This is Your Brain On Awesome Thoughts on the world from a student of the mind


Visualizing cause and effect in the brain

Two of the biggest challenges facing neuroscientists involve visualizing the brain on the one hand, and influencing it on the other.  These two have a lot to tell us about the brain individually, but what would be truly powerful would be combining the two in one study.

This is just what a group of researchers at MIT are trying to accomplish, pioneering a new method called "opto-fMRI" that uses the visual information provided by fMRI with the ability to activate specific neural circuits by using optogenetics.

For those of you unfamiliar with these techniques, fMRI is essentially a way of visualizing neural activity by observing blood flow in the brain.  The idea is that, as particular areas of the brain function at a higher level of activity (eg, if they are used in some task that is being performed), then the body will send more blood to that area in order to keep them well-nourished and functioning correctly.  fMRI essentially monitors this blood flow over time, piecing together a map of neural activation that can show connections and circuits between brain regions.

Visualizing the brain is all well and good, but it doesn't allow us to actually influence particular neurons or circuits.   This is where optogenetics is particularly useful.  It involves breeding mice (or worms, rats, etc) that express particular kinds of proteins that are sensitive to certain wavelengths of light (called channelrhodopsin).  These proteins exist in the nervous system, and when their "target" color of light is shown, they cause the neurons they're associated with to fire.  This allows for a very fast-paced control over the nervous systems of these animals, achieving a level of precision we do not usually have.

You can probably see where scientists are going with the combination of these two techniques.  By having one technology that lets us visualize the entire brain, and another that allows us to influence a very specific location in the brain, we can start to investigate how that specific region might connect with other areas that span long distances (relative to the brain, at least).

This is a pretty new technology, so we'll have to wait and see what researchers come up with by using these techniques, but the potential applications for such a technology are quite exciting.  By being able to see the distal connections between many locations in the brain, we'll gain a better understanding of the interconnected web of neural activity associated with all kinds of behaviors.

via MIT News


Why empiricism will always be imperfect

A new year is upon us, and that’s always a great time to clean out the skeletons in your closet.  So without further ado, let’s take a look at Jonah Lehrer’s explanation of “the decline effect” (published in The New Yorker last month). Lehrer describes this odd phenomenon whereby statistical significance of previous scientific findings seems to decrease with age, as we get further and further away from the time that it was initially reported in literature.

As any scientist can tell you, the holy grail of an experiment is a low p-value, a statistical measure that tells whether your findings are indicative of an actual effect, not just randomness and chance. This sounds fairly straightforward – of course we want to find things of actual importance, rather than being lulled into a false discovery by arbitrary data – but it turns out to be  much hazier than a simple “yes” or “no.” P-values depend on a number of factors that can change the statistical outcome of your experiment. Things like experimental design, subject choice, even the time of day can have drastic effects on the results of an experiment.

Scientists’ answer to such imperfections is to run the experiment over and over in a number of different environments. This is the beauty of scientific empiricism; at its best, it has the ability to extract truth from the noisy world around us. However, as Lehrer notes, there is one variable that we never change: the fact that people are the ones running these studies. This statement may seem annoyingly obvious, but it’s incredibly important to consider for any scientific study. While the empirical process is designed to provide an objective method of analyzing data, humans are inherently imperfect at being objective and unbiased, and this can manifest itself in the conclusions we take from our studies.

Suppose that you run a study with 90 subjects. The first 80 subjects show a fantastic result. You eagerly begin working on your forthcoming journal article, ready to share your findings with the world. However, upon running the final 10 subjects, you find that this result almost totally disappears. Bummer. An objective machine might say “maybe there isn’t anything here after all” and move on.  But people aren’t objective, and they’ve got a stake in giving the world something that is deemed significant. So you decide to leave out those last few subjects, citing them as outliers and thus non-representative of the general population, and publish an article. A few years pass, and a number of researchers (less invested in your discovery) decide to take another look at that paper.  They replicate your experimental design, but they fail to replicate your stellar results.

I don’t mean to cast a shadow of doom and gloom over the scientific enterprise. I just want to remind everyone that as long as human beings carry out scientific work, human faults will continue to plague our results. If we hope to come to an understanding of the world around us, it is important that we accept and anticipate the flaws inherent in our system.

via The New Yorker


More Memristor Action

Wow, many apologies for cutting off the (relatively) constant drip of science goodness I've had going on for the last few months.  The past few weeks have been super hectic (I just got back from an interview in Seattle).

I've had to spend all of my writing time working on an article on memristors for the upcoming edition of the Berkeley Science Review.  To that extent, I thought I'd share this interesting lecture by one Leon Chua, the original mind behind memristors and a huge supporter of their emergence into the scientific world today.

I'm not going to go into a ton of detail (you'll have to wait for the article for that!), but this is a general lecture on the ways in which memristors might be applied to physical models of the human brain.

(for those of you who have no idea what I'm talking about, check out this post on a team that is creating software to be used with memristor circuits)

Essentially, Chua is arguing that brains are already made up of memristors (though obviously not in the same sense that our circuit boards are).  He points to the well-known behavior of synapses as strengthening/weakening their connection depending on whether the two neurons involved fire at the same time.  This is a process called Hebbian learning, and Chua suspects memristors are just right for this job.

It's a bit long, so feel free to skip around to the parts that seem more interesting to you, but well worth the watch if you like thinking about how other physical systems might do things similar to natures method of biological computation.

