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26.12.12

Dystextia

There's a fascinating, very short report out in JAMA marking the first case where text messaging abnormalities were the first signs of a neurological abnormality.

The paper, "Dystextia - Acute Stroke in the Modern Age", documents the case of a pregnant woman who suffered a small "acute ischemic infarction" (stroke) in her left insula (below). As per medical radiological tradition, the right side of the brain image represents the left side of the patient's brain, because they flip them (supposedly because that's how they see the patients when they're facing them?)




She was brought into the emergency room after the following text message conversation with her husband about their baby's due date (P - patient; H - husband):

H: So what’s the deal?
P: every where thinging days nighing
P: Some is where!
H: What the hell does that mean?
H: You’re not making any sense.
H: July 24, right?
P: J30
H: July 30?
P: Yes
H: Oh ok. I’m worried about your confusing answers
P: Butithink
H: Think what?
P: What i think with be fine

What's interesting about this is that the patient had been hypophonic (soft speech) due to a recent upper respiratory illness, which the authors conclude may have masked her strange speech patterns:
"As the accessibility of electronic communication continues to advance, the growing digital record will likely become an increasingly important means of identifying neurologic disease, particularly in patient populations that rely more heavily on written rather than spoken communication."
While this is a cool presentation of modern technologies encroaching upon the medical world, what's fascinating to me, from a neuroscientific perspective, is the location of her stroke and its effects. In 1996 Nina Dronkers scanned the brains of 25 patients with apraxia, or the inability to coordinate speech movements, and found that 100% of the patients had lesions in only one spot: the left insula (which was also found to be lesioned when she performed MRIs of Broca's original patients).


This is an old argument, but provides strong evidence that the insula is an important player in coordinating speech movements.

Even if that "speech" is actually just texting on your iPhone.


ResearchBlogging.org
Ravi, A., Rao, V.R., & Klein, J.P. (2012). Dystextia: Acute Stroke in the Modern AgeDystextia Archives of Neurology DOI: 10.1001/jamaneurol.2013.604
Dronkers, N. (1996). A new brain region for coordinating speech articulation Nature, 384 (6605), 159-161 DOI: 10.1038/384159a0
Dronkers NF, Plaisant O, Iba-Zizen MT, & Cabanis EA (2007). Paul Broca's historic cases: high resolution MR imaging of the brains of Leborgne and Lelong. Brain : a journal of neurology, 130 (Pt 5), 1432-41 PMID: 17405763

21.12.12

The Monster Under the Bed

The piece below was written last night by my PhD advisor, co-author, collaborator, friend, and mentor, Robert T. Knight, M.D. I'm posting it verbatim without comment, with his permission.

*****

Children often worry about the monster under the bed. Fortunately, adults can assuage that scary feeling with warmth and love and children eventually learn that monsters are a figment of their imagination. Now the monster under the bed is real, and the fear inside of the children of the land is palpable. Sadly, the horrible loss of twenty precious little joyful kids is only the surface of the damage the young man with the assault weapon inflicted on our children.

Yes, children are resilient – and some pundits will say ‘don’t worry, kids will deal with it with no long-term damage in most cases’. Don’t believe them for a minute. Being tough and resilient is different from having the magic of childhood ripped away.

We adults have collectively elected to inflict this on our children. And I do not mean only the NRA officials, the gun lobbyists, the gun-company owners or the politicians who implicitly condone ‘guns of war’ entering our schools. I mean all of us, all adults who are collectively responsible for the precious gift of childhood. We have all abdicated our solemn obligation to our children.

What to do? First, we need immediate changes to how we deal with gun ownership in this country. As a neurologist, I am required to report to the Department of Motor Vehicles any patient who is having cognitive changes such as marked Alzheimer’s disease that precludes him or her from driving safely. Similarly, I am required to report anyone with a likelihood of losing consciousness that is not under control with medications. Any rational person would not want someone losing control of their car and plowing into 20 defenseless children in the local schoolyard, yet we let the same carnage happen with a gun in the hands of unstable people. Perhaps we need to examine whether health care professionals have a responsibility to report patients with a propensity for violence to gun licensing agencies. We already have such a reporting requirement for anyone who is actively suicidal or homicidal.

And to what end are we deluged with guns? So that gun enthusiasts can handle their sleek toys and feel the power of weapons that have now been turned against our children? The logic that each American has the inalienable right to any firearm is profoundly flawed. By this line of thought a ‘gun enthusiast’ should be able to have a 50-caliber armor-piercing machine gun. Presumably, the excitement derived from shooting one projectile would be magnified by shooting an even bigger missile of death. Assault weapon aficionados should logically agree that owning a bazooka is their right. Why not surface-to-air missiles providing an even bigger rush?

All this so that we can have a ‘silent militia’ to protect our country? A ‘silent militia’ is a concept that exists only in the minds of the paranoid: we already have the greatest and most loyal fighting forces ever assembled on the face of the earth. Or so that we can ‘Live Free or Die’? Spare us all the John Wayne movies – which, by the way, I thoroughly enjoy. A word about NRA members is warranted. Let me divulge that I was a shotgun owner and hunter as a kid in rural New Jersey, like virtually every other boy in my small rural town. I am a supporter of the Second Amendment to the Constitution and certainly all NRA members feel the same. But most NRA members do not support unbridled access to guns that have no place in hunting and are vehicles of war.

Why are we at this juncture? How is it that twenty innocent children could be slaughtered so easily, by a disturbed 20-year-old with a lethal military-grade weapon? Let’s look inward. The failure to stand up to the powerful gun lobby is a failure of our collective responsibility to protect our children. Look not to the NRA Headquarters; look to yourself, YOU are responsible. Lack of action is action.

How do we break this cycle of adult irresponsibility that plagues the nation and has taken joy from so many family members in Newtown? What, then, to do? Obviously, new licensing approaches is a must. Current Federal laws on gun purchase need to be extended to gun shows, internet and inter-personal sales. I’d go further. I’d personally prefer a recall of all assault weapons -- a move that has worked well in other countries. But I must assume this is a non-starter in the USA. Rather, we, the protectors of childhood, should lobby our elected officials to ban the sale of assault rifles, large clips, armor piercing-bullets and body armor. These sales are unconscionable – it is simply unheard of in other first-world nations.

