some time before this meeting is over… In any case, she alerted everyone to the fact that notions such as copyright are entirely alien to the current undergrads, and that should get publishers thinking indeed. Those undergrads will be our customers, i.e. scientists, in due course.

Apart from the publishing session, I enjoyed conversations about the latest blows in the ongoing “does-kiss-and-run-exocytosis-even-exist” debate, and about the non-reproducibility of computational neuroscience papers. That one (from Yale’s Ted Carnevale) floored me completely – models are mathematics, after all! How can they not be reproducible? Carnevale explained that essential code pieces are missing from most computational papers, and that the journals should insist on having these code modules deposited in a publicly accessible database such as his ModelDB. We’ll think about it for sure. Any other computational neuroscientists want to chime in?

Cori Bargmann wins my crown for best lecture of the day, for her fine exposition of behavioral circuits in C. elegans.

And again I was disappointed in my efforts to get a half-decent dinner (shoeleather-dry hamburger at the sports bar across from the convention center…), and after spending some time at a late evening stem cell ‘data blitz’ I gave up on trying to find the MIT party as it was raining miserably. Really, Atlanta as a conference venue isn’t winning any points with me.

Redesigning scientific publishing

The most striking news for me at the®evolution in Scientific Publishing session yesterday was that fewer than 100 people showed up, even though prominent posters advertising the discussion greeted all attendees on their way into the meeting. I guess neuroscience journal editors are going to have to figure out how to navigate the brave new world of scientific publishing without much help from readers.

For those of you who haven’t been following the debate, there are a couple of linked hot-button issues that publishers have been dealing with over the last few years. One is whether journal content should be available to anyone (open access) or only to subscribers or site license users. Another is how journals should make the transition from print to web publication, which includes the question of who’s going to pay for our work once journals move away from print subscriptions as a major revenue source. (If you doubt that journal editors add value by publishing your work, ask yourself why you don’t just post a description of the experiment on your own website and skip all that pesky peer review hassle.) Like the rest of us, the editors of the Journal of Neuroscience are trying to figure out how to keep the community happy and the journal sustainable at the same time, and this session was their attempt to bring society members into the conversation.

The panel included people from the American Physical Society, the librarian organization SPARC, Science magazine, Highwire Press, Elsevier and PNAS. We heard some cautionary tales – when PNAS tried making their content freely available after one month in 2000, they had an 11% drop in subscriptions, and when the APS tried asking high-energy physicists to pay for publication in the early 1990s, many of them stopped submitting their work to the journal. But there were also some success stories, including several journals at which authors or third parties can pay to make articles free online at publication. At PNAS, about 20% of authors take this option. Donald Kennedy of Science emphasized that his journal is available to virtually all scientists through site licenses, though Andrew Watson, who edits the open-access Journal of Vision, challenged that view in the question period, calling the discussion “too nice”. He had a point: I’m not sure that someone unfamiliar with the debate would have been able to determine which panelists disagreed with each other on what issues.

Day 3

Today I spent part of the afternoon at the Nature booth that the company has set up here at the meeting. Lots of people dropped by, some to chat about their interest in getting involved in editing, others to talk about their papers, and still others with general questions about the way things work behind the scenes. One question I get asked a lot is whether there is any way to tell if a paper that you’ve just written is something that Nature Neuroscience would be interested in publishing. I can certainly rattle off a list of traits that tend to characterize papers published in high profile journals, but I don’t know how helpful that is. One thing that has become clear to me in my own experiences writing papers, and in talking to authors, is that it is extremely difficult to objectively evaluate one’s own work. When you’ve spent a year or two conducting experiments and then writing them up, it is quite hard to step back and get a sense of how important or interesting the work is to a broad audience. Partially because of this, we do offer authors the option of submitting a Presubmission Inquiry to gauge the journal’s interest in a potential submission. This is easy to do, but the effectiveness of this depends critically on writing a useful description of the work. Quite often authors will describe the work in very abstract terms, or mainly describe the conclusions that they have drawn from the work, rather than what experiments were conducted. The most useful thing for an editor is to get a concise description of the science that was done, as well as it’s motivation and a brief statement of what is learned from it. For us to give useful feedback about whether the work is likely to be appropriate for the journal, the abstract should not be too abstract.

The evening brought the annual MIT Picower party. This year it was held at a large club in the Midtown area of Atlanta, and was totally packed. I would say there were well upwards of 1000 people in attendance, talking, drinking and dancing. Attendance was tilted towards the younger end of the SFN attendee spectrum, but there were quite a few faculty in attendance as well. When I left at around 1 things showed no signs of slowing down…

Talk about peer review at SfN

One important thing I get out of this meeting is the opportunity to talk with scientists about how the journal is doing and what we might improve. People seem generally happy with the papers that we’re publishing, but I’ve gotten a lot of interesting suggestions too.

The most controversial one was that we should publish the reviews of accepted papers (anonymously) online. Some people loved this idea, saying that reviews contain a wealth of information, from the reasons that the referees found the work exciting to the potential limitations of the authors’ approach, which would be especially helpful to scientists reading papers outside their field. Another potential advantage would be to make the editorial decision process more transparent to readers. Knowing that the reviews would be posted might also influence referees to write them more carefully and do a better job of citing references to document their concerns about novelty or conceptual advance.

