Cosyne, Day 1

To sum up day 1: I forgot my phone charger and all my toiletries and managed to lose my notebook by the end of the first lecture…! But I brought my ski gear, so there’s that. Mental priorities. For other days (as they appear): 23, 4

Motor controlTom Jessel gave the opening talk on motor control. The motor cortex must send a command, or motor program, down the spinal cord but this causes a latency problem. It takes too much time to go down the spinal cord and back to have an appropriate error signal sent back (in case something goes wrong.) To solve the problem, the motor system keeps a local internal copy (PN, left). A simple model from engineering says that if you disrupt this gating, you can no longer control the gain of the movement and will get oscillations. So when Jessel interferes with PN activity, a mouse that would normally reach directly for a pellet instead moves it’s paw up and down in a slow forward circle – oscillating! I think that he also implicated a signal that directly modifies presynaptic release through GABA in this behavior.

(Apologies if this is wrong, as I said, I lost my notebook and am relying on memory for this one.)


Azim E, Jiang J, Alstermark B, & Jessell TM (2014). Skilled reaching relies on a V2a propriospinal internal copy circuit. Nature PMID: 24487617

Clay Reid & The Brain Institute

Sounds like a band name, huh? As I jet off to Cosyne, this article seemed appropriate:

As an undergraduate at Yale, he majored in physics and philosophy and in mathematics, but in the end decided he didn’t want to be a physicist. Biology was attractive, but he was worried enough about his mathematical bent to talk to one of his philosophy professors about concerns that biology would too fuzzy for him.

The professor had some advice. “You really should read Hubel and Wiesel,” he said, referring to David Hubel and Torsten Wiesel, who had just won the Nobel Prize in 1981 for their work showing how binocular vision develops in the brain…

“Torsten once said to me, ‘You know, Clay, science is not an intelligence test.’ ”Though he didn’t recall that specific comment, Dr. Wiesel said recently that it sounded like something he would have said. “I think there are a lot of smart people who never make it in science. Why is it? What is it that is required in addition?”…

He is studying only one part of one animal’s brain, but, he said, the cortex — the part of the mammalian brain where all this calculation goes on — is something of a general purpose computer. So the rules for one process could explain other processes, like hearing. And the rules for decision-making could apply to many more complicated situations in more complicated brains. Perhaps the mouse visual cortex can be a kind of Rosetta stone for the brain’s code.

It’s a fun read about the goals of Clay Reid and of the Brain Institute as a whole. I’m always dubious about using the visual system as a model for anything subcortical, and for implicitly assuming that non-cortex is less important than cortex. And what about long-time scale modulation? But for all that, they’re doing pretty cool stuff up there.


Monday open question: Do you have a personal website? Is it useful?

As I’ve mentioned, the past few weeks have seen potential new faculty members come and go from my institution. I decided to look them up online to see what I could find. Did they have a twitter account? A personal web page? Out of ten, one had a twitter account and none had a personal web page. I went back to the three (specialized) potential faculty members from the last round and while two had a lab web page, I couldn’t find the lab web page of the third (I know where they ended up)!

The advantage of a twitter account is: people are going to be talking about you, and you won’t know about it if you can’t see it. It seems straight-forward if a bit of work.

But a personal web page is different. It doesn’t take tons of work, particularly once you’ve set it up. All it needs to have is your name, a list of your interests, your CV, a list of your work, a way to represent you. It’s the modern business card, really. Once you are a faculty member and have a full lab web page I think it goes away but before then – why not?

Can anyone speak to whether they have one and whether it’s actually been useful?

Update: From Artem’s comment below, why web-presence is important for researchers

Update 2: From an anonymous twitter comment: “I find it very useful. When I give a talk somewhere, >50 people visit [their personal page] and download papers & ask better q’s at talk.”

Unrelated to all that, 2/21 edition


Sculptures covered in beeeeeeeswax

“An extraordinary coup, one of the greatest kingdoms in India had fallen into the hands of an order of esoteric yogis

How to bury your treasure:


Great new blog by Steve Shea covering all the neuroscience preprints posted to bioRxiv

The Turing Dog Test

For those of you who remember that Mutual Information Coefficient paper, too bad, you probably shouldn’t be using it. Just use Mutual Information instead. (I work with a lot of information theorists and I don’t know anyone who ever even thought about using MIC.)

How to deal with a lot of comparisons: explanation of FDR

k-means clustering in GIF form:



Evolution is a special kind of (machine) learning. See also: Genetic Algorithms

Twitter cliques:


Using slime mold to reengineer Iberian railways. I would have just used a computer.