The NRA leadership should be ashamed that they are not advocating strongly for this change. Of course, as usual, shame seems to be tempered by profit. The bottom line is money in the pockets of the NRA leadership, their lobbyists, and the gun company owners. Every retirement fund or company holding shares in any company making assault weapons for public purchase needs to divest all their holdings NOW. If they don’t comply, WE must remove our funds and use our purchasing power by boycotting these companies. Neuroscience and common sense has shown that the fear of public shaming is perhaps the biggest stress anyone can endure. Maybe we circulate the names of the top 100 NRA leaders, lobbyists and automatic weapon manufacturers, making sure we know where the purveyors of death reside.

Am I being extreme? I certainly hope so. The NRA is not the problem. We – the adults of the United States of America – are the problem. We have abdicated our sacred responsibility to our children. Do not expect politicians alone to change this. Only the concerted efforts of all of us will change a culture of gun violence. People who fail to act now must assume partial responsibility for the next death of a child. Stop the Monster Under the Bed before the fabric of childhood freedom, safety, happiness and magic is irretrievably cut.

Robert T. Knight, M.D.
Professor of Psychology and Neuroscience
University of California, Berkeley

28.11.12

Video games give kids dementia?

PANIC.

As much as I enjoy silly people, I really dislike jumping on the silly person bandwagon here but I feel compelled to counter nonsense with real sense.

As Vaughan Bell over at mindhacks has repeatedly noted, Baroness Greenfield of Oxford likes to turn to the press to talk about how video games, the internet, and other generally fun things are ruining the brains of our children.

In response, Ben Goldacre has made a simple request of the Baroness: publish your findings in a peer-reviewed study.

This has yet to happen.

Over the years many reasonable, intelligent, knowledgeable, practicing scientists like Vaughan, Ben, Dorothy Bishop, NeuroSkeptic, Dean Burnett, and others have tried to counter the Baroness's claims through appeal, humor, sarcasm, etc.

But the Baroness keeps making public claims to the media such as, "Several scientific studies have suggested that playing an excessive number of computer games or spending too much time surfing the internet can have a physical impact on the brain," with the implication that this change is bad.

But truth is better than fear, and neuroscientist Daphne Bavelier recounts almost a decade of her research regarding the effects of action video games on the brain and cognition in her recent TED talk. Yes, they change the brain. But this change can be good (edit: softened the language here from "is good", since this is a complex issue).

The reality? Action video games, such as first-person shooters, improve attention, visual perception, cognitive control, and a host of other executive functions. This research began with a accidental finding by C. Shawn Green that he and his video-game playing friends were performing much better on attention tasks than non video game playing control subjects. This culminated in their 2004 Nature paper, "Action video game modifies visual selective attention". Since then their research has progressed quite well.

And is peer-reviewed.

Dr. Bavelier gives a fantastic talk, and it's one that I've added to my now-growing list of good neuroscience TED talks.

Watch the video below to see the real scientific evidence regarding the effects of video games on the brain. I'd love to know what evidence the Baroness's has to counter.



ResearchBlogging.org
Green, C., & Bavelier, D. (2003). Action video game modifies visual selective attention Nature, 423 (6939), 534-537 DOI: 10.1038/nature01647

16.11.12

Face processing in the brain: "That was a trip"

There's a cool new (open access!) case study out in the Journal of Neuroscience by my friend and colleague Josef Parvizi. The paper, "Electrical Stimulation of Human Fusiform Face-Selective Regions Distorts Face Perception", is an analysis of a single subject, Ron Blackwell (he gave his name freely), an engineer from the Bay Area.

Mr. Blackwell had experienced seizures since he was a teenager, but for decades his medication had staved them off. Slowly, however, the medication became less effective, at which point he agreed to undergo surgery to remove the epilepogenic tissue from his brain.

As part of the pre-surgical mapping to determine where in his brain the pathological tissue was located, Dr. Parvizi and the surgical team implanted Mr. Blackwell's brain with passive recording electrodes. This technique, known as electrocorticography (ECoG), is an important aspect of my research. Dr. Parvizi and I have written and are writing several ECoG papers together.

The nice thing about this technique is that it gives you the best of both worlds in terms of human brain imaging: knowledge of both where in the brain is active as well as when the brain is active. Normally, brain imaging is non-invasive, meaning we don't usually perform brain surgery and open up the skulls of our research participants! Surprising, right?

Because of this there's always a trade-off between where and when. With functional magnetic resonance imaging (fMRI) I know down to the millimeter what parts of the brain are active--even the deepest regions of the brainstem. Sadly, however, we can only get a snapshot of this activity once every second or so. This is a fundamental limitation of both the technology and the signal we're measuring.

EEG, on the other hand, gets thousands of data points per second, allowing me to know precisely when the brain is responding. The skull, however, blocks some of the brain's electrical activity making it very hard to know where the signal is coming from. It's like having 10 speakers each blasting music in another room and trying to figure out which speaker is playing which song when all you can hear is a BOOM HMMMMM blur of noise through the wall. (MEG is a little better, but it still has its limitations.)

ECoG doesn't suffer from these limitations because the signal is being recorded directly from the brain's surface.

Of course, there is still a basic limitation here, and that is that ultimately these imaging techniques mostly only give us information about correlations between brain activity and behavior without being able to tell us about causal relationships.

It's like if I have you running on a treadmill and record muscle activity from your arms. When I make the treadmill move faster, you run faster and your arms move faster! The correlation between your movement and the treadmill speed is so strong, in fact, that it can't be due to chance.

"Aha!" I exclaim, pleased with my experimental cleverness, "look at that correlation! The arms must be critical for running."

Of course, all it takes is one person who is missing an arm to run on that treadmill to disprove my hypothesis.

As I've said many times before, this is why working with people with brain lesions is so important to neuroscience and why I work with such patients. If a person who has a lesion to a brain region thought to be responsible for an emotion or behavior of interest can still experience that emotion or do that behavior then that is not where that behavior is located in the brain, regardless of how many imaging studies show activity in that region.