Either way, I promise more regular posts from now on...that is, until my next interview period 🙂

via (detailing a conference on memristors last February)


Shedding light on the supposed link between MMR and autism

As you may have noticed in the past few months (if not years), there is quite a bit of concern about the possible link between autism and vaccinations. If you were to look at almost any properly carried out independent study, you'd find that most of these allegations are completely ridiculous. Nevertheless, sensational claims seem to have a knack for outshining the factual evidence that contradicts them. The autism/vaccination "link" has caused a number of parents to intentionally avoid vaccinations for their children, resulting in a number of unnecessary deaths, including the recent outbreak in whooping cough in California.

It all started with a paper written by Andrew Wakefield in 1998.  In the paper, he describes a number of children who had recently undergone vaccination for MMR (measles, mumps and rubella) and supposedly began showing signs of autism shortly thereafter.  The author suggested that the MMR vaccine was causing these children to develop their symptoms.

Twelve years and who knows how many un-vaccinated children later, we finally get the truth: the original paper was rife with manipulation and deceit.  In an article published in the British Medical Journal, Brian Deer recently took a critical look at the original paper, checking up on each patient and getting the facts straight regarding many of Dr. Wakefield's claims.  Here is a quick list of errors that the author found (taken directly from the article):

  • Three of nine children reported with regressive autism did not have autism diagnosed at all. Only one child clearly had regressive autism.

  • Despite the paper claiming that all 12 children were “previously normal,” five had documented pre-existing developmental concerns.

  • Some children were reported to have experienced first behavioural symptoms within days of MMR, but the records documented these as starting some months after vaccination.

  • In nine cases, unremarkable colonic histopathology results—noting no or minimal fluctuations in inflammatory cell populations—were changed after a medical school “research review” to “non-specific colitis”.

  • The parents of eight children were reported as blaming MMR, but 11 families made this allegation at the hospital. The exclusion of three allegations—all giving times to onset of problems in months—helped to create the appearance of a 14 day temporal link.

  • Patients were recruited through anti-MMR campaigners, and the study was commissioned and funded for planned litigation.

The journal that originally published this paper has finally rescinded the article, more than a decade later.  Unfortunately, during that time many young children and newborns went without a critical component of healthy living in the modern world.  Moreover, the suspicion it effected in the general public may take generations to sort itself out.

The scientific process is usually an efficient way of arriving at some sort of truth about the world. Unfortunately, the truth is also easily obscured by faulty reporting and self-interested research. The threads of trust that lend credibility to scientific enterprise are fragile, and cause unknowable damage when cut. As scientists and science advocates, it's our responsibility to ensure that this trust remains as strong as possible.

Further reading:
Coverage in Slate (for those who don't have access to the journal or who don't have the time to sift through a full article)


Total body transplant. ‘Nuff said.

Maybe it's just me, but as a neuroscientist, the idea of brain transplants is both terrifying and awesome at the same time.  There's something quite unsettling about thinking of a head that is separated from its body, yet still in function, but that also doesn't mean that's impossible.   This is an interview of one Dr. White (who unfortunately passed away recently), a neurosurgeon for many years, and one of the only people to carry out one of the more controversial and complicated procedures I have ever heard of: the total body transplant.

Now, before you get all riled up about the ethical implications of this, a few notes.  One, we're not talking about human beings (yet), but rather monkeys and other kinds of animals (which, depending on your disposition to animal cruelty, still leaves this in moral peril).  Two, these experiments were carried out decades ago, and as far as I know they don't go on presently.

So what exactly is going on here?  Well, essentially Dr. White wanted to take the organ transplant to another level.  We already have medical procedures that can replace one person's heart, lungs, kidneys, etc. with artificial or transplanted replacements, but what about the whole shebang?  What about the entire human body?

As with most procedures this invasive and risky, Dr. White started performing the operation on non-human primates and other animals.  The operation involves effectively removing the entire head from it's original body, cutting off the head of another animal (of the same species, although Mars Attacks! may disagree), and then reassembling the head onto its new body.

This is particularly tricky to pull off because of the delicacy of many essential components of the nervous system.  Surgeons had to be extremely careful not to damage any of the cranial nerves as well as any tissue that was exposed.  However, when all was said and done, they managed to place a monkey's head on a new body, and watch as the monkey successfully carried out various simple functions with its new machinery.  Spooky.

Now, you might be asking "why the hell would anybody want to do something like this (insert your curse on mankind for the abomination it has created here)."  Well, in truth, there are all kinds of situations where one might benefit from a new body, perhaps the most obvious of which is with tetraplegics.

Imagine being in a horrendous accident in which you lose all function of your body from the neck down.  You can still think just as before, but now you have lost almost all ability to carry out your everyday life.  In a world in which total body transplant is a viable option, gaining mobility again might be entirely possible, provided that you had a body to work with, and here's the tricky part.  Technically, the procedure needs two people to work.  One head, and one body.  Where might this second body come from, you might ask?  Well, that's a question I'll leave to the philosophers and politicians, but one possibility is from people who are clinically "brain dead," or who have perfectly functioning bodies, but nobody upstairs to direct them.

Anyways, I've said too much, so I'll just let the video do the rest of the talking.  Whether you think this is morally acceptable or not, it's still an amazing feat of biological engineering and surgical precision.  It sends chills up my spine, I just can't tell if they're the good kind or the bad kind.