Who is getting hired in neuroscience?

I am always a bit jealous by how organized the field of academic economics is when compared to, well, anyone else. To get an academic job, young economists put up their one “job paper” into some sort of database for prospective employers to evaluate (also, they do not do postdocs). This gives them a large dataset to analyze. fivethirtyeight has a nice analysis of what the people looking for an academic economics job are working on (there’s more in the link):

Neuroscience does not have an equivalent database, unfortunately. But I do run the neurorumblr, which aggregates neuroscience faculty job postings. They often break down what type of research they are looking for candidates to accomplish into broad categories. There are currently ~95 job postings: here is what they are looking for.

Neuroscience jobs
I was surprised by the number of computational positions; a large chunk of them are computational and cognitive which leads me to think they may be EEG/fMRI postings? I’m not sure.

Also, “cognitive” is the new “psychology”.

 

Why is reporting on health and science so bad? Because the reporters can’t do their jobs.

Imagine this scenario: a sports reporter is asked to cover an emerging conflict in the Middle East. The sports reporter, never particularly keen on international affairs, is on a deadline and looks to see what they can use. There’s in-person video of the central events in question, but our journalist friend doesn’t have the necessary background or context to fully understand what happened. Is there something else? A press release from the US government and from one side of the conflict in the Middle East? Sounds like our sportsman is good to go! Just copy and paste the exciting bits, add in the little bit of context that our intrepid soul already has, and bingo. News has been reported!

Later, it turns out that our poor reporter has been duped! The press release from the Middle East was nothing but PR, empty words of propaganda to make things seem more important and interesting than they really are! Our friend from the sports section sighs, wishing he had asked someone who knew about this kind of thing who would have known what to look out for.

In a similar vein, Vox has an article asking why so many articles on health (and, let’s admit it, science) are junk. The culprit is identified as clearly as in our example above: coverage by those who don’t know, or don’t care. See:

The researchers found that university press offices were a major source of overhype: over one-third of press releases contained either exaggerated claims of causation (when the study itself only suggested correlation), unwarranted implications about animal studies for people, or unfounded health advice.

…When a press release included actual health advice, 58 percent of the related news articles would do so too (even if the actual study did no such thing). When a press release confused correlation with causation, 81 percent of related news articles would. And when press releases made unwarranted inferences about animal studies, 86 percent of the journalistic coverage did, too.

…Unfortunately, however, this isn’t a perfect world. Many journalists are often covering science in the morning, and the courts in the afternoon. We are under heavy pressure to meet multiple deadlines every day, and some of us lack the time, sources, or background to properly vet the studies we’re reporting on.

So we rely on scientists and on press offices to guide us through research, even though, clearly, we shouldn’t.

Wait – what? The problem is the scientists and press offices? Because reporters are too overworked or unqualified to do their job properly? It sounds from the quote above that reporters are just parroting what a press release says without actually reading the source material. It sounds like reporters aren’t doing their jobs. But rather than accept the blame, they are trying to avoid the responsibility.

Unless I am mistaken, the job of a journalist is not to overlay press releases with a thin veneer of impartiality. Their job is to synthesize new information with their existing bank of expertise in order to convey to a naive audience what is or isn’t novel or important. Conversely, the job of a PR department – which derives from the incentive structure – is quite clearly to hype new research. Does anyone think that a press release from a corporation is written to be as truthful as possible, rather than putting as good of a spin on it as possible?

If the reporter knew enough about the field, they would be able to check whether or not the things they were writing were true. Where in the paper does it say this correlation exists? Is there an exaggeration? How much?

If they are unable to do that, what are they doing? Why should I read science or health journalism if they are unable to discern fact from fiction?

Monday open question: Which neuroscientists have most influenced your thinking?

With the release of the NIH BRAIN Initiative grants, it’s become clear that there’s a big disconnect between members of the different subfields: people working molecular neuroscience, cognitive neuroscience, systems neuroscience, etc. I’m just as bad as anyone else so I thought it may be useful to know who are the, say, five most important influences to their work?

