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?

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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.
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Reset

... 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.


Saturday, November 28, 2009

Collision course

In an earlier post about responsibilities, DrDoyenne commented:
It's also important to realize that PI and trainee may not be compatible because of personality, work-ethic, and other differences. Neither need be in the wrong...just different. I read about many incompatible relationships in science blogs (usually written by the trainees), and the blame seems to be dumped on the PI. There are certainly bad mentors, but more often it may be simple incompatibility or a failure on the part of the trainee to understand why the PI is so hard on them.
I have been thinking recently of how true this observation is and how I have seen it play out in my relatively short time in science.

The transition into my postdoc has been a difficult one, and recent weeks have been particularly trying. Earlier in the month, I was exchanging emails with Bear over revisions for a manuscript resubmission. At some point, I made a comment about my frustration. I was a bit surprised a few days later--after having gone through a couple of more rounds of emails regarding the manuscript--to receive a message from Bear saying he was sorry to hear that I was having a tough time, but he thought that most postdocs do. He went on to briefly share his own experience of being a postdoc, worrying about not publishing, and ultimately deciding to pursue own interests, even if it meant "working on the side". I had already decided that this is what I should do, but that email provided additional impetus and encouragement.

Regarding that email, I tweeted*: As crazy as he drove me sometimes, I am really fond of my grad adviser. He continues to provide encouragement and advice. LadyScientist replied: That's really rare. And priceless. Sounds like you had a good one.

This brought a wry smile to my face because I daresay some who were in Bear's lab would debate that--vehemently. Hell, even I might have debated it at some point.

Too often, trainees have an unreasonable expectation for (a) consistent application of the same standards across all trainees, (b) rational behavior uninfluenced by emotional state, (c) consistent, professional, and formal mentoring. I know this because at some point, I had these naive, idealistic ideas. I have a feeling that this rarely happens. Let's face it, as much as we like to depict them as strange, otherworldly creatures at times, PIs are people too. They have unique personalities and styles, which don't always mesh with those of their trainees.

It took me some time to figure out a few important things about Bear's style. Bear expected his trainees to be independent. But he expected more out of those who were highly self-motivated and committed. There were times he was pretty aggressive with certain trainees during meetings. Some people would respond defensively. Others would just shut down. At times, I would get pretty upset and angry, but I tried not to react on those emotions. It was particularly frustrating, though, when he let others slide. I eventually came to realize that when he nailed me to the proverbial wall in a meeting or landed a snarky comment, it was because he expected more out of me. Bear pushed those who would respond (eventually) in a productive manner--that is those who would go search the literature or design and execute the experiment to address the question, knowing if he asked it again, we would have an answer. I learned that I should not take his affronts as personal insults. I would still feel that initial, primal reaction, but I no longer let it stick around for days. Because of his style, Bear forced me into situations that required me to think for myself. His personality forced me to be sure of myself and to display confidence even when I didn't feel it. I left his lab with a level of independence and confidence that, when I started grad school, I could not have imagined possessing. Some of Bear's personality traits that drove me crazy were what helped me become that strong, independent scientist, and realizing this allowed me to leave with an amiable relationship with my Ph.D. mentor.

Of course, now I have a new personality to contend with. Guru has presented a unique challenge. He is pretty damn impossible to read because he is so reserved. On a couple of occasions, he has called me out (one-on-one) because I seemed less than thrilled about something. Guru is also much more involved in research--not to the extent of working in the lab himself, but being very involved in experimental planning and design. I recently realized this is one reason that I have been frustrated about research: It is difficult for me to identify my intellectual contribution to my project because it was defined in such detail when I started. Some people would consider having a defined research plan a good thing. I'm not opposed to having a research plan, but I also like having some latitude within that plan or the ability to pursue a 'side project' of interest. There are many good arguments on both sides (i.e. defined plan vs. letting a trainee sort it out on his or her own or single project vs. multiple projects), but it largely boils down to differences in style and personality. Just as it did with Bear, it has taken me some time to define certain elements of Guru's style. I have also realized that I have been much more timid in my interactions with Guru than I ever was with Bear. My hope is that I can use this knowledge to find some compromise that will work for both our personalities. Otherwise I fear I will end up (a) working on something I'm not particularly invested in, (b) losing some of my fire for research, (c) butting heads with Guru during my remaining time in his lab, or (d) some combination of the three.

* Don't worry, PhysioProf, I know how you feel about Twitter.

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Saturday, November 21, 2009

Great Expectations

I am still a mere, lowly postdoc. However, I have a very clear idea of what I want to do with my life, at least professionally speaking. In my view, my time as a postdoc is not solely to expand my knowledge base and repertoire of techniques, or to publish fabulous papers, or to become a more independent scientist, although each of these things is important. It will be a few years, yet, before I am ready to begin searching for my dream job, but this is the time that I am defining an image of the career scientist I want to be--which involves pondering issues such as those described here. I likely have a naive and/or idealistic view of some things, which is why I am posting them here--for discussion with the commentariat.

At the end of last week, I posed the question of what responsibilities a PI has to his or her trainees. DrDoyenne provided some great responses (You should go read them!). She raised the important point that both the PI and the trainee have responsibilities in the relationship. She is absolutely right. It is difficult to discuss one without the other.

This question of responsibilities, both on the part of the mentor and the trainee, is a critical one but is often taken for granted. I think most students and postdocs have perception of what their responsibilities and their adviser's responsibilities are. The same can be said of the PI. However, we rarely discuss these matters (at least based on my experience and observations). There is no handbook or contract clearly stating each party's responsibilities. Instead we assume that the other person knows what is expected of them. When someone doesn't meet those expectations, there is a great deal of frustration, anger, passive-aggressive behavior, in-clique bitching, and, on occasion, bandying of the phrases like "it's your/his/her fucking job". I would like to clarify that I have never been told to-nor have I ever told anyone-that "it's your fucking job". But similar phrases have been thrown around by parties in private conversations.

