The Open Science Debate: Part 1.5 – open access roundup
A roundup of sources of rumination about what Open Science could look like, plus promising-looking tools and resources representing what Open Science looks like today
Rapid dynamics of hippocampal spatial representation in echolocating bats
Review of recent research that demonstrates hippocampal place cells in echolocating bats tune their spatial selectivity to match the spatial acuity of incoming sensory information
Chronicles of a Graduate Student Let Loose in Europe (Part 2)
Senior graduate student Georgia Panagiotakos collects memorable quotations at the 61st Lindau Meeting of Nobel Laurates
Chronicles of a Graduate Student Let Loose in Europe (Part 1)
Senior graduate student Georgia Panagiotakos details her experiences at the Cortical Development conferences in Crete, Greece
Hello again,
I’m (finally) working on my report on the Colloquium on Rethinking the Future of Scientific Communication (is it May already?), and I remembered that one of the organizers, Nader Rifai, had recommended this great series of articles on scientific writing published by the journal Clinical Chemistry, of which he is editor in chief. So, before I forget, here is the link:
ClinChem Guide to Scientific Writing
By the way, as neuroscientists you may or not be familiar with Clinical Chemistry, but if you are interested in open science and new publication models, Dr. Rifai might be a good person to pay attention to. As the other organizers put it (approximately) over drinks the night before the colloquium, if you want to know how journals should be evolving over the next 5 years, just look at what Nader was doing last year.
That’s all I have for now, but stay tuned for more activity soon!
-Nick
While scouring Pubmed for published articles featuring Stanford Neuro-student authors for a recent post, I had two thoughts.
1) Students in the Stanford Neuro program were on a hell of a lot of papers
2) There was definitely a better way to highlight those papers than a retrospective every 6-months that took forever to type up and even longer to actually read (see thought 1).
Thus was born a new semi-regular feature for the neuroblog: PhDs in Press – of which this post is the first example.
Part shameless publicity, part proud bragging, part intra-program PSA, this feature will highlight recently published articles featuring an author (or authors) who is a current member of the Stanford Neuroscience Ph.D program.
[Note regarding the mechanics of this feature: This is purely through the magic of an ongoing My NCBI search for the names of Neuro PhD students. I wouldn't be surprised if there were some false negatives in the data set. Neuro students - let me know if I've missed your paper, and I'll gladly add it.]
Without further ado, and with many congratulations to the authors, the papers:
First Author papers:
- Jaimie Adelson (Adelson et al 2012)
- Niru Maheswaranathan (Maheswaranathan et al 2012)
- Jack Wang (Wang et al 2012)
Second through n-th Author papers:
- Branden Cord (Byers et al 2012)
- Lief Fenno (Byers et al 2012)
- Emily Ferenczi (Akam et al 2012)
- William Joo (Tasic et al 2012)
[Continue reading below the fold to allow link functionality above]
Read the rest of PhDs in Press »
This afternoon (April 2nd), Drs. Sebastian Seung and Anthony Movshon met at Columbia University to debate the topic of Connectomics. Moderated by Radiolabs Robert Krulwich and science writer extraordinare Carl Zimmer, these two eminent neuroscientists talked for an hour on what connectomics brings to the field of neuroscience. For those of you not familiar with connectomics, it is the effort to use high-throughput histological tools (such as serial electron microscopy) to provide an extremely precise wiring diagram of the brain (or practically, of small volumes of brain tissue). Sebastian Seung (Professor of Computational Neuroscience, MIT) is an outspoken proponent of connectomics as way to illuminate fundamental truths about how the brain functions, Anthony Movshon (Professor and Director, Center for Neural Science, NYU) represented those neuroscientists who disagree with Seung regarding the critical necessity of connectomics for understanding the computations of the brain.
During the debate, a small group (50-60) of Stanford Neuroscience students, post-docs and professors were watching together. 2 senior graduate students, Astra Bryant (Knudsen, Huguenard labs) and Nick Weiler (Smith lab) were live-tweeting. For those of you who missed out on the action, you can vicariously re-live the debate by reading our archived tweets below. It is currently unclear whether an official transcript/audio recording of the debate will be made available. When/If it is we’ll update this post with the links.