For me, the names would have to be (in no particular order):

1. Eve Marder

2. Bill Bialek

3. Rachel Wilson

4. Krishna Shenoy/Mark Churchland

5. Cori Bargmann

Nobel Prizes in Neuroscience (Updated)

After O’Keefe and the Mosers winning the Nobel prize this year, I was wondering how many of the prizes have been for neuroscience research (directly). From the full list, these seem to be the winners:

  1. The Nobel Prize in Physiology or Medicine 2014
    John O’Keefe, May-Britt Moser and Edvard I. Moser
    “for their discoveries of cells that constitute a positioning system in the brain”
  2. The Nobel Prize in Physiology or Medicine 2013
    James E. Rothman, Randy W. Schekman and Thomas C. Südhof
    “for their discoveries of machinery regulating vesicle traffic, a major transport system in our cells”
  3. The Nobel Prize in Physiology or Medicine 2004
    Richard Axel and Linda B. Buck
    “for their discoveries of odorant receptors and the organization of the olfactory system”
  4. The Nobel Prize in Physiology or Medicine 2000
    Arvid Carlsson, Paul Greengard and Eric R. Kandel
    “for their discoveries concerning signal transduction in the nervous system”
  5. The Nobel Prize in Physiology or Medicine 1991
    Erwin Neher and Bert Sakmann
    “for their discoveries concerning the function of single ion channels in cells”
  6. The Nobel Prize in Physiology or Medicine 1981
    Roger W. Sperry
    “for his discoveries concerning the functional specialization of the cerebral hemispheres”
    David H. Hubel and Torsten N. Wiesel
    “for their discoveries concerning information processing in the visual system”
  7. The Nobel Prize in Physiology or Medicine 1977
    Roger Guillemin and Andrew V. Schally
    “for their discoveries concerning the peptide hormone production of the brain”
    Rosalyn Yalow
    “for the development of radioimmunoassays of peptide hormones”
  8. The Nobel Prize in Physiology or Medicine 1973
    Karl von Frisch, Konrad Lorenz and Nikolaas Tinbergen
    “for their discoveries concerning organization and elicitation of individual and social behaviour patterns”
  9. The Nobel Prize in Physiology or Medicine 1971
    Earl W. Sutherland, Jr.
    “for his discoveries concerning the mechanisms of the action of hormones”
  10. The Nobel Prize in Physiology or Medicine 1970
    Sir Bernard Katz, Ulf von Euler and Julius Axelrod
    “for their discoveries concerning the humoral transmittors in the nerve terminals and the mechanism for their storage, release and inactivation”
  11. The Nobel Prize in Physiology or Medicine 1963
    Sir John Carew Eccles, Alan Lloyd Hodgkin and Andrew Fielding Huxley
    “for their discoveries concerning the ionic mechanisms involved in excitation and inhibition in the peripheral and central portions of the nerve cell membrane”
  12. The Nobel Prize in Physiology or Medicine 1961
    Georg von Békésy
    “for his discoveries of the physical mechanism of stimulation within the cochlea”
  13. The Nobel Prize in Physiology or Medicine 1950
    Edward Calvin Kendall, Tadeus Reichstein and Philip Showalter Hench
    “for their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects”
  14. The Nobel Prize in Physiology or Medicine 1949
    Walter Rudolf Hess
    “for his discovery of the functional organization of the interbrain as a coordinator of the activities of the internal organs”
    Antonio Caetano de Abreu Freire Egas Moniz
    “for his discovery of the therapeutic value of leucotomy in certain psychoses”
  15. The Nobel Prize in Physiology or Medicine 1947
    Carl Ferdinand Cori and Gerty Theresa Cori, née Radnitz
    “for their discovery of the course of the catalytic conversion of glycogen”
    Bernardo Alberto Houssay
    “for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar”
  16. The Nobel Prize in Physiology or Medicine 1944
    Joseph Erlanger and Herbert Spencer Gasser
    “for their discoveries relating to the highly differentiated functions of single nerve fibres”
  17. The Nobel Prize in Physiology or Medicine 1936
    Sir Henry Hallett Dale and Otto Loewi
    “for their discoveries relating to chemical transmission of nerve impulses”
  18. The Nobel Prize in Physiology or Medicine 1932
    Sir Charles Scott Sherrington and Edgar Douglas Adrian
    “for their discoveries regarding the functions of neurons”
  19. The Nobel Prize in Physiology or Medicine 1906
    Camillo Golgi and Santiago Ramón y Cajal
    “in recognition of their work on the structure of the nervous system”
  20. The Nobel Prize in Physiology or Medicine 1904
    Ivan Petrovich Pavlov
    “in recognition of his work on the physiology of digestion, through which knowledge on vital aspects of the subject has been transformed and enlarged”

16.2% 19% of the awards have gone to neuroscience!

