The first day (Saturday) I was presenting all afternoon, which left me too exhausted to return until Sunday around 11.  Since then, I’ve been hanging out at the Theme F poster sessions – these have been unbelievable.  I’ve also attended a large number of the large lectures (including Elizabeth Spelke, Richard Morris, Steven Laureys, Francis Collins, and May-Britt Moser), all of which have been quite enlightening.

Poster highlights thus far include the entire perceptual decision-making session this morning, a poster on a beautiful new tool for controlling social stimuli (truly an incredibly creative idea), a nice poster on neuroimaging children with William’s Syndrome by Dr Tricia Thornton-Wells at Vanderbilt, and an equally-interesting poster on early visual processing of valid currency.  If I can get author permission, expect to hear a great deal more about these in the coming weeks.

This afternoon I’ll be wandering around the poster floor and exhibitor booths.  If you see a poster you think I’d enjoy, or you yourself would like me to come check out your work, feel free to comment below or contact me on twitter (@M_ostlyHarmless, hashtag #sfn09).  I’m looking forward to providing more complete and satisfying coverage when I return later this week.

1.  authors now have a great incentive to publish in PLoS journals, and

2. this could be a wonderful data set to mine for those interested in both the public and scientific reception of open access publishing

PLoS has published an xls file containing all the article-level metric data, which can be downloaded here.  I’ve played around with the data for a few minutes and a few things become clear rather quickly.

First, though I love the potential for interactivity which is a hallmark feature of the PLoS journals, it appears to be very infrequently used.  Of the 11059 research articles included in this data set, only 651 (~5.9%) have one or more ratings, while only 29 (< 0.3%) have 3 or more ratings.  I find this quite surprising – though I’m personally quite reluctant to comment on, leave notes on, or rate a peer-reviewed research article, that’s in large part due to my present academic standing (I don’t even have a Bachelor’s degree yet).  What authority do I have to say anything about the research of another lab?  This isn’t to say I never have something to say, but if so, I’d write a post here.  Conveniently, PLoS is also keeping track of blog trackbacks and mentions (though I’m sure there are mentions not counted in these metrics).  Examined this way, the situation appears a bit less bleak: 1196 of the 11059 included research articles (10.81%) were mentioned in at least one blog post (have a non-zero number of trackbacks).

The second obvious feature of the data set is that, as one would expect, a small number of articles appear to be viewed an enormous number of times (the 70 most-viewed articles, which amounts to .63% of all research articles, account for over 10% of all article views).  A notable example is one of this year’s media darlings published in PLoS One, “Complete Primate Skeleton…” with over 56000 views in just 2.5 months (the data go through 7/31/09).  Papers like this contrast starkly with the mean, which is closer to around 2100 views for a research article.  It’s likely that there are similar reasons for the large number of views for many of these other articles.  In the future, I’ll try comparing number of views to time since publication (a factor PLoS readily acknowledges skews these metrics) – perhaps this number simply reflects a trend towards publishing in open access journals in recent years.  PLoS is doing a great job of tracking blog references to papers, but perhaps there could be a similar metric for popular media mentions (such as Google News results/queries?).  This would be the interesting metric for understanding (and maybe factoring out or accounting for) the role of mass media in article popularity.  If researchers are working to gauge the influence of their article among their scientific community, pure page-views, especially when driven by media outlets, may not be the best metric.

Number of citations found in PubMed Central vs those found in CrossRef for each article (n = 11059)

Finally, it becomes clear that the various citation-tracking services (specifically, CrossRef, PubMed Central, and Scopus) have quite disparate results.  Even if we ignore Scopus for now (the folks at PLoS acknowledge an issue with their database in the ALM FAQ), we can see that there is not generally a 1:1 relationship between the number of citations ascribed to PubMed Central and number of citations ascribed to CrossRef.  I’m sure someone out there has a (or a number of) good reason(s) why this is the case – but it does seem a bit strange.

So what does this early data tell us about open-access and community-focused publishing?  Most importantly, despite all the encouragement on the part of PLoS and the blogging community, it appears that the enterprise of bringing an interactive discussion to an article (rather than having the discussion take place in the comments of blog posts) has been largely unsuccessful.  I find this at least a bit baffling – it’s not at all uncommon for readers (often researchers) to post comments on blog posts discussing peer-reviewed research using their real name.  If the trackback feature is working properly, anyone reading the original research article is just a click away from seeing this feedback.  Why the willingness to post a comment in one place, but not the other?  Or, take the 5-star rating system – this is a quick way to post a very general reaction to a paper.  The mean of the average ratings of the 651 rated papers is 4.16 – should this be taken as an indicator of very high average quality of research published in PLoS journals, or a signal that there is an inherent selection bias in those rating articles?  I know that personally I have a very tough time rating anything 1/5 (even my iTunes library reflects this – there are something like 1000/6000 songs rated 4+, and the remainder are unrated).   The problem here appears to be the lack of anonymity.  There’s, I think, a simple solution to this problem.  Now, when you look at a rated article (for example), you can see the user who rated it.  I think it makes complete sense to require a user to be registered to rate an article, but s/he should also be given the option of anonymity.  Requiring sign-in would still be useful for filtering out spam ratings (in ensuring only one rating per user, etc), but would allow users to post more honest reactions to articles.  Though it’s not unfeasible to institute a similar system for comments or text notes, I think those should be tracked to a particular user.

