Saturday, December 19, 2009

What's in a name?

"What's in a name? That which we call a rose/ By any other name would smell as sweet."

Thus says Juliet in Shakespeare's Romeo and Juliet. Admittedly, it is possibly one of the most overused quotes of Shakespeare, but in a way (albeit, perhaps a strange and slightly creepy way), it basically sums up my view on the continuing debate of how we define chemistry, biology, and everything in between.

Although this has subject has been a matter of discussion for quite a long time, it has become the center of rather heated debate since the announcement of the 2009 Nobel Prize in Chemistry. The row has been highlighted in a number of blogs and journal editorials including this one in ACS Chemical Biology (a hat tip to Brent Stockwell for the tweeted link). Essentially some folks feel that understanding ribosome structure and function is not Chemistry at all, and it's certainly not the first time in recent years that the Chemistry Prize was awarded for elucidation of molecular functions/interactions of cell-derived molecule These folks feel that the Nobel Prizes in Chemistry are being "stolen" by biology.

Of course, this is really about ruffled feathers and the debate over what "real chemistry" is.

In my opinion, if you're looking at how atoms and molecules behave, bond, and interact, then it's chemistry--whether it's propylene or a P450. Ergo, biochemistry (or chemical biology or biological chemistry or whatever else you want to call it) is chemistry. For that matter, a lot of toxicology and pharmacology are chemistry. Compartmentalization of core sciences (with reference to research) is becoming increasingly difficult--and that's not necessarily a bad thing. There is a continuous spectrum of work running from chemistry to biology to physics. To impose arbitrary divisions between these disciplines and between subfields of these disciplines implies that science is a static thing. It isn't! Science is a changing, moving, dynamic entity.

Admittedly my "world view" of chemistry has been shaped--and some might argue, skewed--by the environments in which I've studied and trained. My undergraduate study was in a "Department of Chemistry and Biochemistry", and even though my degree says B.S. in Biochemistry, there was a strong emphasis on the core chemistry curriculum. This is probably why I chose to apply to graduate programs in chemistry departments that were strongholds for biochemistry. I have a Ph.D. in Chemistry, but my graduate work focused on protein chemistry and enzyme kinetics. There was honestly little division between chemistry and bio-related studies at PSU. This was perhaps aided by the fact that the medical school campus--home to formal departments of biochemistry and pharmacology--adjoined the arts and sciences campus--home to formal departments of chemistry, physics, and biology. The alliance was further promoted by inter-/multi-disciplinary programs, centers, and institutes for structural biology, biophysics, and chemical biology (to name a few) that brought together investigators from the medical school and A&S. There no sense of animosity that a chemistry professor was doing "too much" biology or that a pharmacology professor was doing "too much" chemistry. I daresay, most of them would be hard pressed to define where chemistry (or physics) ends and biology begins.

There is a dark side to the integration of biology, chemistry, and physics. Some have developed the attitude that if there is no biological application, then the work is unimportant. That is utter nonsense. Much of our understanding of the mechanisms by which enzymes act was originally based on analogies to well-characterized chemical reactions. We must take care not to stray into this form of scientific elitism.

Chemistry, biology, physics... We cannot disregard the foundations for our interdisciplinary work. Nor should we attempt to segregate those branches of study that have successfully integrated these core sciences. Our disciplines have evolved an interdependence and, thus far, have thrived in it. There many exciting discoveries yet to come, which would be impossible in the absence of collaboration and integration.

Friday, December 11, 2009

Is there an app for that?

I have been known to express rather strong feelings regarding seminar etiquette and the lack thereof. In recent years, a growing focus of my ire in this regard has been mobile devices. Initially we (speakers and audiences alike) had to deal with folks failing to turn their phones to vibrate. Of course, a vibrating phone can still be a distraction when the entire row can feel it vibrating every ten minutes, and the owner of said phone (who decided to sit in the center of the room) keeps leaving to take the call and then returns to the same center seat. But I digress.

With the emergence and affordability of "smart" phones, we must now contend with people texting and emailing in, what they believe, is a discrete manner. There is little discretion in your buzzing pocket and blindingly bright screen, which can be rather distracting to your neighbors during a seminar.

However, this week I witnessed a new seminar 'sin' made possible by the iPhone.

Sitting toward the back of a large, dark, toasty auditorium, about halfway into the seminar, I was trying very hard to follow what was going on and jotting down notes in my book. As I started to return my gaze to the screen, I was distracted by someone a few rows in front of me, fiddling with her iPhone, showing something to her friend. The usual aggravation began creeping in.

