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...


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


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.