This scenario brings us to what I view as the first responsibility: establishing clear, reasonable expectations. Of course, expectations (should) change. They are not one-size-fits-all-forever. Expectations are influenced by where we are at and where we are going, both personally and professionally, on the part of the PI and the trainee. Although this may be temporally a first responsibility, it is one that should be revisited throughout a trainee's tenure.

There are two parts to this responsibility, which I would argue, initially fall on the PI. The first is establishing expectations for trainees. New grad students may have very little (or even no) experience working in a laboratory. Even if they do have more substantial experience, it is as an undergrad RA, in a company, or as a tech in an academic lab, which are completely experiences from doing dissertation research, and with distinct expectations. Postdocs, of course, have research experience, but the culture of every lab is different. It is important for the PI to help define that culture by establishing certain expectations. These may include but are not limited to:
  • ballpark figure of hours/days a week the trainee is expected to be in the lab
  • responsibilities in the lab outside of research such as maintaining equipment or inventory
  • expectations for scientific engagement outside of research such as seminars, conferences, courses, and scientific reading
  • attendance and etiquette for meetings
I distinctly recall a few months after I joined the lab, Bear called a meeting with all the grad students. Bear was not one to engage much in formal mentoring activities, but in that meeting, he spoke with us about things that he thought were important to becoming a successful scientist. In addition to providing very useful advice for new trainees, it also established some of his expectations... and I took it as such.

The second part of PI's responsibility here is to establish some expectation of what trainees should expect from the PI. This goes back to the idea that every lab has its own culture. Every PI has a unique personality, schedule, and style, which most assuredly affects how the lab is run. Some PIs are very involved in research, day-to-day. Other PIs are mostly hands-off. Either way, the PI's style dictates what a trainee can expect from the PI. How much help or input should I expect from my PI when it comes time to write a manuscript/prepare a presentation/design an experiment/search for job? A PI shouldn't have to provide a decision tree for trainees but should give some idea of how involved he or she is when it comes to research and training.

The trainee also has responsibility in this establishment of expectations. First off, PIs rarely make frivolous comments regarding things trainees should do. You may think your PI is talking solely because he is enamored by the sound of his own voice. But when your PI prefaces a discussion with "This is what it takes to be successful in this field", you should probably interpret that as "This is what I expect you to do while in my lab". If you have some concern about what your PI expects of you or what you can expect from your PI, ASK YOUR PI. Your lab mates can provide useful information about the PI's style and expectations, but there are limits to that information. Their information may be based on assumptions because they never asked, not to mention circumstances may be very different. Expectations are only a starting point. As a trainee, you have to set some expectations for yourself. Ultimately, as a trainee, you have to take responsibility for your own career.

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The epic battle of Pitar and Belle

As you may have gathered from my midweek post, the past few weeks in science have been pretty crappy for me. The first half of this week was particularly rough and was not helped by the fact that I started the week sleep-deprived from working furiously to finish revisions on a manuscript from Bear's lab, required by PITA reviewer (who we shall refer to as Pitar, henceforth). Moreover, this wasn't just any manuscript, but one of the major projects I worked on in Bear's lab, the one for which I was awarded an NRSA in grad school, the one that I carried out almost singlehandedly and thus carried the name of only one other author aside from myself and Bear.

Pitar basically wanted to see every piece of data we mentioned in the manuscript. This included controls, negative data, and data that looked almost exactly like other data that was already in the manuscript. Yes, I understand, there's a whole heap of lying, data-manipulating bastards in science these days, so Pitar cannot be expected to take my word that when I say data for thing 2 looks like data for thing 1. Still this made my life miserable. Pitar has no concept of what went into making the figures in the paper presentable, clear, and quite frankly beautiful. Nor does Pitar care.

Bear and I decided that most data requested would appear as supplementary figures, which meant they didn't have to be as beautiful as figures in the main paper. But me being me, and my name being associated with this work, I could not bring myself to just put the standard analysis program output into the supplemental. The 1/2-pt lines and 6 pt font just looks amateurish. So I spent hours resizing, ungrouping, deleting, adding, copying, pasting, regrouping to make the figures at least look decent. After working into the wee hours of the morning Monday, my shoulder, elbow, wrist, and thumb hurt from all the clicking and typing, and my ass and back ached from hours of sitting in a hard chair. I was so exhausted that I couldn't think straight enough to write comprehensible figure legends, so that had to wait until after I had gotten a few hours sleep--and when I should have been doing ELISAs or Westerns or something in Guru's lab. I will admit that insanity of trying to get so much done in such a short period was really my own damn fault--due to procrastination.

Either way, I got it done and addressed all but one main bullet and one sub-bullet Pitar fired through modification of a main figure or addition of supplemental data. I truly hated the fact that Pitar made it one of 'those' papers, where there were supplemental figures than figures in the main text. Bear sent in the revisions early in the week.

The long wait began.

And ended. I received word from Bear yesterday that the manuscript had been...

ACCEPTED!

It was so nice to end the week on a high note, even if it was a note from my past.

Hopefully it is an omen for the week(s) to come.

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Thursday, November 19, 2009

What the hell did I do to you?!?!

I think I have expressed previously that I am one of those strange people that absolutely loves science. The process, the work, the discoveries... Science is an integral part of my life. I often speak of science in anthropomorphic terms.

And now I'm trying to figure out what the hell I did to her. Why does she hate me now? Why is there so much general suckitude when it comes to research and science these days?

When I started my postdoc, I took on two somewhat related projects. The person who previously worked on one of them (we'll call project A) had been gone for over 6 months. The other project (B) didn't even have preliminary data.

I came to realize as I tried to get project A off the ground, that the supporting data for it was almost nonexistent for the in vitro system. And that data from the in vivo system was notoriously difficult with regard to quantification and reproducibility--this from the people who actually did the work. So I tried a different approach, which kind of worked the first time, worked beautifully the second time (early this summer), utterly failed the third time (a few weeks ago), and provided a negative result in a different cell line (sometime last week).

