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

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:


Unrelated to all that, 2/7 edition


(above: “the dangers of women voting”)

A down week as I came down with a cold. Normally I write up everything for my blog on Saturday or Sunday morning but this week I was unable to write anything coherent. So enjoy these links!

On the web

Multilevel mating success in water striders

Meaning is a subtle concept. On translating (part of) Leopardi’s Zibaldone

Even though there is a clear category distinction: pondering the limits of anthropomorphism

Which neuroscience conference should you go to? It really depends on the bars.

This is why rent sucks in San Francisco. I once plotted the amount of housing in Portland, OR (metro) vs SF-Oakland; despite having drastically fewer people, Portland had built more housing over the past ten years!

TruliaPriceMonitor_Scatterplot_Jan20141I have a thing for maps and infrastructure: US bus and Amtrak routes

“Higher status people were also more likely to help themselves to candies that were intended for children”

Genetic determinism: why we never learn – and why it matters

Hits a little too close to home. If Harry Potter was submitted to an academic journal

Because no one uses Google+. Multi-platform use of social media

Ecology is everywhere. A living nest!

It’s been a good week for pretty pictures. The 2014 Sony World Photography Awards

Unexpected complexity in fMRI imaging

Heterogeneity increases group decision making. I talked about this a bit before on this blog.

Picture of the week

elephant“With four parameters I can fit an elephant, and with five I can make him wiggle his trunk.” – Enrico Fermi [initially misattributed to John von Neumann, sorry]

Tweet of the Week



Unrelated to all that, 2/1 edition

On the blog

I talked about a paper that attempts to sort out how animals communicate with others of their own species – and whether they might be listening to what other species have to say.

I also gave the lowdown on a debate on the Connectionist mailing list. Neuroscience today is attempting to understand planetary motions, kinematics, statistical mechanics, and quantum mechanics all at once. Let’s try a bunch of different things.

Then I was curious about what the most popular papers in neuroscience were. Hint: it’s all about humans and cognition. Because if there is one thing that people like, it’s thinking about themselves. I made the word cloud above from the most popular papers; here are the word clouds from the rest.

Finally, I let you know that the Boston Review is concerned with only the most important of questions: Are dogs people?


This is how I foresee the Superbowl turning out. Please don’t kill that dream.

Hidden hierarchy in string quartets

What does Google want with DeepMind? I had heard that they are essentially buying the company to buy the talent, not the product but take that with a grain of salt.

24 short films to watch

Great lab websites. Apparently more labs should use a WordPress template.

Truly an outstanding paper: “Background and aim:It is unclear how total sock ply and thickness are related when more than one sock is worn.”

A disguising of tailors, neverthriving of jugglers, sitting of judges, temperance of cooks, and a superfluity of nuns.

‘”I’m not very likely to get laid today, so instead I’ll fight with someone,” seems to be the thought pattern here.’

When has rigour in a computer science proof led to insight?

Is theory dead in Economics? Apparently not.

How farming reshaped our genomes.


Your weekly image:

Your weekly tweet:

Unrelated to all that, 12/6 edition

Can you believe it is December already?

On the blog

I addressed the difference between ‘learning socially’ and ‘social learning’. I find the idea that behavior can adapt without any direct learning occurring to be quite fascinating.

I also discussed how visual object recognition can improve when other modes of information, such as semantic concepts, are added.

Finally, I discovered that I am either a liar or a crackpot.


David Dobbs wrote an article titled ‘Die, selfish gene, die’. My impression was that the idea that he was attack was not the one that is presented in the book The Selfish Gene, but rather some kind of strawman. In fairness, Dobbs backtracked on his twitter pretty quickly and clarified his point by restricting it quite heavily. While the writing is undeniably great, the article itself is fairly misleading which leads me to wonder whether that makes it good or bad science writing? I was going to post on it, but my fear got the better of me and I decided I didn’t know enough evolutionary theory to feel comfortable attacking the article. Jerry Coyne does the job that I wanted to do, with more authority though probably also more venom.

See 100 years of breed ‘improvement’ (pictured above)

The average grade given at Harvard is an A, and one professor is ‘bravely’ fighting that grade inflation by giving a second private, meaningless, grade.

The role of genes in learning across species; a great new blog!

We are seriously defunding the NIH

A shepherd has 120 sheep and 5 dogs. How old is he? When kids are taught to a test, the problem-solving skills they develop are not necessarily the ones that you want them to.

This is a synaptic vesicle! It’s crazy busy

The Stanford Prison Experiment is widely cited, but remember that the average is not the whole: individual participants reacted in very distinct ways.

No, humans are not chimp-pig hybrids. Apparently that was a possibility?

