Oddly inspired.

I'm...it's really bad timing, but a recent article I found on a blog has inspired me to write about actual science.  Sadly, due to the combined effect of my ongoing relocation and next week's planned schedule, you will have to wait until September to read about it. 

Which, you know, given that it looks like yet another project I've worked on has hit the "this isn't getting published" zone from my past postdoctoral position (I had one in grad school, despite yearly attempts for about four years after graduating to get my advisor to act in some positive manner towards it), is saying something.

In short, I think the trick is to select research projects that require effort to progress - not effort to keep them from collapsing into a singularity from which nothing can escape. 



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Trifling Thoughts.

1.) I really was hoping to go for a couple of more years before having to deal with a poorly behaving high-power RF amplifier.

2.) Whenever someone says that quantum mechanics should be understood at an intuitive level, I wonder if they never had to occasionally take solace in the mathematics earlier on in their education.  While it was fleeting during intro E&M at university, the intermediate E&M class did have me routinely finding some sanity in mathematics.  Perhaps my intuition is just exceptionally poor, of course. 

3.)  Given all the hoo-ha about AFM recently, I thought this was interesting and timely.

And there's a good ending point for today......


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Angry Birds: Academia

The title is just what I think would be a thoroughly hilarious game for one's smartphone.  However, as I am a cranky postdoc (at least until early next year), I have found the franchise thoroughly helpful for those moments where I need to kill a minute or four in lab waiting for something to incubate/boil/equilibrate.

While I am tremendously interested in chemical microscopy of all sorts, various online discussions of a recent Science paper regarding AFM studies of single molecules of reactant and products reminded me of the somewhat odd excitement over "seeing" something.  Your eyes are limited spectrometers that can only deal with photons, and many don't appreciate the signal processing involved between your eye and your brain.  Now, if we could do electrons and neutrons as well, I'd be less worried about our restricted optical window.  Heh.

I keep meaning to post long overwrought thoughts about NMR, lipid bilayers, and the scurrilous treatment of valence bond theory by some people, but don't hold your breath.  Maybe once I clear my to-do list further, I'll have the cognitive energy to do so.

Question for any who might be reading - is there an opposite of "minimal publishable unit"?  When you have a ~ 15 page article in a solid journal along with another ~ 15 pages of supplementary information, maybe you want to see about splitting that work up.  Especially if you're citing the SI in the main article. 

I'll go topple over some structures now.....






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Starting off 2013.....

I hope that everyone's 2013 looks to be promising and full of potential in all possible areas.

While I did manage to post more in 2012, I think more substantive/research literature-oriented posts are called for here.  I suppose I should look into figuring out how to insert well-formatted equations to help with this goal, although I suspect I will find it easier to just generate the equations elsewhere and then insert them as images.  I do not expect to accurately predict one of the Nobel Prizes again, though. 

I contemplating bringing up the ACS panel suggestion to have people complete a doctoral degree in 4 (no more than 5) years to a couple of biological chemistry faculty I know, but I realized that this would cause such severe trauma they'd never recover.  Because - thankfully, this wasn't me - I know people who did a Ph.D. in chemistry (bio focus) who did take 8 or 9 years to finish the degree, and they were uniformly in certain labs whose aspirations were borderline insane.  If it takes your students that long to finish a Ph.D., you are doing something wrong.

We will see how far I get with my various scientific self-improvement goals this year (read up on relativistic QM/QC - I have a borrowed copy of Dyall & Faegri's text, kind of poking through it slowly; my going-on-a-couple-years goal of getting Shaik & Hiberty's text on VB theory under my belt; and more on my various programming self-study projects).

And now back to pushing the limits of knowledge further......

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Speak of the devil....

...and the devil, he shall appear.

A recent discussion at the Curious Wavefunction briefly touched upon the role of (macro)molecular crowding in biochemical studies.  I am presently preparing to see whether a certain set of experiments are feasible, and in some of the potential tests, I am adding a fair amount of crowding agents to my samples. 

The samples that have those crowding agents are presently the only ones that exhibit any enzymatic activity.  The other samples are dead, biochemically speaking.  One of the "dead" samples does exhibit complex formation in one of my alternate tests, but that's it.  Further tests are needed, of course, and it's certainly possible that I can retain enzymatic activity in the other samples upon logically adjusting my current protocols.  But perhaps there's a lesson here to be learned.




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Lit Links

So, in case any were wondering, my area on the East Coast was mostly spared the wrath of Hurricane to Post-Tropical Cyclone Sandy.  Some rain, a bit more wind, but not many power outages in the immediate area.  I am however fairly well prepared for any mystery zombie apocalypses that might arise (from the dead).  I hope that all of you reading who were subject to its furor endured the storm as well as possible.

In any case, some bits of possible interest -

1.) PNAS has a special feature this week on "the Chemical Physics of Protein Folding."  Sadly, it's behind a paywall for the time being.

1.5.) Related to this, I once mentioned a while back in a comment (I believe over at the Inquisitive Ket) about one of the less-important reasons Levinthal's paradox never really bothered me, namely, that proteins aren't really free to sample all possible conformations due to their interactions with other proteins (even indirectly due to crowding), the solvent, and with itself.  In any case, it's always interesting to see people carefully examine these sorts of questions in the recent literature.  

2.) Gaining structural insight occasionally takes a while.  It also reminds me of the utility of neutron science for biochemistry - the ability to use contrast variation using selective deuteration make it possible to probe multicomponent systems.  And let's not forget that one can also use neutrons for spectroscopic measurements. 

Anyway, back to the actual science…..  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!