Of course, we can't go around lesioning peoples' brains!

So how else can we get at causality?

Brain stimulation.

Imagine the treadmill scenario again. This time I can shock your arms while you're running. So I shock the muscles, and they twitch, and you shoot me a nasty look, but you don't really break your stride.

"Huh," I think, "but the correlation between the arm muscle activity and running is so strong... but if I disrupt his arm muscles he doesn't stop running. Strange."

So I begin recording leg activity. And again I see a huge correlation. But I'm cautious about making any strong claims yet. This time, I'm smarter, and I hook your legs up to my electrical stimulator and set you running on the treadmill.

This time when I send that shock, your quads spasm and you collapse. Eureka! A triumph for science! The legs are where running happens.

As I sitting at home, nursing the black eye you gave me once your leg stopped spasming, I pride myself on a job well-done.

This analogy (minus the black eye, I believe) is what Parvizi's paper added to our understanding of how and where the brain processes faces.

Parvizi also implanted Mr. Blackwell's brain with a stimulator at the site thought to be important for face processing. Check out the figure below:


Parvizi and his group took advantage of a fortuitous situation wherein an fMRI scan of Mr. Blackwell showed clear differences between face and non-face processing activity in the same regions where they happened to have the ECoG recording electrodes implanted. This allowed them to look at face processing in Mr. Blackwell's brain in both fMRI and ECoG.

Furthermore, they also had a stimulating electrode there.

And check out the video below to see what happened to Mr. Blackwell's face perceptions when he was stimulated.

VIDEO LINK

"That was a trip."

No kidding.

I really respect this paper because of its combination of methods to converge on correlational and causal links between brain and behavior, which are often sorely lacking in cognitive neuroscience.

ResearchBlogging.org
Parvizi J, Jacques C, Foster BL, Withoft N, Rangarajan V, Weiner KS, & Grill-Spector K (2012). Electrical stimulation of human fusiform face-selective regions distorts face perception. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32 (43), 14915-20 PMID: 23100414

29.10.12

Update on Crowdsourced Letter of Recommendation

A couple of weeks ago I put out a call for a letter of rec from the Internet. Since then I've gotten a lot of requests for an update. It seems like I hit a chord with the academic science blogging and outreach communities. Before I get to specific details of the responses I've received, I have a few comments.

First, I'm honestly blown away. I'm so damn happy to hear that any of this stuff I've been doing for the last few years means anything to anyone. The positive feedback in this blogging/writing world is rare and I'm humbled and reinvigorated as I'm reminded of why I'm doing this.

As an academic and a scientist putting yourself out into the public at all--especially when you use your real name--opens you up to a lot of criticism. Academic researchers think you're wasting your time when you could be doing "real work". The Internet snark machine is happy to jump on any error you make and let you know how stupid you are. And you can easily fall into the page-view trap of writing pieces just to drive traffic, moving you ever farther from useful, constructive scientific discourse.

People often ask why I do this. I've summed it up thusly over on Quora:
Social media is a way for me to continue sharpening my understanding of difficult concepts. The time investment isn't important to me--my job is to learn and discover, and this is another aspect of that. And if in the process I make something more clear and accessible to a possible future scientist, all the better. No scientist achieved their breakthroughs because they communicated less.
This whole public communication thing helps me find holes and weaknesses in my thinking. Sure, it's also fun sometimes. And I like to know that people think the stuff I know is interesting. But deep down it's about continuing my training and making my thinking less lazy.

As for the letter, the why of that is summed up in my associated statement to the hiring committees that I'm including along with the letters themselves:
Much of my outreach and education efforts exist in an invisible space where metrics and assessments cannot easily reach. To try and give an index of my extracurricular outreach, education, and science communication efforts I reached out to my digital network of people who read my blog, watch my videos, and follow my writings on twitter and other social networks. I asked them to submit to me a statement of what—if anything—my blogging, public speaking, etc. has meant to them. Below is an unedited collection of the comments I received: some anonymous, some pseudonymous, and some signed.
As I said above, many academics think this online social media stuff is, at best, a waste of time and at worst an exercise in the narcissistic pursuits of an egotistical sell-out.

What I'm trying to do is provide some metric that shows that any of this might be useful or helpful, and to show that it does have some positive impact that can be wrapped up nicely into a metric that can be easily referenced.

As of today I have about 20 letters from people ranging from a C*O of a huge tech company, Quora as a company, clinical workers, undergrads, PhD students, post-docs, and a tenured faculty member, a health care professional, and others.

Some are hundreds of words, some are tweets. This process has itself spawned a meta-article about the process.

But I've still got a few more days before I hand everything over the the search committees. And it will be many months before I know if they even give a shit. In the mean time I'm going to continue doing what I'm doing armed with the knowledge that maybe it matters to someone out there.

Thanks everyone.

14.10.12

Voyteks and Guerrilla Science at SfN!

If you're at the Society for Neuroscience Conference in New Orleans right now, my wife Jessica and I each have a poster, plus one special feature.



My wife is presenting one of only 9 dynamic posters this afternoon. This is a new format SfN is trying out that incorporates multimedia into their poster format.

Her dynamic poster is at 1pm today over in aisle JJ, and is titled, "User Experience Design for Children's Neuroscience Education" and is about creating their Ned the Neuron education eBook (now available for the iPad!) I'm currently waiting for our napping son to wake up, but I should also be there around 2pm.

My scientific poster is tomorrow (Monday) morning over at CCC58. It's titled, "Phase/amplitude coupling supports network organization in human frontal cortex" and it doesn't totally suck. (Seriously I'm pleased with this research, so if you're at all interested in functional coupling, cognition, ECoG, and/or signal processing, come by!)

Finally my zombie neuroscience collaborator and fellow guerrilla scientist Tim Verstynen and I have an unofficial poster up over at GGG35 titled, "Advances in neuroprosthetics for Detroit law enforcement personnel: Building a better RoboCop today".

It's worth checking out. You can also download the reprint here (PDF).

TED pulls pseudoscience talk

A few months ago TEDxCharlotte released a video from its event of a guy named Randy Powell just talking a bunch of pseudoscientific-but-grand-sounding nonsense about "Vortex Mathematics".

