2014 Nobel Prize in Chemistry Hijacked by Physicists

This year, all three laureates are physicists!  All three earned their doctoral degrees in physics, after all.   And 'super-resolved fluorescence microscopy' - come on, that doesn't sound chemical at all! 

Where is the outrage? 

:) Read more!

Chiming in with a #ChemCoach entry

Here's my contribution to the ChemCoach Carnival, for what it's worth.


Your current job.

I am a postdoc in an actual chemistry department on the East Coast (USA) doing a mix of physical chemistry, biochemistry, and spectroscopy, along with dashes of molecular biology, computation, and misery. 

What you do in a standard "work day."

No such thing as a standard work day for me -  I'm presently slogging through heaps of molecular biology in order to validate a protocol for producing uniformly 13C/15N labeled protein (mostly since my PI isn't yet comfortable with how we do things in the 21st century).  Earlier this year, for example, I was doing everything from NMR on inorganic solids (after effecting some probe repairs on my own) as well as some p. chem. of lipid mixtures, in addition to protein NMR (solution and solid state). 

What kind of schooling / training / experience helped you get there?

 I was a biochem/chem undergrad (did my undergrad research in a biophysics lab - lasers and magnets, what more could one wish for?) and did my Ph.D. in an honest-to-Buddha chemistry department, doing biophysical chemistry.  I was briefly diverted into a year at a cancer research institute doing biophysics/soft matter-oriented work (that was a trip, let me tell you), but returned to my chemical roots. 

How does chemistry inform your work?

Just the other day I was trying to get this horrendous mix of inorganic chemicals to go into and stay in solution, actually - and people say there is no chemistry in biochemistry!  Heh.   My perspective on many of my scientific interests is rooted in my chemical background - for example, signal transduction could be translated as essentially controlling the rates of chemical reactions across interfaces, after all.  It's a rather essential component of what I do on a daily basis.

Finally, a unique, interesting, or funny anecdote about your career

I was at a conference where I spoke to the colleague of this scientist who had written a paper I had read and digested multiple times, as it was extremely germane to my interests.  He noted that said scientist had never followed up on this particular aspect since they found that obtaining reproducible data was far too tricky.  I should have realized then that my project might have been a bit ambitious, but I persevered and did manage to get reproducible data.  It just took another 2.5 years on top of the 2 years I had spent working on said project.....  Read more!

To The Classroom!

A recent post at Chemiotics sparked some old, dimly remembered memories from my grad school days as a gen. chem. TA leading weekly discussion sections.

Now, general chemistry is, from what I can figure, is a slightly different beast than organic chemistry.  At the universities I attended, the class was also a requirement for physical science and engineering majors, and could make up a substantial fraction of the class given the strength of the engineering programs at my alma maters.  Organic chemistry tended to draw from a smaller student pool - outside of the legion of premeds, it was populated by those with chemistry & biological science majors, as well as the expected chemical/materials engineering students. 

Back to general chemistry - this situation leads to walking an incredibly tricky path so as to keep the material interesting, relevant, and not too off-putting to anyone in the audience.  In short, no one is entirely happy with things, but one might consider that a sign that everyone is getting what they need in the final accounting, although not necessarily what they'd prefer. I'll be a bit obnoxious as usual here and suggest that gen. chem. can be an opportunity to demonstrate chemistry's status as the central science to a diverse audience, if done well. 

Back to the premed issue, though - I think what perturbed many of us is the attitude that arises in a class with a significant premed population.  I won't belabor this point with various horror stories (as we all have them), but, for example, the majority of the "point lawyering" I experienced was from premedical students.  In all of those cases I can still remember/wrote down for the record, none of them involved an actual grade breakpoint (e.g., they were nowhere near the boundary that would have resulted in a different overall final grade).

Of course, perhaps what we need is a different model for medical education.   Or maybe not.  Perhaps what we need is to be reminded of the difference between education and training.  Learning about something that may not be transparently applicable to your post-university career plans is not the end of the world.  A radical idea, I know. 

Obligatory mention - congratulations to the new Nobel laureates! 

P.S. - If anyone wants to share their horror stories teaching undergraduates, please share in the comments.  Read more!

