The Mechanisms Underlying Grantsmanship are Not Fully Understood

I was editing one of the lab's papers today, and came across the classic grant/paper sentence, "The mechanisms underlying ... are not fully understood."  Do you ever see that sentence outside of science? So I went to Google Scholar and searched for "mechanisms underlying" and "not fully understood"  to find the first usage of it.

If you search for each term individually, you will find hundreds of references dating to the nineteenth century.  They were both common scientific phrases, but it took time for them to be combined.

If you search for the two phrases combined, the earliest link is to a book review from 1920, but skimming the document, I could not find either phrase.

The next reference comes from a 1950 paper, "THE SIGNIFICANCE OF THE "ONE-MINUTE" (PROMPT DIRECT REACTING) BILIRUBIN IN SERUM'," although they use each fragment in different sentences:

"The mechanisms underlying the renal excretion of bilirubin are still obscure." (I like that twist, I'm going to steal it.)

"The factors governing the speed of diazotization of bilirubin in serum are not fully understood."

It was not until 1962 that the full power of the phrase was unlocked almost simultaneously by two papers, "Physiology of acclimation to low temperature in poikilotherms:"

The degree of compensa- tion is different in different groups of animals (2, 3) and the mechanisms underlying this compensation are not fully understood.

 and "The inflammatory response to a foreign body within transplantable tumors."

This response seemingly lies in the stroma and, although mechanisms underlying the inflammatory reaction in normal tissues are not fully understood...

The science world would never be the same.

Do Whatcha Wanna*

While some PIs eventually learn to take pride in their "grantsmanship," I doubt anyone is happy with the grant system.  Nominal scientists spend their time trying to raise money rather than doing actual science.  We award grants based on people's paper trail, and then go tell them to teach, train, proselytize, and, oh yeah, publish.

I don't have a well thought out solution to the problem, but I do have a half-baked one: treat scientists like start-up companies.  My idea comes from two strains.

Cause it makes you smile if it sounds dope
When I read The Double Helix, the biggest surprise to me was that Watson and Crick discovered the structure of DNA as a side project.  They both were working on other projects - I can't remember what, but I think it had to do with invertebrates - and would sneak off together to try and piece together the crystallography data.  And Watson kept having to appease his advisor that his main project was indeed moving along, and apply for fellowships.

The lessons I took from this (and this is simplistic) are that people work best on things their interested in, and trying to make them work on a specific project is counterproductive. This may be my experience, but I know many people who toil away on mediocre projects when they yearn to do something else.** Yet, when we apply for grants, we make people write up specific projects that by definition may not yield interesting results. So what do we do if we stop writing grant proposals?

Scientists and startups
One of my favourite essayists is Paul Graham.  He's an angel investor (venture capitalist) who biannually runs a startup bootcamp to identify and train tech entrepeneurs.  When he decides whether to invest in a company, he almost ignores their business plan, because nascent companies constantly change plans.  What he focuses on are the founders, and he looks for specific traits: determination, flexibility, imagination, naughtiness, and friendship. Founding companies is extremely demanding, with a high failure rate.

Entrepreneurs and scientists share a lot of similarities.  They're both trying to do something new, which means exploring a lot of idea space, and modifying the plan as results come in.  They both have to overcome failure, whether it's experiments not working, or users not signing up. The rewards are asymmetric, with the best projects doing orders of magnitude better than the average. The best scientists and founders are not necessarily those that are the smartest, but the best hackers and hustlers.  And both groups waste a lot of time trying to raise money.

Ten years ago, venture capitalists evaluated startup companies the same way we evaluate grants today: they'd ask for a business plan, and then fund based on that.  But they've realized another model has better yield: ignore the business plan, and fund the founder.  My proposal is that scientists do the same.

Rather than have people spend weeks writing a fellowship, filled with scientific justification and wedged-in hyphotheses, let's run a scientist boot camp.  Take a month, send people off to Woods Hole (or wherever), and have them slap together a project.  See who stays up late.  See who tries something spectacular, fails, then whittles it down to something manageable.  See who hacks together a solution to a problem.  And fund them, for whatever the want to do, proposal unseen.

In the end, I don't think the cost is that high: some flights, a month's pay for the students, and a couple supervisors.  You'd save a lot of grant reviewers' time.  You'd build camaraderie between the students that may last as they venture back to their home institutes.  And you might end up funding successful scientists rather than people with good credentials.