Carl Zimmer mentioned it in his evisceration of TED's weak science draw (specifically Philip Zimbardo's talk) which lead me to ask a question about the talk over on Quora.

Specifically, I asked, "Is Randy Powell saying anything in his 2010 TEDxCharlotte talk or is it just total nonsense?" It got a lot of great answers (which is what I was hoping for) including the currently top-rated response from Jay Wacker, Stanford professor of theoretical physics:

Wow. Such fucking bullshit. Well, I am theoretical physicist who uses (and teaches) the technical meaning of many of the jargon terms that he's throwing out. And he is simply doing a random word association with the terms. Basically, he's either insane a huckster going for fame or money doing a Sokal's hoax on TEDx I'd bet equal parts 1 & 2.

and this one from Joshua Engel (one of my favorite Quora users):

This is one of the reasons I'm not crazy about TED talks. The argument is gibberish; not a single point makes any sense. But without a transcript, it's tricky for me to make a point-by-point refutation. I have to stop, transcribe, then explain. It's a slow and tedious process. The question is, is anybody engaging in that kind of critique for the talks that aren't obviously deranged? Or is everybody just accepting what they hear and then letting the video move on to its next point? Video is a poor way to make an argument. It's a good teaching tool, since it's very convincing when the subject is actually valid. But it's equally good at making an invalid argument with little opportunity for critical thought.
 You can get a feel for Mr. Powell's work in this video:


Well it would appear that TED has officially responded by removing Mr. Powell's talk from their TEDx YouTube channel. Specifically, TED editor Emily McManus left this response on my Quora question:

Randy Powell's talk onstage at TEDxCharlotte 2010 came under criticism for its lack of scientific validity. Criticism came from mathematicians and science writers as well as threads on specialist science and math blogs and other online communities. Members of the TED and TEDx teams watched the talk, sought further advice from experts, and ultimately agreed that the criticisms had merit and were serious enough to warrant removal of the talk from the TEDx official YouTube channel, in compliance with our policy.
Randy Powell was given several opportunities to directly defend his work, but did not do so. In a phone conversation with members of the TED and TEDx teams on September 12, 2012, Powell stated that his brief onstage talk at TEDxCharlotte did not include complete data on his work. He could not point us to that data online during the call, but agreed during the call to email TED his data, including a detailed 10-page paper, for a further independent review by a mathematician and possible replication of his experiments by a physicist. Neither the paper nor any other data was ever received. We consider the matter closed.
In response to this incident, TEDx has clarified its policies on the scientific validity of talks and is working with independent TEDx organizers to help them access more and better resources for vetting speakers.
Personally I don't think that removing the content to scrub its record is the best way to go but it's interesting to see that TED is at least taking some steps to clean up its scientific appearance.

7.10.12

Crowdsourcing a Letter of Recommendation

I've got a huge favor to ask of you all.

At the behest of some of my friends and colleagues I have decided to go on the academic job market earlier than I expected and apply for a (very) few tenure-track faculty positions. My chances are slim, but several people have told me I should take a shot since the cost is low.



Over the course of running this blog for just shy of three years I've had some amazing conversations and interactions with all of you, however these kinds of conversations are hidden from the traditional academic metrics, and that sucks.

In addition to a research statement, part of the job applications require letters of recommendation as well as a teaching statement.

I've decided to include as an additional letter of recommendation and as part of my teaching statement a recommendation from... well... the Internet. From you all.

If anything I've written on this blog or elsewhere, any lecture I've given, any research I've done has had an effect on you (positive or negative I guess), I would be immensely grateful if you would be willing to take a few minutes to email a statement to me explaining how.

bradley.voytekgmailcom


Send me as long or short of a note as you'd like. Because academia is such a hierarchy-obsessed group, the more information about your real-world self you can include, the better: name, title, university or industry affiliation, etc.

But please know that I don't care as much about those things. I'd love to hear from you regardless of your job/title/pedigree. In fact, I personally believe the more non-academics I've reached the better.

If you ask me to keep your comments anonymous, I will do so. If you want to just leave an anonymous comment on this post, I'll be moderating them all, so I will receive your comment but it won't be published here.


Maybe you liked something I wrote on here, Twitter, Quora, the SciAm guest blogs, O'Reilly Radar, whatever. Maybe you liked my TEDxBerkeleyGoogle, or zombie talks. Or hated them. Maybe brainSCANr inspired you to hack your own scientific project or maybe you saw a lecture I gave in real life or on Google Plus. Some of you may have started reading this blog as an undergrad and are now off doing amazing things as graduate students, or in industry.

If anything I've done online has had an impact on you, please let me know.

We in the scientific blogging community are always looking for alternative metrics. But we rarely ask on another for help. I'm asking now.

The idea of having a letter of recommendation from the Internet seems awesome to me. I really hope this works.

(And if you're curious, you can read the draft of my Teaching Statement (PDF) and check out my publication record.)

20.9.12

NeuroImage paper: "A method for event-related phase/amplitude coupling"


For those of you who haven't noticed, the title of this blog is "Oscillatory Thoughts" which really does refer to my research interests. The gist is this: neuronal activity oscillates and these waves play an important role in our cognition.

This latest paper of mine published in NeuroImage (accepted PDF version), "A method for event-related phase/amplitude coupling", is--as you can infer from the title--a method describing a different way of analyzing neural data than has been used before.

Voytek NeuroImage 2012 Fig 2 theta/gamma phase/amplitude coupling

This was a method I developed as I moved past the work from my (surprisingly highly-cited) Frontiers in Human Neuroscience paper and on toward the research that makes up part of my research I'll be presenting at SfN. In the figure above (Fig. 2 from the paper) I give a schematic of what phase/amplitude coupling (PAC) is, but essentially it means that the phase of the slow part of the neuronal oscillations gives you information about the strength of neuronal firing in that same general brain region.

Normally this metric is calculated across some arbitrary length of time, meaning you can't get much information about when this coupling occurs. In this paper I simply took a standard regression-based approach to calculating this coupling and perform it across a series of time-locked trials. This provides a simple time-resolved measure of PAC.