Project B had to basically be started from scratch. It took a couple of months to get the in vitro model system up and going, thanks to one crucial detail left out of the methods section of one group's papers. After that problem was solved, I had to get the Western blots to work, dealing with trying to get efficient transfer of proteins of interest and the fact that the commercially available antibodies are crap (one band my ass, Santa Cruz). This finally started to show some promising results this summer as well. But I again ran into the problem of reproducibility, trying to figure out whether it's the crap antibodies, differences in experimental conditions, or just something that I screwed up. And then there was writing and revising a protocol for the in vivo work, which I was looking forward to.

Other things I've worked on have either just not worked or have given wonky results that require additional troubleshooting/control experiments. The real-time PCR was screwing up intermittently, which in the end, required setting up every experiment twice to get usable results. Regarding one completely unrelated idea (which I felt was a good idea and a nice reflection/application of my previous training), the guy heading the core facility that I need to use is a butt munch--ignored me once, blew me off the second time, was curt the third time, and is ignoring me again.

So basically the past couple of months have sucked (even if you don't count the shit I've been dealing with outside of science).

Yesterday I'm perusing the RSS feeds for new PubMed entries on topics of research interest. And I find an 'early edition' PNAS paper that is basically describing my project B, with in vitro and in vivo data (using different but closely related model systems). I thought I might actually cry (when it comes to my life, it takes a lot to make cry). I still have to read the paper in detail. I might be able to salvage something of my work, but it definitely steals my thunder.

I realize that all of this is 'part of science'. But that doesn't really make me feel better. I've been having a very tough time this year, scientifically speaking. I keep telling myself that it's important to encounter adversity at this stage of my career, so I can (hopefully) deal with it better in my independent career. That it's "character building". But that doesn't make it any easier.

In recent weeks, I had decided that it was time to start considering alternative projects, for a myriad of reasons. In a way, this most recent development may just be another cutting of ties to current projects to push me into another one. It still doesn't entirely remove that feeling of science kicking me when I'm down.

Well, time to suck it up and get back to it.

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Friday, November 13, 2009

Responsibilites: Open forum

A question for my readers:
In your opinion, what are a PI's responsibilities to his or her trainees?
The concept is thrown around in several blogs, conversations, and even in today's editorial in Science by Bruce Alberts. However, it's not something that has been clearly defined, and I daresay, there are many opinions on this. Of course I have my own thoughts on this, but I'd like to hear some other opinions before I post my own this weekend.

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Tuesday, November 10, 2009

Word of what?!

I've been working on revisions for one of my manuscripts from Bear's lab. I realized today that I did not have the final draft that was originally submitted--you know, the one I should be revising. Not disastrous because most of the revisions are supplementary figures (controls, negative data, etc.). Anyway I wrote Bear asking him to send the submitted manuscript as a Word document, so I can get on with my stuff.

As I was reading his response, my brain saw, "Here is the Word of life". I paused. Bear has been known to joke, mock, and use some rather colorful phrases.

Then I realized that my brain had misinterpreted. The email actually read, "Here is the Word file", which makes so much more sense.

The question remaining: Was the misinterpretation a product of the current splitting headache? The feeling of exhaustion? Or my desperate desire to get this manuscript out of my life for good?

Sometimes there are no easy answers to life's questions.

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Survival of the...?

Less than a month after closing its merger with Wyeth, Pfizer announced its latest restructuring plan yesterday. This involves establishing five central R&D sites, 4 in the US and 1 in the UK. Details on the restructuring are slim, but it is reminiscent of the current GSK model.

Also not discussed in the press release: How many scientists will be losing their jobs. Given that Pfizer will be reducing R&D ops at 3 sites, consolidating its R&D sites in Connecticut, and completely shutting down R&D ops at several other sites, the news ain't gonna be good. This follows on news last week that Johnson and Johnson could be cutting up to 8000 jobs. No one seems to know what sort of layoff numbers will be emerging from the Merck/Schering-Plough merger.

Unfortunately this is part of the life cycle of big pharma. They assimilate other companies and then the pruning begins. I don't think this is really anything new. Just ask someone working for Monsanto 15 years ago... which became Pharmacia... which was acquired by Pfizer. There are many other examples. I don't know how numbers laid off in recent years compare with mergers of previous decades (yes, I'm a lazy blogger and have not consulted Wikipedia on this), but mergers and layoffs are nothing new (just like the valleys in NIH/NSF funding are nothing new).

Perhaps this is why I was struck by this comment on Derek Lowe's* post on the subject:
I am Synthetic Organic chemist about to graduate from a reputable group. I am so frustrated with these pharma layoffs and thinking to go to academics. So what do you guys think, is academic job is better in present context?
Of course, one has to wonder what he (or she) means by an 'academic job'.

If he means associate professor position, as interpreted by commenter OrgChemRedundant, then my answer would be 'HELL NO!'. You don't, or at least in my mind shouldn't, pursue that career path as a backup plan. Need I really explain why?

If he means working as a bench chemist in someone's lab, then it's worth considering. Some university departments/institutes have been investing heavily in organic chemists, setting up what I can best describe as mini-biotech groups within academia. These entities utilize chemists to synthesize hits from high-throughput screens, compounds for groups without synthetic capacities, problematic syntheses, etc. To some extent, you're still at the mercy of the grant cycles, but you may be more insulated from the economic swings. You might also be making less money than you would in pharma.

This also highlights a previous discussion we've had here: There are options outside of academia and big pharma. There are those companies that we buy all our solvents and chemicals from. There are many smaller companies, like Cayman Chemical and Santa Cruz Biotechnology, that specialize in classes of compounds or targets for bio-related research. There are smaller companies that big pharma is outsources some of their synthesis to.