Recommendation engines for science papers and useful guides to reference managers (h/t Prerana Sresthra)

Best practices for behavioral experiments in headfixed mice. Read and be learned.

Same movie, different posters:


Friends with benefits

tl;dr: Rodents will help each other get out of trouble, though they will help each other more if they are related. Social learning in rodents can require information transmission between ACC and amygdala, and the strength of synapses in mPFC dictates social status.

He wanders into the room and stops – someone else is peering at him out of a tiny plastic cage. Wandering over he must decide: should he help him out of the cage? Or let the creepy situation remain creepy, and leave them stuck in there?

Rats, it turns out, aren’t big fans of creepy situations and will actively go out of their way to help their furry compatriots escape from their cages. Not only will they help other rats escape their cages – even if they don’t know them – but if they find a bite of chocolate they’ll hand over some of that as well. [Though if you look at the data: the little bastards wait half a week before they get around to doing it.]

Screen shot 2014-02-08 at 11.27.27 AM

That’s fine but things can get a bit sinister when the rats aren’t just strangers but strangers that appear different. When they find another rat trapped in a cage that is of a different strain, the free rats would rarely attempt to let the trapped rats loose. This isn’t purely a matter of rats being different from one another, but rather of rat-features that they weren’t familiar with. When rats were housed with rats of different strains, they would help other rats of that strain out. Individuals of that outgroup had been ‘humanized’, so to speak. Yet, own-group preference wasn’t innate – if they weren’t housed with other rats of their own strain, they wouldn’t help them, either. For an example, watch this movie from the paper (which I can’t directly embed).

We already know a bit about the neuroscience of empathy and social structure in rodents. A mouse that observes a fellow mouse receiving painful shocks in a certain area of their cage will learn to avoid that area through pure social observation. However, they learn better when it is a sibling that is being shocked than when it is an unrelated rat. This learning requires a region of the brain known as the anterior cingulate cortex (ACC), though the region can be inactivated during later retrieval and recall without affecting the behavior. It also requires the amygdala, not just for learning but also for later retrieval and recall. During learning, the ACC and amygdala are connected by strong (theta) rhythms, potentially to transmit information between the areas.

Screen shot 2014-02-20 at 10.58.38 AMAnother factor guiding social behavior is social status. Status affects behavior on a range of levels, from how decisions are made to how healthy an individual is. It is pretty surprising to me that in rodents, social status can be directly changed by changing the strength of synapses in the medial prefrontal cortex (mPFC). I’ve only ever seen a broad neuromodulator like serotonin do something like that, though I would hesitate before suggesting that they two mechanisms were connected. On the other hand, mPFC is upstream of serotonergic areas so increased synaptic strength could mean increased serotonin!

Ben-Ami Bartal I, Rodgers DA, Bernardez Sarria MS, Decety J, & Mason P (2014). Pro-social behavior in rats is modulated by social experience. eLife, 3 PMID: 24424411

Ben-Ami Bartal I, Decety J, & Mason P (2011). Empathy and pro-social behavior in rats. Science (New York, N.Y.), 334 (6061), 1427-30 PMID: 22158823

Wang F, Zhu J, Zhu H, Zhang Q, Lin Z, & Hu H (2011). Bidirectional control of social hierarchy by synaptic efficacy in medial prefrontal cortex. Science (New York, N.Y.), 334 (6056), 693-7 PMID: 21960531

Jeon D, Kim S, Chetana M, Jo D, Ruley HE, Lin SY, Rabah D, Kinet JP, & Shin HS (2010). Observational fear learning involves affective pain system and Cav1.2 Ca2+ channels in ACC. Nature neuroscience, 13 (4), 482-8 PMID: 20190743

Meerkats: a non-human history (because meerkats are people too!)


OK, this is probably the greatest thing I’ve read in a while. “Thought-provoking” as they say:

In truth, though, I was drawn to the darkness of meerkat life. Beneath the kid-friendly surface, a Shakespearan drama was unfurling in those South African burrows. It was like watching King Lear or Titus Andronicus acted out by suricates with brains the size of walnuts.

A typical meerkat inhabits a world of revenge, suffering, and endless toil. The cuddly characters of the show were regularly stung by poisonous asps, lifted off camera in the talons of enormous raptors, or (most common of all) expelled from the group like Old Testament exiles, lost to wander in the desert until they expired from thirst. Even the ‘successful’ meerkats, the ones permitted by the matriarch to have children and live with the group, had lives that resembled Victorian factory workers, spending almost all of their waking hours on the tedious dual tasks of lookout duty and grub-hunting…

And yet I firmly believe that meerkats and other higher-order mammals do have a history, of a sort. I’m not talking about the natural history of biologists, which is concerned with their average lifespan, their feeding habits, their reproductive cycles. I mean the history of historians. This type of history, the kind I enjoy doing and reading, is grounded in imaginative leaps that bear a core resemblance to those of the novelist or poet. It’s about putting your own experience of the world to one side and trying as hard as you possibly can to imagine someone else’s experience. What is it like to live in a meerkat society? On what internal principles do they organize themselves? What do they dream about? When they gather in the desert at night and make high-pitched sounds as a group, are they singing? What is meerkat subjectivity?