As always I have made the code used for this measure available on my website (zip file). A special thanks also goes out to Philipp Berens and his MATLAB CircStats toolbox.

My work is isn't earth-shatteringly cool, but I believe it's useful. And it does seem to provide new information about the task-specificity of PAC.


Voytek NeuroImage 2012 Fig 3 theta/gamma phase/amplitude coupling

And potentially information about PAC between brain regions:


Voytek NeuroImage 2012 Fig 5 theta/gamma phase/amplitude coupling



This NeuroImage paper moves my work a tiny step forward, and is but one piece in a cluster of work I hope will be coming out over the next year or so. As I said in my Frontiers paper post, the reason I find these neural oscillations so interesting is because,
We don't know how different brain areas communicate to give rise to cognition. There's a complicated code that we don't understand. This nested oscillations idea might connect the really low-level physiology of the brain with high-level cognition that requires communication between a lot of brain regions. And it ties it all nicely together into a cool communication system where different low frequencies could act as "switches" to bias information flow between brain regions.
This method provides researchers with a new way of testing for transient changes in oscillatory communication. Unless you're really into methods, it's probably not worth reading, but I'm really proud of this one.


This work was financially supported by the (sadly defunct) American Psychological Association Diversity Program in Neuroscience grant 5-T32-MH18882 (to B.V.) and the National Institute of Neurological Disorders and Stroke grants NS21135, NS21135-22S1, and PO40813 (to B.V. and R.T.K.) and NS40596 (to N.E.C.).


ResearchBlogging.org
Voytek B, D'Esposito M, Crone N, Knight RT (2012). A method for event-related phase/amplitude coupling NeuroImage DOI: 10.1016/j.neuroimage.2012.09.023

30.8.12

Allen Institute for Brain Science

Yesterday I gave a talk at the Allen Institute for Brain Science (twitter) about my work on brainSCANr and how it integrates with their Allen Brain Atlas.

view from my hotel room
For those of you not familiar with the organization it was started by Paul Allen, co-founder of Microsoft. So far he's invested about $500,000,000 of his own money to allow the Institute to prosper. They've got several concurrent projects going on, namely looking at gene expression in the human and mouse brain, connections between regions, and so on.

They made a splash about 5 years ago with their Nature paper, "Genome-wide atlas of gene expression in the adult mouse brain" and then again in 2009 with their Nature Neuroscience paper, "An anatomic gene expression atlas of the adult mouse brain". It's my understanding they've got a huge new Nature paper coming out soon as well.

And they recently just hired consciousness neuroscience research extraordinaire Cristof Koch away from Caltech to be their Chief Science Office. Although shorter than we'd hoped, it was really nice to be able to sit and chat with him about my research and future directions.

Why are these papers so cool? Honestly it's mostly because of the amazing technology driving their massive data collection efforts. They've got an enormous facility with hundreds of scientists and automated robotic data collection systems just tearing through terabytes of data.

They were also really interested in my work with Uber... it was a pleasant surprise to meet a group of scientists who understood the importance of working with software engineers, data visualization people, and so on.



data collection facilities

It's clear Paul Allen and the Institute have built a very data-driven, tech heavy team. Their goal is not only to collect all this data, but to share it with everyone.

These are my people.

Over dinner last night there was a lot of excited talk about the future of data in neuroscience. I've said it before--and it's nice to sit with a group of scientists who agree--that I think it's arrogant to believe that the person who knows what best to do with the data that I collect is me.

And that philosophy is built into the Institute.

Don't get me wrong, they are doing amazing things with their data internally, but they really do hope that researchers will take their data and run with it and do things they couldn't imagine (which is I guess why I was invited).

They've put together what is probably the most user-friendly neuroscience data site I've seen that allows researchers to explore and play with data.

tool to explore point-to-all gene expression correlation maps
trying to get a handle on all the information!
brain data art
loving the OHBM Space Needle art

I really believe these kinds of endeavors will be the future of neuroscience: data-focused and engineering-heavy with a huge scientific team running in parallel to take part in the data exploration and to guide hypothesis-driven research.

I can't wait to see more efforts like this start popping up in the next few decades.


ResearchBlogging.org
Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, Chen L, Chen L, Chen TM, Chin MC, Chong J, Crook BE, Czaplinska A, Dang CN, Datta S, Dee NR, Desaki AL, Desta T, Diep E, Dolbeare TA, Donelan MJ, Dong HW, Dougherty JG, Duncan BJ, Ebbert AJ, Eichele G, Estin LK, Faber C, Facer BA, Fields R, Fischer SR, Fliss TP, Frensley C, Gates SN, Glattfelder KJ, Halverson KR, Hart MR, Hohmann JG, Howell MP, Jeung DP, Johnson RA, Karr PT, Kawal R, Kidney JM, Knapik RH, Kuan CL, Lake JH, Laramee AR, Larsen KD, Lau C, Lemon TA, Liang AJ, Liu Y, Luong LT, Michaels J, Morgan JJ, Morgan RJ, Mortrud MT, Mosqueda NF, Ng LL, Ng R, Orta GJ, Overly CC, Pak TH, Parry SE, Pathak SD, Pearson OC, Puchalski RB, Riley ZL, Rockett HR, Rowland SA, Royall JJ, Ruiz MJ, Sarno NR, Schaffnit K, Shapovalova NV, Sivisay T, Slaughterbeck CR, Smith SC, Smith KA, Smith BI, Sodt AJ, Stewart NN, Stumpf KR, Sunkin SM, Sutram M, Tam A, Teemer CD, Thaller C, Thompson CL, Varnam LR, Visel A, Whitlock RM, Wohnoutka PE, Wolkey CK, Wong VY, Wood M, Yaylaoglu MB, Young RC, Youngstrom BL, Yuan XF, Zhang B, Zwingman TA, & Jones AR (2007). Genome-wide atlas of gene expression in the adult mouse brain. Nature, 445 (7124), 168-76 PMID: 17151600
Ng L, Bernard A, Lau C, Overly CC, Dong HW, Kuan C, Pathak S, Sunkin SM, Dang C, Bohland JW, Bokil H, Mitra PP, Puelles L, Hohmann J, Anderson DJ, Lein ES, Jones AR, & Hawrylycz M (2009). An anatomic gene expression atlas of the adult mouse brain. Nature neuroscience, 12 (3), 356-62 PMID: 19219037

7.8.12

The Adventures of Ned the Neuron!

