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Archive by category: Noah Gray

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Vote for "Method of the Year"

Last year, the editors of Nature Methods chose a “Method of the Year” (MOY) and the winner was next generation sequencing. This feature included an editorial, commentaries, news features and other types of content discussing the winning technique.

This year, the editors want input from the scientific community. Go here to see the nominees and cast your vote. Interestingly, you can vote positively or negatively for a technique as well as leave comments in discussion forums. Although the ultimate choice will still remain an editorial decision, at least the editors will get feedback from the community.

This is some great use of Web2.0 to get the community engaged and I hope that you will participate.

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Moving to Nature Network

Another blogging hiatus on the old "Action Potential" blog. Sorry about that. However, the news is now that I have become a neuroscience editor for Nature, I will be taking my show on the road to a new site, and will be blogging on Nature Network. My new blog is called Nothing's Shocking (10 points to whomever knows the reference) and will pretty much follow the same fast and loose style that got me into trouble here. I hope you'll come take a look. There are already two posts up (besides the obligatory introductory trash), with more to come:

What does mirror self-recognition really mean?

Janelia East and the quest for round scientists

I've greatly enjoyed my year+ on AP and want to thank all of the readers and commenters who provided me with the incentive and motivation to continue doing this. Let the debates continue...

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Getting into and out of character

A great discussion over at Nature Network inspired me to initiate a similar conversation here at Action Potential. Corie Lok asked the question "What is fair play in the blogo/commentosphere?" A fair question indeed. The responses have produced some interesting discussion fodder, but got me thinking about my own experiences on several science blogs. Although this conversation is equally applicable to any type of blog, let's stick with those dedicated to or mainly engaged in conversations about science.

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The science of dignity

A recent Nature news article regarding the latest battle on the animal research front takes us to Switzerland. There, the University of Zurich and another research institute are taking a case to the Swiss Supreme Court arguing against the rulings of a lower court, which banned two primate-based experiments that had been approved by the Swiss National Science Foundation. The proposed experiments were said to potentially offend the dignity of the animals, according to an external advisory board, overruling a decision by the veterinary office (responsible for animal welfare) who allowed the experiments to proceed.

This stems from a change in Swiss law back in 2004, which suggested that the dignity of animals had to be considered (see Article 120). As the accompanying editorial points out, using a subjective concept like dignity as our guiding compass in determining the moral legitimacy of research proposals is not only absurd, but dangerous.

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Turning web traffic into citations

Our June editorial discusses the relationship between web traffic and citations. Specifically, can one predict how well any particular paper is cited years after publication, based solely on the number of downloads it receives immediately following its appearance online? Our preliminary analysis suggests that this relationship not only exists, but is surprisingly strong.

I’ll leave you to read the editorial for more of the background as to why we examined this relationship, but I will repeat a few keys things here. The main purpose of this post is to provide more of the details behind the data and analysis, and to initiate a good discussion.

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Retraction reaction redux

I apologize for the long time between posts. Things have been busy and I hope to have more for you soon. In the meantime, I wanted to toss out something to tide you over.

A recent Nature editorial extends the previous discussion that began in the AP post "Retraction reaction", concerning the retraction of a paper from the lab of Nobel Prize winner Linda Buck. The editorial touches on the issue of a significant weakness in the scientific process. Namely that save for a select few in the "know", the community-at-large rarely learns of what went wrong in a study, leading to its eventual retraction. This is indeed a concern and an on-going problem.

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Nature Network Journal Club: Curbing cocaine addiction using gene therapy

The next installment of the Nature Network Neuroscience group journal club is now live. The paper discusses a potential therapeutic strategy involving the upregulation of the dopamine receptor D2R that may be beneficial in the treatment of cocaine abuse and addiction.

The contributor discussing this paper for the neuroscience group is Áine Duffy, a postdoctoral fellow at Weill-Cornell Medical College in New York. I want to thank Áine for her participation.

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Nature Neuroscience turns 10!

Our May editorial takes a brief look back at some of the history of Nature Neuroscience. We also present some of the most-cited papers over the past decade. This is an interesting exercise, as it provides an opportunity to reflect on the interests of both the authors and readers over the past decade.

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Nature Network Journal Club: Giving sounds the silent treatment

The next installment of the Nature Network Neuroscience group journal club is now live. The paper provides evidence that in unanesthetized animals, sounds are sparsely represented in the auditory cortex.

The contributor discussing this paper for the neuroscience group is Lizzie Buchen, a science writer for Discover Magazine in New York. I want to thank Lizzie for her participation.

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Big Pharma and academia becoming more and more cozy

I recently attended the Alzheimer's Disease Keystone meeting in Keystone, CO and became more acutely aware of something than ever before: academia and drug companies really like one another. Sure, the latter always loved the former, since collaborating with university-based scientists often made the publications arising from the private sector look a little more legit. On the contrary, the reciprocity in this relationship has not always been there. There is without a doubt some sub-disciplinary differences in this complex relationship, but in the basic science departments that I lurked around, if you were associated with a company (or worse, left academia for a position there, succumbing to the power of the Dark Side), there was always talk of whether or not you could be trusted. Because companies need publications to prove the legitimacy of their product, right? And the legitimacy determines how much money everyone makes, right? So with such conflicts of interest, could the scientist, or the data being produced by these people, be trusted?

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Nature Network Journal Club: Neuronal dynamics mediate efficient coding

The next installment of the Nature Network Neuroscience group journal club is now live. The paper discusses the role for brief adaptation in the improvement of population-based encoding accuracy during sensory information processing.

The contributor discussing this paper for the neuroscience group is Adam Packer, a graduate student at Columbia University in the lab of Rafa Yuste. I want to thank Adam for his participation.

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What to do with your unfunded proposals - place them in a centralized repository?

I would say no. Grant proposals are a precious commodity, especially in this day and age of reduced funding and evaporating money. However, in a recent Nature correspondence, Dr. Noam Harel describes his vision for a centralized grant repository, ideally open to the public, where researchers could place their best ideas, allowing various funding agencies to discover the plans most-suited to their respective agendas. Dr. Harel likens this potential web manifestation to something like eBay, Facebook or Google, but for scientists and funding agencies. A more apt analogy might be Monster.com, with both sides searching for their ideal match, and a long-term relationship (perhaps I am now making it sound more like eHarmony.com...).

When it comes to the integration of scientific communication and technology, I am extremely optimistic, and although I don't reject Dr. Harel's idea entirely, I just don't see it taking off in its presently-proposed form.

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Nature Network Journal Club: Getting a GRASP on synapse location

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.

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Nature Network Journal Club: Sticky matters configuring a synapse

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.

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Nature Network Journal Club: Drug craving and internal state

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.

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Neuroscience and Web 2.0: Participation may vary

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.

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Nature Network Journal Club: Crossing the threshold to consciousness

The next installment of the Nature Network Neuroscience group journal club is now live. The paper is attempting to understand the neural mechanisms that distinguish between conscious and unconscious processing, and is from a collaborative group in Paris.

The contributor discussing this paper for the neuroscience group is Alfredo Pereira, Jr, an adjunct professor at São Paulo State University. I want to thank Alfredo for his participation.

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Pet sematary

A woman in the US has decided that she loved her pit bull (named Booger) so much, that having him all over again is definitely worth the $150,000 price tag. I saw this story in the BBC, reporting how a Korean company, RNL Bio, has taken its initial order for pet dog cloning, the first such venture of commercial scientific canine cloning (a pet cat was first cloned in 2004). The lead scientist at RNL Bio, Dr Lee Byeong-chun, had previously worked with disgraced stem cell scientist Dr Hwang Woo-suk, whose fraudulent publications created quite a stir (we referred to that scandal on Action potential here.)

The client, Bernann McKunney, gave RNL Bio ear tissue from "Booger", preserved by an American biotech firm before the dog died 18 months ago. Ms. McKunney had become quite devoted to her dog after she claimed it saved her life, coming to her aid while she was being attacked by another dog, an encounter that cost her an arm. For those of you wishing you had the six figures required to re-create your close canine companion, never fear, RNL Bio's marketing director, Cho Seong-ryul believes that the cloning costs should come down to be under $50,000, as the industry begins to "take-off".

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Nature Network Journal Club: Special delivery of an anesthetic

The next installment of the Nature Network Neuroscience group journal club is now live. The paper is on selective nociceptor inhibition, from the lab of Clifford Woolf at Harvard.

The contributor discussing this paper for the neuroscience group is Damien Samways, a post-doctoral fellow at St. Louis University in the lab of Terrance Egan. I want to thank Damien for his participation.

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Harvard open-access policy – can you please be more specific?

The Faculty of Arts and Sciences (FAS) at Harvard University voted Tuesday to adopt an open-access policy, providing a free repository for finished papers, according to a recent press release. This move will allow for greater dissemination of scholarly work conducted at Harvard, says Stuart Shieber, a professor at FAS. Shieber states that a combination of a restrictive publishing system and the “astronomical” cost of journals have led the Harvard professors to support such a venture. An official description of the proposal that was actually discussed by the FAS on Tuesday is here.

As my colleague from Nature Precedings, Hilary Spencer, points out in a recent Nature Network forum, this entire policy is very vague with regards to what is meant by the scholarly article or the "final version." Is that the final, journal-produced PDF? The peer-reviewed, unpublished, non-copy-edited version? The non-peer-reviewed pre-print? According to an analysis written up on TheScientist.com, this mandate would require that published articles be submitted. However, go back and re-read the original proposal and tell me where it says that explicitly.

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Nature Network Journal Club: Manufacturing new hair cells is for the birds

The next installment of the Nature Network Neuroscience group journal club is now live. The paper focuses on the generation of new hair cells from avian mesenchymal tissue.

The contributor discussing this paper for the neuroscience group is Shelley Batts, a graduate student at the University of Michigan. I want to thank Shelley for her participation.

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What are you doing for Darwin Day?

The Darwin Day celebration was initiated by Dr. Robert Stephens and was held at Stanford University on April 22, 1995 to celebrate the scientific accomplishments of Charles Darwin. In subsequent years, the event was changed to be on or around the birthday of Darwin (February 12, 1809) and has had many illustrious speakers take part, including Richard Dawkins and Donald Johanson. The celebration has become a global one, with museums, academic institutes, private foundations, and others sponsoring some form of a tribute to this famous scientist.

A consolidated list of this year's events, held around the world, is here. Tell us what you plan to do on Darwin day, and if you take part, report back here on what you learned, disagreed with, or experienced. If we get a nice response here, perhaps we can prepare an event synopsis for ARJ, in case their readers miss out on the celebration.

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Science and Engineering Indicators 2008 = Scary Stuff

In mid-January, the Science and Engineering Indicators 2008 was released by the National Science Board. The goal of this report is to provide quantitative information about US science for private and public policymakers, as mandated by law.

This study is full of interesting information, and feel free to point out any gems that you dig up. For now, let's focus on a couple of sections, namely science education and the section entitled "Public Attitudes and Understanding." In science education, there are both reasons to cheer and be alarmed; as for the public understanding of science....be afraid...be very afraid.

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Next installment of Nature Network Neuroscience journal club

The next installment of the Nature Network Neuroscience group journal club is now live. The paper is on somatosensory processing in sensory and motor cortex, from the lab of Carl Petersen in Lausanne.

The contributor breaking down the paper for the neuroscience group is Eric Thomson, a post-doctoral fellow at Duke University in the lab of Miguel Nicolelis. I want to thank Eric for his participation in this new endeavor.


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CALL FOR CREATIONIST PAPERS: at the Answers Research Journal

Answers in Genesis, a self-described Christianity-defending ministry dedicated to enabling Christians to defend their faith and to proclaim the gospel of Jesus Christ effectively, recently launched a new publication, Answers Research Journal. Their mission:

Addressing the need to disseminate the vast fields of research conducted by creationist experts in theology, history, archaeology, anthropology, biology, geology, astronomy, and other disciplines of science, Answers Research Journal will provide scientists and students the results of cutting-edge research that demonstrates the validity of the young-earth model, the global Flood, the non-evolutionary origin of “created kinds,” and other evidences that are consistent with the biblical account of origins.

As their parental organization teaches, "facts" don't speak for themselves, but must be interpreted. All I can say is..........Wow.

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Monkeys master mental math

ResearchBlogging.org

Everyone has had that awkward moment at a cocktail party or at the lunch table:

You: Congratulations on the little one; she's beautiful! When was she born?
New mother: Thank you, thank you. Well, let's see, I've kind of lost track, but with today being January 14 and her birthday being December 17...
You: Oh, so she's already 5 weeks old then. Wow!
New Mother: Uhh...no. She is exactly 28 days old.

Although mistaken mental math has embarrassed us all, we humans still reign supreme in the nonverbal representation of numerical values, right? A new study in PLoS aimed to find out by directly comparing rhesus monkeys and college students on the same arithmetic task.

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Online journal club at Nature Network

I apologize for the blatant promotion, but I wanted to bring your attention to a new forum designed to spur on discussion involving interesting neuroscience papers. I categorized this under "What's new in NN?", except here, the "NN" is different: Nature Network. This platform has been around for some time now, but I am new to it. I recommend that you check out the site, as it aims to connect scientists on both the local and global levels (but unless you are in Boston or London, the local part is still being rolled out).

In the Neuroscience group, we are starting an online journal club featuring interesting papers from any journal for discussion. These journal clubs will be written up by experts in each respective field (except those that I do; I am going to fake my way through whatever topics don't get covered by the experts...). These experts will be students and post-docs discussing somebody else's work, in the classic spirit of a journal club.

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Open access in neuroscience

A new policy in the Journal of Neuroscience demonstrates the current push towards open access publication. Researchers can pay to have their article freely available immediately upon publication, starting with all articles submitted as of January 1, 2008. It is interesting, because J Neurosci words the new policy a bit like an experiment, essentially telling the authors and funding agencies to put their money where their mouth is. If they want open access, as many are calling for, they can help support it. Hopefully we can return to this policy in 6 months or so to see how many authors took this option, and who funded those choosing to "pay for play."

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Easing back into it

Well, now, it has been a nice long break since the last post, but time to get this blog rolling again here in 2008. Let's start light, while I finish cooking up the stuff I want to discuss. Let's return to a request I buried in a previous post that received no response:

With regards to moving on, I have plenty of ideas for new discussions, but would also like to offer up the concept of "reader-generated content." If I receive enough participation, I'm willing to discuss what you find interesting as often as you send me promising topics. For now, let's set the modest goal of one reader-selected topic every 2 weeks, and go from there. If you would rather keep your communications and ideas private, feel free to email me at 'Actionpotential' at natureny dot com.

This can take any form, including a nomination for a new study that you think might stimulate conversation, or for clarification on a Nature Neuroscience paper that was recently published (I especially encourage the non-scientist readers to take us up on this offer!).

In addition, if you haven't noticed, we have been working on a modest facelift of the blog homepage, with more organization and categorization. I'd love to hear any feedback on any of these new aspects and will take any other suggestions that might make the blog more user-friendly. Here's looking towards a captivating survey of neuroscience in 2008!

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Brain doping

Anyone who follows the sports world is well-aware of the concept of doping, in which athletes participate to establish an edge over the competition. This goes back a long ways and includes more famous examples like the East German Olympic machine, and the sprinter Ben Johnson, but also the more recent examples of Todd Landis, Marion Jones and, of course, Barry Bonds.

Competition seems to do that to people, clouding their judgment, confusing their ideals, pushing them to a point where it seems almost immoral not to give yourself any and every possible advantage. Well, doping is extending beyond the physical and entering the realm of cognitive capacity. A new commentary in Nature, written by Barbara Sahakian and Sharon Morein-Zamir of Cambridge, argues that the increased use of "cognitive-enhancing drugs" poses a number of serious ethical issues that can no longer be ignored.

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Learning from your horrible mistakes

ResearchBlogging.org

Staying on the genetics theme, a recent Science article suggests that a particular variant of the dopamine receptor (D2) causes some people to poorly learn via negative reinforcement. The A1 allele, as this variant is known, has previously been linked to increased vulnerability of addiction.

The researchers recruited volunteers, who performed a learning task while lying in an fMRI machine. Individuals with the A1 allele (at least one copy) were equally successful at selecting a targeted "good" symbol reinforced with positive feedback (the display of a "smiley face") as those individuals completely lacking the A1 allele. However, when the task was changed such that negative reinforcement drove the learning (subjects were asked to avoid the "bad symbol"), those individuals with the A1 allele failed to perform as well as their A1-lacking colleagues.

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The final installment

With this entry, I hereby retire from reporting on the details surrounding Dr. James Watson's race row. The subject of IQ and race may rage on in this blog, but it is time to move past the tabloid reporting. Fittingly, I felt that we should return to where it all began...with the release of a new book. Here is a review on Dr. Watson's Avoid Boring People by Jerry Coyne, a geneticist at the University of Chicago. Dr. Coyne paints a complex picture of the author, and attempts to be rather candid, succeeding for the most part. In addition, he does not hide his obvious admiration for the man. You can feel free to contrast Dr. Coyne's review with the opinion of another critic. No mercy given by that Nature editor.

With regards to moving on, I have plenty of ideas for new discussions, but would also like to offer up the concept of "reader-generated content." If I receive enough participation, I'm willing to discuss what you find interesting as often as you send me promising topics. For now, let's set the modest goal of one reader-selected topic every 2 weeks, and go from there. If you would rather keep your communications and ideas private, feel free to email me at 'Actionpotential' at natureny dot com.

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When it rains...it pours

I don't know what it is about Jim Watson and my blog posting, but every time I mention him (as I did in my previous entry), something else pops up and I have to talk about him again. While doing my morning reading, I stumbled upon an entry from the DrugMonkey blog that was simply too good to pass up. Jim Watson is more mixed race than anyone thought, with 16% of his genes likely to have come from an African great-grandparent, as reported in the Sunday Times.

[12/12 - MAKE SURE YOU CHECK THE UPDATE. CLICK BELOW TO CONTINUE READING.]

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The column that Dr. Watson needed to read

There was a great Op-Ed piece in the NY Times yesterday, written by Dr. Richard Nisbett, that provides a nice set of studies challenging the notion of inherent intelligence differences between races. Dr. Nisbett communicates these findings to the reader in a very clear fashion, providing good information for those of you who followed the news and debate underlying the Watson scandal.

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"All the News That's Fit to Print" (except the part about potential conflicts of interest)

Since the recent fall-out of the recent NY Times OP-Ed piece discussing the use of fMRI to predict the inclinations and feelings of swing voters is still fresh in our minds, I wanted to simply provide the link to a recent PLoS ONE paper that touches on the general concept of the media reporting on science.

Continue reading ""All the News That's Fit to Print" (except the part about potential conflicts of interest)" »

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Antidepressants and caloric restriction, what's the connection?

ResearchBlogging.org

If it exists, it must be a tenuous link, right? Well, at least in C. elegans, it is definitely not. Linda Buck and colleagues revealed, in a recent Nature article that drugs modulating the serotonin system in the worm can increase lifespan. Caloric restriction has been a well-documented means to enhance longevity in animals ranging from rodents to worms. We have only recently begun to mechanistically understand why eating less allows us to live longer (remember the sirtuin genes?)

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Extraordinary claims require extraordinary evidence

A tangent related to the primate cloning paper has understandably received less attention, but deserves its own thread. In the same issue of Nature containing that paper, an accompanying editorial described how Nature, for the first time, implemented a relatively new policy by seeking the independent confirmation of this particular "high-risk" finding (or "strong claim") during the review process.

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Cells reverting back to their youth

ResearchBlogging.org


Since we had a long and involved conversation on the role of embryonic stem cells in research, as well as how this issue is politicized by both sides of the debate (with additional discussion here), recent news insists that we post a follow-up on Action Potential.

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Infants inherently interpret intentions?

ResearchBlogging.org

While we are discussing infants, development and nature vs. nurture, it is fitting that Nature just published a new article describing the social evaluation skills of pre-verbal infants (6-10 months old). In a nicely-designed experiment, researchers allowed infants to view a toy as it was made to climb over an obstacle. Near the top, another toy would either help the first toy complete the ascent, or impede its progress by pushing it back. When then allowed to choose one of the second two toys for playtime, the infants overwhelmingly chose the "helpful" toy over the "hurtful" toy. In addition, infants were much more likely to choose "neutral" toys (ones that neither helped nor hindered the first toy's progress) over hurtful toys and helpful toys over neutral toys. Interestingly, these preference biases evaporated when the eyes (very prominent on the toys) were removed. This suggests that if the babies did not recognize the toys as "individuals", partiality to helpfulness made little sense, and was thus irrelevant.

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Genetic control of intelligence

ResearchBlogging.org

No, this isn't another post about Jim Watson; the title is just a shameless ploy to draw in the search engine crowd... It is relevant though, as you'll soon see. I've been meaning to talk about this next topic for a couple of weeks now, but have been distracted with unexpected news stories, editorial discussions regarding the review process, etc. A recent study in PNAS has demonstrated a significant interaction between nature and nurture that influences intelligence.

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Confidential comments – your opinion

Discussion is heating up regarding a new proposal that could change the face of peer review in neuroscience. At the PubMed Plus leadership conference this past June, sponsored by the Society for Neuroscience, the creation of a Neuroscience Peer Review Consortium was proposed.

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Science for the masses

Everyone is fascinated by science. When discoveries advancing our knowledge of the brain are made, these get extra attention. Why? Because we want to understand how we think, feel and function. When scientists discuss their research with the general public, people usually believe them, not dwelling on the details, but instead focusing on what implications a particular study might have on their own thoughts or opinions. This makes sense, because the general public is not in a position to evaluate the technical merits of most neuroscience manuscripts. That is why we have the peer review system and academic journals, like Nature Neuroscience. Once the study is reviewed favorably and is published, the general public can then be told of the exciting new progress.

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Open Laboratory 2008 - last call for submissions, but I'll just take your comments

Science blogging is becoming a fairly large entity, if you haven't noticed. NPG alone sponsors seventeen of them. Launched in January 2006, Scienceblogs.com has had over 50,000 posts and 555,000 comments on 66 blogs. This is a good thing for both the general public and for science, as again the internet proves its worth by easily bringing together populations of people who may have only rarely mixed otherwise.

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Notes from Action Potential's far-flung correspondents

Well, it's the last day of the meeting and time to start sharing what you have learned. I invite all SfN attendees to comment on an interesting talk, poster, experience, etc... that they had or saw at the meeting. I'd like to take advantage of this forum to get an interesting discussion going regarding anything from specific research findings, science policy, or gossip. Questions are also welcome. To get the ball rolling, I am going to repeat a comment here that was submitted under the previous blog entry, from Dmitry:

In case you also are at the SfN conference and were present today on a wonderful talk by Gazzaniga, I've got one stupid question. He finished by telling some story about his son losing a row competition and it was supposed to be an advice for young scientists. Unfortunately I didn't completely get the point (because of my English not being perfect). Could you briefly retell it?

If anyone can help out, it would be appreciated. So let's have it, I'm interested in hearing your thoughts from the meeting.

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Retracting creationism

I decided that all of Action Potential's many readers down at SfN are probably in need of a little lift at the halfway point of the mother of all neuroscience meetings. It has been almost 3 days of non-stop data input and your brain, if not full, wishes it were. So let's take a brief interlude from the rigors of neuroscience to discuss a lighter and more relaxed topic: Creationism.

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CSHL neuroscience is shrinking

Although the Watson scandal was more public and hit faster, there has been another crisis brewing at CSHL for going on a year now that has been discussed in whispers at meetings and through emails, but let's organize all of these free associations and questions into a single place and ask the big question:

What is going on with neuroscience at CSHL?

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Scintilla - a required application for surveying science blogs

This is an entry that should have been written back in June, a time that pre-dates my involvement with Action Potential! Back then, nature.com incorporated and launched a new free service called Scintilla that collects data from hundreds of news outlets, scientific blogs, journals and databases and then makes it easy for the user to organize, share and discover exactly the type of information in which he or she is interested.

Scintilla incorporates interesting features from several different Web 2.0 technologies including The Hype Machine (aggregation), Google Reader (checking selected sources), last.fm (recommendation engine based on other users’ activities), and del.icio.us (social network based around content). It is pretty slick and easy to use. For the content producers, here is a statement from NPG. They even have an interesting solution for science bloggers concerned about losing advertising revenue to those reading through this service.

Give it a try and tell me what you think.

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Watson steps down from CSHL position - a lot of hot air

In a statement issued today, Dr. James Watson resigned as Chancellor of Cold Spring Harbor Laboratory. This is an important event for CSHL, which is now relieved of making more difficult decisions regarding Dr. Watson's future. Although Watson's fund-raising abilities were unparalleled, and he built the lab to what it has become today, in order for CSHL to move forward, he had to leave.

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Patience, fairness and getting the girl.

ResearchBlogging.org

No, Action Potential is not going to start giving dating advice...yet. I just needed a catch-all title for a catch-all blog entry. After last week's ugly Watson debate, I figured that I would return to research science and have a little fun updating you on some recent primate research. The usual caveat applies to this entry, as with many of mine, that the neuroscience links are tenuous. Of course, that depends on your definition of neuroscience. Since mine is quite broad, it looks like we can proceed.

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He said what??

James Watson, current chancellor of Cold Spring Harbor Laboratory, shared the Nobel Prize in 1962 for his contributions leading to the discovery of DNA structure. I guess his expertise in molecular biology and genetics has also provided him with a unique insight into the relationship between intelligence and race.

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Neuropod: neuroscience on the go

Have a busy schedule ahead of you, but wishing you could stay current with cutting edge neuroscience discussion? Well fret no more. Nature, in partnership with The Dana Foundation, has launched Neuropod, a neuroscience-based podcast.

Each month, Kerri Smith will report on some of the interesting happenings in the world of neuroscience research. This month, Kerri discusses the relationship between cognitive enhancement and warfare, how stress contributes to memory formation, learning from brain imaging, and why chili peppers might have a future in anesthesiology.

Remember to check back each month for a new episode, or better yet, sign up for the free RSS feed to have the podcast delivered straight to your desktop (paste this link in your media player). Let me know what you think of this format, as we want your feedback to make this feature an interesting and entertaining tool.

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What kept Einstein smart…

ResearchBlogging.org

…may have been the fact that he didn’t watch the Baby Einstein videos, distributed by the Walt Disney Company. A recent study by researchers at the University of Washington determined that those babies who regularly watched the supposedly stimulating videos actually scored more poorly on an assessment survey of language development. All research was conducted through phone interviews of over 1,000 parents of children between 2 and 24 months of age.

This has Disney in an uproar. They have challenged the quality of the research, the competence of the researchers, and the intelligence of the University, whose president has chosen to stand by the work and the press release bonanza that this study has created. Why do companies suddenly become experts in basic research only after the emergence of findings against their products? Would this attack on the excellence of the research exist if the opposite outcome had been true, and the videos actually enhanced language skills? Of course not. But that would have made for quite an interesting sticker label on the package –

“****New research determines that Baby Einstein videos enhance language development!!**** (however, we at the Disney Company have reason to believe that this study was conducted in a poor and sloppy manner and the potential remains that this DVD may hinder cognitive growth. Please watch at your own risk)”

It is senseless to debunk a published, peer-reviewed manuscript as non-rigorous without statistics, an independent study, or other credible evidence to back up such accusations just because you disagree with the outcome. However, in the defense of the company, their #1 concern seems to be the inflammatory, and potentially result-distorting, press release that was issued by the University. I agree that parts of that blurb leave much to be desired with regards to the facts (the University must know that very few parents out there are actually going to sit down and read the full article to make their own assessment of the study's merits, especially if they don't have full-access rights to the article.) But upon reading the response of Disney's CEO to this press release, credibility erodes when it begins to look like his "high road" talk against an inaccurate, malicious press release is just a front, allowing him to proceed to bash the article itself. Of course, the president of UW reciprocated.

Disney has started to go down the appropriate path by working with an expert to assist them in interpreting the new findings, but even she was quoted in a Nature news feature as saying:

“"There are some valid conclusions in [the new study] that warrant additional research. I'm cautious, but it makes sense."

Disney should leave the research to the researchers, and the peer-review to the journals. If Disney is truly concerned and dedicated to the education of our youth, instead of fighting such studies, perhaps they should attempt to learn from them and encourage further dialogue amongst child development researchers, allowing both the company and the public to understand the full impact of their product. Meanwhile, one author of the DVD study suggested that watching anything, even American Idol, could be better for juvenile language development than these videos. Well, I don’t intend to encourage my children to watch reality TV anytime soon, but I also won’t be spending $370 on the Baby Einstein box set either. For the record, the American Academy of Pediatrics recommends no television for children under the age of two.

By the way, what ever happened to reading and conversation as language learning tools?

ZIMMERMAN, F., CHRISTAKIS, D., & MELTZOFF, A. (2007). Associations between Media Viewing and Language Development in Children Under Age 2 Years The Journal of Pediatrics, 151 (4), 364-368 DOI: 10.1016/j.jpeds.2007.04.071

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Politicking for a mate

ResearchBlogging.org

In Washington DC, coalitions are always formed, with prominent congress(wo)men establishing a staunch public stance on controversial topics, usually to increase their own popularity with certain constituencies, and/or to increase their power. But what about the little-known, junior representative who backs the political giant? What does s/he get? Usually, a nice transportation funding package for the home state, ensuring future votes, or the gratitude of the senior official, perhaps leading to a future seat on an important committee. Well, it seems that chimpanzees operate in much the same way.

Although this won’t be the first time that someone compares Washington politics to monkey business, a new study in Current Biology exposes some of the intricate policies that exist in the world of male dominance amongst chimps. While these great apes may cooperate on a variety of tasks designed to help the colony as a whole, there is a fierce competition amongst the males for dominance and, of course, females. In order to ensure a dominant position, stronger males form coalitions to achieve and maintain status within the group. Once the alpha male is in place, these coalitions are sustained. What is unclear is what benefits the “supporters” derive from protecting and promoting the status of another male.

In the current study, the authors found that when females were ready to mate, the alpha male seized the lion’s share of the opportunities, as expected. Interestingly, they went on to describe that the way other males supported their leader was to protect him during his mating attempts. In return, the alpha male from this particular colony paid in full with the only currency that has long-lasting value to his cohorts: mating opportunities for themselves. The alpha male was much more tolerant of the mating attempts initiated by chimpanzees that supported his own copulatory tendencies the most, and interfered with the reproductive advances made by non-supportive males. It seems that the advantage of even a little access to receptive females is enough of a carrot to entice weaker males to defend Darwinian law and make it easier for the most-fit male to pass on his genes. For the alpha male, the allure and rich compensation of being on top trumps the instinct to fend off every potential rival, leading to the relinquishment of a handful of valuable mating attempts. Therefore, as in Washington, the price of remaining in power for a chimp is to make life easier for your friends and downright miserable for your enemies.

Duffy, K., Wrangham, R., & Silk, J. (2007). Male chimpanzees exchange political support for mating opportunities Current Biology, 17 (15) DOI: 10.1016/j.cub.2007.06.001

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Another way for the sirtuins to enhance longevity

ResearchBlogging.org

What do obesity and Parkinson's disease have in common? Strains on our current health care system? Well...yes, but apparently another answer is the sirtuin family of deacetylases. A new study published in Science claims that controlling the activity of sirtuin2 (SIRT2) can be neuroprotective against alpha-synuclein pathology.

The sirtuins are better known for their influence on aging, with many studies demonstrating an increase in the lifespan of several different organisms if these genes are activated. One way to turn on these genes is by stressing an organism, for example through caloric restriction, leading to the activation of SIRT1. SIRT1 can also be directly activated by Resveratrol. Mice that overexpress SIRT1 exhibit several properties associated with a restricted diet, and increased longevity, including low cholesterol, low blood glucose, and low insulin levels. Interestingly, increased SIRT1 expression and/or activity delays the Parkinson's pathology associated with aggregating alpha-synuclein.

SIRT2, another sirtuin family member, is mainly expressed in the brain and is known to be involved with cell cycle regulation, however, the variety of substrates that have been identified for this deacetylase (including tubulin, histones and p53) suggests that it may serve in several cellular capacities. A group at Harvard decided to reduce the expression of SIRT2 through RNAi or small molecule inhibitors, and found that, unlike SIRT1, reduced expression and activity of SIRT2 protected against neuronal cell death in culture and even in a Drosophila model of Parkinson's. Although not completely confirmed, one possibility for the differences discovered regarding the activity levels and neuroprotection between the different sirtuin isoforms is that SIRT1 and SIRT2 act in opposing manners when influencing signaling pathways, with each deacetylase providing checks and balances against the other's actions.

It is exciting that we are beginning to gain an understanding of the signaling systems that influence aging, with the sirtuins exhibiting a knack for extending lifespan, including the maintenance of good health through our digestive systems, and apparently now in our brains. I suspect that we can expect much more from sirtuin research.

Outeiro, T., Kontopoulos, E., Altmann, S., Kufareva, I., Strathearn, K., Amore, A., Volk, C., Maxwell, M., Rochet, J., McLean, P., Young, A., Abagyan, R., Feany, M., Hyman, B., & Kazantsev, A. (2007). Sirtuin 2 Inhibitors Rescue -Synuclein-Mediated Toxicity in Models of Parkinson's Disease Science, 317 (5837), 516-519 DOI: 10.1126/science.1143780

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Public opinion forums in research: fad or fundamental?

If one comments on the merits or an aspect of a manuscript in a public forum, but nobody ever reads it, does your opinion exist? That is the question I asked myself today after seeing that Neuron has added a feature to its website designed to provide the readers of selected papers the opportunity to comment on the findings. They say that this was in response to community feedback. I don’t doubt that such feedback exists, as I have heard similar things in my travels, but at this point in scientific publishing (at least in neuroscience), it seems that the idea may still be well ahead of its time.

Neuron’s forum is not the first for this sort of thing, as PLoS and PLoS ONE have had such an entity from their respective beginnings. Now, admittedly, I have not done a careful analysis of how many articles can actually boast even one comment made by the public, but I have made it a habit to always click on that little link imploring me to read comments made by my colleagues whenever I navigate over to a paper that has such a feature. I have seen very few postings, and those that I have seen (on PLoS ONE in my case), were actually posted by the authors themselves.

I am enthusiastic about the idea of a place for the community to provide feedback on publications, as such forums give a voice to anyone willing to speak their mind. This is unlike the website Faculty of 1000, in which only selected scientists are invited and required to provide opinions about the work of their colleagues.

But it seems that either too few are confident enough to make any statements (good or bad) on the record regarding a paper, in case their opinion ends up being short-sighted, or too few care enough to spend the time required to construct a succinct, insightful comment that is unlikely to yield them any benefits. And, to return to my question at the beginning, for those few that dare to comment, is anybody reading these opinions?

Neuron is taking the right approach and has commissioned top scientists to “get the ball rolling” and make comments on the featured manuscripts, but after that initial windfall subsides, we will see how many more postings are made. Let’s just give it some more time to sink in. With everyone beginning to use the web more and more for almost everything, I’m sure that this initial drought of forum comments will give way to a more robust dialogue, making public opinion forums a fundamental part of scientific research participation.

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Paranoia in research – justified or not?

I just returned from attending my second Gordon Research Conference in two months and I am surprised by what I have seen and heard. Or should I be? Gordon Research Conferences (GRC) were started in the 1920's by Dr. Neil Gordon of Johns Hopkins University as a means to foster direct communication between scientists working in specific disciplines. The "spirit" of the GRC was to present unpublished data, making the meeting a cutting edge presentation of the latest and best findings from top laboratories. These days, one is considered a cavalier presenter if your talk includes data that are mere days from being accepted for publication, let alone including novel findings that are provocative, but may not as of yet be fully developed, and nowhere near ready for submission to a journal.

I am all for presenting older results, as some recent historical perspective often enriches the understanding of any new findings that are presented. This "review" also helps to educate the students and post-doctoral fellows attending the meeting, the conferees most likely to be less familiar with the history of the field. But I didn't see any chances being taken at the meetings that I attended, which likely reflects the nature of scientific research today, at least in particular disciplines. With academic positions few, the number of PhD-holding ambitious young scientists many, I guess I can't blame presenters for hoarding their most precious findings, so as to protect them from the "vultures" looking for the next great idea to pursue, or experiment to conduct, ready to call the kidnapped results their own intellectual property. However, this policy of data protection is bad for science and can transform a meeting into a delicate social interaction where one never knows if the person to whom he/she is talking will be the one to run back and duplicate a result, rushing to publish it quickly (unfortunately, given the competition of today, being the first to publish a key result may make the difference between getting tenure or finding a new job and home.) Therefore, the intellectual exchanges that are the hallmark of small meetings, and often the source of the best criticism for one’s work, are severely dampened.

I think that Dr. Gordon would be disappointed if he saw that his vision of small, intimate, cutting-edge meetings where scientific ideas can flourish and intermix had digressed to a state that differs little from the stereotypical large meetings (like SFN) where novel, unpublished findings are a rarity. For the record, here is the mission statement of the GRC:

"The Gordon Research Conferences provide an international forum for the presentation and discussion of frontier research in the biological, chemical, and physical sciences, and their related technologies...placing a premium on the "off the record" presentation of previously unpublished scientific results and on the consequent ad hoc peer discussion."

It is sad that our intellectual pursuit of knowledge through scientific research has become just like any other business venture...cut-throat, stressful, with a healthy dose of paranoid conservatism attached to everything. And to think, in my undergraduate naivety, I thought that by going into science I was going to avoid the abuses and misadventures that came with pursuing a career in corporate America.

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The stem cell debate continues...

Let's move the debate from an earlier thread in a different direction, as I am getting a bit bored by that discussion. By the way, for those keeping score, Dr. Condic's response to the editorial in question was published in the July issue of Nature Neuroscience, and went live today.

Last week, President Bush vetoed another bill that would have allowed research on embryonic stem cells to go forward in America. Is Bush reflecting the current opinion of the country? A recent USA Today/Gallup pool says that he is not. Between 4/13/07 and 4/15/07, the poll asked 1,007 adults nationwide this question: "As you may know, President Bush has said he will veto a bill to expand federal funding for embryonic stem cell research. Do you think Bush should or should not veto this bill?" 31% said that he should, 64% said that he should not, while 5% were uncertain. In another recent poll published last week in Science , 60% of infertility treatment patients (over 1,000 in the poll) stated that they would prefer to have their unused embryos used for research purposes rather than having them destroyed or adopted by another couple.

Thus, it seems that the minority opinion is currently ruling on this issue, as it has for quite a long time. In fact, in all polls I could find dating back to 2001, when any group of people were asked if the federal government should support embryonic stem cell research, a majority always answered yes. So let me play the devil's advocate for a moment; since President Bush was elected twice, this begs the question of how relevant the debate over stem cell research really is in the mind of the average voter! Where do you think this debate sits on the political front? Is this even one of the most critical debates pertaining to federal scientific funding? I'd love to hear your opinions.

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Dissemination before peer review.

The physics community already has theirs. Now biology has its own site dedicated to the informal discussion of unpublished results. A new site launched this week, Nature Precedings, allows scientists to upload unpublished manuscripts while they are under consideration at a journal, perhaps inciting conversation and feedback regarding the work even before the article is accepted. In this day and age of caution and paranoia surrounding results (go to any scientific meeting these days and count the number of presentations that focus on published results vs. those that highlight unpublished ones), how do you think this will impact the neuroscience and publishing communities?

I see a definite place for this type of resource, providing a repository of additional data and user comments regarding techniques and discoveries, as a complement to the volumes of published papers that have undergone reviewer-mandated quality-control measures. But change comes slowly, especially when change involves freely releasing one's precious data that have taken years to amass. I am skeptical as to how quickly this concept will integrate into the world of neuroscience. With the ease at which data can be anonymously reproduced and subsequently submitted, I feel that many neuroscientists will be cautious about what data they are willing to let go for free.

However, as a counter, this type of system works well for the physics and mathematics community (plenty of discussion fodder here)...

This is an experiment that should be interesting regardless of its outcome, my favorite kind.

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