(Having slept on this, I am downplaying the logistics  here.  For example, working with mouse models would be difficult in a one month course. But there are pretty common, useful mouse lines like Thy1-GFP/ChR2, and you could even try a BYOM system if the mouse quarantines were modified for the unique situation.)

*In honor of Treme.

** I realize even mediocre projects need resolution.  Sometimes its better, though, to just pull the plug.

A Walk Along the Paper Trail: A Cannabinoid Trail Mix

It's grant writing time here at the Paper Trail, which means reading lots of papers to cite in the background section of the grant.  I'm going to cover my favourite paper that I've discovered, which shows that endocannabinoids can directly modulate taste receptors.

More than meets the tongue


Flavour is a tricky perception.  It's obviously dominated by how things taste, but also influenced by olfaction, and internal states like hunger.  Recordings from rat gustatory cortex show that other sensory modalities are represented as well, like sensorimotor information from the tongue, or temperature.

While some of these modalities are directly encoded in cortex, others are represented indirectly, through hormones and neuromodulators.  The most famous of these is leptin.  Leptin is released by fat cells (adipose tissue), and is bound by leptin receptors in the hypothalamus and sweet taste bud cells (TBCs).  Leptin is an anorexigenic mediator, which means it suppresses appetite.  What's really cool is that leptin doesn't just act centrally:  if you record from TBCs in mice, you'll find that leptin decreases the firing of sweet TBCs.

The Munchies


In contrast to leptin, endocannabinoids are orexigenic mediators (appetite stimulants) that were known to work through CB₁ receptors in the hypothalamus and forebrain.  In the paper I'm covering today, Yoshida and colleagues showed that endocannabinoids (henceforward ECBs) can act orexigenically directly on sweet receptors themselves.


They started by recording from the taste nerve innervating the anterior tongue.  In wild type mice, the taste nerve responded to a variety of tastants, including NaCl, sucrose, quinine, etc (panel A, below).  To see the effects of ECBs, they injected the endocannabinoid 2-AG i.p., and again recorded from the taste nerve and found that 2-AG increased the response to sweet tastants  (panels A, B). They also tested the dose-dependence of 2-AG, and found it saturated at approximately 1mg/kg body weight.

Endoannabinoids increase sweet response; CB₁ -/- mice have no increase.
From Yoshida et. al. 2010.

Next they repeated the experiment in CB₁ knockout mice, and found that the knockout mice had normal responses to all tastants.  However, when they injected the ECBs, there was no increase in the sweet response. This shows that ECBs can enhance the sweet response, and that the CB₁ receptors are essential for that modulation.

To see the behavioural effects of ECBs, they measured how often the mice licked a liquid source.  To make the task more interesting, they mixed quinine (a bitter tastant) with sucrose at different concentrations.  At all the concentrations tested, the lick rate increased in mice injected with the ECBs.  CB₁ knockout mice, however, had no difference in lick rate.

Next, to verify that ECBs work directly on TBCs, they isolated TBCs and recorded from them directly.  They used a transgenic line that expressed GFP in sweet cells, under the promoter for T1r3 (expressed in umami cells as well). Using a glass microelectrode, they recorded extracellular action potentials from the isolated TBCs in response to sweet tastants (see below).  Then they bath applied 2-AG and found that the firing rate increased in response to sweet tastants.

2-AG enhances TBC response to sweet tastants.
From Yoshida et. al. 2010.

They tested the response over a variety of concentrations, and found the EC50 for 2-AG was 0.1 ug/mL.  They also verified the ECBs worked through the CB₁ receptor by applying antagonists against CB₁ and CB₂.  Only the CB₁ antagonists were able to block the ECB enhancement. In the final figure of the paper, they performed RT-PCR and immunostaining to verify CB₁ was present in sweet TBCs.

It's amazing to me how often the brain seems to modulate in depth.  There are endocannabinoid receptors on the tongue, and in the hypothalamus and forebrain.  And it occurs across modulators as well, as leptin is expressed in all these places.

While I jokingly titled the review "the munchies," the body expresses endogenous endocannabinoids, and these levels inversely correlate with leptin levels in the blood. And while the effects of endocannabinoids are obvious on the tongue, I don't think it is quite as clear in the brain.  It would be interesting to record from gustatory cortex while animals were under the influence of endocannabinoids to see how the representation changes.  You could sell it to the NIH under the drug addiction program.