I've been itching to announce this for months, but I've been biting my tongue. Now I can finally let the neuron out of the bag.

Ladies and gentlemen I'm proud to introduce to you a joint project between my wife Jessica Voytek and our friend Erica Warp: The Adventures of Ned the Neuron! To get the important pitch out of the way first, please go contribute some money to their Kickstarter campaign to help them get started if you want to help.


Also, please consider following their company on Facebook. I promise they're not spammy.

For several months now Jessica and Erica have been working on their company, Kizoom, to develop the first of what I hope to be many science education eBooks for kids. The fact that this is being built using open or semi-open tools and platforms is also pretty amazing.


Note that I'm in no way connected to this company, though the obvious disclosure is that my wife and I are financially entwined and, as unbiased as I try to be, I of course cannot be completely so. I mean, I'm writing this post, aren't I? But... as a new father I'm coming to appreciate more and more the joys of well-written, scientifically accurate educational materials.

So who are Erica and Jessica and why should you trust what they write?

Erica earned her PhD in neuroscience from Berkeley working on spinal cord development. She published three super cool papers during that time, one each in Nature, PNAS, and Current Biology. I promise you she knows her brains.

Jessica is the primary author on our brainSCANr paper which we published in The Journal of Neuroscience Methods earlier this year. She earned her Masters degree in Information Management and Systems at Berkeley, which she completed while very pregnant with our son. Not only does she know her brains, she's also technically and artistically very savvy.


The two of them have been working hard on this baby of theirs (that's them celebrating after submitting their NIH grant). They have managed to put together a book that is fun and interactive for kids (their target audience) while being educational and totally neuroscientifically accurate.

No neuro nonsense. Just good science and good fun.

So many of us neuroscientists complain about the poor public understanding of our field that it's time for us to stop being critics and start trying to make the changes we want to see. And that's what I love about Kizoom and The Adventures of Ned the Neuron: two very smart neuroscientists and techies are putting themselves forward and trying to make science more approachable to the most scientifically vulnerable group.

Kids.

Erica wrote the story and drew the early artwork while Jessica has been working on getting the whole thing coded up, animated, etc. Basically the techy nerd work.

What's impressed me the most is that, throughout all of this had work, they've also been doing a lot of science outreach and communication for kids. Jessica worked for the Girl Scouts for years, including developing a cookie booth finder to help people locate the nearest Girl Scout troop selling cookies in their area!


In May Jessica and Erica volunteered at a Girl Scout event to teach young women about neuroscience and the brain with the help of Ned the Neuron!


We also recently learned that, out of the thousands of abstracts and poster submissions to the Society for Neuroscience Conference this October, their poster "User experience design for children's neuroscience education" has been selected as one of nine in the new "Dynamic Posters" session.

What's that? Well, according to the email they received,
A dynamic poster is an electronic version of the current paper-based format, displayed on an LCD screen rather than a poster board. However, it’s more than just an e-poster, which is typically an electronic - but still static - PDF version of a paper poster. Embedding multimedia content is encouraged such as videos, slides, animated charts or graphs, scrolling text, or a 3D rotation of a model. A dynamic poster presentation is designed for face-to-face interaction: like a regular poster presentation, the dynamic presentation will be driven by the primary author while attendees visit the poster. Some text elements of the poster will always be viewable for browsing by people walking by or waiting for their turn to speak with the presenter. Other parts of the poster will be operated by the presenter, who can click on and play a video or enlarge a graph to better illustrate a method or result.
I definitely applaud the Society for Neuroscience for finally taking this kind of tech-based approach.

I wish I could convey to you in words the emotional love the both of them have for this project. I'm really proud to have seen it grow from nothing into a nearly completed project. Please check it out and consider helping if you can.

Thanks everyone.

ResearchBlogging.org
Voytek JB, & Voytek B (2012). Automated cognome construction and semi-automated hypothesis generation. Journal of neuroscience methods, 208 (1), 92-100 PMID: 22584238
Warp E, Agarwal G, Wyart C, Friedmann D, Oldfield CS, Conner A, Del Bene F, Arrenberg AB, Baier H, & Isacoff EY (2012). Emergence of patterned activity in the developing zebrafish spinal cord. Current biology : CB, 22 (2), 93-102 PMID: 22197243
Marriott G, Mao S, Sakata T, Ran J, Jackson DK, Petchprayoon C, Gomez TJ, Warp E, Tulyathan O, Aaron HL, Isacoff EY, & Yan Y (2008). Optical lock-in detection imaging microscopy for contrast-enhanced imaging in living cells. Proceedings of the National Academy of Sciences of the United States of America, 105 (46), 17789-94 PMID: 19004775
Wyart C, Del Bene F, Warp E, Scott EK, Trauner D, Baier H, & Isacoff EY (2009). Optogenetic dissection of a behavioural module in the vertebrate spinal cord. Nature, 461 (7262), 407-10 PMID: 19759620

1.8.12

The deception ratchet

The recent admission by Jonah Lehrer of fabricating quotes in his latest book has caused a lot of schadenfreude, bloviating about the "state of journalism", etc. People are writing a lot about what this "means".


I've been critical of Jonah Lehrer in the past because of his seemingly blind exaltation of neuroscientific findings but noted that this is a symptom of the state of cognitive neuroscientific research in general. After all these years, I believe I've finally identified the major root source of my scientific frustration.

Lies of omission. Intentionally leaving out critical information with the intent to deceive.

Again, this post isn't about Lehrer, it's about how Lehrer reflects the state of neuroscience. Specifically, this post is about the pervasiveness and problems associated with lies of omission. While I will discuss this in a neuroscientific and science reporting context, I think it is a more generalizable issue.

In that post linked to above, my friend and fellow neuroscientist Dan left a very insightful comment mirroring a discussion I had on twitter with Noah.





