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How to be a neuroscientist




Bradley Voytek Cognitive Neuroscience New Phrenology fMRI

(Image source: The Roots - Phrenology)







You just got brain-mesmerized!







Let me break down these points.

1. "Is curiosity a singular thing?"



Bradley Voytek PNAS basal ganglia prefrontal cortex striatum





Or, as I say in my chapter:






Editor's selection: Neuroscience
This post was chosen as an Editor's Selection for ResearchBlogging.org
Editor's selection: Social Science
This post was chosen as an Editor's Selection for ResearchBlogging.org

brainSCANr: Paper rejected and Health2.0!

(This is cross-posted from the brainSCANr blog)




Bradley Voytek Jessica Voytek brainSCANr careMAPr Health2.0





You can see the rapid demo prototype here:

Bradley Voytek Jessica Voytek brainSCANr careMAPr Health2.0





What do people think about the idea? Any suggestions?


Something ghoti with science citations

Science has a lot of problems. Or rather, scientometrics has a lot of problems. Scientific careers are built off the publish or perish foundation of citation counts. Journals are ranked by impact factors. There are serious problems with this system, and many ideas have been offered on how to change it, but so far little has actually been affected. Many journals, including the PLoS and Frontiers series, are making efforts to bring about change, but they are mostly taking a social tactic: ranking and commenting on articles.

I believe these methods are treating the symptom, not the problem.

Bradley Voytek drunk ghoti

Publish or perish reigns because our work needs to be cited for we scientists to gain recognition. Impact factors are based on these citation counts. Professorships are given and tenure awarded to this who publish in high-ranking journals. However citations are biased, and critical citations are often simply ignored.

Bear with me here for a minute. How do you spell "fish"? g-h-o-t-i: "g-h" sounds like "f", as in "laugh". "o" sounds like "i", as in "women". "t-i" sounds like "sh", as in "scientific citations". This little linguistic quirk is often (incorrectly) attributed to George Bernard Shaw; it's used to highlight the strange and inconsistent pronunciations found in English. English spelling is selective. You can find many spelling examples that look strange, but support your spelling argument.

Just like scientific citations.

Bradley Voytek scientometrics

There are a lot of strange things in the peer-reviewed scientific literature. Currently, PubMed contains more than 18 million peer-reviewed articles with approximately 40,000-50,000 more added monthly. Navigating this literature is a crazy mess. When we created brainSCANr, our goal was to simplify complex neuroscience data. But now we want to shoot for more.

At best, as scientists we have to be highly selective about what studies we cite in our papers because many journals limit our bibliographies to 30-50 references. At worst, we're very biased and selectively myopic. On the flip side, across these 18+ million PubMed articles, a scientist can probably find at least one peer-reviewed manuscript that supports any given statement no matter how ridiculous. Don't believe me? Here's my first whack at a questionable series of statements supported by peer-reviewed literature:

Human vision extends into the ultraviolet frequency range1, possibly mediated by an endogenous violet receptor2.


The effects of retroactive prayer are well-described in improving patient outcomes1. Herein we examine the hypothesis that such retroactive healing is mediated by an innate human ability for "psi"; that is, for distance healing mediated by well known quantum effects2.

What we need is a way to quickly assess the strength of support of a statement, not an authors' biased account of the literature. By changing the way we cite support for our statements within our manuscripts, we can begin to address problems with impact factors, publish or perish, and other scientometric downfalls.

brainSCANr is but a first step in what we hope will be a larger project to address what we believe is the core issue with scientific publishing: manuscript citation methods.

We argue that, by extending the methods we present in brainSCANr to find relationships between topics, we can adopt an entirely new citation method. Rather than citing only a few articles to support any given statement made in a manuscript, we can create a link to the entire corpus of scientific research that supports that statement. Instead of a superscript number indicating a specific citation within a manuscript, any statement requiring support would be associated with a superscript number that represents the strength of support that statement has based upon the entire literature.

For example, "working memory processes are supported by the prefrontal cortex"0.00674, gets strong support, and a link to PubMed showing those articles that support that statement. Another statement, "prefrontal cortex supports breathing"0.00033, also gets a link, but notice how much smaller that number is? It has far less scientific support. (The method for extracting these numbers uses a simple co-occurrence algorithm outlined in the brainSCANr paper).

My citation method removes citation biases. It provides the reader a quick indication of how well-supported an argument is. If I'm reading this paper and I see a large number, I might not bother to look it up as the scientific consensus is relatively strong. But if I see an author make a statement with a low number--that is, a weak scientific consensus--then I might want to be a bit more skeptical about what follows.