Though this data reveals some initial reluctance within the community to adopt this particular means of scientific dialogue, I’m optimistic that as the myspace and facebook generations grow to be competent graduate students and scientists we’ll have a more open and interactive culture of science.  It’s absolutely fantastic that PLoS released this data, and I hope in the near future they release increasingly-detailed metrics that can be further mined for interesting usage and publication patterns.  I really do think that the future of the scientific publishing “industry” will be in managing and profiting from usage data rather than scientific discourse.  The guys at Mendeley seem to understand this, and certainly are on their way to having a very impressive data set to work with.  Knowing what articles tend to cluster in researchers’ libraries (and references sections of articles) will allow for the creation of an iTunes Genius-like algorithm for suggesting papers – an absolutely killer feature many labs (and hopefully institutional libraries) would certainly be willing to pay for.

For further information about the PLoS Article-Level Metrics and the prospect of community-oriented science communication, check out the (non-exhaustive) set of links/articles below.  As always, I’d love any feedback you might have, so feel free to comment or email any thoughts/ideas/criticisms.

PLoS Journals – measuring impact where it matters – this post is especially interesting

Improving Science Through Online Commentary (Eagleman & Holcombe, 2003) [PDF]

PLoS Takes a Giant Leap Toward Science 2.0

EDIT: new links/posts/mentions

PLoS Article-Level Metrics Home

A Blog Around the Clock: Article-Level Metrics at PLoS

For example, let’s say there is a single neuron responsible for perceiving a circular disc. When a disc is flashed, this neuron fires, and you have a vivid perception of a circle (well, as vivid as a circle can be).  Without this neuron, you would not perceive a circular disc, even if it were sitting blatantly in front of your eyes, which were accurately transmitting information to your visual brain.  This is a fairly straightforward, though grossly simplified account of how we often think about vision (but instead of single neurons, we usually consider enormous, brain-wide networks of neurons working in teams; but see Quiroga et al, 2005 for an observation which may suggest otherwise).  But what if we presented this circle in a way that made it difficult to see – say, it is flashed very dimly – so that you sometimes see the circle like normal and sometimes miss it completely.  What is that neuron up to in the time before we show the circle that causes it to be more or less likely to fire, thus leading to your perception of the circle?

A recent study published in the 3/4/09 issue of the Journal of Neuroscience by Matthewson and colleagues used EEG to test this idea – what is different about the global electrical activity in the brain when a hard-to-see flash is perceived compared to when it is not perceived?  To test this, the research group used a phenomenon called metacontrast masking, in which a short initial flash is rendered undetected by a surrounding flash that follows (here, the researchers used a circular disc, flashed for 12 ms, followed by a ring around the disc presented ~50 ms later for 24 ms).  Subjects (whose brain activity was being recorded with a spidery EEG cap) reported whether or not they detected the first ‘target’ circle (there were ‘catch’ trails in which no target was presented to make sure subjects were paying attention).  This type of stimulus allowed the researchers to gather EEG data over a roughly equal number of trials in which the target was detected and undetected.

The main finding was that a certain band of ‘brain waves’ (cortical oscillations) before the target was flashed were able to differentiate between trials in which the target was detected and undetected.  These oscillations, in the alpha band (a frequency range centered at 10 Hz, typically associated with decreased vigilance and alertness), when measured locked to onset of a fixation cross that came onscreen before the target, were found to have different phases for detected and undetected trials.  Since the alpha rhythm is rather slow, which often suggests a greater number of neurons firing in synchrony, the authors suggest that this phase difference reflects a different cortical susceptibility to visual stimulation.  When the target was presented at one peak of the oscillation, subjects were much more likely to report perceiving it – at different times of the rhythm, the visual cortex was more receptive of input.

Personally, I find this result quite fascinating.  I’ve been working to see if there’s a critical error in the methods used or analysis performed, but it seems like the authors were very careful in their work – this finding appears, by my best understanding, to be legit and important.  Though I’ve mentioned throughout this post the possibility of using brain state to predict perceptual state before the stimulus is shown, I want to be clear that this is not what the authors of this study did.  All this analysis and classification of alpha states was done after subjects were long-gone.

