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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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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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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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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Black boxes and rigor.

There was a thought-provoking post over at the Curious Wavefunction regarding a Nature op/ed piece on the increasing "black boxification" of modern biological research.  While it is both concerning and makes for an easy bit of mockery, I have to sometimes wonder where one can draw a line.  For example, it's been fairly typical (in my experience) for some specific physical/spectroscopic method to be introduced in a manner consistent with one's expected minimum physical chemistry background.  It's not uncommon for there to be a step or two which is essentially "and we take this result from classical mechanics/electrodynamics" or "this is actually a result of a certain mathematical theorem/relation" in such an introduction.   Some might claim that there's a huge difference between not knowing a technique relies upon a particular mechanism versus (for example) not having worked out a laborious series expansion for a particular term that yields the desired form in that case.  But I would view it as a caution - what happens if you stumble across a case where, in fact, you need to go back and rederive the expression for a term since some parameter or limiting case has changed?  Naturally, you find that if you end up relying upon that method in your research to any significant extent, you are going to dig in deeper.  You will figure out what the limiting cases are, and where any approximations are likely to break down. 

Of course, here I'm reminded that there is a difference between being able to contend with the formalisms of an argument and being able to develop a more physically rooted intuition for said argument.  I suspect many of us have encountered the "it's not rigorous enough" student somewhere along the line - they're the ones who find the experimental nature of scientific research a bit troubling and are worried that we're not careful enough with our mathematics.  We don't want to go in that direction either, of course.  Well, those of us who are scientists and not just frustrated mathematicians, at least.  I'd like to think that there can be a fruitful synergy between the two - when one is able to invoke physical intuition is a good time to develop one's mathematical skills and understanding, and then later on apply that mathematical expertise to a new problem where intuition is lacking at the start. 

I have more stuff to blather about, as it distracts me from extremely unfortunate technical difficulties in my own research.  Stay tuned. Read more!

Some random thoughts....

Or, Structures, Struggles, and Teaching People How to Make Nuclei Dance.

So, a few issues of interest and/or importance to yours truly. This is going to be short.


1.) Vaults! I've suddenly become very entranced with both their structural (39-fold dihedral symmetry for the win!) and functional (no one really knows what they do!) beauty. The structure of rat liver vault at 3.5 Angstroms was recently published (see here) – they were able to clearly assign the major vault protein (MVP) to the electron density, while the other proteins and ribonucleic acid is still up in the air. The internal dimensions of approximately 620 Angstroms in length and 400 Angstroms in diameter is enough to encapsulate most entities within the cell. There's some mention that they might interact with lipid rafts, given some sequence homology considerations. Amusingly, since the number of coordinates and structure factors exceeded what could be put in a PDB file, it's been deposited under three separate accession codes.

2.) I mentioned not too long ago that I'm having some issues with our resident BIAcore (surface plasmon resonance) system. Let me describe to you a representative issue with the current chip and setup: The baseline for the control surface after being coated with buffer and blocking agent is significantly lower than the original baseline. It is possible we have a bad chip, or a bad instrument (some sort of drift in the optical components), or something else. So while troubleshooting and such is going on, it brings to mind a major difference between my current work and former work in terms of nature and aspect. With the SPR setup, it's a unit that is, for lack of a better phrase, a single entity. Sure, we can remove and insert sensor chips, and it's controlled by the adjacent computer, but it's basically a large self-contained box. I can't really go peeking inside, checking things out for myself since it's a shared facility instrument. Back when I was boldly going where no one had gone before in the world of NMR, it was all modular and accessible. I had a oscilloscope checking on the forward and reverse power going to and coming from the probe (remember, in ssNMR, one works with higher RF powers than in solution, typically), I could break out the network analyzer to check the performance of the probe or an amplifier/frequency generator, I could open up the probe to see what chaos might have befallen us, I could always quickly toss in a standard sample (adamantane, KBr, glycine) to quickly assess how far off-course we might have strayed.... I could change filters/attenuators in an appropriate fashion to see where misery was striking at the heart of my experiment. And there was a sense of general, simple assessibility – I could use any network analyzer that I could borrow from someone in the department to check what I might see with my lab's. I could always repack a chemical standard with new material from scratch without it being a big deal or expenditure of time. I could examine the raw data to check and see if the FID was starting at a maximum or minimum (there's a way to check the angle in the SPR software, but it doesn't seem to be something most people do), for instance.

I suppose it's a matter of personal experience – my graduate experience was analogous to the laboratory where I worked as an undergraduate (where we did primarily EPR and time-resolved optical spectroscopy). I – as a general rule of thumb – like to know what's going on at a certain foundational level. I am not a fan of being told, “Yeah, you need to call the company and ask.” I expect with time I will get more used to such commercially available instrumental setups, but until then, I shall lament this state of affairs.

3.) I have a wild bug up my nose about the issue of how to best teach NMR to people. I think most people familiar with magnetic resonance first become acquainted with it via the module in introductory organic chemistry classes, with maybe a mention of it in the introductory physics sequence. Now, I don't really think that there's anything wrong with this – when I was taking organic chemistry, I had the inspired thought, “Hey, protons are spin-1/2 particles, but so are electrons....what about coupling those spin-1/2 particles with nuclei that are spin-1/2 particles? Could we correlate nuclei to electrons? This could be useful for metal-containing systems, since you've got unpaired electrons!” I did some math, and then I found out who George Feher was, and then my moment of insight became bittersweet. I had a few extra drinks that weekend to get over the disappointment, and now that I've told my “how I independently rediscovered ENDOR” story, I won't be tempted to tell it again for a while. However, back to the question - what about the next step? It seems that most people get a “structural determination via spectroscopic/physical methods” sort of class, where they also get into additional methods such as IR, UV/Vis, mass spec, and the like. But, let's say that I become science czar, and I mandate that NMR be removed from this class and be included in a one semester (or equivalent) course in NMR. What else should we teach in this course? How broadband should its audience be – should we let biochemists who have a thing for structural biology expect to get something out of it as well? What about physics majors who are plotting on becoming chemical/molecular physicists and possibly develop the next generation of NMR experiments and applications? How much “death by operator algebra” should we have in this class? What kinds of experiments should be include in the lab component? I have my own ill-formed opinions at this point in time, but it's been fun to mull over on my own and I thought I should share.


And just like that, I'm gone....

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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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