LabRigger is a how-to blog with a fresh look (kudos for the design and typography) that already has many interesting and relevant posts up for scientists who like to build. (You know who you are…) Furthermore, it seems especially geared toward neuroscientists and physiology folks. I’ve already added this one to my browser’s bookmarks.

Here are some of my favorites from quickly perusing the site: Printable bolt size charts, Tips on intrinsic optical imaging, Comparison of high NA, low mag objectives, and my favorite, Catalogs as textbooks. (I still remember a neuroscience faculty member here at MIT who told me that he brings science catalogs along on his vacations as “leisure reading” to stay up-to-date on new tools and to generate ideas for experiments.) In fact, I wanted to read just about every post on this blog and I think you will too! And if you’re the author of this blog, please introduce yourself in the comments, too.

It’s a centralized commenting location for all major neuroscience papers. Every recently published paper has a page that you can find by browsing or searching. You can leave comments anonymously, and you can request follow-up emails when others comment. ThirdReviewer currently indexes all papers from 11 major journals, including Neuron, Nature, J Neurosci, and Nature Neuroscience.

Check it out and opine: The Third Reviewer
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A few days later, Henry Markram, leader of the Blue Brain Project at EPFL, sent off an e-mail to IBM CTO Bernard Meyerson harshly criticizing the IBM press release, and cc’ed several reporters. This brought a spate of shock media into the usually placid arena of computational neuroscience reporting, with headlines such as “IBM’s cat-brain sim a ‘scam,’ says Swiss boffin: Neuroscientist hairs on end”, and “Meow! IBM cat brain simulation dissed as ‘hoax’ by rival scientist”.  One reporter chose to highlight the rivalry as cat versus rat, using the different animal model choice of the two researchers as a theme.  Since then, additional criticisms from Markram have appeared online.

Find out more after the jump.

In the aftermath, IBM has stood behind the announcement, citing for Network World their team’s involvement with “Stanford University, University of Wisconsin-Madison, Cornell University, Columbia University Medical Center, University of California-Merced and Lawrence Berkeley National Laboratory” as defense.  Who are the researchers they are standing behind?  According to Modha’s blog, they are:

• Stanford University: Brian A. Wandell (Prof of Psychology, Electrical Engineering), H.-S. Philip Wong (Prof of Electrical Engineering)
• Cornell University: Rajit Manohar (Prof of Electrical Engineering)
• Columbia University Medical Center: Stefano Fusi (Prof of Theoretical Neuroscience)
• University of Wisconsin-Madison: Giulio Tononi (Prof of Psychiatry)
• University of California-Merced: Christopher Kello (Prof of Cognitive Science)

For this neurodude, it is interesting how this disagreement may be symbolic of the gap that still remains between neuroscience and AI.  Markram is a neuroscientist turned technologist, while Modha is a computer engineer who wants to derive technological insight from biological  systems.  They are approaching the ideal of reverse engineering the brain from very different perspectives, and its only natural that they value different milestones.  The IBM team, even with the additional professors on their team, still lacks mainstream neuroscientists to help validate their claims.  That being said, the public realization of this could be a positive thing for both fields.  Although some frustration has resulted from this, this could be a great opportunity for the breakdown of walls between these fields.

In the end though, it does seem like Markram has a point.  The IBM press release clearly went too far.  Whether the angry public e-mail was the best strategic way to make the point remains to be seen.  It will be interesting to see what the next move from the IBM team will look like.

I’m a fan of it because it is an open-access journal featuring a “tiered system” and more.  From their website:

The Frontiers Journal Series is not just another journal. It is a new approach to scientific publishing. As service to scientists, it is driven by researchers for researchers but it also serves the interests of the general public. Frontiers disseminates research in a tiered system that begins with original articles submitted to Specialty Journals. It evaluates research truly democratically and objectively based on the reading activity of the scientific communities and the public. And it drives the most outstanding and relevant research up to the next tier journals, the Field Journals.

I’m a big fan of the variety of specialty journals they have:

• Aging Neuroscience
• Behavioral Neuroscience
• Cellular Neuroscience
• Computational Neuroscience
• Enteric Neuroscience
• Evolutionary Neuroscience
• Human Neuroscience
• Integrative Neuroscience
• Molecular Neuroscience
• Neural Circuits
• Neuroanatomy
• Neuroenergetics
• Neuroengineering
• Neurogenesis
• Neurogenomics
• Neuroinformatics
• Neuromethods
• Neuropharamacology
• Neuroprosthetics
• Neurorobotics
• Synaptic Neuroscience
• Systems Neuroscience

From the Neuroscience Wikipedia initiative:

SfN is calling upon members to harness the power of Wikipedia and support the Society’s mission of promoting public education about neuroscience.

Wikipedia, a free online encyclopedia, has become one of the major sources of information used by the public.