Now, what I’d really like to see is a group perform the predictive version of this experiment – keep a running monitor of alpha power and present hard-to-see stimuli at different phases of the alpha oscillations.  If this finding is robust, and computational power is plentiful enough, this experiment should be feasible and yield a positive result.  I’m really excited to see developments like this study, along with several others from the past year, concerning what’s happening neurally in the period before a stimulus is presented or a motor act is performed.  In our efforts to piece together an explanation of human behavior (both subjective experience and objective action) in terms of neural events, this kind of work is just as important as understanding the effects of these behaviors (perception and action) on the brain.

What do you think?  If you’re experienced with EEG experiments/analysis, I’d love to hear a more in-depth evaluation of the methods used in this paper.  Leave a comment, or email me at neurotechnica on gmail.

Having been a huge fan of the first Houston exhibition, I was excited to learn that Body Worlds would be returning this year.  This time, it’s called “Body Worlds 2 & The Brain, Our Three-Pound Gem” (which naturally had me excited).

To start off with, this exhibit is extremely expensive for a museum showing.  My (student!) ticket came out to be $21, and standard adult admission is $25.  There’s definitely not enough to this exhibit to warrant that kind of ticket price (though I’d still suggest attending if you somehow missed the first Body Worlds showing).

Also, for those of you with a strong interest in neuroscience (like myself), Body Worlds 2 is definitely targeted towards a general audience.  There isn’t anything that isn’t taught in PSYC 101 or an intro neuroscience course, but it’s pretty cool that it’s presented in a very readable and exciting way.  The “three-pound gem” part seems to be an afterthought, though, as very little of the exhibit itself is geared towards the brain.  There are lots of wall hangings that briefly introduce different aspects of modern neuroscience (like development, personality, emotion, creativity, memory, consciousness, disease, etc).  These amount to little more than you’d find in a Time or New York Times article, and some even contradict each other.  One (I don’t remember which) attributed long term memory to  “the back of the brain”, and also defined “instantaneous memory” to be the type of memory used to remember a phone number (this is the classic example for working memory).  But, in general, these provide an interesting & broad overview of the more interesting parts of neuroscience.

So what brain-related plastination specimens are shown?  Like before, there are plastinated coronal, saggital, and axial slices of adult brains, as well as several specimens from stroke victims (slices & whole brains).  There are at least 2 examples of the entire nervous system (brain, spinal cord, and large peripheral nerves), which are very impressive and interesting to see, as well as one specimen from an Alzheimer’s disease victim.  The coolest brain-related specimen, I thought, was a cast of the cerebral blood vessels.  The structure is absolutely beautiful.  Also, several of the full-body plastinations placed a great deal of emphasis on the brain, like “The Ponderer“, which is a man seated comfortably in a contemplative pose w/ much of his brain exposed.

As far as the full-body plastinations go, there are some very creative examples on display.  It won’t do anyone much good for me to try and describe them, but there are at least 3 or 4 that I was very impressed with.  Gunther von Hagens is truly an artist.  The full-body specimens are much more artistic this time than they were in the previous exhibit, so perhaps those alone could be worth the price of admission.

It surprises me that they’re marketing this exhibit as focusing on the brain.  Aside from the wall hangings, there isn’t really any additional brain-related content this time around.  There is, however, a large and very interesting display of human development, from conception to birth.  This part of the exhibit should certainly be the main attraction, but for whatever reason (probably support from the Mischer Neuroscience Institute), the brain was this year’s focus.

Overall, I was a little disappointed in Body Worlds 2.  I guess I was expecting to be as impressed as I was the first time, which I unfortunatley wasn’t.  Don’t get me wrong, Body Worlds is a wonderful opportunity to see real human bodies and what happens to them as we age & suffer disease.  The full-body plastinations are as impressive as ever, if not moreso, and the neuroscience blurbs on the wall will hopefully further promote awareness of neuroscience as an important discipline.  But if you’re expecting something new and brain-centered, Body Worlds 2 isn’t quite there.

What: Body Worlds 2 & The Brain, Our Three-Pound Gem

Where: Houston Museum of Natural Science

When: until Feb 22

How (much): $21 for college students, $25 for adults, $17 for members (buy here)

Worth it? Depends on who you are.  Definitely check it out if you missed the first Houston showing, but otherwise, there’s not much new to see here.

The authors do an excellent job describing the merits of blogging about science – namely, quick peer review and dissemination of information to a larger audience than a journal or trade publication would reach.  They cite several examples of science blogs being used as educational tools in the K-12 classroom.  My favorite example of these is Cognitive Daily, written by Dave and Greta Munger (Dave is also the founder of ResearchBlogging.org, an aggregator for quality blogging about peer-reviewed research).  The husband-and-wife duo dissect recent publications in the cognitive sciences and do a great job explaining the findings in a clear and concise way.  I also really enjoy their ‘casual friday’ posts in which they conduct their own experiments through online polling software and analyze the results in a future post.  Dave and Greta even organize their posts into convenient categories that K-12 teachers can use to supplement their curriculum.