If you really want to go the pharma route, whatever the reason, here is a piece of advice that I heard during a talk by an 'old' chemist at Merck. He had been at the company for 20 or 30 years and, over those years, had worked on one particular biological target multiple times. The project was tabled, and almost killed completely, multiple times, mainly because drugs against the target did not appropriately treat the indications they were developed for. Ultimately he had the satisfaction of seeing a drug make it to the market that truly changed lives, one case he witnessed personally. By that point, he was a division head, but the pride and satisfaction was clear. He was trained as an organic synthetic chemist, but one message he had for his audience was this: Even in pharma, simply being a synthetic chemist is not enough; you have to learn and understand at least some of the biology and physiology of the system you're working on.

Honestly, we could turn this into a fill-in-the-blank statement. Science--at the very least, chemical and biological sciences--has changed. For most of us, we can no longer pick a small niche and just stay there, speaking only with our niche-mates. There's a reason multi-/inter-disciplinary training has taken off--and it's not just because of NIH investment in such training programs. It's because we can no longer just be a(n): enzymologist, molecular biologist, organic chemist... As grad students, we may train to become one of these things, but that doesn't mean we can't or shouldn't learn other things. We don't have to become experts in every other field, and the truth is, we can't. However, we can pay attention to what's going on in other fields, to understand the big questions that other scientists are studying, to learn what challenges other labs are facing. That's the way we will make progress. And that's the way we will (professionally) survive.

* Derek Lowe's blog In the Pipeline is an excellent read if you're interested in drug discovery or what's going on in the pharma industry.

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Sunday, November 8, 2009

The morning after

After some late night, therapeutic baking, I realized that yesterday's post was sort of a downer. I had not originally intended for it to be such, but it seems that the blogging center of my brain takes unintended detours sometimes. I considered taking it down because (a) it was a bit depressing, and (b) it's very personal. But it is part of who I am, so it stays, at least for now.

Part of the original intention of the post was this. I know a couple of grad students who are entering the dissertation phase swing by periodically. Generally grad students view the defense date with this great sense of dread. They see it as a day where their fate hangs in the balance, the day that decides whether they become a Ph.D. scientist or not. However, I think, under most circumstances in science grad programs, the truth is your fate has already been decided before you set foot in that room. At least, this has been my experience and the experience of basically every Ph.D. I know. You may have a committee member that gives you a hard time, maybe more than one, but they are usually the ones that have done so in every committee meeting you've had.

You should absolutely prepare for your defense, polish your presentation, practice. You're talking about something that you've invested in for years, something that you are the world's expert on. You should take pride in your work, and part of that is presenting it to your colleagues in a polished, professional manner. You've been working toward this for a long time. Don't forget to enjoy the achievement.

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Saturday, November 7, 2009

Bittersweet

Today marks the one year 'anniversary' of my dissertation defense. I think for most people D-day is an intense and emotional day. It is the culmination of years of hard work, commitment, frustration, successes, doubts, failures, beer bets--and that's just the research.

Generally in my program, and especially in my lab, there was rarely a question of whether your committee was going to pass or fail you. This removed some of the tension associated with the event--despite my adviser joking at group meeting the same week that the event would hopefully be cause for joyous celebration. Even so, the thought of standing in front of your peers and mentors explaining, in less than an hour, what you've contributed to science over the past five years is nerve racking. I was one of three grad students that started in Bear's lab the same year. I was the last to defend, and the other two had already gone to their respective postdocs in distant states.

My preparation for my defense that day was this: I didn't show my face on campus until an hour before my early afternoon defense. I didn't look at the presentation. I went for a run. Then I went to my favorite coffee house for breakfast with my dad and uncle who had driven eight hours for my defense and with my husband. I knew that I had the presentation down cold. I knew all the data. I knew the mechanisms. I had spent a lot of time immersed in the central questions, pondering and thinking, over the past years, and very intensely in the past months. Spending time rehashing everything that morning would only serve to stress me out further. I was nervous enough without that.

When I did arrive on campus, I pretty much bypassed my lab altogether. I setup my computer in the lecture room, checked the lighting, made sure the laser pointer and remote for the computer would work, that the animations were fine. And then I tried not to think about it. My lab, my committee members, and a few other colleagues filtered in. I did not freak out when one of my committee members was a no-show because I knew that I had my quorum. And again there was no reason to stress me out further.

Bear gave me a very complimentary introduction. I was touched, although he came pretty damn close to making me cry. I stood on the opposite side of the room from computer (and coincidentally, my committee); I had planned this so I would not spend my time getting tangled in cables or staring at the computer screen. Initially I was so nervous my hands were shaking, but after about five minutes or so, I settled in and settled down.

I think most students dread the closed session with their committee. There is something dark and ominous about it. The truth is, I actually enjoyed the closed session. My committee members were the traditional older, white, tenured professors, which I think many students associate with cranky and confrontational--especially with female scientists. But these men were fantastic--thoughtful and engaged. We spent the better part of an hour speculating and debating hypothetical mechanisms for a phenomenon I had observed, not in a way that was confrontational but rather collegial and intellectually stimulating. It was the kind of moment that captured the essence of why I chose grad school in the first place.

It was great to have my family there, especially my dad and husband. They had both been wonderfully supportive throughout grad school, listening to me go on and on about things and people and policies that they knew nothing about. It seemed right that they get to experience that big day and the subsequent celebration.

There was one thing missing that day. My mom. She had died just a few months before, after fighting cancer for nearly two years. I spent a relatively small percentage of that time with her. Some days, even now, I regret not taking more time away from graduate school to spend with her. Yet before that thought can even fully form, I remember how important it was to her that I finish what I started and that I not let her disease interfere. She decided early on that she was not going to let cancer keep her or those she loved from living their lives. A nurse, she worked full-time in an oncology clinic until a week before her death. Just days before her death, she was protesting that I had chosen to postpone my defense, even for a couple of months. She was certain that I could do great things, and she'd be damned if anything stopped me. She bragged about me to the MDs she worked with and the MDs who treated her. That's what mothers do, I suppose.

It still seems wrong that she wasn't there to experience the fulfillment of a work that she supported for so long. Honestly it hurts more now than it did a year ago. Maybe because there were so many other emotions vying for my attention a year ago. Maybe because the second year is so often harder than the first. Either way I look back on that day and experience the definition of bittersweet. Maybe because this past year hasn't been a picnic. But hopefully, next year I will be able to look back on D-day with a little less bitters and a little more sweet.