Updated 4/5/12: The video of the debate
For the official announcement of the debate, see the Radiolab website, here.
The debate was organized by NeuWrite.
Enjoy, and feel free to contribute to the discussion either in the comments, or by tweeting with @stanfordneuro.
Part shameless publicity, part proud bragging, part intra-program PSA, this post is all about articles, published in peer-reviewed scientific journals, featuring work by the students of the Stanford Neuroscience Ph.D program.
Since last July, the current graduate researchers (and recently-minted alumni) have produced an admirable volume of scientific research, some of which has been published in the form of journal articles. As the authors in question tend not to go around bragging, I’ll be doing so on their behalf.
To that end, what follows are two lists detailing the results of an afternoon spent spelunking through Pubmed. The first list contains the names of current (or recently graduated) Stanford Neuro students who are first authors on articles published since around June ’11 (date arbitrarily chosen). The second list contains the names of Stanford Neuro students who are second through n-th authors on papers published within the same time period. Click on an individuals name to see the full paper title and abstract.
Congratulations to all the recently published authors in the Stanford Neuro program!
(Grad students: Apologies for any author/paper left off the list – let me know and I will gladly add you - Astra)
First Author papers:
- Sergio Arroyo (Arroyo et al 2012 *co-first with Corbett)
- Corbett Bennett (Arroyo et al 2012 *co-first with Sergio)
- Poh Hui Chia (Chia et al 2012 )
- Lief Fenno (Tye et al 2011 *co-first with Kay Tye, Sung-yon Kim and Rohit Prakash)
- Emily Ferenczi (Mattis et al 2011 *co-first with Joanna Mattis and Kay Tye)
- Patrick House (House et al 2011)
- Mariko Howe (Howe and Barres 2012)
- David Kastner (Kastner and Baccus 2012)
- Sung-yon Kim (Tye et al 2011 *co-first with Kay Tye, Rohit Prakash and Lief Fenno)
- Joanna Mattis (Mattis et al 2011 *co-first with Joanna Mattis and Kay Tye)
- Rohit Prakash (Tye et al 2011 *co-first with Kay Tye, Sung-yon Kim and Lief Fenno)
- Andreas Rauschecker (Rauschecker et al 2011)
- Jana Schiach Borg (Schaich Borg et al 2012)
- Nicholas Steinmetz (Steinmetz and Moore 2012, review of Gregoriou et al 2012)
- Saul Villeda (Villeda et al 2011)
- Jack Wang (Wang et al 2012)
Second through n-th Author papers:
- Ron Alfa (Bader et al 2011)
- Astra Bryant (Paz et al 2011)
- Matt Carter (de Lecea et al 2012)
- Branden Cord (Pasca et al 2011, Byers et al 2011)
- Lief Fenno (Byers et al 2011, Mattis et al 2011, Paz et al 2011, Tye et al 2011, Yizhar et al 2011, Zhang et al 2011)
- Lisa Gunaydin (Mattis et al 2011, Anikeeva et al 2011)
- Logan Grosenick (Anikeeva et al 2011, Tye et al 2011)
- William Joo (Sweeney et al 2011)
- Li Li (Yoo et al 2011)
- Jana Lim (Greer et al 2011)
- Ivan Millan (Liu et al 2012)
- Kira Mosher (Villeda et al 2011)
- Daniel O’Shea (Mattis et al 2011, Yizhar et al 2011)
- Scott Owen (Bader et al 2011)
- Georgia Panagiotakos (Osterhout et al 2011)
- Rohit Prakash (Mattis et al 2011, Goshen et al 2011, Abilez et al 2011)
- Aslihan Selimbeyoglu (Rauschecker et al 2011)
- Sergey Stavisky (Sussillo et al 2012)
- Gabriela Suarez-Mier (Taniguchi et al 2011)
- Nathan Woodling (Liang et al 2011, Grabrucker et al 2011)
- Kelly Zalocusky (Witten et al 2011)
[Continue reading below the fold to allow link functionality above]
Read the rest of Stanford Neuro Peer-Reviewed Publications »
I haven’t made much of a dent in my own writings about Open Science yet – I’ll get that up either tomorrow night (doubtful) or this weekend. However, in anticipation of Friday’s colloquium, here is a roundup of some of my favorite sources of rumination about what Open Science could look like, and some of the most promising-looking tools and resources I’ve encountered that represent what Open Science looks like today.