SfN’s Public Education and Communication Committee (PECC) recently reviewed the main Wikipedia neuroscience overview section and entries on 10 major branches of neuroscience. Many of the entries were still under construction and incomplete.

SfN aims to improve and expand Wikipedia’s neuroscience content by encouraging members to edit and contribute.

Well done, SfN!

I’ve been remiss in posting this article that was featured in the HHMI Bulletin a few months ago, but Neurodudes was mentioned in an article about blogs and science, along with our friend Andrew Hires’s excellent Brain Windows blog.

Indeed, researchers would do well to blog more than they do. The experience of journals such as Cell and PLoS ONE, which allow people to comment on papers online, suggests that researchers are very reluctant to engage in such forums. But the blogosphere tends to be less inhibited, and technical discussions there seem likely to increase.

Moreover, there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

]]> http://neurodudes.com/2009/03/04/nature-its-good-to-blog/feed/ 1 http://neurodudes.com/2008/05/13/pbs-not-so-neuroscience-savvy/ http://neurodudes.com/2008/05/13/pbs-not-so-neuroscience-savvy/#comments Tue, 13 May 2008 04:22:47 +0000 Neville Sanjana http://neurodudes.com/?p=460 Salon has an interesting piece condemning a recent PBS show purportedly on Alzheimer’s treatment but really more of a sketchy informercial. The program concerns a neurologist with tenuous ties to UC Irvine who advocates SPECT (single photon emission computed tomograpy, a technique which, similar to PET, uses a radiotracer) and some unfounded preventative treatments for Alzheimer’s. The neurologist Bill Amen has appeared on many big-name media outlets including CNN, the Today Show, and Fox News (and the real sign of media success — Oprah) although his approach to Alzheimer’s detection and treatment is lacking in scientific credibility:

“SPECT scans are not sufficiently sensitive or specific to be useful in the diagnosis of A.D.,” neurologist Michael Greicius , who runs the Stanford University memory clinic, and has a special interest in the use of functional brain imaging in the diagnosis of A.D., tells me. “The PBS airing of Amen’s program provides a stamp of scientific validity to work which has no scientific validity.”

Continued pontification on neuroethics issues after the jump.

Looking at Amen’s website, you can find all sorts of “neuro supplements” (many of them seem to be similar to basic multivitamins, probably not harmful but not really neuro treatments in any specific way) and more intriguing products like the $4.95 online Amen Brain System Test which “is a valuable tool to help determine if there are problems in the prefrontal cortex, anterior cingulate gyrus, basal ganglia, temporal lobes or deep limbic system.” Really? Anterior cingulate? Deep limbic system? Hmmm.

Although people are certainly getting duped by Amen who is out for a quick buck, he is likely indicative of a larger trend. Namely, cashing in on the public’s desire to apply modern neuro research to improving their own health. (After all, that is how/why a lot of neuroscience is funded.) Some of this type of stuff is legitimate and that’s fine, but a lot of it won’t be. How could Amen get promoted through many “respectable” media outlets? Didn’t anyone try to check out his claims? Amen’s response to the critical Salon article makes no headway in providing scientific support for his treatment. As Stephen Colbert might say, his response smacks of truthiness. Where are the neuroethicists and neuroscientists on this one? Shouldn’t they be complaining to the news outlets and reminding them of their duty to fact-check the reports made on their shows? And yes, I mean interviewed guests too. General popularity should not be conflated with scientific approval. People who make scientific claims need to be checked on!

This issue seems to be a pertinent one these days, as demonstrated by this front page NYT article (NYT, login) on the absurd use of ex-military as news analysts and their propagandistic use by the Pentagon. Truthiness seems to be all the rage right now. Let’s hope facts come back into the picture before bad neuroscience leaves a lasting bad impression.

On a more positive note, I’d be curious to hear any opinions on what kinds of products based on preliminary results from neuro research should be allowed and how the scientific community can become more active in approving what’s good and what’s not. I do think that we will soon have many neuroscience entrepreneurs and not all of them are going to have PhDs. What products can be trusted? Maybe we need a forum for reviewing and rating these products — even one based on feedback from users. Ideas?

Here’s a neat new website. It’s a repository of quantitative information on biological things (eg. organisms, biomolecules, etc.) Some stuff I found while glancing through:

Number of mRNA/cell in E. coli: 138

Volume occupied by all RNA in E. coli: 6%

Average gene length in mammals: 16.6kb

Average gene length in nematode C. elegans:  4 kb

Mutation rate per genome per replication in humans: 0.16 mutation/genome/replication

Average time between blinks in humans: 2.8 sec

Amount of photons necessary to excite a cone in humans: 100

Citations are included for most numbers too. The database seems a little sparse on neuroscience topics, so go over and contribute some numbers!