Dan said:
1. [Lehrer] wrote many blog posts, long-form articles, and books. In all cases, he had the luxury of space to add nuance to his articles (my point in an earlier comment).
2. He clearly isn't a scientist but he's shown that he can read and understand a large swath of scientific literature. He read enough that he must of come across articles that contradicted his ideas.
3/4 Is the big question. We know significant research exists that contradicted many of the stories he wanted to tell. When he came across those contradictory findings, did he convince himself that they weren't good science or did he actively ignore them to cherry pick the studies that fit his stories?
Dan's points 3/4 are basically talking about lies of omission. While Lehrer admitted to fabricating some quotes and then lying to cover up that fabrication, my deeper concern is how easy it is to commit a lie of omission and how hard such a lie is to uncover.

How can you possibly prove someone didn't know something when the accused can so easily feign ignorance?

Every time I hear about the insula being the "disgust" part of the brain, or oxytocin being the "love chemical", or dopamine being the "addiction chemical", I cringe. Normally I would say this is my curmudgeonly annoyance at oversimplification, but as Dan noted anyone who spends even a minute doing a search of the literature on PubMed will find tons of contrary evidence against the tidy narratives often reported in media accounts.

For example, the insula is also associated with a whole barrage of behavioral and cognitive functions.

There are two issues wrapped up here: one journalistic and one scientific.

Journalists are, in theory, supposed to fact check, but how can they check facts on scientific minutia in which they are not trained? Who is culpable? And are scientifically savvy journalists who follow the press release about a new scientific finding at fault if they don't address the complexities (when the allure of a neat behavioral narrative is so strong)?

Now the second problem comes down to evidence fishing. I'm sure many neuroscientists who have analyzed their data have encountered an anomaly. Maybe an unexpected brain area showed significant activation to your task. Maybe your treatment group had an unusual response. How do you handle these discrepancies?

The wrong way is to go to PubMed, search for the name of the brain area and the name of your task or drug or whatever, find some abstracts that talk about the two, and just go ahead and cite those and pretend like it's common knowledge that the insula "processes disgust" and leave it at that.

But I promise you this happens. A lot. I've seen it happen.

In both cases, journalist and scientist alike have committed sins of omission. The savvy journalist knows that their story is too simple, but man it makes for such a better story. The scientist just needs to add that little citation to show that their annoying finding is already known and therefore not worth discussing (because it doesn't fit their paper's narrative).

In a fantastic review of self-deception in unethical behavior, Tenbrunsel and Messick "...identify four enablers of self-deception, including language euphemisms, the slippery slope of decision-making, errors in perceptual causation, and constraints induced by representations of the self."

Honestly I can't recommend this paper highly enough; it's easy to read and fascinating.

The part that is most relevant to the discussion at hand, however, is on the ethical "slippery slope" that I'm calling "deception ratcheting":
The second component of the slippery slope problem is what we call the “induction” mechanism. Induction in mathematics is as follows. If a statement is true for N = 1, and if the statement for N + 1 is true assuming the truth of N, then the statement is true for all N. The way this works in organizations is similar. If what we were doing in the past is OK and our current practice is almost identical, then it too must be OK. This mechanism uses the past practices of an organization as a benchmark for evaluating new practices. If the past practices were ethical and acceptable, then practices that are similar and not too different are also acceptable. If each step away from ethical and acceptable practices is sufficiently small, small enough not to appear qualitatively different, then a series of these small steps can lead to a journey of unethical and illegal activities.
This happens in journalism just as it happens in science. If, as a scientist (or journalist), you witness some lazy brushing away of a surprising finding then you, too, will be more likely to do the same. And when your future students (or assistants) see you doing the same, then they become more comfortable with deceptions and lies of omission as well.

Tenbrunsel and Messick argue that such systematic, generational drift is caused by our large-scale errors in attributing causation to deception:
Acts of omission are a third reason as to why perceptions of causes are in error. Whereas lies of commission are direct misstatements of the truth, lies of omission are acts of deception that occur because someone withholds information that deceives the target. A failure to take an action, i.e., disclose the truth, makes it more difficult to ascertain responsibility, not only for others but also for oneself. Consider the situation in which you are selling a car. Is it your responsibility to inform the buyer that the car has had several unexplained malfunctions or is it the buyer’s responsibility to ask? Phrases or euphemisms such as “buyer beware” reveal the answer: moral responsibility shifts from the agent to the target under situations characterized by acts of omissions. Ritov and Baron’s (1990) work provides empirical support for this intuitive motion, demonstrating that acts of omission are viewed as more acceptable than acts of commission. Acts of omission, then, because they blur the assignment of responsibility, can create self-biased perceptions of causes, shifting blame from self to others. In such circumstances, it is highly likely that individuals’ propensity to engage in unethical behavior increases, because shifting responsibility to others allows one to divorce oneself from the moral implications of their actions.
Errors in perceptual causation allow us to distance ourselves from the ethical issues at hand. We erroneously believe that we cannot fix the problem, because it is a people and not a system issue. We also falsely believe that it is someone else’s problem, either because they are to blame or because the responsibility is someone else’s, not ours. While different from hiding the ethical implications of our own actions, this form of self-deception removes the ethical decision from our backyard, thus watering down the ethical demands of the situation.
The whole style of writing popular amongst the "Big Idea" crowd pushes for errors of omission in favor of a tight story. This is such a minor sin--one for which you almost certainly cannot be caught--that the allure to commit the lie probably overwhelms any inner voice of caution. But once you take that first deceptive step, you are statistically more likely to be willing to baby step your way farther and farther in service of that tight story.

Until in the end you're plagiarizing your own copy, making up quotes, and lying to fellow journalists.

By this point you should be asking yourself, "how well does this Tenbrunsel and Messick paper represent our state of knowledge on this topic?"

So caveat lector. Listen to the notes that are being played, but listen more carefully to the notes that are not being played.

And for you writers and scientists out there, beware the easy allure of the deception ratchet.

ResearchBlogging.org
Ann E. Tenbrunsel, & David M. Messick (2004). Ethical Fading: The Role of Self-Deception in Unethical Behavior Social Justice Research, 17 (2), 223-236 DOI: 10.1023/B:SORE.0000027411.35832.53
Chang LJ, Yarkoni T, Khaw MW, & Sanfey AG (2012). Decoding the Role of the Insula in Human Cognition: Functional Parcellation and Large-Scale Reverse Inference. Cerebral cortex (New York, N.Y. : 1991) PMID: 22437053

23.7.12

Why we play

Someone on Quora asked me answer this question:

"Why does our brain crave entertainment? And should we give in to its cravings?"