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Pop culture views of women in science

DrDoyenne (over at Women in Wetlands) is posting an interesting series on the stereotypes of female scientists in TV/movie fiction. I recommend going over and checking it out. It starts here.

Saturday, October 31, 2009

Followup on 'Progress?'

A few weeks ago I posted about the number of female Nobel laureates and how that number reflects trends in science. This week Science published a roundtable interview with the four women who took Nobel Prizes in STEM fields this year. The web version includes an extended audio version.

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Thursday, October 29, 2009

Clone wars

It seems like more than 9 days has passed since my last blog post. The past week has been pretty crazy with several very long days/nights in the lab, urgent experiments getting dumped in my lap at the last minute, struggling with my own long experiments--you know, the usual travails of the typical postdoc (or grad student). Throw in there a program retreat with a large number of grad students (meaning late night after-parties and thus < 8 h sleep over two nights) and a minor medical procedure that, among other things, required me to give up real food and coffee for >40 h (the latter was painful-literally) and be up at some godforsaken hour this morning. Upon discharge, I was instructed to go home, rest, and avoid 'activities that require you to think or act quickly'. So I think that leaves sleeping, watching crappy daytime TV , re-reading Harry Potter, and blogging. I've hit 2; I'll get to the others later.
It starts at the top, with the administrators and the PIs. It then filters down to the lower ranks--the postdocs, the grad students, the research associates. It really is an insidious plague. And despite the dramatically different landscape, the acknowledgment of its presence, the discussions of alternatives, it still continues to spread. I am referring to the ridiculous assertion that success as a scientist requires one to remain in academia. Yes, this is a sweeping generalization. Yes, there (probably) are PIs out there who are happy with whatever career choice their trainees make, so long as their trainees are happy with the decision.

But there remains a pervasive attitude that if you are a productive student/postdoc and leave academia to pursue other career options, then you made a mistake or cracked under the pressure or some other term equated with failure. (Chall was recently the center of this perception at her new job.) In many graduate programs, you're essentially presented with two career options: research in industry or research in academia. And many PIs seem to consider a move to industry as the ultimate betrayal (after all, Pfizer and Merck are actually run by Voldemort and Darth Vader, right?).

It's satisfying to have someone follow in your footsteps, so to speak, to want what you have, to create 'clones' of yourself. Some PIs, though, can't seem to understand why on earth any good trainee would want something other than a tenure-track position at an R1 university. Some even seem to take it as a personal insult that a trainee would choose any other path. Some go so far as to tell their trainees that they will be wasting their lives, should they choose something else.

Now I think I've made my career aspirations pretty clear. I do want the students, the postdocs, the lab (even if it's in a basement somewhere)... but that is my decision. I don't assume that every other postdoc or grad student wants that. There are two innate problems with making such an assumption.

The first is practical: There simply are not enough faculty positions available for every trainee. So by telling your trainees that a tenure-track position is the only worthwhile job out there and pushing them toward that career path, you're setting them up for failure. Depending on how deeply that notion gets ingrained, your trainee may find impossible to be truly happy with any other job because your voice is always in the back of her (or his) mind reminding her of where she went wrong, that she couldn't make it, that she failed.

The second is personal, but may come as a shock to some PIs: Not every individual with a Ph.D. wants to run his/her own lab at an R1. Furthermore (and you may want to sit down for this one), not every individual with a Ph.D. wants to stay in research. The reasons for not wanting to start a lab or not wanting to stay in research are vast. Too vast to even tackle here. Occasionally a trainee may simply lack confidence, and a word of encouragement may be just what he or she needs to start down that path. However, a PI shouldn't pressure anyone to pursue an academic research career just because he/she thinks it's the right decision for that trainee.


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Tuesday, October 20, 2009

We're not alone

Maybe it's just me... but I don't really interact with any professional women in areas outside of science. So sometimes I lose sight of the fact that women in other fields are facing the same challenges and questions that women in science, are. I caught a 'teaser' for the NBC/MSNBC special report series "A Woman's Nation", and I decided to take a look. The series is actually an extension of The Shriver Report (as in First Lady of California) from the Center for American Progress. I have not read the entire report yet, but here is one excerpt that caught my attention:
For the vast majority of women (and men for that matter), reaching a C-suite level position is not very likely (or perhaps even desirable). The statistics on educated women entering the workforce and the early but encouraging research we have outlined suggesting that women are highly effective in senior-level positions would lead one to ask:
  • Why aren’t women more equally represented at senior levels of the business organizations?
  • Why is the number of women at the top still so small?
  • Why are there so many leaks in the pipeline of women into leadership in corporate America?

... Among the many reasons women hop off the career ladder is work-life conflict. Two options that many women pursue to address these conflicts are: “opting out” (or downshifting) and pursuing entrepreneurial careers.

... many highly educated women leave their employers prematurely due to the barriers they encounter in the workplace and the challenge of integrating work and family.13
But opting out is not simply a response to inflexible schedules and problems rectifying work-family conflict... women are more likely to leave the workforce because their jobs are not satisfying or lack meaning. Many women, especially those at midlife, opt out because they do not feel valued.14

A second option for women is to take on a reduced work schedule, working part time or job sharing. This approach, like opting out, is viable only for those families that can afford to live on less earnings. Women are far more likely than men to pursue reduced-hours arrangements in order to accommodate their caregiving demands. Unfortunately, employers appear to have an almost inexplicably high level of resistance to establishing part-time professional positions.

Many highly skilled women seek professional part-time roles where they can contribute in meaningful ways, only to find that such roles pay poorly, are marginalized, and often do not include benefits (not even on a pro-rated basis). The result is a serious talent drain that would be very easily remedied by employers simply letting go of an outdated belief that professionals and managers work full time.

Sound familiar?

Sunday, October 18, 2009

Fashion faux pas?