We live in a world where the entirety of scientific knowledge is easily available to us. Why aren't we leveraging these data in our effort to uncover truth? Why are we limiting ourselves to a method of citations that has not substantially changed since the invention of the book? My method may have flaws, but it much harder to game than the current citation biases that only give us the narrowest slice of scientific support. My citation method entirely shifts the endeavor of science from numbers and rankings of journals and authors (a weak system for science, to say the least!) to a system wherein research is about making statements about truth. Which is what science should be.


Robinson KA, & Goodman SN (2011). A systematic examination of the citation of prior research in reports of randomized, controlled trials. Annals of Internal Medicine, 154 (1), 50-5 PMID: 21200038


Top 10 neuroscience TED talks





Oliver Sacks




Jill Bolte Taylor



Henry Markram




Vilayanur Ramachandran



Sebastian Seung




Bradley Voytek brainSCANr

Gero Miesenboeck




Michael Merzenich


Jeff Hawkins







Christopher deCharms


Dan Gilbert


Daphne Bavelier



Gabrielle Giffords' brain surgery: Decompressive hemicraniectomy

So the big news this weekend was the terrible shooting in my home state of Arizona. The highest-profile victim was congresswoman Gabrielle Giffords who, as of this writing, is recovering from surgery after being shot in the head.

Most early reports of her shooting listed her as dead. My belief is that this is because people hear "shot in the head" and immediately translate that into "dead". Many surgeons would, as well.

However, according to the BBC, Giffords' surgeon, Peter Rhee, was "a former military doctor who served in Afghanistan" and her neurosurgeon, Michael Lemole, "removed half of her skull to give the [brain] tissue room. The bone is being preserved at a cold temperature and can be reattached when the swelling subsides."

The article does not, however, explain this procedure very well, and so I thought I'd give a little bit of an explanation.

This surgery is known as a decompressive hemicraniectomy. I've published research with people who have had this procedure, blogged about that work, talked about it a TEDxBerkeley last year, and even got picked up by Mind Hacks and Wired for it. Here's what the skull of a person who has had this surgery looks like:

Bradley Voytek Journal of Cognitive Neuroscience Giffords Hemicraniectomy

And in 3D:

This surgery is amazing. As I said in the last piece, I worked with a surgeon at San Francisco General Hospital, Geoff Manley.


There is a scale that is used to describe someone's neurological state after a head injury. This is known as the Glasgow Coma Scale (GCS), which is a numerical scale ranging from 3 to 15, which 3 being nearly dead. A person who shows up with a GSC of 3 can even be viewed as a lost cause, with very little chance of survival. Points are assigned based upon observations of the eyes, movement, and verbalization by the patient. A 3 would mean the patient does not open their eyes to any stimulation, has no movements, even in response to pain, and makes no sounds.

One of the patients we worked with in my study had a GSC of 6 in the field, which dropped to a 3 by the time he got to the hospital. That subject

...underwent an emergency decompressive hemicraniectomy and removal of the subdural hematoma because of his rapid neurological deterioration. At the time of EEG testing, he was doing remarkably well and had no evidence of any residual neurological or behavioral deficits.

Another patient:

Subject 1 sustained a gunshot wound to the left frontal lobe anterior to premotor and motor cortices. His Glasgow coma scale (GCS) was 14 on admission. The patient was taken to the operating room for debridement of the gunshot wound, and a decompressive hemicraniectomy was performed to prevent further neurological deterioration from increasing ICP [intracranial pressure] from the initial penetrating brain injury. At the time of EEG testing, his memory, attention, and motor function were normal and he did not have any frontal release signs. Of note, the patient is currently back to school.

Now, of course I'm not a medical doctor, have no details about Congresswoman Giffords' medical state, or anything like that. But hearing that her neurosurgeon performed a decompressive hemicraniectomy gives me hope that she may well recover from this attack.

Anyway, I hope this serves as a way of some explanation of what her surgery was, and why it was performed.

EDIT: I've written an even simpler explanation of this over at Quora:

Basically, the gunshot caused tissue damage of the actual brain tissue. This leads to swelling. Of course, the head is an enclosed space, so the brain tissues can only swell up onto the skull causing compression and threatening to cut off blood supply or down, through the opening at the base of the skull (foramen magnum) causing a herniation (in this case, and "uncal herniation"). This swelling down onto the brainstem stem compresses the tissues there, damaging the neurons. The brainstem neuronal structures are responsible for basic functions required for life such as respiration and maintenance of consciousness. Damaging these tissues leads to rapid degeneration of status, coma, and then death.

EDIT #2: Looks like CNN's Dr. Gupta agrees with me.