Initially I was going to decline, but when I thought about it, it started to sound like an increasingly fun challenge. Here's my full response:

*****

In short, yes, "entertainment" is beneficial to our neural health. And yes, for various definitions of "entertainment" we should absolutely "give in"!

There is a reason that young mammals play and frolic.

It's practice.

Lion cubs and wolf pups at play are learning motor skills. They're learning how to hunt to survive.


via Bite Dose

Classic research from the 1950s by my friend and Berkeley teaching mentor Marian Diamond proved that mammals raised in "enriched environments" (with toys, running wheels, etc.) had less neural death (or more neuronal growth) in their brains. They learned better, were healthier, etc.

I'll just let Dr. Diamond tell the her own story (via the Society for Neuroscience History of Neuroscience Autobiographies):

It turns out that the Hebbs allowed their children’s pet rats to run freely around the house, and this gave Hebb an inspiration. After a few weeks of free roaming, Hebb took the rats to his lab to run mazes and compared the results with maze-running by rats living in laboratory cages. Interestingly, the free-ranging rodents ran a better maze than the locked-up rats. Hebb speculated that rats confined to small unstimulating cages would develop brains worse at solving problems than animals growing up in a stimulating environment like a large house with hallways, staircases and human playmates.

From Hebb’s observation the Berkeley team got the idea of deliberately raising baby rats in two kinds of cages: a large “enrichment cage,” filled with toys and housing a colony of twelve rats; and a small “impoverished cage,” housing a solitary rat with no toys. Indeed, the rats growing up in a deliberately enriched environment ran better mazes than the “impoverished rats” raised in unstimulating confinement. And like the bright and dull rats that Krech and his colleagues had already tested, the deliberately enriched rats had more of that particular brain chemical, acetylcholinesterse, than the impoverished rats. This time, however, it was apparently nurture at work, not nature...

The research process involved removing the brain of a laboratory rat, chemically fixing, or preserving, the brain tissue andmaking thin slices of it (20 micra thick), viewing the slices undera microscope, then very carefully measuring the thickness of the cerebral cortex from the rats raised in both kinds of cages, enriched and impoverished. I did see variations: The enriched rats had a thicker cerebral cortex than the impoverished rats, but the difference was not the sort you could observe casually. You had to compare the brain tissue under the microscope, and the cerebral cortex of the enriched rats was only 6 percent thicker than the cortex of the impoverished rats. Nevertheless, it was highly statistically significant; nine cases out of nine showed a 6 percent difference. This was the first time anyone had ever seen a structural change in an animal’s brain based on different kinds of early life experiences. Could it really be true?

I took another year and repeated the experiment with nine more animals. Then I started to get excited. It was about 1963 by then, and my life was really hectic. I now had four children, Catherine, Rick, Jeff, and Ann and was only at the university half time, doing demanding, pioneering work in the lab. In some ways, that period is hard to recall. But I do remember very clearly the day I took the results over to show David Krech. I ran across campus with the papers in my hand and laid them out on his desk. He stared at them, then at me, and immediately said, “This is unique. This will change scientific thought about the brain.” It was a great thrill—truly an emotional high—to sit with him and share that moment.

In 1964, we published the results in a paper by Diamond, Krech, and Rosenzweig called “Effect of Enriched Environments on the Histology of the Cerebral Cortex.” And a year after that I found myself standing in front of a session on the brain at the annual meeting of the American Association of Anatomists.

We were at a hotel conference room in Washington, D.C., and I was truly scared. There were hundreds of people in the room—very few of them women—and this was the first scientific paper I had presented at a big conference. I explained the projects as calmly as I could, people applauded politely, and then—I’ll always remember this—a man stood up in the back of the room and said in a loud voice, “Young lady, that brain cannot change!”

It was an uphill battle for women scientists then—even more than now—and people at scientific conferences are often terribly critical. But I felt good about the work, and I simply replied, “I’m sorry, sir, but we have the initial experiment and the replication experiment that shows it can.” That confidence is the beauty of doing anatomy. Ed Bennett used to say to me,“Marian, your data will be good from here to eternity, because it’s based on anatomical structure.” Eternity is a long time, of course. But so far—and it’s been thirty-four years—Bennett has been right. And the man in the back row? My entire research career and some of the many scientific findings that stemmed from it will continue to show how wrong he was in the pages ahead....

We know that this applies to humans to some extent, too. For example, even briefly practicing a new skill, such as juggling, can increase your motor cortex grey matter volume. Practice and play is most certainly good for the brain.
I don't have the time to hunt around right now, but I'd be shocked if there wasn't a whole wealth of academic research looking to the evolution of playing behaviors and their role in species fitness and survival.

My guess is the running theory would be something like this:

  • Play is simulation. It's Practice.
  • Low-cost practice can prepare you for high-cost survival situations (such as fighting or hunting).
  • Animals that have practiced are more likely to survive the high-cost scenarios for which they've practiced.
  • This type of practice and play is therefore beneficial for survival (which increases the chances of procreation).
  • To encourage this type of behavior, mammals are "rewarded" for playing.
  • These neurochemical "rewards" in response to play are what we refer to as "entertainment".

Note that so far I've only focused on physical play. But humans, being the social primates that we are, also find social practice entertaining as well. It's good for us to practice socializing and learning social structures in low-cost scenarios, so we watch TV, read books, go to performances, chat online, play multiplayer videogames, and so on.

We interpret the observations of social interactions or the simulation of social behaviors as "entertaining". But what we really might be doing is practicing how to interact with one another in a low-cost setting.

You don't want to piss off king monkey or your future possible offspring supporter when you only get one chance in real life.


ResearchBlogging.org

Draganski B, Gaser C, Busch V, Schuierer G, Bogdahn U, & May A (2004). Neuroplasticity: changes in grey matter induced by training. Nature, 427 (6972), 311-2 PMID: 14737157