Yoshida R, Ohkuri T, Jyotaki M, Yasuo T, Horio N, Yasumatsu K, Sanematsu K, Shigemura N, Yamamoto T, Margolskee RF, & Ninomiya Y (2010). Endocannabinoids selectively enhance sweet taste. Proceedings of the National Academy of Sciences of the United States of America, 107 (2), 935-9 PMID: 20080779

The Death and Life of Great American Neuroscience Department

Unless your university's name ends in "rd," your neuroscience department will inevitably go through boom and bust cycles. Washington University recently went through one, losing Rachel Wong, Josh Sanes, and Jeff Lichtman. Similarly, Cold Spring Harbor lost Zach Mainen, Holly Cline, Roberto Malinow, and Karel Svoboda. Those institutions are now trying to rebuild with young faculty like Daniel Kerschensteiner, Dinu Florin Albeanu, and Stephen Shea

When I started grad school at Duke, it was ranked in the top 10 neuroscience departments (whatever that's worth). Seven years later, it has dropped to ~ #20, and lost five senior faculty (with rumors of more).  And the department is now starting the rebuilding process by hiring a new chair, Stephen Lisberger.

Having lived through the death spiral of a department, I figured I'd write a post-mortem of what went wrong.  This will be a from the benches report, as I don't know what was said among faculty.

1. Insufficient leadership

Around the time I started grad school, the department appointed a new chair.  Rumor has it that the choice was between Larry Katz, and Miguel Nicolelis, but for personal reasons neither of them could be appointed chair.  So a third person was picked.

I've always been baffled by the business world's obsession with leadership, what makes a leader, how to identify leaders, etc.  I thought leadership was just another important aspect of business, like management, or logistics. Now, having experienced a leadership void, I can understand. As far as I could tell, the department had no direction, no focus of research, or any way to distinguish itself from other departments. I rarely received any e-mails from the chair, or any other senior scientist.* People just did their work, in whatever direction it happened to go.  Which leads to the next point.

2. Lack of community

Duke Neurobiology, rather than being a cohesive department, was just a collection of labs in the same building.  There were few collaborations between labs. People in the lab next door would publish exciting, high impact papers, and no one would know.  There was a happy hour on Friday's with intermittent attendance. The lunch room was in the corner of the building where only a few labs went to it.

I realize that community is an intangible thing, and won't make up for deficiencies in intelligence or dedication.  And that other neuroscience departments may not have communities either.  But after reading Peopleware, and reading about teams of people working towards a common goal, I feel something was missing.  Simple things like centralized lunch rooms, or quarterly e-mails about papers from the department would have gone some way towards making people part of a group rather than data machines stuck to a desk.

3. No forward momentum

Science is a Red Queen race. In order to maintain your standing in the wider community, you need to continually improve: incorporating new techniques, trying new systems, asking new questions. For a department, this usually takes the form of hiring new faculty. Duke tried to do that, and held faculty searches four years in a row, looking for both junior and senior faculty.  Which resulted in one junior hire.

The inevitable result of this was that once the department stopped growing, it immediately started shrinking. Senior faculty were continually getting propositioned by other departments until one offer was good enough. And each faculty that left made it easier for the next to leave.

4. No money

Duke, as a "young" university, has a small endowment compared to other institutions. There are relatively few sponsored professorships for senior faculty. Other departments that go through boom/bust cycles are in similar positions, where they can hire young faculty, but can't match offers to retain them.  I have some Moneyball-style ideas for how a department can compete by hiring under-appreciated scientists, but that's for another blog post.


In the press release announcing Lisberger as the new chair, Lisberger said all the right things:

“I look forward to bringing excellent young scientists to the Department of Neurobiology. I hope that graduate training in Neurobiology can become a focus of the institution and will strive to help the neuroscience community achieve a level of interaction that makes the whole much greater than the sum of the parts."

Hopefully he can turn things around, and improve the brand of my degree.  It can only go up from here.

* Rumor also has it that the chair asked songbird and primate researchers whether they could switch model systems to mice.

A Walk Along the Paper Trail: Bitter Trail Mix

While my previous walks along the paper trail have focused mainly on olfaction, my ultimate goal is to study taste perception.  Since the last few walks have been about olfactory receptors, I figure it would be natural to transition to taste receptors.