Before I get to the meat of today’s post… Traffic has been up to my little blog since one frequent visitor and commentator decided to make an example of me (but in a mostly constructive way). So, welcome to new readers. I hope you continue to drop by. If you want to know more about where I’m coming from, check here and here.

Now onto the main course...

For various reasons, I've been thinking back on a debate that I had more than once with a fellow grad student. She held that there's only one way for a woman in science to dress if she wants to be taken seriously. Her contention was that if a woman dresses in a feminine manner, if she shows any leg, if she wears a top that even hints that she has cleavage, then she'll get a male colleague's attention, but she creates a scenario in which he cares more about her ass than he does her science. Or male colleagues will just dismiss her out of hand. Her claim was that if a woman wants a man to respect her intellectually, then she has to hide her sexuality, her femininity--wearing pants, suits, and tops that are more masculine cut and that hide skin and curves. She shares the attitude of Ms. Mentor, which is frumpy is better than fashionable in professional interactions. This mentality is shared by many American-born female scientists in academia. I say American-born because I've seen many foreign female scientists--particularly European--who seem to be quite comfortable wearing figure-flattering dress or sleeveless top among their male counterparts.

Women want to be accepted as equals in science. That shouldn't mean that we have to imitate the men in our fields in attitude and dress. We shouldn't have to hide behind our clothes. A skirt shouldn't be a red flag, screaming, "Hey, there's a chic in the room." They know already! It's not as though we've been drinking Polyjuice Potion so we look like dude #1.

I think that this attitude holds us back. It is a self-imposed restriction. We are telling ourselves and other women that we can't be ourselves. It's true, that regardless of culture, gender, or occupation, most people behave differently at work than they do with friends or significant other, but some degree of personality comes across in professional interactions. For many people, personality is reflected in personal style. I happen to feel more confident when I feel good about my appearance and when it is representative of my personality. It wasn't that long ago that I really began to find my personal style and learn what flattered my figure, and it wouldn't have happened without a very good friend--a female postdoc who experienced a similar revelation months earlier. Giving my appearance a little time and consideration can change how I carry myself (especially if my day is starting off pretty crappy). Although I do it for myself, other people notice when I pay attention to my appearance. It is rare that I feel marginalized or objectified for wearing attractive, stylish, distinctly feminine clothing.

I selected a professional but distinctly feminine outfit for my dissertation defense: a black pencil skirt, a floral print top that just covered my shoulders, and three-inch heels. I did not get a single smart ass or derogatory comment from Bear (who is pretty notorious for saying what he thinks to his trainees without any filter). My committee--which was entirely over 50 men that day--did not treat me any differently. We had a very collegial, animated debate over the proposed model. I did not feel as though I was not respected for being an attractive, confident woman--quite the opposite really.

My aforementioned grad student friend would probably have been shocked and appalled by my choice of attire for my dissertation defense. In my experience, women take note when a male scientist dresses fabulously, but don't view it in a negative light. So why do some women seem to take offense when another female scientist chooses to show her style? Are perceptions of female scientists generally so heavily swayed by how they choose to dress?

I'm done with it. I'm a woman in science and I have decided that it's ok for me to dress like a young, confident, stylish woman (even if I'm not all those things all the time). And if anyone has a problem with that, they can bite me because I do good science and that's what matters.


Saturday, October 17, 2009

Don't hate me

Maybe it has something to do with the fact that I actually took Monday as a holiday, in keeping with our institute's list of official holidays...

Or that it's not a gray, gloomy day...

Or that I had an awesome, if brief, Friday evening with Paramed...

Or that I was convinced it was a regular (by banking standards) workday for a good 60 s or more as all the alarms in our apartment were screaming at 5:30 this morning for us to get our asses out of bed...

But I'm actually looking forward to a Saturday in lab. Maybe this is a sign that I'm getting my research mojo back.


Saturday, October 10, 2009

Whoa. Where did that come from?

Note: I have no idea if these ramblings will make any sense. If they don't, I blame the horrendous cold and the cold medicine. Actually I probably shouldn't blog 'under the influence', but I'm going to anyway.

Making life-changing decisions is hard. Making the actual change is infinitely harder. That's when the real work begins, and it usually takes years. After all, they're not week-changing decisions. You take that first step. You start on your way. You keep your head down. You're watching your feet because the trail is can be rocky, your footing unsure, and you don't want to fall on your face right out of the gate. You keep going this way for a little while. Then you look up and see what's really in front of you. Sometimes it knocks the wind out of you.

When Paramed and I made the decision to move to the Northland so I could do a postdoc at BRI, we knew it wouldn't be easy. There were events prior to and after the decision that made us question if we'd made the right
one, not so much from the career standpoint, but because we were moving even farther away from family. We had no idea, though, just how hard the change would be. Even though we were both ready to move on, it was
tough leaving PSU City. We spent the first 5+ years of our marriage there, and it was the first place where we established a set of friends and habits that were completely independent of our families. Having spent our entire lives in the southern US, moving to the Northland was a HUGE culture shock. Plus it's always a challenge to walk into a group as the newbie, trying to figure out where you fit in and establish connections with the people. On top of this, there was a massive emotional roller coaster involving Paramed's plans and future for the first 9 months we were here. All of this is to say, for the past several months, I've been keeping my head down, watching my feet.

Then, over the past few weeks, many small things--blogs, conversations, ramblings of the subconscious, etc.--that caused me to look up, see what's in front of me regarding my career track, and say (initially at least), "What the hell did I get myself into?" To be honest, I'm a little jealous of Dr Becca, who said this week:
What seems to be most highly valued is having a real focus throughout your career, as opposed to flitting about learning a million methods in different fields.

... realizing that this is what is desirable in a New Investigator candidate, a sneaky grin crept onto my face because I was also realizing that I have GOT IT.

I'm jealous because I don't have that. I chose a different path, a different field, and it seems I've been trying to rationalize this to myself recently.