Why do we not have a Meerkat history? It all reminds me a bit of the George R.R. Martin novellette Sandkings (the pdf is easily google-able.)

Edit: Silly me. Here are some meerkats for you:

Monday open thread: Is tool development slowing down?

My institution is on the hunt for a new neuroscience faculty member or two and the past two weeks have seen ten candidates come and go. All of them are doing awesome science, but what struck me was the lack of people making new tools or techniques. The institution I am at likes to think of themselves as quite cutting edge, so I had assumed that I was going to report to everyone on what the hot themes and tools were. Instead, only one candidate was working on a new tool. I’m not even looking for something fantastically new, really: a new statistical analysis or a new take on an imaging set-up (SPIM?) would have made me happy.

After seeing plenty of new things in faculty talks the last few years, I have to wonder: is tool development slowing down? Were the last few years the tail end of a transient boom of channelrhodopsin etc? Are we in the ‘exploit the tools’ cycle before another round hits? Or was my observation just a fluke?

Oh, and if anyone was wondering, apparently 50% of all neuroscientists live in Cambridge, MA. Who knew?

Unrelated to all that, 2/14 edition


On the blog

On Monday I tried to ask what are the fundamental problems of Systems Neuroscience. There are some good comments in there.

I also tried to share my feelings about doing science – as in, why do I bother doing it at all? For me, it’s all about having an aesthetic sense. David Schoppik shared a good interview with Sir John Sulston, one of the original researchers in the worm field.

On other blogs

I kind of hesitate to link to this, but there’s a kerfuffle going on where Lior Pachtor is accusing Barabasi and Kellis of fraud (article 1/3). It’s pretty vicious and most of the accusations seem to fall pretty far short of fraud and are instead a case of over-selling. Accusing a fellow academic of fraud is just about the worst thing one can do, and serious charges require serious evidence. Still, it’s worth reading.

Scientists strap fake dinosaur tail on chickens to discover how T-Rex walked. Srsly

Rethinking how the sensory cortex works. There’s more integration of different sensory modalities than you’d think.

Speaking of integration, sometimes it’s best not to do any of it with personal libraries

Fish have it easy in schools, because they do a lot of drafting

Loess explained in one GIF:

The sieve of selection. C. elegans ftw

Two depressingly bad – in the number of factual inaccuracies – by David Graeber and Barbara Ehrenreich on play in animals. What’s more depressing is the number of non-scientists linking to them.

Humans: not-so-special

Does trend-chasing explain financial markets? There’s at least some pretty graphs in there.

How to kill a paper in review that you don’t like.

Here are some lessons from genetic algorithms on neural network structure that I’m not sure we’ve really learned.

Fish are stupid because their lives suck:

Science is an aesthetic practice


One of my friends recently hired – or had foisted upon her – an undergraduate to help her do research. “How do you stay motivated?” he asked her. “Uhh” she responded.

We’ve all been there. Doing science really sucks, a lot of the time. Add to that the common list of other deficits with this career: little money, tons of work, no real respect, etc. So why do we do it?

While I was on the microscope I was thinking these very thoughts, and decided to write an article about it on Medium. One of the points of writing this blog is to get better at writing, so I used the chance on Medium to do something a bit different.

The point of the article is that, while there are many reasons one could do science – and I know the reasons are probably pretty heterogeneous among my peers – the reason that I in particular do science is for aesthetic reasons. Essentially, the impulse to do science is the same impulse that drives someone to an appreciation of art. It is a cultivation of an appreciation of the beauty of the world. I’m not sure what motivates an Artist to create Art, though it seems that my few vain attempts have been about creating something beautiful for other people. But to me science is more like stumbling through an art gallery: it isn’t about creating something for other people, but rather finding something beautiful for myself. Once found, I can fit it into my mental blueprints of the world and reflect on it as I would a fine work of art. Perhaps that’s a bit selfish, but it’s what keeps me going.

Go read it, and please feel free to send any constructive criticism on it my way!

Mammalian brains (via Labrigger)

mammalian brainsThis is just too great. Here’s a bunch of mammalian brains, to scale I imagine (via Labrigger who cannot find the original content owner, unfortunately)