One thing that struck me is how many names I don’t know, especially for people who, apparently, did really foundational work. I need to bone up on my history of neuroscience. Also, neuroscientists, don’t expect another award for ~7-8 years (*coughDeisserothBoydencough*).

*I’m including the 1973 prize as the (lone?! update: Pavlov!) psychology prize. Not sure whether to include the 1994 prize for GPCRs?

Updated: As commenter alf pointed out, I forgot Golgi and Ramon y Cajal! Which is depressing. And he’s right, last year’s work on vesicular transport could largely be seen as a neuroscientific prize.

Also Pavlov, because of the weird way the committee described his work.

Monday open question: How long will it take to “solve” the brain?

Let’s do a quick calculation…

At the largest neuroscience conference, SfN, there are maybe 30,000 scientists who show up. Let’s pretend that this is about 1/3 of all neuroscientists (probably an underestimate) so we get 100,000 of us suckers.

Now let’s pretend we could assign each one of them a neuron that we wanted them to study. And let’s pretend that we were going to try to understand mice because, well, why not. There are ~71,000,000 neurons in the mouse brain according to Wikipedia.

This means that the mouse has about 700 neurons per neuroscientist.

There are ~10^11 synapses in the mouse brain, or about 1400 per neuron. That means there are roughly 980,000 synapses per neuroscientist.

Additionally, inside of each neuron is a whole bunch of molecular machinery that we don’t understand. Here is a simplified schematic of one of these pathways (dopamine):

molecular pathways

I have no idea how many of these pathways there are, nor how they interact. They’re kind of complicated.

Now let’s go up a step and remember that you can’t study a neuron in isolation because you have no idea what it’s inputs are or what it is outputting to. So now we need people to investigate sets of networks. And how those networks interact with each other. And how that interaction affects the physical world. And so on.

And all this is just for a mouse.

Whenever you hear, “but we’ve been studying [Alzheimers/Parkinsons/anything else] for thirty years!” remember what we’re dealing with.

The only way we can understand the mammalian brain without precisely measuring every single step of this is to find regularities and make theoretical models that can generalize from what we know to make predictions about other parts of the system. Otherwise, the hope of “understanding the brain” at all in our lifetimes is hopeless.

 

 

The beauty of brain science

hippocampus

Photo by Jason Snyder

There has recently been a few articles on a “theory of the brain”. Gary Marcus started us off with an editorial in the NYT concerning the Blue Brain Project:

Biologists — neuroscientists included — can’t hope for that kind of theory. Biology isn’t elegant the way physics appears to be. The living world is bursting with variety and unpredictable complexity, because biology is the product of historical accidents, with species solving problems based on happenstance that leads them down one evolutionary road rather than another.

Vaughan Bell had a good commentary:

This reflects a common belief in cognitive science that there is a ‘missing law’ to be discovered that will tell us how mind and brain are linked – but it is quite possible there just isn’t one to be discovered.

And around the same time Neuroskeptic reviewed a paper on a similar topic, asking how we reconcile single neuron views of information transfer with network (oscillatory) views).

I take issue with the idea that neuroscientists can’t hope for beautiful theories of the brain. Just look at that picture of the hippocampus above! Does this look like a disheveled, random assortment of neurons to you? The brain is just bursting with structure – but the tools and investigations into that structure are too young to know everything about it. So far.