Why do I always wake up 5 minutes before my alarm goes off? I find that I can do this on trips even when it is not my normal waking-time.

Upping your theory game. Something that neuroscientists really need to do.

In the journals

A multiplicative reinforcement learning model capturing learning dynamics and interindividual variability in mice (pubmed)

Optogenetic activation of an inhibitory network enhances feedforward functional connectivity in auditory cortex (doi)

Dietary choice behavior in Caenorhabditis elegans (doi)


Your weekly image:

Your weekly tweet:

Unrelated to all that, 11/22 edition

On the blog

I’ve been trying to find links to neuroscience, and economics/biology/ecology, resources for people who want to hear something serious. and the Stanford NeuroTalk podcast are both good, and I recently found this set of excellent talks from the NIH.

I discussed how ‘wise’ crowds are, and when that wisdom might fail. It is actually not straight-forward when you should listen to what other people have to say, despite what some in the Economics field thinks.

Whether or not neuroscience is ready for open, ultra-collaborative work is a big question. There are a couple of projects that would probably qualify for that title right now – those being Open Source Brain and OpenWorm – but the more I think about it the more I find that there is no good consensus of what are the big ‘open questions’ in neuroscience. I am beginning to wonder if a resource for collaboration over the internet might be a valuable product…

I also found a couple of cool links on how adaptable people are (and how difficult it is  to separate phenotype from genotype!) and how surprisingly fluorescent arthropods are.


Because it is known. Prophecy Sciences wants to use neuroscience to improve hiring/sports.

Dear traveller: please don’t think ill of us. We are the last generation. And we are immortal.

Probably a bad idea. Let’s not give this kid a billion dollars.

Let’s do all of it. Doing the things that you’re not supposed to do with Google glass. Can I say that I for one don’t understand the glass hate?

If you stay there too long, you won’t be the same. Are the Andes the most rapidly evolving place on the planet?

I can guess which numbers are even with 95% confidence. Why brains are not computers (ed: except maybe they are, they’re just doing different inference).

Because you want people to understand your stuff. On why engineers and scientists should be worried about color. Very worried.

In the journals

The intrinsic dimensionality of plant traits and its relevance to community ecology. DOI: 10.1111/1365-2745.12187

Toward a neural basis for social behavior. DOI: 10.1016/j.neuron.2013.10.038

Symmetry in hot-to-cold and cold-to-hot valuation gaps. DOI: 10.1177/0956797613502362

Spatial memory and animal movement. DOI: 10.1111/ele.12165


Your weekly image (the newly discovered ‘plant hopper’):

Your weekly tweet:

(Ignore this: 3YG65VYNY7MK )

Unrelated to all that, 9/27(ish) edition

Okay, I’m finally back from traveling and appeasing the various authorities in my life. That means I’ll be back to my regularly-scheduled programming. Meanwhile, links!

From the blog

David Hubel passed away, which was sad. But then Colin Camerer won a genius prize which is happy, but does not take away the sadness.

On other blogs

Is it fun to be a professor? Apparently, yes.

How to make better (cleaner) figures. A link to another link roundup, but the first item is too good to let go

Can math explain history? And a Q&A. This is something that I’d love to comment on but don’t feel like I have the historical background knowledge for any proper critique.

What it’s like to attend one of those spam conferences you (or, at least, I) get emails about.

On error bars.

The Emperor Gladwell is naked. Don’t click the link but do the google news method first!

These are the most cited papers in behavioral economics.

Tamarins whisper when they think they’re being overheard

Are male and female brains different, or are male brains just bigger (because males are bigger)?

In the journals

Interaction rules underlying group decisions in homing pigeons

Goats favor personal over social information in an experimental foraging task

On the sister blog

Bach was a thug and Mozart was pretty crude

A truly majestic animal

Context, people, context!

Some recent photo finds

Unrelated to all that, 9/20(ish) edition

I’ve been in beautiful Portland, Oregon the past few days for my Grandmother’s 100th (!) birthday. We’ve had several celebratory dinners and brunches; I’m completely exhausted yet my Grandmother keeps on truckin’. At one of the dinners there was a slideshow of pictures from her life and it’s almost unimaginable how much she’s seen; she grew up in rural Alberta (her mother at one point had a pet bear, no joke), and she remembers seeing the troops marching off to war in World War I and listening to the King’s Speech.

All of the cousins on that side of the family gathered together in one place for the first time in twenty years – we have lived pretty far apart, from all across the US to Canada (Vancouver) to Mexico to South Korea to the UK. Seeing everyone as adults for the first time, it’s striking how many similarities there are between children who have lived in pretty distinct families and environments. It makes me think there might be something to this whole genetics thing…

Anyway, here are your links for last week:

On the blog

I discussed some success from neuroscience, and why, though ‘bumpology’ in the popular press may not be informative, the science is useful to scientists.

