Prize ponderings

There have been some particularly interesting and worthwhile points made on the blogosphere over the last two days in the wake of the Nobel announcements.

1.) The success of small/investigator-driven/table-top science.  Actually, this applies to more than just the Chemistry Prize - see here for some comments regarding this year's Physics Prize. 

2.) Are we doing ourselves a disservice by discussing and debating the Nobel ad infinitum?  Is trying to find one to three people to recognize for a certain (set of) accomplishments really the best option?  How much of this is a holdover from how science used to be conducted pre-1900?  I happen to especially like Paul's Chemical Hall of Fame idea, and am willing to participate.  (I may want to nominate a physicist or two, though.*)

3.) Chemjobber brings up the interesting point as to whether the "mix" of chemistry that gets highlighted due to the Prize announcements is the one the community wants to present to the public. 

4.) There seems to be a sense that we need to circle the wagons a bit before the central science withers away.  I can't entirely disagree with this one.  I've been told multiple times that some of the questions I've stumbled over while doing biological chemistry regarding underlying questions of (mostly) physical and inorganic chemistry aren't really fundable, at least relative to the biological question with which I'm engaged.  You can only try and spin questions into applications for so long and so far before it gets tedious.


5.) I would read this post over at Everyday Scientist if you haven't already.  I'm in the same sort of boat as a bio/physical chemist.  I look at the Physiology/Medicine Prize and see work like in vitro fertilization and the H. pylori work recognized, and vast amounts of cell biology and systems physiology in their ranks (immunology, olfaction, neurobiology, and so on).  I view biochemistry as something which is securely rooted within the realm of chemistry.  Of course, this makes me wonder - while the issue of communicating chemistry to the public has been a discussion topic in various contexts over the years, maybe we also need to open up the lines of communications between chemists.  I'm not entirely sure how to go about doing this right at the moment, but I am definitely open to ideas.  

Of course, perhaps this is all just colored by my spectroscopic tendencies - if I can fit it into a coil,  cuvette, or beamline, consider my interest piqued.  Biological, chemical, geological, material, or physical. 

As always, the comment section is open. 

*: Erwin Hahn and Albert Overhauser.  Spin echoes and the Overhauser effect.  You know you want to agree with me! Read more!

Stuck in the middle with you.....

So, due to recent research efforts, the path to enlightenment - well, at least, reasonable progress on a project - has become clearer.  Of course, it entails going back and preparing otherwise identical samples, albeit with a different labeling scheme.  Naturally, this will require some optimization.

In other news, I've recently been inspired to think about how to characterize extremely nasty and messy mixtures of appallingly complex and egregiously sensitive molecules.  My initial thought was that I should just let other people do this sort of thing.  However, I had a number of uncharitable thoughts about certain areas of the research community and realized that I should think more carefully about this situation.   I then had the notion that I need to do what my blog name suggests and think about things with less than precise site-specific chemical resolution for a bit.  I can layer on some perfectly reasonable physical parameters and other particular measures of interest.   Some people will complain, but then again, there are always those sorts.

Another unrelated topic I've been pondering - just how "open source" is chemistry?  How many of us have data trapped in proprietary formats in backup discs or external hard drives?  How often have you had to grudgingly use readily available software in ways it should never be used since more appropriate software doesn't exist or is egregiously expensive for the extent one needs it? Any information, griping personal anecdotes,  or interesting reads on the topic would be appreciated.

That will be all for tonight, I'd say.

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Generality and Contingency.

There's an interesting post over at In the Pipeline regarding the nature of how enzymes work, and it has inspired excellent comments (as is par for the course at ItP).  One notion comes up that if so-called generalized mechanisms can't be devised, it's a failure of sorts for chemists.

My question - the photosynthetic reaction center is an enzyme (oxidoreductase).  Dinky soluble proteins that do isomerizations are enzymes.  Metalloproteins that rip apart chemical bonds are enzymes.  Some proteins float around in the cytoplasm.  Others are embedded are in a membrane of some sort or another.  Others exist at a membrane/solution interface.  Others are extruded from the cell to go do their thing in the cell's environment.  So, how general can a mechanism be for an enzyme? 

One of the things that is often brought up is that there's an element of historical contingency to consider when examining the history of life on this planet.   While we obviously can't just throw up our hands in defeat to try and understand the mechanistic details of biological chemistry, neither can we truck along without acknowledging that context and history are important aspects of the grander scheme.

If that is still not comforting, perhaps one can find some solace in Kornberg's reminder to trust in the universality of biochemistry.  Consider it a tradeoff - while your one enzyme might not shed light on all enzymes, it can shed light on the same enzyme (or similar ones) across many organisms, from the modestly-scaled unicellular beasties to the gargantuan eukaryotes that now populate the Earth.  Read more!

Cultural Differences

There was an interesting post over at In The Pipeline last week about the differences between chemists and biologists, in particular the nature of how chemists and biologists conduct research presentations in mixed company. As the vast majority of my experience is in academic environments, I will not claim that any of the following observations necessarily extends beyond the weed-ridden walls of academe.

1.) Biochemists do aspire to make details of individual preparations something that can be avoided. Certainly, for those of us who are not working with wretchedly ill-behaved proteins (at least on occasion), we can basically just describe the protocol in broad terms (overexpression, cell lysis, clarifying the lysate, and the chromatographic methods/other procedures). I've done that without specifying buffer compositions in exacting detail before. Also, we are trying to make things as routine and unexciting as possible - preparing protein constructs with cleavable affinity tags; expressing eukaryotic in bacterial cell strains that compensate in various ways for not having all of the innate eukaryotic metabolic machinery; using multi-well plates for spectrophotometric assays of various sorts. We would like for things to be boringly reliable, rest assured.

2.) One fundamental problem with presenting material to mixed audiences is that your own people are in attendance waiting to pick your stuff apart. Not necessarily in a malicious manner, of course - well, at least not always. In short, you might decide to go light on the detailed mechanistic enzymology (say, for sake of example, you are an enzymologist) in your latest talk, but what then happens in the Q&A session? Your fellow enzymologists pepper you with a dozen intricate mechanistically oriented questions in no time at all. Six months later, you present again in front of this mixed audience. You have included adequate enzymological detail in your talk and slides. The cell biologists and analytical chemists yawn, and the synthetic chemists wonder why you're boring them with this information. And now you'll never break the chain.

3.) Biology fundamentally means working with living organisms. I sometimes have the impression that chemists who haven't ever done any substantive biochemistry or biology research don't fully appreciate this distinction in the visceral way that those of us who have fallen to the Dark Side do. If it takes a week for something to grow up, then that is what we do. We can't just toss it on a hot plate to speed things up. Conversely, not everything can be stashed in a freezer to wait until tomorrow (although when it can, we do appreciate it). There's also the price of doing interesting biology/biochemistry, where the efforts to make things boringly reliable in point 1 are nowhere near being implemented.

There's certainly more I could eventually think of, but these were the major points I wished to mention. I, personally, do my level best to make my points as understandable and transparent as possible when giving a talk. Of course, given that some of my ideas involve slaughter by spin Hamiltonian, it can be easier said than done...... Read more!