After a moment, I realized she wasn't just fiddling with her iPhone, but she was taking pictures of data slides. I found this unfathomable and completely inappropriate.

Perhaps, though, I was overreacting. So when I returned to the lab, I inquired of my science tweeps: Is it appropriate to covertly photograph data slides during a seminar?

From a limited sample set (n=4), the answer was a resounding "no". I think Zen put it best: "When you have to ask if it's okay to do something 'covertly', the answer is almost certainly, 'No.'" (Note added in proof: Zen has more to say with the additional context not allowed by Twitter. So do others.)

Looks like I have another rule to add to my "Guide to Seminar Etiquette". Now the question is how do we deal with things like this?

Thursday, December 10, 2009

Everyday (lab) living

Last weekend I went on a slightly obsessive-compulsive cleaning spree in my tiny kitchen and consulted Martha Stewart's Homekeeping Handbook (hey, it was a gift... and actually quite useful) to refresh my memory on cleaning the coffee maker (which I highly recommend doing-my homebrew is fantastic this week). As I was flipping to the appropriate section, I noted a page headed: "Six Things to Do Every Day". According to Martha, we should do the following daily:
  1. Make the bed. Because "Tidiness begets tidiness"
  2. Manage clutter.
  3. Sort the mail.
  4. Clean as you cook.
  5. Wipe up spills while they're fresh.
  6. Sweep the kitchen floor.
There are explanations for each, which I (mostly) redacted, but this list makes sense when you think about the things that you spend so much time on during weekly/monthly/semi-annual cleaning. They are the little things that can be managed quickly when they are still little things (a book here, a glass there) but can quickly grow into behemoth monsters if you wait.

Similar things happen in labs. We decide to file papers A through D over the weekend, wash X tomorrow, put away Y later, order Z this week, and before we know it, we can't find our desks for the piles of papers, our benches have descended into chaos, we can't find anything, and we can't run experiments because we're out of reagents. So I got to thinking, what would Martha's list look like if she worked in a lab? Thus I bring you "Six Things to Do Every Day: Science Edition". (You will note some redundancy.)
  1. Manage clutter. Some scientists have a place for everything: every pipette, tip box, tube rack, reagent, etc. When they're done with an experiment, everything goes back in its place. I was not this person in grad school; I am now, and it saves me so much time looking for things.
  2. Update your lab notebook. We want results, but documentation is equally important*. In academic labs, many scientists are not particularly vigilant in this regard. We scribble down notes on post-its, gloves, paper towels. We shove the printouts of our raw data, graphs, or Westerns in the notebook. Then we transfer everything to our notebook maybe once a week. Doing this daily--both the writing and the scrapbooking (as I refer to cutting, pasting, taping, or otherwise affixing raw data and other bits of paper to the notebook)--offers several advantages.
  3. Wipe up spills when they're fresh. Because it really pisses people off when they have to clean up after you; it's disgusting and potentially hazardous, seeing as they have no way of knowing what the dried up gunk is.
  4. Plan out your next day's experiments. I find that I am most productive and efficient when I plan my next day's experiments before I leave for home. This gives me a focused task to accomplish when I walk in the next day, so I can started right away. Although this may seem obvious to some, planning out experiments includes checking supplies to ensure that you have what you need to run the experiment. If you don't have the supplies, then you know what you need to beg or borrow before you are elbow deep in samples. Speaking of supplies...
  5. Make a list of reagents and supplies that are running low. Make an actual list on a post-it or note card or whatever, not a 'mental note' because mental notes have a greater tendency to disappear. Once a week, source and order whatever is on your list.
  6. Scan literature search RSS feeds. The sheer volume of research being published in any given area is astonishing. Much of it has no bearing on our personal/lab research interests, but there are jewels out there as well. RSS feeds for saved PubMed searches or articles in press from publishers are a great way to stay on top of what's happening now. Others may have longer attention spans than I do, but I find whenever my article feeds go beyond ~20 new entries, then I have a tendency to scan through without paying much attention to the title. Taking 5 minutes to scan through the feeds every day helps keep me from skipping over those gems.
My list is not the be-all, end-all. So what does your list look like?