I also posted a link to a classroom experiment designed to illustrate how trade may have developed. This is a great example of how economics should progress – experimentally – especially when one considers how sophisticated economic thought has been historically.

Additionally, there was a great paper that was recently published on how oxytocin can regulate social reward. As an addendum, it was pointed out to me on twitter that the serotonin receptor under discussion can sometimes be found on the postsynaptic glutamatergic (excitatory) cells; this is something I want to look into more.

Finally, I stirred up a bit of a fuss by accusing Gary Marcus of hating computational neuroscience. I’ll admit to being in a bit of an…ornery mood the morning I wrote that, and Gary pointed out that he, in fact, does not hate computational neuroscience. I think we have a difference of opinion on precisely what is an impressive advance in AI and what neuroscience has contributed to it. I’m working on a post going into that in more detail, so look out for that. I meant to try to have more of a discussion with him on it, but I’ve been surprised by how much I’ve had to do in lab and with my relatives…

On other blogs

Digging into the details, the Hot Hand does exist but it really sucks

The case of the disappearing teaspoons! An article from pubmed.

A freshwater flea, magnified

This has always been my favorite Calvin and Hobbes

How does fMRI work?

Is it possible to recover from a setback in academia like this?

Yelp for journals!

Medium seems like it’s just Kuro5hin remade (everything old is new again)

Dogs are perfectly happy to socialize with robots

Why the paradox of choice might be a myth

In the journals

Individual personalities predict social behaviour in wild networks of great tits (Parus major)

Nectar thieves influence reproductive fitness by altering behavior of nectar robbers [Mostly just an excellent title]

Sex differences in the influence of social context, salient social stimulation, and amphetamine on ultrasonic vocalizations in male and female prairie voles

Nucleus accumbens response to gains in reputation for the self relative to gains for others predicts social media use

Surprised at all the entropy: hippocampal, caudate and midbrain contributions to learning from prediction errors

On the sister blog

Tel Aviv has a fantastic street art scene, but my favorite work is from Broken Fingaz

Death metal robots!  That is all.

There are some bizarre and awesome subreddits out there, and these are a few that I would like you to know about

I found a really cool gif illustrating how a motor works, go look at it and be learned

What is happening in the Great Plains is tragic and scary

Dali and Bunuel made a movie. It was weird.

Advice for academics

Some 74 percent of professors aged 49-67 plan to delay retirement past age 65 or never retire at all, so let’s face it, you need help.  Here are some resources that will be update as I find them (or they’re pointed to me!).  This will be perma-linked in the upper right-hand corner!

Currently in no particular order (will organize later):

You and your research by Richard Hamming.  A classic which everyone should read.

Some modest advice for graduate students by Stephen C. Stearns

A survival guide to starting and finishing a PhD by Nathan Yau

How to get tenure at a major research university by Sean Carroll

Pro-tips for graduate students (especially in bio/statistics): parts one, two, and three

Choosing a PhD program: what’s important and what’s not and How to choose a PhD program

How to get into an animal behavior graduate program: an outline, getting good recommendation letters, and getting research experience

Having the courage to build your own non-academic career path by Carla Davidson

Getting the right kind of mentorship by Mark Christie

A Guide and Advice for Economists on the U.S. Junior Academic Job Market by John Cawley

Advice for Acadmic Authors by Kwan Choi

Writing Tips for Ph.D. Students by John Cochrane

Ph.D. Thesis Research: Where do I Start? by Don Davis

The Young Economist’s Guide to Professional Etiquette by Daniel Hamermesch

A Few Tips for Being a More Sucessful Graduate Student by Darren Lubotsky

How to Survive Your First Year of Graduate School in Economics by Matthew Pearson

Q&A: Experienced Advice for “Lost” Graduate Students in Economics by Ariel Rubinstein

Giving an Academic Talk by John Shewchuck

The Complete Guide to Getting into an Economics PhD program by Miles Kimball

How North American ecology faculty search committees work by Jeremy Fox

Sources: 1

Unrelated to all that (January 16th edition)

Wait, there’s a paper with ‘neuroecology’ in the title?  I’m sold! Well a review of a paper, really, but they did it better and more thoroughly than I could.

That’s…that’s a lot of dopamine and depression.  Scicurious has a series of articles on the link between dopamine and depression.

See schizophrenia isn’t all that bad, you should be thankful really.  And really, the culture that you live in shapes your schizophrenia.

See, being a psychopath isn’t all that bad, you should be thankful really.  This is more evidence for the importance of ‘neurodiversity’.

Maybe if they were psychopaths they just wouldn’t want more friends.  On the Dunbar number, and why we can only have so many friends.