The naysayers are equally passionate, telling me that posting reviews would place an additional burden on the referees, making them more reluctant to review and probably leading them to express their opinions less candidly. People worry that allowing a large number of readers to see the reviews might increase the odds of someone identifying a referee. One scientist said that editors would be dodging their responsibilities by posting the reviews online, making it look like we were trying to shift the blame for the decision onto the referees. Others note that many flaws identified during the review process will have been fixed by the time the paper is published, so the criticisms raised by referees are no longer relevant.

I’m sympathetic to these concerns. Of course we would never post reviews without the permission of the affected authors and referees, and I don’t advocate making it a regular habit for all accepted papers. On the other hand, I can imagine that it would be helpful to readers in certain cases. It will be a while before we decide whether to try it, but in the meantime, I’d be interested in your opinions on the subject.

SfN, Day 2

The first full day of SfN. My favorite lecture was Wilfried Denk’s, about applications of non-linear optics. The idea of mice carrying miniaturized fiber-optical two-photon scopes on their little heads is not totally new, but still awesome. He also mentioned ‘second harmonic imaging’, which can deliver information about orderly molecular arrays and membrane voltage in living cells. Finally he reported on efforts to automate EM imaging of serial sections and the subsequent threedimensional reconstruction – a project that if successful (in the sense of yielding a widely applicable methodology) could make the lives of many grad students a lot easier.

Other lectures today felt less inspiring as they stuck closely to published material. What really got me miffed though was the difficulty of procuring a decent lunch in downtown Atlanta. Few options made for verrrrry long lines. The area is also an amazingly ugly concrete jumble. Folks, I’m so nostalgic for New Orleans! Plenty of good food there!! Hopefully the town will come back, in spite of all the bad news (discouragingly, the papers recently reported that New Orleans’ population now is about 40% of pre-Katrina times…)

Fun nighttime socials made up for some daytime scientific disappointment. Nature Publishing threw a very classy party at the Sundial Restaurant, slowly rotating high above downtown. I was astonished to hear Morgan Sheng, Moses Chao and Bartlett Mel all speak (some) German! Very good, guys, keep it up 🙂

I’m not supplying any links tonight (it’s gotten late with all the partying!) but I may add some later once I get a chance to google for second harmonics… I shall see y’all at the Nature booth tomorrow afternoon!

First Day…

I flew in Thursday night for the Friday auditory physiology satellite meeting organized by Xiaoqin Wang and Yale Cohen. It was an interesting meeting – in addition to posters and morning talks on new research findings, an afternoon session was focused exclusively on methods. A wide range of auditory neurophysiologists gave 10 minute slide presentations of training techniques and the details of their preps. It is widely acknowledged that training animals on auditory tasks tends to be harder than training them on visual tasks, which I think made everyone inclined to share tips and techniques.

Today brought the start of the main meeting. I also missed Gehry’s talk, but made it to the visual coding session, which featured some nice talks. The poster session was, as always, more about running into people than about absorbing many new results, but for me that is one of the best things about this meeting. You run into everyone…

SfN 2006, Day 1

I flew in this morning and thought I would easily make it to Frank Gehry’s talk at noon, but this being my first time in Atlanta it took me a while to find my hotel, so I missed it. Bummer. Do write in and let me know what he spoke about. I assume he was less controversial than last year’s “Neuroscience and Society Dialogues” speaker 🙂

I poked my head into the symposium on the ongoing efforts to cure Parkinson’s with dopaminergic neurons derived from ES cells (progress is being made, though as usual the goal seems to recede as we approach it), and learned about synaptic scaling from Gina Turrigiano’s polished presentation. Michael Sendtner however made my day when he told me that Bavarian politicians were impressed by our recent editorial on a new competitive university funding scheme in Germany (in our June issue). Bavarian politicians are a notoriously crusty bunch, very hard to impress. This scary guy is the prototype of homo politicus bavariensis – the Munich airport is named after him…

See you in Atlanta?

The big SfN neuroscience bash is coming up fast, starting this Saturday. We are sending quite a big delegation, including our chief editor Sandra Aamodt, my colleague Josh McDermott and myself, plus John Spiro and I-han Chou from Nature. You’ll have a chance to meet us at the Nature booth, #1832 in the Exhibitors’ Hall, where we’ll be holding court (ahem…) for about an hour each. Tentatively, you can shake hands with Sandra on Sunday afternoon from 3:30 to 4:30, and yell at me on Monday from 2 to 3 p.m. Times may change. Current info and other editors’ booth hours will be posted on a chalkboard at the booth. Our marketing colleagues tell me they’ll distribute free journal copies and other goodies at the booth, and they’ve also put up a special SfN 2006 webpage to give you easy access to the most recent neuroscience coverage by Nature Publishing.

This blog should see some real action as my colleagues have solemnly promised to post their impressions daily! So check back often. If you think I should come by your poster or slide talk, please post a comment with your abstract and abstract number. I look forward to meeting y’all (and to hearing those wonderful Southern accents again!)