Some minor notes.

The reason they're making your son take chemistry?  Because they're mean.  Or perhaps because they hold to some archaic notion that education is about broadening one's horizons and tempering the intellect, not just about preparing one for any particular career path.  I haven't decided. 

Small-molecule synthetic chemistry in the NY Times?   A pleasant surprise to see in the national newspaper of record, at least last I checked. 

Microbial physiology via NMR.  So cool.   Also, kind of jealous.  I really need to get some awesome stuff done sooner rather than later.

I think that will be all for the evening.


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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!

A perhaps idiosyncratic view.

So, as it turned out, I called this year's Nobel Prize for Chemistry.  While I am now curious if I have any Elven ancestry (Elrond had that gift of foresight, right?), I feel I should note the following for those feeling that biochemistry isn't really chemistry.

I like biological chemistry since, in my view, it allows me to explore so many areas of chemistry.  I've synthesized isotopically enriched small molecules, I've purified proteins, I've been able to work with multiple spectroscopic and physical measurement methods in detail, I've examined paramagnetic inorganic solids with both success and failure, I've spectroscopically dissected multicomponent organic solids, I've had to explore certain types of self-assembling systems, I've cranked through theoretical treatments of metalloenzyme catalysis as well as polymer chemistry to make sense of my data over the years.....it's been a good time.

Extending from that, I like chemistry since it is perfectly situated to go hopping over boundaries.  I don't see why I shouldn't be able to figure out signal transduction pathways just because I'm a chemist.  I don't see why I should humbly hand over fundamental questions about the theoretical basis for spectroscopic methods to the physicists.   

Although right now biochemistry is giving me a headache.  Speaking of which, back to it.....

P.S. - A hearty congratulations to both Serge Haroche & David Wineland as well as, of course, Robert Lefkowitz & Brian Kobilka! 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!

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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Sunday Contemplations

It's been a lively time on the chemical interwebs.

The entire chiral space dinosaur story is kind of getting tedious at this point. While the allegations of plagiarism certainly needs to be investigated, adjudicated, and resolved, I was most intrigued by the post here at the Curious Wavefunction. I find it convenient that he brings up the famed geologist Charles Lyell - there is a personally beloved example of what might be termed geological/geochemical contingency that I perpetually bring up at these moments.

Xanthine oxidase. You may or may not remember this enzyme from undergraduate biochemistry (well, for those of you took such a class). I mention it since it is a fairly well-known example of an enzyme which uses molybdenum as a cofactor. There are a number of molybdenum-utilizing enzymes that organisms use. However, it has been observed that certain organisms prefer to use tungsten. These are usually so-called "extremophiles" (deep-sea hydrothermal vents, in particular), where tungsten is more abundant than molybdenum, as well as needing to do chemistry at higher temperatures and under far more anoxic conditions. Perhaps it is not as dramatic as the sorts of substitutions that have been bandied about by some (hello, #arseniclife!), I will admit. But it bears consideration - how might multiple perturbations along these lines shape and remodel biochemistry?

(For anyone who wants more info on the above, I'd suggest first checking out the work of Michael Adams at the University of Georgia. If you are just curious about a point I bring up, let me know so I can reference you properly.)

The other interesting point that was brought up, IMO, was the idea of convergent evolution. This relates broadly to the idea that there are going to be certain physical "boundary conditions" one has to consider. My latest book of interest on this is Living at Micro Scale - the Unexpected Physics of Being Small by David Dusenbery. Here, the focus is on microorganisms and - to recall Edward Purcell - life at low Reynolds numbers.

I don't have anything interesting to note about DHFR since I neither deal with drug discovery nor with the biochemistry of DHFRs. Although I wonder - what if that paper hadn't shown up in J. Med. Chem.? What if it had ended up in a more general-audience biochemistry journal? Would there have been the same response? Would anyone have even noticed it on the chemistry blogosphere? I wonder.

Anyway, I'm going to contemplate lipid bilayers, detergents, and how they are clearly conspiring to make my life difficult. 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!

Nobel Notes

Thumbs up to the Nobel Foundation for their decision regarding Ralph Steinman's laureate status. I always felt that the rule was to make sure nominations of those who have passed on were not submitted in the first place. Now, whether or not one agrees with this is a separate issue.

Given that my professional interests are not very immunological or astrophysical, I don't have any particularly incisive commentary about the Physiology/Medicine or Physics Prizes.

A followup to a comment elsewhere - Tom Wainwright passed away in 2007, so unfortunately he would be ineligible for a Nobel. Given that Aneesur Rahman and George Vineyard have also passed on, Alder is really the only "founding father" of MD who would be a possibility.

On the off chance it is a magnetic resonance Chemistry Prize this year, I will not be sarcastic and post "but it's just applied physics! Why are applied physicists winning Nobel Prizes?" I'll actually just write a short blurb on what was so cool about the new laureates' research. (All other fields of physical chemistry being recognized are fair game for such commentary, though.) Read more!

A Modest Response

Yet another round of science Nobels have been given out. And once again, the chemistry committee decided to award it to scientists who studied polymer synthesis by a multicomponent macromolecular assembly in a crowded, aqueous environment. They even had the gall to use crystallographic methods to study it!

This is definitely not chemistry. No way at all. I mean, synthesis, macromolecules, polymers, crystallography, people wanting to understand macromolecular structure and function at an atomic and molecular level? How can this be chemistry? Someone explain that to me, will you?

Unless, of course, it *is* chemistry. But that couldn't be. Could it? It's all quite troubling.

P.S. - Still alive, looking for a new position, staying on my toes. Read more!