Reblog this post [with Zemanta]

Wednesday, December 2, 2009

(Not quite) seven months of Biochem Belle

DrugMonkey has issued a call for the Twelve Months of Blogging. Since I just joined this community in June, mine is 7. Without further adieu:
  • June: The why first. I have decided, at last, to add my voice to the (female) scientist blogosphere.
  • July: I don't recall ever having a formal discussion on this topic in graduate school, but I thought I had a reasonable idea of who should be listed as authors on a manuscript...
  • August: A few days ago I was thinking about my lack of productivity this week, largely attributable to attending cool science talks but also failed controls in experiments and meetings with Guru and collaborators (why the hell can't a meeting take less than 2 hrs in this friggin' place?).
  • September: Has it really been 2 weeks since a last posted?
  • October: The editorial in the current issue of Cell outlines new guidelines for supplemental materials for Cell Press publications.
  • November: Today marks the one year 'anniversary' of my dissertation defense.
  • December: ... in which I pull my head out of the sand and out of my ass.
Reblog this post [with Zemanta]


... in which I pull my head out of the sand and out of my ass.

Recently there has been much wailing and gnashing of teeth--some in the blog, much more outside of the blogosphere. The past couple of months have been really intense; not only has research been painfully lackluster, but there was a whole heap of other crap outside of science (that I won't go into right now). I am no good at compartmentalizing, so each thing feeds into the other, particularly because science is such an integral part of who I am. Add to this that on the order of 30 hours of my weekend plus another night during the week is spent alone (as Paramed is working), I have way to much time to think, contemplate, overanalyze, etc., etc.

So I took the four-day weekend to reset. During the course of those four days, I think I spent a grand total of 1 hour focused on research to draw up a plan of action. The remainder of the time was spent sleeping, watching TV, writing creatively (which I haven't done in months), working on a 12 year old's reading list, watched a Lord of the Rings movie, and other general miscellany not associated with work. It was wonderful. And just what I needed--even if that makes me a "bad" postdoc.

Yesterday afternoon I took some time to think about what I don't like regarding current affairs (mine, not the world's), what I want out of my life right now, what I should be doing... In a span of thirty minutes, I had filled a page with goals that I could and should implement in short order. Many of these ideas center around restoring some sense of balance (a topic I commented preached on early in this blog's existence, but which seems to have gotten completely out of whack for me) and making the most out of my remaining time at BRI. In a neater and more comprehensible form than what I freewrote, here's what I came up with and why:
  • Use my time more efficiently. Time sinks in my life (like e-mail, Twitter, and coffee breaks) have been growing. It's not just the time they consume directly, but the disruption of focus and thought processes that they cost. I have too much shiznit to get done. Of course, it's not just at work, but at home as well. Because of Paramed's wacky schedule, I am carrying a large burden of the household chores, and I need to be more efficient in that regard.
  • Get my last manuscript from Bear's lab published. I've been clinging to this one. It's really interesting stuff, and some of the experiments that I did still astonish me. It's just there's so much more that could/should have been done, but it was the end of the line. I need to let this one go, and trust Bear and his lab to polish the edges, so I can focus on what I'm doing at BRI.
  • Connect with other postdocs in the research community at BRI. For better or worse, my postdoc lab is not particularly social. It seems that each person has one or two other people in the lab that s/he talks to (whether about science or nonscience stuff) on a regular basis, and breaking into those tiny cliques is difficult. But there are gaggles of postdocs and other scientists in the research community affiliated with BRI. So I am going to be more engaged in the community, starting with the monthly journal club and postdoc socials. There is really no excuse for not meeting other postdocs.
  • Focus on my health. I knocked off a couple of concerns in the last few months, but I have let things slide with regard to diet and exercise. I know that the healthier I am--the cleaner my diet, the fitter I am--the more energy I have. And given the experiments I'm planning for the next few months, I'm gonna need all I can get.
  • Focus on what I can do here to mature as a scientist. I have been quite focused on the research aspect (and independence therein) during my time at BRI, thus far. However, there are many other things that go into being a good scientist and having a successful independent career, like grant writing, presenting, managing, networking, etc. There are many opportunities at BRI and in Guru's lab to develop these skills and resources, and I should take full advantage of them. Honestly, if I leave BRI without a good network, someone should give me a kick in the ass.
  • Figure out how to communicate clearly/calmly/confidently with those in authority. I cannot explain it, but I seem to forget how to speak around Guru sometimes. I have to learn how to communicate with him more effectively. And with other PIs, administrators, etc. I have a feeling that one day my academic "life" might depend on it.
  • Create slots of "protected" time with Paramed. Life is insane for us both. We may never feel like we get "enough" time together. Right now I'm just looking for a few--literally, 3 or 4--hours together a week, during which I am not cooking/working/cleaning/revising and he is not working/at school/doing homework.
  • Establish some social connections that are not built on professional ones. Yeah, I pretty much suck at this. Always have. But I'm going to try. Maybe.
  • Learn to find happiness where I am. 'Nuff said.