First, a great post by Richard Poynder on his blog Open and Shut, which touches on most of the issues I raised in my own post this weekend about the mess journal publishers (and particularly Elsevier) have gotten themselves into with their support for RWA. In the end, while he certainly doesn’t let them off the hook, he makes the case that the research community is equally oblivious to a gaping chasm of unsustainability in the current scientific publishing system.
Open Science Philosophy:
- These pretty much sum it up, but if you want to read lots more words, following are some more verbose resources.
Is the Open Science Revolution for Real?
- Ok I already linked to this David Dobbs article in my last post, but it’s still one of my favorite discussions of the many issues involved in evolving the scientific publishing model. He breaks it all down for you. Great introduction to the debate.
Read the rest of The Open Science Debate: Part 1.5 – open access roundup »
Thanks to nomination by Kelly Z, David Bochner and I will be attending a colloquium on the future of scientific publishing this Thursday, sponsored by Stanford University Libraries, Highwire Press, and the Journal of Clinical Chemistry. In preparation, I have been doing a lot of research into the current debate over the role of traditional publishers, and models for what a future, more open publication system might look like. In the spirit of open discussion, I thought I would share my thoughts here and invite the Stanford community to comment and post your own ideas and responses, which I would love to share with the colloquium this week.
Below is Part 1, in which I discuss the rise and fall of the controversial Research Works Act this winter. I end with a number of links for further reading about the controversy and resources which discuss the new models of scientific publishing which are being aired.
Part 2, which I will post next weekend, will describe the state of the Open Science movement in more detail, and summarize the discussions we have during Thursday’s colloquium.
Part 1 – Ding Dong, the RWA is Dead!
One doesn’t frequently have the opportunity to envision a mob of angry scientists, chanting slogans, lab coats a-flapping, brandishing acetylene torches and tuning forks, marching to storm the fortress of the status quo. However, this is precisely the image that has been conjured up in recent weeks (1) to describe the furious stream of blog posts, op-eds, and twitter streams emanating from the corner offices of labs across the country, denouncing prestigious journals and publishers as ‘enemies of science’ (2).
The proximal cause of the all this agitation in the academy is a bill called the Research Works Act (3), introduced to the US Congress by Reps. Darrel Issa (R-CA) and Carolyn Maloney (D-NY) in December. In essence, the RWA proposes to roll back the NIH’s 2008 Public Access Policy, which mandates that the results of all NIH-funded research must be made available for free on the web within one year of publication (4). That is, NIH made the argument that since taxpayers were funding the research, they should not have to pay again to see the results.
The academic publishing industry strongly disagreed. Two of the main backers of the Research Works Act were international publishing giant Elsevier (which has made significant donations to both the bill’s sponsors (5)) and the Association of American Publishers (AAP) (6), who asserted that the NIH’s current policy amounts to government sponsored piracy, and violates the copyrights held by scientific journals and publishers.
This is where the angry mob comes in. Read the rest of The Open Science Debate: Part 1 (Ding Dong, the RWA is Dead!) »
General by .
For a recent neuroscience journal club, I presented several papers on echolocating bats. Under the premise that “bats are awesome” (F. Collman, personal communication), what follows are the major points from my presentation. The slideshow below contains parts of my presentation including figures from several relevant papers. A disclaimer – I will be vastly oversimplifying the research, and presenting only a fraction of what the authors discovered and discussed. For less concise descriptions of the research in question, interested persons should read the appropriate papers.