I wrote a piece on Medium (because it formats purty pictures well) on the beauty of the brain, and what a ‘theory of the brain’ would mean:

At first glance, the brain is a mess. More like a tangled ball of yarn than a finely woven tapestry, every combination of neuron-to-neuron is in there, somewhere. Yet look a little closer and this complex structure devolves into very clear regularity. I could take you on a tour of the waves of Purkinje cells, straight-backed like military men, reaching their arms out to passing fibers shooting up from a distant province. I could show you the shapes of the hippocampus where memories are created, messages washing down step by step. I could show you the round columns of barrel cortex, clear to your eye, that precisely mirrors the pattern of whiskers that eventually stimulate them. There is so much visible structure in here that we’re still attempting to unlock.

The points I was trying to make are:

  1. Brain science is super young! There’s still tons to know
  2. We actually do have some pretty good candidates for theories of the brain, though the list is far from complete
  3. One key to creating any theory is to understand the boundary conditions, ie the physical constants and constraints on the system. This is as true in Physics as it is in Biology, and we’re very far from understanding them (note also: this is a big problem with Blue Brain – it’s just an epileptic cortical column with no inputs!)
  4. A ‘theory of the brain’ will ultimately be meaningless, or pointless. It won’t tell us what we want to know; rather, we will need multiple overlapping theories for them to have any use.

Stem cell scientist Sasai commits suicide

Yesterday, it appears that stem cell scientist Yoshiki Sasai committed suicide. Sasai, as head investigator, was involved in the recent stem-cell paper retraction though he did not appear to have been a part of the fraud itself:

He titled his missive, “Apology regarding the paper retractions.” He wrote: “I am deeply ashamed of the fact that two papers of which I am an author were found to contain multiple errors and, as a result, had to be retracted.”

Part of what so shamed him, he said, was his failure as a mentor. “As a deputy director of our center, with responsibility for nurturing young researchers, I feel a deep responsibility for what has happened…”

Sasai was devastated by the retraction, saying in his letter that “it has become increasingly difficult to call the STAP phenomenon even a promising hypothesis.”

But Obokata hasn’t given up. She’s trying to replicate the research under video surveillance at the same institution where Sasai apparently committed suicide.

There are two really good comments on this tragedy so far. The first is a deeply personal story from Michael Eisen:

I don’t know all of the details, but the parallels between the two cases are haunting. As was the case with my father, it does not seem like anyone thinks Sasai was involved in the fraud. But as the senior scientists involved, both Sasai and my father bore the brunt of the institutional criticism, and both seem to have been far more disturbed by it than the people who actually committed the fraud.

It is impossible to know why they both responded to situations where they apparently did nothing wrong by killing themselves. But it is hard for me not to place at least part of the blame on the way the scientific community responds to scientific misconduct.

Read it and think about it. In a similar vein, rxnm on the pressures that cause this misconduct:

And what about everyone else? Journals, colleagues, scientists, journalists? Do we really need hero narratives? The splashy results that will “change everything”? The hype machine it is out of fucking control. We are adopting the language of biz-speak bullshit and starting to buy into these empty non-values about techno-utopian revolutionaries and lone geniuses. We all participate in the culture of valuing glam, prestige, prizes. Who gets the 8-figure grants while everyone else struggles to stay afloat? Who can I get a selfie with at SfN? Who gets to stamp their name all over the culmination of decades of work by hundreds or thousands? We’ve become cultish: around people, journals, technologies, institutions. As if these are things that matter more than the colleagues around us, or our own integrity. It’s pathetic, and we can be better.

Why would robots have heads?

Or conversely, why is your head near your brain? Sensory organs came before or after cephalization? In other words, do we have a head because it is advantageous to be able to respond quickly to quickly changing incoming sensations (vision, audition)?

This is interesting:

However, flatworms differ from more advanced animals in that their mouths are in the center of their bodies, not at the anterior end.

 

“The members of the HBP are saddened by the open letter posted on neurofuture.eu” (updated x2)

Truly, the Human Brain Project has become sad 😦 Here is their response to the neurofuture petition that I talked about on Monday (in PDF only, for some reason):

The members of the HBP are saddened by the open letter posted on neurofuture.eu on 7 July 2014, as we feel that it divides rather than unifies our efforts to understand the brain. However, we recognize that the signatories have important concerns about the project…

What are the concerns of the open letter? The open letter expresses the concern that these goals are so unrealistic that they will damage all of neuroscience, and states that not enough is known to take on such a challenge. We share this uncertainty. However we contend that no one really knows how much neuroscience data is currently available because it has never been organized, and that no-one even knows how much data is needed to begin such an endeavour. Reconstructing and simulating the human brain is a vision, a target; the benefits will come from the technology needed to get there. That technology, developed by the HBP, will benefit all of neuroscience as well as related fields. Many other areas of science have demonstrated that simulation can be a tool to create new knowledge, not just to confirm existing results.

Take that for what you will; it’s a fairly corporate/academic response. Meanwhile, neurofuture has a comments section which is fairly interesting. Here are some good ones:


The first is scientific: the leadership of the Human Brain Project has no experience in creating mathematical formalisms for representation of dynamical systems on multiple temporal and spatial scales. Without such formalisms, it is very unlikely that the complexity of neural models will be manageable, and the existing ad-hoc methods for modeling will remain firmly in place. The project statement on "Mathematical and Theoretical Foundations of Brain Research" claims that the theoretical research will magically come from "outside" the Human Brain Project but this appears to be mostly magical thinking. The current organization structure makes it obvious that independent thought from outside cannot possibly penetrate the upper echelons of power of the Human Brain Project. Which brings me to my second point. The second issue is organizational: the Blue Brain Project has earned a reputation of secrecy and extremely hierarchical authoritarian approach to scientific management, which suggests that rather than the stated goal of unbiased and objective collection of data and tools, the project is likely to result in promoting the agendas and pet project of a small group of people at the top of the hierarchy. There simply is no evidence for an open-minded and exploratory culture in the existing Blue Brain Project, and there is no chance for such culture to emerge without a complete remake of the organization structure, from pyramid to a flat decentralized structure. Without a way to promote diversity in thinking, the Human Brain Project will mostly be about control and power, rather than any meaningful scientific goals.

July 7, 2014, 2:07 p.m.
Ivan Raikov. Okinawa Institute of Science and Technology. Japan


Research on the human brain of this magnitude should be inclusive of all approaches and technologies that have been providing advancements on understanding the brain. The current suggested approach of a bottom up simulation is akin to trying to understand the laws of gases by simulating the collisions of an Avogadro number (6.022×10^{23}) of particles. This is unnecessary and also fruitless: there was thermodynamics before statistical mechanics and even the latter does not derive the laws of gases from simulations; it uses first principles, validated against the phenomenological theory of thermodynamics. For the brain, the approach should also be two-pronged: a top-down (from function and behavior to structure)-- "the thermodynamics" part, and a bottom up (neuronal level interactions)-- the "statistical mechanics" part. Simulations aid both directions, but they are only useful within the context of experimental evidence.

July 7, 2014, 9:40 p.m.
Zoltan Toroczkai. University of Notre Dame. United States

Personally, I considered applying to one of the partner-projects, but found the goal to be unclear and the decision process to be absolutely not independent, I therefore considered this would be a pure waste of time. If Europe wants to move on in this area of research, then they do not only need to focus on learning more about the human brain, but also using it to do something useful with. Generally, a lot of this work is done at a very low level, while higher level understanding may be sufficient to do other things with, e.g. neural networks have been around for ages, while we actually don't properly understand how they work in the brain. There are however other models of the how the human brain works that are at a higher level and seem to work pretty well. The project should cover more work that is around using the outcomes of or deals with creating a human brain without making a one-by-one copy of the brain itself, while still offering the same functionality.