I think what it comes down to is that 'finding yourself', figuring out what you want to do with your life isn't a linear path for everyone. It certainly hasn't been for me. I briefly described my background when I first started this blog. Growing up where I did, I didn't know any scientists, and there certainly weren't any opportunities to do research as a high school student. I had loved science from the outset, but it was a long time before I considered it as a career. When I made the decision to pursue a career in science, I was almost done with my BS and jumped straight into grad school. I didn't take/have much time to explore areas outside of chemistry/biochemistry. I gravitated to biochem, but as a grad student, I was fascinated by more heavily bio/biomed-related research. Bear encouraged his grad students to keep up with what was going on in the literature outside our area of interests. I took that to heart. And I became intrigued by two fields that were quite far removed, in both content and techniques, from my graduate work.

Ultimately I chose one of those fields--immunology--for my postdoc work. Part of my reasoning was that immunology is constantly changing and evolving. There is really no shortage of questions and problems to work on. There is certainly a place in immunology for biochemistry and for tools emerging from chemical biology labs, which are not being widely used. I wanted the change work on something that was really important, to work in a field where a novel discovery has the potential to change medicine. And, for reasons that I can't even explain to myself, it just felt right. Maybe that's a poor reason to choose a new field, but it was one of mine, nonetheless.

Of course, that decision has brought a lot of things with it--like learning (obviously) immunology and, perhaps not so obviously, (re)learning cell signaling and physiology. I also realize that this choice all but guarantees taking a second postdoc before I start searching for my 'dream job'. Even then, it could very well count against me with some search committee/study section members that I switched fields. No one is guaranteed success in science, but sometimes I'm afraid that I might have made it much more difficult for myself.

But then I consider that one smart, successful immunologist decided to give me a chance--a chance to learn the field, yes, but also a chance to bring a fresh outlook to the project. He didn't bring me in and send the biochemist to purify antibodies or quantify binding constants. He gave me a problem that needs a biochemical perspective but is immunological at the core. Yes, it's been a bit rocky, but isn't almost every new project? And it's been exciting to see that the systems and pathways we're studying are slowly gaining more attention and interest--both in academia and industry.

I like this quote from Susumu Tonegawa in a recent piece in Cell about taking risks in science:
I keep telling young people, if you want to accomplish anything you have to be an optimist... You have to control you own life. You have to ask yourself why you do science. To put it bluntly, publishing papers in prestigious journals should not be the goal of a scientist. The goal is to discover something, to do something important.
In the end, it comes down to this: I chose to take a risk. I might fail. In fact, there's a good chance that I will fail--many times. I might even fail miserably. When I fail, I have to remember why I'm in it--for the thrill of the discovery, for the chance to have an impact--and pick myself up and go back again. And have as much fun as I can along the way.

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Thursday, October 8, 2009

As I was saying?

Just a couple of days ago I was commenting on the dearth of female Nobel laureates in chemistry and physics.

But then the 2009 Nobel Prize in Chemistry was announced, and Ada Yonath was among the triumvirate--the first woman in 45 years.

Tuesday, October 6, 2009

Progress?

Needless to say, the announcement of the 2009 Nobel Prize in Physiology or Medicine created quite the buzz in the science blogosphere, perhaps a bit more than usual because, for the first time, it was awarded to two women (and some white guy). This is fantastic...

...but it made me wonder about how often Nobel Prizes in sciences have been awarded to women.

The answer: 14 women in 106 years. Of those, 10 (including yesterday's announcement) have been in Physiology or Medicine.

It's interesting that the contributions of women in physics and chemistry were recognized much earlier than physiology. Marie Curie was awarded Nobel Prizes in Physics AND Chemistry in 1903 and 1911, respectively. Yet no woman has been awarded a Nobel Prize in either of these disciplines since the 1960s.

The selection of Nobel laureates is a bit of mystery to me. I don't think that this is some conspiracy by the Royal Swedish Academy to keep women down. I do think, however, that it is a reflection of general trends in sciences, namely that women have integrated into medicine and life sciences more rapidly than physical sciences. This is based entirely upon my own personal experience, and I haven't taken the time to research the statistics for this post. There were quite a few women (tenured/tenure-track/research) in departments under the purvey of the medical school at PSU, and in my current department at BRI, I know of at least 4 female faculty without looking at directory. In the chem department at PSU, there was a single female tenure-track professor when I started grad school--they did add another to the ranks during my time there. A senior research associate professor in my graduate lab relayed the experience of being told by a very famous organic chemist that women were physically too weak to do chemistry. WTF?

Is there some part of the process in physical sciences that selects for high levels of testosterone? It seems to be an issue of retention of women in the upper echelons. There were (and still are) three female faculty in the chem/biochem department where I did my undergrad (although that department did not have a PhD program). When I started grad school (in chemistry), our class was nearly half female. So what happens to them? My education and research has always tended toward biochemical/biological, so if I ever get my dream job, it will most likely be in med school or life sciences department. But, even though there are more women in medical/life sciences, the numbers don't add up for 'migration' of women from physical sciences.

I hope, by the time I reach the end of my career, that we won't be having these same discussions, that we won't be surprised when a woman--or two--take home a Nobel Prize in science.

Monday, October 5, 2009

Moving on

I realize that I've been feeling sorry for myself when it comes to research lately. I've decided that enough is enough. It's time to get over myself... move on... and get this shiznit done.

Goodbye, Safari... and good riddance!

I have been a diehard Mac person for the past 5+ years--ever since I got my first iBook in Bear's lab. I loved that the operating system didn't crash once a day. That the web browser Safari was functional and fast and didn't lock up.

Well, so much for that last bit. The newest version of Safari is giving me flashbacks to the old Internet Explorer. Ever since I updated it a few months ago (to the version that has tabs and the iTunes-esque view of favorite sites), the damn thing locks up at least once a day, and I have to force quit.

I finally got fed up with it and decided to switch to Firefox (which has had tabs for much longer than Safari). I had used it off and on, mostly if some site wasn't working on Safari. The newest version is sleeker and sexier than previous ones. And I like it. I've got the persona. I've got the tabs. And I've got some great add-ons.

