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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Capitalism.

My non-research career seems to be going well, at least insofar as I can manage to say 2.5 months into it.  Relocation will occur in August, and I will be able to reduce the amount of time I spend on the current commute.  It's been quite an experience, and to be honest, I think it will keep me from being bored for a couple of years at the very least.  

Talk to me in a year, though. Read more!

The Eternal Struggles

I managed to wrap up some experiments for a paper (sent back the revised version just the other day), While doing all of that over the last two weeks and change, I was stimulated to contemplate some long-standing issues off and on.  I figured they might be of mild interest.

The first - I'd like insight and numbers.

There's a fairly famous quote attributed to the late theoretical chemist Charles Coulson on obtaining insight versus just numbers.  My question - why can't we have both?  My  purely anecdotal experiences have suggested that chemists tend to be really ambivalent on this topic - on the one hand, we tend to be annoyed if we can't intuit everything from just a glance at the periodic table and a smattering of semiclassical physics (as I once vaguely alluded to recently), but on the other hand, we're quite quick to complain about things not being rigorous and how it's all just a model.  Other fields tend to be a bit less gripey about this sort of thing in my experience - they've either learned to deal with the indeterminacy or uncertainty, and/or come to grips with the ups and downs of toy models. 

The second - the perpetual translation that goes on in the head of anyone working at an interface.

A long time ago, I had gotten myself into a little back-and-forth because, in short, I was reading with my physics filter on when I should have been reading it with my chemistry filter.  This is hardly new, and it's certainly happened since then, for that matter.  It usually manifests in turns of phrase or underlying assumptions that - for example - aren't anything unusual in one setting but might be a bit odd or worse in another setting.  I'm not sure how to resolve this recurring situation, except to try and be more careful.   Suggestions would be welcomed.     

The third - is biochemistry really just "applied organic chemistry," as I was once informed as an undergraduate and have heard off and on since then?

Please.  One is only fooling the innocent undergraduates with that pompous bit of nonsense.  There's a reason it's called biochemistry - one needs to appreciate and understand how to navigate through the entirety of chemistry.  Once one casts aside the self-completing fantasies of some deluded chemists, it's rather straightforward to see interesting chemistry of all stripes manifest in biological systems.  There are incredible metalloenzymes that can fix nitrogen (nitrogenase), we have a chromophore bound to a membrane protein which experiences a photochemically induced conformational change (bacteriorhodopsin), and of course there's all of the multiple feedback and regulatory pathways that all seem to tie into one another in ever-increasingly labyrinthe but beautiful ways that seem to be well-attacked (to some extent, at least) with the mathematical formalisms of physical chemistry.  And all of that is just the tip of the iceberg.  Read more!

Trifling Observations

The major issue with working at interfaces is that when you need to return to a place of stability, said place of stability often needs quite a bit of attention. You've left it abandoned and unattended, and it will suck up all of your effort until you've returned it to a state of steady reliability. Of course, one never lingers for long, as there either is a new avenue to wander down in one's research or to bring a different project off the back burner.

This tangentially ties into some discussion last month (at a couple of blogs, by my recollection) about how the academic sector does not adequately prepare one for positions in the private sector, at least insofar in chemistry. While numerous wry remarks can be made about the state of the chemistry job market in response to this, it relates - broadly - to the breadth of modern chemistry. Even if you were to organize a curriculum solely for aspiring chemists (here in the US, aspiring engineers and biologists & medical students make up a non-trivial fraction of the general and organic chemistry student populace), you still have to figure out how to make a course palatable for those who may end up working in any number of fields and subspecialties, and will likely end up switching and moving about in any case. The idea (naive as it might be) is that one develops the foundation to pursue anything from synthetic organic chemistry to ultrafast chemical dynamics to chemical biology. Or even all three, if you're feeling adventurous.

Anyway. Read more!

Assorted Awesomeness.

So, I was going to do a post on general bad-assery and things I've found fascinating in magnetic resonance this time around, but it's taking a bit longer due to real-life laboratory fun. I will probably rework it as a really long bibliographic post, and perhaps have some discussion about it here and there. Onto the real-life laboratory fun, with apologies to Gossip Girl....


So, I've been aware of surface plasmon resonance (SPR) as a method for investigating kinetics and thermodynamics for a while now, and generally thought it was an interesting application. You can hardly do any reading in the biochemical literature and not eventually stumble across a paper that uses it. However, it was one of those things which I had never actually done until starting my current position.

Well, in order to further preserve some ostensible anonymity, I will be avoiding explicit details of my current work. The particular interaction I've been thinking about a lot as of late has been between this relatively small (~ 40 kDa) protein which I will call Blair, and this larger oligomeric protein that I will call Serena. Now, Serena prefers to relax in an appropriately tailored buffer, as is not surprising. So while I lovingly prepared Serena in such a buffer, I figured that for the purposes of the SPR experiment, I could just squeeze her into a relatively analogous buffer (minimal change in pH, no dramatic differences in overall ionic strength) that was a standard for doing SPR. I didn't think she'd mind, after all, she can retain her hotness under many conditions, or so I was led to believe.

Well, suffice it to say, after three rounds of SPR, I was mistaken. Now, I've learned how to finally run the instrument like a pro, I know that I need to go above and beyond the minimum for filtering my solutions and centrifuging out the dust in my samples, and can rewrite the scripting code half-drunk (not that I have, just that I can, it's really easy). There were other likely culprits (some potential issues with my controls, some concerns about coating densities) which I eliminated from the list of suspects the second and third times I ran the experiments, so I was making progress there. I just need to tweak the buffer conditions so Serena doesn't get all broken-down and sad on me. Because a hot blonde with great legs deserves better, metaphorically speaking.

Because, after all, how can you not want to see this?



Metaphorically speaking, of course.

One minor MR-related thing that will make my next post all about the spectroscopy – I find the idea of using nuclei other than ¹H in MRI to be endlessly fascinating. I'm very intrigued by the work people have been doing with, in particular, ²³Na – everything from cardiovascular physiology to neurological imaging to muscloskeletal studies. Not to say that I don't spread my love around for all NMR-active nuclei – certainly I'm not the only one to check out this absolutely fantastic website by Pascal Man periodically just to see what's new in the world of quadrupolar NMR – but ²³Na MRI seems to be a bit ahead of the pack, just from my anecdotal observations, in terms of development and rate of progress at the moment. If any MRI pros are out there, I'd love to hear from you, as I am positive I am missing out on some really neat things.

Well, that will be my obliged post for the week. I am going to strive for two posts next week. But don't hold your breath.....

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