July 8, 2014, 9:23 a.m.
Wim Melis. University of Greenwich. United Kingdom

It is surprising that in a project whose goals are to simulate the human brain, a developmental part is totally missing. Thinking that the long childhood observed in the human species has nothing to do with the cognitive success of this species is neglecting one of the main characteristic of the studied species and of its "educated" brain. This lack of developmental studies, both in humans and animals, reveals a major scientific flaw. It misses the opportunity to understand the organizing principles of the human brain and its specificities compared to other animals, and to develop new learning algorithms based on the understanding of the mechanisms used by the fantastic learner who is the human child. 
Furthermore given the clinical and societal issues pushed forward to justify HBP, it is a strategic mistake not to include developmental studies as numerous neurologic and psychiatric diseases have their origin during development (e.g. drug addiction, autism, schizophrenia, epilepsia), and consequences of preterm births (6 to 10% of births, 15 million babies each year in the world) and of other brain insults, neural and cognitive developmental deficits (global and specific), impact of low SES on cognitive development are concerning an important percentage of our fellow citizens (e.g. 20% of the young adults are described as non-efficient readers in national French evaluations!) preventing them to obtain a correct and stable work.  Without research on human and animal brain development, it is doubtful that solutions for these problems will be proposed whereas the economic impact in the EU (and elsewhere) is huge.
Finally giving up on data acquisition is a huge mistake when the recent development of non-invasive brain imaging techniques just unlocks the access to the child brain revealing unexpected results (e.g frontal activation in infants, no specific activation to faces in the fusiform gyrus until late childhood), pointing to our ignorance of even the simplest principles which might explain how an assembly of cells can give rise to thoughts.

July 9, 2014, 7:57 a.m.
Ghislaine Dehaene-Lambertz. INSERM. France

Update: via Prerana Shresthra, there are a couple of other good explanations of the problems some have with the Human Brain Project on Quora:

One of the big dreams of my life are to eventually simulate brains, so a priori I love the idea. Here I will just list some of my objections. I do not speak for anyone else and do not claim full knowledge about the HBP. But I have been following the publicly visible parts for a while. I believe that it is premature because

1) We lack the knowledge needed to build meaningful bottom up models and I will just give a few examples:
a) We know something about a small number of synapses but not how they interact
b) We know something about a small number of cell types, but not about the full multimodal statistics (genes, connectivity, physiology)
c) We know something about a small number of cell-cell connections, but a tiny fraction of all the existing ones
d) We know a few things about how a neuron’s dynamics relates to its inputs, but only for a tiny number of cells and conditions.
e) We know a few aspects of a few neurons that change over time, but again for a tiny number of cells and conditions.
The degree of the lack of knowledge is mindboggling. There are far more neurons in the brain than people on the planet. Any planned bottom-up simulations of the human brain are akin to simulating the entire human society on the planet based on say a random 100,000 word documents sampled from the internet. For simulations, the output is only as good as the knowledge about the system that you put in. Hence, large scale simulations are bound to lead to poor results. In my judgment, the data will not become available in sufficient amounts before the termination of the HBP.

…Understanding the brain is different than going to the moon. We knew where the moon was. We do not know how a simulation of the brain should look like. Any simulation techniques developed at the moment may end up being useless for the kinds of models of the brain that we will eventually need.

(and there’s more!) Go visit Quora to see the rest.

Update the second: Neuroskeptic has a good interview with Zach Mainen, the man responsible for organizing the Neurofuture petition.

Monday open question: What have you read that inspired you in science?

In a twitter discussion of inspirational scientists, I realized that a more interesting question was whether other scientists had particular papers or books that had profoundly inspired them.

For very young me, the answer would clearly have been Jurassic Park. This made me want to do science to the extent that several friends and I found a microscope and had one of us (not me) pick their nose until it bled so that we could look at the DNA in the blood, with grand visions of cloning near at hand. Needless to say, this did not work – it turns out that you can’t see DNA under a 40x microscope.

More near at hand, the text that continues to fascinate and inspire me is a book by Joshua Epstein and Robert Axtell, Growing Artificial Societies. This presents a simulation of behaving agents in a land called the Sugarscape. Epstein and Axtell then try to show what happens as these agents live and die in this brutal land. The idea that one could simulate the rules of life and use it to understand how living creatures create societies was breathtaking to me – much more so than something so abstract as Conway’s Game of Life. To this day, that is why I want to understand the clockwork neuroscience that drives organisms as they interact with each other and the ecological environment.

A suggestion by someone else was David Marr‘s Vision: A computational investigation into the human representation and processing of visual information. Marr died of leukemia tragically young, but his sketch of how to attack the problem vision is still considered fundamental. Here are some selections from the book and reading it one is left 35 years later marveling at the intellect behind it.

So what readings have influenced you? I want to read them!