Including fire.fm, which runs a feed from last.fm, which I am loving. Fee-free, commercial-free, personalized web radio. What a concept. Ever since I stopped driving to work about 3 years ago, I basically stopped listening to standard FM radio. I typically only listen to iTunes stations for a short time because (a) crappy quality, (b) buffering, (c) talk/commercials, and/or (d) music selection. So I am very much enjoying listening to high quality radio and discovering some artists that I've never heard before. Looks like its time to update my iTunes collection!

Now I just have to figure out how to move all my bookmarks from Safari to Firefox...

Saturday, October 3, 2009

Over and under

I have a confession. I feel like an impostor.

This is nothing new exactly. When I was finishing by undergrad and made the decision to attend grad school, I feared my advisers were think I was crazy... or stupid... or unprepared. I worried that that I wouldn't get into a graduate program... so I applied to 14 programs.

When I started grad school, coursework and proficiency exams made me feel as though there was so much more that I should have known already. I feared that I wouldn't be good enough or smart enough for the labs I rotated in. Being accepted to my first choice lab did little to allay those fears.

It was Bear* who first made me realize that I had placed limits on myself. I had always worked hard, but I had never been able to see myself making it as a PI at a research university. I had resigned myself to pursuing a career at a PUI** until Bear gave me his vote of confidence.

Now I'm in the postdoc phase, and I still have these feelings of not being good enough for where I'm at. These are the things I sometimes think about when I wake up in the middle of the night and can't go back to sleep (which is what I get for taking pseudoephedrine before bed). Those subconscious thoughts and feelings come to the surface and won't be ignored. Did I really contribute anything to new to Bear's lab? Did my committee really think I had proven myself worthy of a Ph.D., or did they just let me out because I had a job? Why the hell did Guru take me on as a postdoc? What was I thinking, switching to a field I know so little about? I try to be completely honest about what I have and haven't done. Does he regret his decision in hiring me? I'm in a department with brilliant people doing amazing things--what can I possibly contribute?

I feel overwhelmed by the tasks in front of me and underwhelmed by my perception of my intellect and abilities. It's particularly difficult to talk myself out of these self-doubts when I've had a couple of crappy research weeks (you know, the ones where you have trouble getting the simple, straightforward experiments to work). I don't really have anyone at BRI with whom I've established a close enough relationship to talk about these things.

I don't know if this will ever get any easier for me (I hope it does). Despite all these doubts, I won't let go of that dream of running my own lab. Sometimes I'm not sure if it's stubbornness or insanity or a true belief that I can and will do it. I'm absolutely afraid of failing, but I'm more terrified of never trying.

* Don't think for a moment that Bear was the Carebear sort. He could be--and indeed was--an ass on occasion. There were times he made me feel like a complete idiot, but there were also times that he let me know very matter-of-factly what I had going for me and the potential that he saw.

** I think I've said this before, but just to reiterate: I think there is nothing wrong with a career at a PUI. I did my B.S. at such a place and had a lot of fantastic profs, without whom I wouldn't even be in science. I just don't think it's
my gig.

Still not going to read it

There seems to a slight glitch with one of the email subscriptions for Cell Press: the ToC for Trends in Biochemical Sciences has been sent to me EVERYDAY this week.

Or maybe they're just being persistent in an effort to increase readership. I'm not falling for it! Not this week at least.

Thursday, October 1, 2009

Cell Press: Supplements not information dumps

The editorial in the current issue of Cell outlines new guidelines for supplemental materials for Cell Press publications. The contention is that, although supplements are a unique and "powerful advantage of online publishing", they have become dumping sites,
Unfortunately over the years supplemental material has evolved into a seemingly limitless repository for additional “stuff”: a wide range of control experiments, preliminary next-step experiments, data responding to specific reviewers concerns, results that just “don’t fit” within the main paper, extended discussions,and methodological details. It has become a mechanism for expanding the overall content of a paper without any delineated change in editorial standards.

In designing the new framework for supplements, the editorial board is imposing "conceptual" limits, as opposed to rigorous length limits. They designate three major "conceptual categories" for supplemental material:
  1. data that "provides deeper support for the points made in the main paper"
  2. large data sets and multimedia
  3. methodological detail
The idea is that the paper should be understandable to nonexperts, and the supplement should provide details that are important to experts (i.e. critical for repeating or building upon experiments described). Furthermore, each section of the supplement must be linked to a table or figure in the paper.

I will be interested to see how this works out. It sounds logical and reasonable and straightforward. In many high-impact factor journals, it is frustrating and sometimes even difficult to follow what the authors have done. My personal opinion is that the main paper should be able to stand on its own. I shouldn't need a 20-page supplement to believe the paper. That's what dissertations are for ;)

Tuesday, September 29, 2009

Words aren't always enough

As I was scanning through the ToC alert for last week's edition of
Nature, I saw a correspondence entitled "A communication wipeout by gabbling presenters", in which Dongwook Ko of Charles Darwin University in Australia writes:
I have noticed a trend among speakers at scientific conferences to speed up their oral presentations so that they can compress as much information as possible into their allocated time slots.Talking so fast can create a problem for those in the audience whose native language is not the one being used by the speaker — almost invariably English on today's stage.
I would say that 'talking so fast' actually makes if difficult for many in the audience, even if they are native English speakers. At least, it does for me. I am not an android. I cannot process a gig of data in 5 ┬Ás. And I cannot follow you--or the story--if you're blowing through four slides a minute.

Put another way:
More data ≠ better talk

The best speakers present appropriate background and clear, concise data in a well-organized manner. They also know how to keep to time, for the most part, such that they don't have to choose between flying through 10 slides in the last 4 minutes or running 15 minutes over time. Neither is a good option because you're going to lose some folks either way. Speaking clearly and at nice, consistent pace doesn't guarantee a good talk, but at least it gives your data and your story a chance to prove its worth.