Nobel Notes

I am not even going to try and offer up any predictions or suggestions given last year's surprise.  I will, however, make a few comments, some of which I've mentioned in the past.


Molecular Dynamics

Martin Karplus is usually mentioned here.  Chembark has this folded into a more general computational chemistry prize with other scientists who have contributed greatly in other areas of comp. chem., as has the listing over at the Curious Wavefunction.  Not to take anything away from Prof. Karplus and his extraordinary career, but as was brought up last year, this position betrays a lack of appreciation for the development of MD.  I'm not sure how one could reward Karplus without snubbing the early accomplishments under the rug that showed the power of computational methods to ask questions and provide answers to physical problems.  Of course, it's also entirely possible that an MD prize would be one in Physics, which would be entirely acceptable as well.

GPCRs

While some have noted that a Prize for the recent structural accomplishments might seem premature, I can envision a slightly different scenario.  Kobilka's former mentor, Robert Lefkowitz, did receive the National Medal of Science a few years ago for his pioneering work in GPCRs, and has earned various other accolades over the years.  It's possible that there might be some sort of Prize that involves more on the biochemical side of things, but with an eye (and inclusion of) the structural work.

Magnetic Resonance

Not even going to try since I'll just keep babbling on for a while.

The Kavli Question

Will we ever see a dual Nobel/Kavli Prize laureate?  Or is the work that the Kavli Prizes recognize too interdisciplinary to make it through the Nobel process?  (Cue the whining of chemists who want to eliminate biochemistry from eligibility for the Nobel Prize.  Heh.)

P.S. - Really kind of hoping a physician wins the Nobel for chemistry, a chemist wins the Nobel for physics, and a physicist wins the Nobel for physiology/medicine.  It would be a tremendously hilarious week.









Read more!

Quantum biology - A Rose By Any Other Name?

I believe I may have off-handedly mentioned some of this work somewhere in a blog comment semi-recently, but I suppose some further thoughts would not be out of place at this time.  I bring it up because of this preprint and this article about said preprint.

Clearly, on one level, quantum mechanics - via chemistry - underlies biology.  This is, I suspect, a fairly unoffensive statement.  Chemical reactions are quantitatively studied in a quantum mechanical framework, and I don't see biochemical reactions being much different. 

On another level, direct appeal to quantum mechanical behavior to explain biology can seem kind of silly.  Biology is slow, wet, messy, and takes place at a whole bunch of time and length scales.  I imagine many of us recall the exercise - likely done in an introductory general chemistry course, at least in my experience - where one calculates the de Broglie wavelength for an electron and then, say, a baseball. 

Of course, when one looks at table 1 in the preprint, a light goes on.  Long-range electron transfer in proteins?  The role of tunneling in enzyme catalysis?  Vision - which involves the photochemistry of a protein-immobilized chromophore?  Photosynthesis?  A proposed radical spin mechanism for avian magnetoreception? 

This all reeks of physical(ly predisposed) chemists trying to get their dirty mitts onto a whole lot of funding.  Not that there's anything wrong with that, mind you - I'm presently trying to work "quantum biology" into my CV/resume as we speak. 

But for sake of argument, let's take a look at the Fenna-Matthews-Olsen (FMO) protein from a green sulfur bacterium where quantum effects were observed via 2D electronic spectroscopy.

Yep, definitely a protein.  But what's all of that inside the protein?

Why, it looks like the protein is the wrapping for a photochemically delicious filling of chlorophyll molecules!  I could envision that this is the sort of environment which would be conducive for maintaining some sort of quantum mechanical excitation. 

But what about - for instance - microtubules, which some have suggested play a role in consciousness via quantum mechanical effects?  Why, there's even GTP (GDP) known to associate with tubulin in the structure!  Let's take a look -

Hmmm.  Let's focus on the GTP and GDP, so how about….

Well, that was kind of anticlimactic.  That's it?  That is somehow supposed to sustain and nurture our very consciousness from the harsh decoherent world out there?  I find myself skeptical. 

I suppose that is as good a place to end as any.  I may or may not have more to say in the future after I've had a chance to properly consume and digest the preprint.  While I do find the idea of nature exploiting exciton transport, radical spin pair chemistry, proton tunneling, and so on incredibly exciting - I don't think taking that and wantonly speculating is the best route.   