Unlike olfaction, where it is difficult to correlate percepts like "floral" or "rotten" with individual receptors, the correlation is much easier for taste perception.  Taste receptors have been identified most of the major taste percepts: sweet, bitter, salty, and umami (there are some additional receptors for properties like carbonation and water, but those are considered secondary). The receptors for sweet, bitter, and umami are all G-protein coupled receptors (GPCRs), while sodium is detected by ENaCs.  The one percept that remains somewhat elusive is sourness, where a TRP channel PKD2L1 and a carbonic anhydrase CAR4 which are expressed in sour sensing taste cells, but the full mechanism remains unclear.

Given that background, today I'm going to (read and) review the first paper to report taste receptor activation.

Cyclohexi...blegh


The bitter receptors (T2R) were reported almost simultaneously by the Buck and Zuker labs in March and April of 2000 (I bet there's an interesting story of that race somewhere). Besides listing a bunch of receptors, these papers also found that bitter receptors are all coexpressed in the same cells, and that there is no receptor pattern on the tongue.  The Zuker lab also published an accompanying paper by Chandrashekar et. al. where they showed that individual receptors respond to different bitter compounds.

For Chandrashekar and colleagues to study the T2Rs, they needed to establish an in vitro system, but given that they just discovered the receptors, they didn't know the downstream signaling proteins (at least until the end of the paper).  To get around this they used a G-protein which binds to a broad range of GPCRs, Ga15.  They then expressed individual T2Rs with Ga15 in HEK-293T cells and measured the calcium response following tastant application.

Using this system, they screened a random set of human, rat, and mouse T2Rs against a set of 55 tastants. From this entire screen they reported three responsive T2R-tastant pairs. (They surprisingly don't report this entire response profile. And it's not like supplemental info didn't exist in 2000.)  The pair they focused on is mouse T2R-5, which responds selectively to cycloheximine (panel b, below).

mT2R-5 responds to cyclohexamine. From Chandrashekar et. al. 2000.

They "characterized" the response as having a fast rise time of <1s, which desensitizes within 10s (panel a, above).  They also noted that repeated application of cycloheximine caused smaller Ca²⁺ rises, showing there was desensitization.

Thirty years ago, researchers found that different strains of mice have different bitter sensitivities.  For example, C57 mice don't avoid cyclohexamine while DBA/2J mice do.  Chandrashekar sequenced the mT2R-5s for multiple strains of mice, categorizing the receptors as "tasters" (from mice which could taste cycloheximine) and "non-tasters." The non-taster mT2R-5s had three mutations, including a missense mutation, and when they transfected HEK cells with the non-taster mT2R-5, they found it had a lower sensitivity to cycloheximine (panel d).

In the final section of the paper they fingered gustducin as the G-protein that couples to T2R.  To do this they used a cell-free system, using membranes with mT2R-5, and measured how much gustducin was bound to the membrane.  They found gustducin selectively bound to mT2R-5 in the presence of cycloheximine (top panel), and the K_d of the system was similar to what they found in HEK cells (compare panel b below to panel d above).

Gustducin (GTPyS) binds to mT2R-5 in presence of  cycloheximine. From Chandrashekar et. al. 2000.

And that's the paper.  It's still kinda shocking to me that it took until the year 2000 for just a subset of the taste receptors to be identified. They're right there, on the tongue!  I also appreciated the cleverness of using Ga15 to allow them to record tastant responses (although this trick may be standard in molecular biology).

One problem I have with this paper is that it does not seem very... thorough.  For example, they did not report all their tastant-odorant responses, and from skimming Zuker's later papers they did not report them there either.  Or when they characterized the response, they didn't report a tau for the on or off phases. I realize these numbers may not be completely accurate, but I still want to know them.

My legs are a bit tired from this trek, so I'll stop here.  There's a lot more to know about bitter receptors, for example many people have looked at how different polymorphisms in mammals can effect perception. But that is for another time.

CHANDRASHEKAR, J., Ken L Mueller1, Mark A Hoon2, Elliot Adler2, Luxin Feng3, Wei Guo1, Charles S Zuker1, §, *, and Nicholas J.P Ryba2, § (2000). T2Rs Function as Bitter Taste Receptors Cell, 100 (6), 703-711 DOI: 10.1016/S0092-8674(00)80706-0