The most substantial portion of the Batts, Anthis & Smith paper is a discussion on what institutions can do to benefit from resident science bloggers, and how this involvement can benefit the bloggers in return.  Their primary suggestion is for institutions to create an aggregator, similar to Seed Media Group’s ScienceBlogs, which organizes all the blogs kept by members (be they staff, faculty, or students) of an institution by category and has a portal that displays recent posts and comments.  This kind of thing is already being done at Stanford (here).

I think there are some inherent problems in the “institutional blogging” solution which Batts et al propose.

First, I imagine being hosted by and promoted through your institution would influence the content of your posts.  It would be difficult (and perhaps not even permitted) to critique work done at one’s own institution or new policies or happenings about the university.  I doubt absolute censorship would occur except in the most extreme cases, but there would be a conflict of interest, I think.

Additionally, I don’t think that institutional blogging will solve many of the problems in science blogging.  Organizing content by institution doesn’t make much sense – just because I like Semir Zeki’s blog (http://profzeki.blogspot.com) doesn’t necessarily mean I’ll like or be interested in other blogs by UCL professors or students.  Instead, I’d like to be given ready access to other blogs that deal with similar (though somewhat unique) subject matter.  This is where ScienceBlogs really shines – they have a great collection of diverse and high-quality blogs that deal with all manner of topics, and they organize their content into “channels” of related blogs.

Thus, I think an open version of ScienceBlogs which allows (most) all submitted blogs to be indexed and aggregated would have the best potential for bringing together interesting and varied science content.  To avoid reliance on a single site, perhaps the site (OpenScienceBlogs?) could aggregate from RSS feeds and just display the content of the feed on the portal site, while linking to the original post for comments.  Or, plugins could be written for WordPress, TypePad, Blogger, etc that could make all this content aggregation relatively seamless.  Each blog could be tagged with different attributes, such as Topic (evolution, neuroscience, physics, etc), Institution, Author Information (student status, major/concentration, class year), and type of blog (research, pop sci, multi-author, etc) to make finding interesting and relevant blogs fast and easy.

This, I feel, would be an optimal way to organize and access content.  Little work would be required on the part of the bloggers (except maybe the installation of a plugin), it would require minimal staff to maintain, and hosting costs would be generally low.  Additionally, this could be combined with the institutional “badges” mentioned in the paper to confer legitimacy to the blogs (i.e., in order to display your institution’s badge, you have to submit posts to an editor or committee for review, etc).  I think it would be fair to institute community quality control measures, like those used by ResearchBlogging.org, to ensure members are posting relevant and appropriate content.  There would need to be some approval process, but it should be rapid and minimal to encourage participation.  This system would funnel readers to blogs that they’re interested in, as well as surround them with similar content they may not have discovered elsewhere.  Bloggers would get more readers, readers would have more to read and comment on and blog about – everyone wins.

If there’s anyone out there that thinks this is a good idea and knows anything about web development, contact me – I’d love to get started on a project like this.  Or if something like this is already around, please let me know.

Other posts/articles about science blogging:

Living the Scientific Life: Science blogs can advance the academic process

The Scientific Activist: Advancing Science through Conversations: Bridging the Gap between Blogs and the Academy (by Nick Anthis, an author on the PLoS Biology paper)

In his recent commencement speech at Caltech to the graduating class of 2008, Robert Krulwich encouraged the new graduates to take an active role in communicating science to the masses.  The speech is recorded and distributed as a podcast episode of Radiolab, titled “Tell Me A Story” – I highly recommend checking it out.  I think it’s really great and definitely worth the listen (however, according to a commenter, parts are not necessarily accurate).  This speech, and Radiolab in general, prove that science isn’t only about fancy math and big words.  There’s the serendipity, the hard work, the new ideas – the “how” and “why” of research. That’s what can and will get the public interested.

We need more people like Robert and Jad, scientists and journalists alike, to step up to the plate and take the initiative to make science open to the public in an informative and engaging way.  I think Jonah Lehrer deserves praise for this.  His blog, along with his many articles in Seed and The New Yorker, are very successful in conveying good, solid information in a readable and interesting way.  Brian Greene is also doing some great things in New York City with the World Science Festival, an event I sorely regret being unable to attend this year.

What do you think?  What role should scientists play in publicizing science?  Is this the job of journalists, or should scientists themselves take an active role in this process?  Comment below, or email me at neurotechnica shifttwo gmail dot com.