FYI - This was also mostly a chance to play around some more with UCSF Chimera.  Just started using it a bit earlier this year, so if anyone has any tips or list of useful tricks, please share!  The structures were generated with this program using PDB ID 3ENI (FMO protein) and 1JFF (tubulin).  Read more!

Something to read.....

Check it out -  a recent article by Nobel laureate Steve Weinberg on the problems facing big science.  It might be noted that the article is very US-oriented, which is only fair as Prof. Weinberg is here in the US.  Still, something that we all should read.

Try to think of the major scientific efforts that have been started or completed in the last 10 years here in the US.  OK, there is that entire NSLS-II project presently going on at Brookhaven which is supposed to run not quite a full $1 billion dollars.  OK, there was also the LCLS at SLAC (the free electron laser which came online a few years ago).  Well, just so no one accuses me of a totally horrible memory, the SNS at Oak Ridge was just shy of $1.4 billion and started up a couple of years back (and they're still building the full complement of instruments to go with the source). 

Hmm.  Maybe we're not neglecting "big science" after all.   If anyone has thoughts as to how to resolve this conundrum, they would be welcomed! Read more!

Break On Through To the Other Side

I was reminded to share this page in light of some recent conversations elsewhere. I would also encourage interested readers to check out the rest of Prof. Sethna's web site - there's a whole lot of great material on numerous interesting topics in physics and "complex systems," as well as what seems to be a nice, modern introduction to statistical mechanics for a wider audience than for whom most texts are intended. (I've only skimmed over it here and there so far - your mileage may vary.) Disclaimer - I am not affiliated with the lab. In fact, my only affiliation with Cornell is that I once dated a girl who lived in Ithaca, and her father worked at the university. Heh.

I will say that many physicists I've known - at least publicly - aren't convinced that they are after finding 3 laws to explain 99% of the behavior in the known universe. Most have far less ambitious goals (like being able to explain superconductivity for non-BCS systems), although I suppose this is their PR problem - they clearly need more Philip Andersons and Robert Laughlins to champion what most physicists are actually interested in, and not just what the very prolific high energy theorists and astrophysicists are putting on the book shelves. Of course, it's not to say that there can't be some excellent synergy going on - there's plenty of fundamental physics going on at neutron sources worldwide, and many groups are interested in using the tools of AMO physics as increasingly powerful probes of fundamental physics.

We can all recount anecdotes from our personal experiences - I met a bio grad student who clearly thought of their project in terms of cartoon diagrams without a number or semi-quantitative thought in mind, the theoretical physicist who thought that explaining his ideas to the experimentalists (or anyone who wasn't actually a frustrated mathematician) was the role of the phenomenology folks, and the chemists who complain about lack of rigor yet still seem desperate to explain everything in terms a first-year chemistry student would recognize. What we should focus on is trying to understand what is useful in such diverse approaches and work from there.

Biophysical chemists such as myself do not suffer from such faults, as we have all of their strengths and none of their weaknesses. We're also very modest. :) Read more!

A Modest Update

Point the first -

- It was remarked to me that my occasional overindulgence for parenthetical remarks in my writing suggests that I am secretly a Lisp programmer at heart. I snickered. It does look like an interesting language to learn, though…

Point the second -

- I was reminded of a thoroughly snarky point I had made to some friends a while back. String theory (or whatever your preferred scheme for quantizing gravity and unifying the fundamental forces) can explain physics. But the really interesting stuff will require using physics to explain the laundry list of actual phenomenona that we have on our platter. So learn your statistical mechanics, as you can then do everything from analyze (to one degree or another) magnetic samples, ion channel clusters in membranes, and socioeconomic behavior.

So love your stat mech and cherish the partition function!

Point the third -

- A recent blog post over at Just Like Cooking sparked a comment, harkening back to a brief digression elsewhere last year. I was of course led astray for a bit, and dug up some earlier papers on the topic. Not that my to-do list is by any means feeling underweight, but I feel it could be edifying (and potentially interesting) to try and work through the idea in a manner that would be fairly accessible to a (more) general audience. So less "death by Hamiltonian," and more "spiced up with Hamiltonians," if one will permit that metaphor. Read more!