The hippocampus is a region of the brain critically important for episodic and spatial memory. Patients without their hippocampi (like the famous patient H.M.) cannot form new episodic memories. Patient case studies such as H.M’s sparked a keen interest in the hippocampus amongst neuroscientists, and there have been great strides in elucidating the neural circuitry within the hippocampus. The question of exactly how that neural circuitry encodes episodic and spatial memory is a matter for many lines of ongoing research and much debate.
One well described phenomenon within the hippocampus, that may play a critical role in the spatial component of spatial memory formation, are hippocampal neurons termed “place cells”. These neurons are driven when the animal passes through a particular region of its environment. Earlier work in rodents demonstrated that when an animal is placed within a particular environment, its place cells tile the entire area, tracking the animal’s movements. The spatial region that any given place cell (called the “place field”) encodes is flexible – changes to the environment (i.e. moving landmarks, changing wall colors, altering odors) will alter the place field. Introducing an animal into a brand new environment will cause an individual place cell to generate a new place field, however returning that animal to the old environment will recall the original place field. Theoretically, the location information provided by place cells could be utilized in the generation of memories. Place cells fire as you move through the world, and the order in which the population fires could be stored as a memory of movement through space. Exactly how this storage could be achieved, and where in the brain it takes place, is the subject of many ongoing research projects. It’s also not what the rest of this post will be about.
Instead, we’ll turn to a slightly different question – one of how sensory information influences the structure of the place fields. Another persistent research question is what exact inputs generate the place field. It seems like common sense that sensory information would play some role in establishing and maintaining the place field, and in causing a place cell to fire as the animal moved through the appropriate place field. As I mentioned about, it is known that altering the sensory information within the environment will cause place cells to change their fields. However, these changes occurred over long time scales (the order of minutes to days). Researchers from the University of Maryland were interested in much quicker changes in place fields – namely, how place cells responded to newly arrived sensory information. Do place cells rapidly alter their fields based on temporally precise sensory events?
Read the rest of Rapid dynamics of hippocampal spatial representation in echolocating bats »
Mr. Keller:
As Publisher of both the Stanford University Press and HighWire Press (a division of the Stanford University Libraries), you understand the value of the free and broad dissemination of knowledge.
You must also appreciate the threat that the Research Works Act (HR 3699) poses to the open exchange of ideas. This exchange is central to scientific progress and is the most fundamental means the scientific community has to return the public investment on our research. In limiting access to publicly-funded research, this act stands against the stated mission of both Stanford University Press and HighWire Press, as well as the motto of Stanford University itself.
I therefore urge you to join other respected members of the Association of American Publishers, including AAAS, the MIT Press, and the University of California Press, in publicly stating their opposition to the Research Works Act.
Sincerely,
Kelly Zalocusky
PhD Candidate
Stanford University
Neuroscience Program
————————————————————-
In case Mr. Keller is not an avid NeuroBlog reader, I have also sent him the letter directly. I encourage my fellow NeuroBlog readers to do the same. Really, truly–feel free to copy, paste, and send this exact letter.
Michael A. Keller can be reached at Michael.Keller@Stanford.edu
Admin Note:
As a colleague and fellow PhD Candidate at Stanford University, I whole-heartedly agree Ms. Zalocusky’s sentiments, and I applaude her for speaking out against the Research Works Act (HR 3699). I hope that readers will join with us in contacting both members of the American Association of Publishers, as well as our elected representatives in national government, in protest of the Research Works Act.
Astra Bryant
PhD Candidate
Stanford University
Neuroscience Program
For those of you still at SfN11 on Wednesday, be sure to visit the final posters from Stanford Neuroscience.
The Stanford Neuroscience affiliates presenting their research on Wednesday, Nov 16 are:
Posters
What has the Stanford Neuroscience community been up to? Find out by visiting our presentations and posters at SfN2011!
The Stanford Neuroscience affiliates presenting their research on Tuesday, Nov 15 are: