Please standby

I had plans for tackling some lab work, house work, and blog posts yesterday. Said plans fizzled out after I started feeling like crap, thanks to Paramed's bug, which also zapped all higher brain function. Sleeping 12 hours helped a great deal.

This morning I get an email from Guru wanting some data for a grant... due next week. I just started working on the project last month. Some of the data requires a little more processing and analysis but can be ready within a day. The other data is more problematic. The experiment has been done, but the data doesn't look great. No one in our lab has worked on this particular model, and it was my first time doing it, so things are far from perfect. I can try to salvage something from it, but it's not really grant quality material, in my opinion. As an aside, I explained the problem to Guru and received a response that there is an art to technique that is an integral part of the experiment, and I should talk to Jack and Jill who have experience with it. He couldn't mention that before I had already done the entire experiment.

Anyway, a critical element for repeating the experiment has been unavailable and was just ordered Friday. I think I'll be able to start the experiment about midweek, and then it will take 3 to 4 long days to crank through. I had already planned to repeat the experiment. Now I'm just doing it on a compressed timetable. So if I disappear from the blogosphere for the next week or two, it's not that I've fallen off the face of the planet. I'm just chained to my bench or sequestered in a dark windowless room, trying to hang on to my sanity.

Best of luck to everyone else this week!

Critical reading vs. reading critically

"I can't believe that's a paper."

This was the statement of a colleague--we'll call him Ronald--upon seeing a manuscript on my desk. To my knowledge, he had not read the paper, or even the abstract, just the title. It was not groundbreaking work by any stretch, but it was a nice little methods paper published in a methods journal. It seems that part of Ronald's disdain derived from the fact that he had used the same reagent to label the same tissue for a slightly different technique. Since it was such an obvious and simple method, which Ronald and others in his previous lab had used under other conditions, clearly it was unworthy of publication*.*When something pisses me off, I am prone to using hyperbole--extensively, as you may note here. Although the statements here are not as absolute as I make them seem, the sentiments therein ring true.

Normally I get along quite well with Ronald, but that simple statement pissed me off, perhaps because it is just one example of a attitude among many postdocs at BRI and, I suspect, science in general. Almost inevitably discussion of a paper or seminar focuses on everything that's "wrong" with it: how they did the wrong experiments, used the wrong model, how limited the scope of the study is, that it's not novel or groundbreaking work... Sometimes they have perfectly valid points, but they seem to dismiss the value of the publication because it's not what they would do. They spend a lot of time thinking about how to invalidate the study and ignore its positive contribution to the field. There are a few exceptions: papers published in top journals of the field (unless published on study in direct competition with their own work) and papers published by colleagues and non-competing collaborators.

In graduate school, we are supposed to learn to read the scientific literature critically. The issue is what that means. Many people--especially trainees--use the first definition of critical: "inclined to find fault or to judge with severity, often too readily". We should be using the third definition: "involving skillful merit as to truth, merit, etc.". We're supposed to be looking for good and bad, right and wrong, founded and unfounded, and all degrees in between. When we finish reading the fucking paper, we should have a clear idea of what the results actually demonstrate, the caveats, and its utility, its contribution to the field.

Scientific publishing, in theory, is about the dissemination of knowledge. Some papers are going to change how we think about science or fill in large gaps of a given question or pathway. But not all papers will be "paradigm changing". Some papers reaffirm and expand upon what we already know; these are critical because, as we have seen time and again, there is usually something wrong with the process if no one can reproduce the results of another lab. Some papers alternative interpretations; even if in the end the alternative is wrong, these should help prevent development of tunnel vision, becoming so enamored of our own hypothesis that we become blinded to other possibilities. And some papers are reports of "simple" methods; these keep us from having to reinvent the wheel every time we do a new experiment and sometimes provide faster/cheaper/more sensitive methods than we had in our repertoire. The vast majority of manuscripts are not going to be published in the Cell/Nature/Science families of journals; this does not mean they are useless. It's time for postdocs (and maybe other scientists as well) to reevaluate how we read papers and determine the worth of a publication.

As an aside for those with access to EMBO Reports, I recommend checking out System Crash, a Science & Society piece about how emphasis on high impact publications and focus on short-term gains are affecting science.

More than they bargained for?

In case you haven't noticed, I really enjoyed my time in my undergrad chemistry program. The department was pretty small. There were around 10 faculty conducting research; each worked with one to four undergraduate students, and a few had a M.S. student working in his/her lab. The real focus was undergraduate education. Even in my largest class (first semester general chemistry with close to 200 students), there was ample opportunity to meet with the professor outside of class and really learn the material. For the most part, professors connected with students, even if they were not a chem/biochem major. Many faculty fostered the interest of their students in science and got them involved in research. I discovered my passion for science in that department.

Perhaps this is why it made a bit sad when university administration more or less mandated that this wonderful undergrad department start a Ph.D. program. The move did not seem to make much sense. There was little (if any) faculty support within the department for such a program. Most of the faculty were there because they wanted to teach at a PUI. The department did not have the facilities and resources to support a robust Ph.D. program. The scope of the program had to be very specific because it was a public university and the flagship school up the road had a large and widely recognized program in chemistry. There was concern among faculty about setting standards for admission and trying to compete with neighboring universities.

Now add to this the delicate balance of trying to keep their status as a PUI to maintain eligibility for many of their grants. My understanding (based on the definition in this report) is that status as a PUI is determined by the total number of Ph.D.s granted across all NSF-supportable disciplines. The university must award, on average, 10 or less doctoral degrees across all fundamental science and engineering departments.  Even if the chemistry program only grants 2 or 3 Ph.D.s a year, they may lose their PUI status depending on the number of Ph.D.s awarded in other departments. Coincidentally some of those NSF-supportable disciplines at the university are now touting their own new Ph.D. programs. (I am not as familiar with NSF as NIH funding mechansims, so I may have misinterpreted. There may be other definitions for PUIs used by different funding agencies. Feel free to correct me.)

Cruising around the web, it's difficult to ascertain just how limited--or widespread--this sort of expansion is (or I'm just not sufficiently perceptive or committed). The NSF survey reports doctorate-granting institutions, not programs/departments. U.S. News & World Report only ranks those programs that have produced 5 Ph.D.s in 5 years, so new programs don't show up.  I know of at least one other chemistry program at a PUI that succeeded in adding a Ph.D. program in the last 5 years. The question is, do we really need more Ph.D. programs? At least in biomedical sciences, the National Academy of Sciences said, "No." The report (now 10 years old) states that the number of Ph.D. graduates (which has been slowly increasing since) was sufficient to maintain the workforce.

So what is the advantage to the university? The driving force is not immediately evident to someone who has been only been on the student side of the line... and who has seen the funding situation deteriorate. Is it just another feather in their cap? Is it meant to add to their prestige? Or is it (more likely) about money? Does the addition of a Ph.D. program allow them to petition the state for more money? Or perhaps draw more in from alumni and benefactors? Is this another example of academic glut or filling a legitimate niche?

Into the void

In a recent discussion about the shifting focus of my project, Guru asked if I wanted to learn super cool method. I did. It was one of the reasons I chose his lab, and I told him such. His response: "You're too shy about telling me these things." This conversation made me realize that I may not have been very clear about what I'm expecting out of my time at BRI... and clarifying what is expected of me.

Oftentimes grad students and postdocs don't speak up, at least not with advisers. On an earlier post about establishing mentor and mentee expectations, DrDoyenne relayed her husbands feeling that trainees "failed to ask questions about what was expected of them or to speak up when they did not understand something". This is equally applicable to other areas of interaction with our advisers. We have a tendency to hide behind a mountain of excuses, and we lose out.



Widening the gap
Many times, when we fail to speak our mind or ask questions, we widen the communication gap between us and our advisers. So why do we do it? I briefly highlighted some reasons in my earlier response to DrDoyenne, but here are a few (expanded) contributing factors in my mind.

Village idiot/impostor* syndrome
*"Impostor" added in response to an excellent point by PhDamned
When you're starting in a new lab and/or new field, you sometimes feel like the village idiot. You don't know all the techniques, the terminology, the data from years of research that have pushed a project forward, the status quo on lab meeting presentations, typical expectations, and so on. You don't want to ask the obvious questions--whether or not they are, in fact, obvious to everyone. When you're the n00b, you can get away with some things, but you're not really sure where the line is. This is exaggerated when you're a postdoc because you already have the Ph.D., which means you should know some of this stuff; at least this is what you tell yourself. So you sit quietly, trying to understand what's going on, feeling completely lost.


Mule syndrome
Science selects for trainees possessing some sense of independence and persistence. This statement contains more truthiness, if you've decided to follow the tenure track. Independence and persistence are good--in the appropriate context. However, some of us could be described as stubborn as mules, which sometimes keeps us from asking for help when we need it.

High IF
Not impact factor, but intimidation factor. For some, speaking to anyone in a position of authority, is enough to silence them. This is feeling can be intensified by the adviser's standing in the institution/field (big cheese=high IF) or a trainee's perception of the adviser's personality. Regardless of the reason, when we feel intimidated, we tend to avoid interactions, especially if we are bringing in problems instead of solutions. And when we are forced into interactions, we hold back.

Past is present
We are all human, which means we carry our experiences and memories into current and future situations. If we've had difficult interactions with our current adviser or an adviser in the past, then we are hesitant to risk putting ourselves in a similar situation again. We also look to colleagues' interactions with our advisers. We hear "horror" stories from past or current lab members about how critical/apathetic/irrational/(insert your own key word) the PI is in one-on-one interactions with them. We sometimes let these shape our own interactions with our advisers--missing the point that other lab members' interactions and perceptions are colored by their own personality and experiences.

Other planet complex
This is a point we've touched on previously. Sometimes we connect with our advisers. We speak and she/he understands what we're saying and vice-versa. Other times it's almost as though we are on different planets speaking different languages. It's frustrating. We think we know what our advisers want/are asking and respond accordingly, only to realize they want something else entirely--and we can't figure out what that is.

Bridging the chasm
The communication gap between adviser and trainee must be closed if we're to have a productive and long-lasting relationship, something which will impact our careers. How do we do that? That's one I'm still working on, but this is my view so far: Try to figure out the major cause for the gap and adapt. There are some things we cannot change, like our past experiences or our advisers' personalities, but we can change how we react to them. For instance, I have to remind myself that Guru is a very different adviser than Bear, and I need to adjust how I communicate with him. We can also look to colleagues that do seem to communicate effectively and evaluate what they do differently.

In all this, though, we have to keep a clear idea of the purpose for this relationship. This isn't about making your adviser a drinking buddy or establishing a "sunshine and rainbows and lollipops" relationship with him/her. For me, this is about making me a better scientist and future mentor. I will not always like what Guru (or any other adviser) has to say; the critical point is that I appropriately interpret what he's saying and that I find my voice and make sure it's heard.

Choices: Graduate program edition

It's that time of year. The applications are in. Undergraduates (and others) around the country are waiting to hear if they've been accepted or invited for an interview. In less than three months, they will have decided where to spend the next 3 to 7 years. Between now and then, they will be gathering intel--scouring websites, talking with PIs and students, visiting campuses--which will inform their impending decision.

The whole process can be overwhelming. I was pretty clueless going in. I knew I wanted to pursue biological chemistry research. I had found professors whose research I was interested in. Beyond that, I didn't know what to expect or what I was looking for in a graduate program.

My undergraduate training was at a mid-sized state school in a small department, which encompassed chemistry and biochemistry. My experience and interactions there certainly influenced my views of what I wanted. I gravitated toward programs that had a similar atmosphere. This meant programs that were highly collaborative and multi-disciplinary in practice. I was weary of departments and labs in which PIs talked about collaborations with people across the country or half way around the world, but never mentioned working with colleagues in the department. I recently described my philosophy regarding divisions between disciplines and subfields of chemistry and biology, a philosophy I held even as a prospective Ph.D. student. I felt then (and still do) that it is difficult to integrate and advance related disciplines if a department imposes rigid barriers between them. I realized later that the rigid structure often went along with a seeming lack of collaboration within the department. I also stayed away from programs in which there seemed to be a great deal of tension between students and their PIs. This was largely rooted in a lack of self-confidence. I could not envision myself going head-to-head with an adviser on a regular basis, nor could I imagine being silent or deferential during repetitive conflicts, especially those unrelated to research. I also could not see myself doing well in a cutthroat department.

I heeded the advice of my undergrad professors. Dr. D told me to find the student who had been in the program the longest, who would have the most experience with the program, the most reason to be bitter, and usually the most honest responses. If you talk to that person and he or she doesn't regret joining the program, then that's a good sign. I did just this on my visit to PSU. Someone else suggested asking basically everyone I met about the typical length of a Ph.D. in their program and how long they had been there. In chemistry, an average beyond five years was viewed as problematic. An issue that revealed itself was that many programs stop providing funding to students after six years; in some of the same programs, it was not unusual to take that long or longer to complete a Ph.D.

Dr. K, another undergrad instructor, counseled me to not pick a program if there were not at least two advisers that I could see myself working for. Although Bear was my first choice for mentor, I saw the wisdom of this advice play out in my program. There are several reasons you might (have to) pass on your first choice PI. You might realize that you'd rather be mauled by hyenas than work for your "dream" adviser once you do a rotation in his/her lab. A PI's funding situation may not allow him/her to take a new student the year you arrive; hopefully this is something you would know before choosing a program, but there is no guarantee. If the PI has a tenure review and doesn't get it, he/she may choose to go somewhere else. Or there may be a high level of interest in a given subfield the year you join. Among my first year colleagues, there were 8 people vying for 6 spots in three labs. Needless to say, two didn't get into the labs they wanted. One of them found a suitable alternative; the other postponed joining a lab for almost another year. The point is things happen, so it's good to have more than one option.

Looking back, perhaps one of the most important things about the application process was figuring out what I really wanted. The questions I asked myself were just as important as the ones I asked others. What was most important to me: sexy science or sanity? What was I willing to compromise on? Was an ultra-competitive or a collaborative environment right for me? I spent time thinking about my experience and my level of comfort and confidence. As a prospective grad student, I didn't have much of any of those. I chose the program where I could see myself succeeding at research that excited, where I would learn from my instructors, my adviser, and other labs. It was a good program--a great one in my book, actually--but not the "best" of my choices (at least according to the U.S. News and World Report). But in hindsight, it was the best program from me. I went in as a timid undergrad but left as a confident scientist. And that's what it should really be about.

The future of the Scientiae carnival

Scientiae is facing a crisis--where does it go from here.

If you're new to the blogosphere (and maybe even if you're not), Scientiae is a monthly carnival built around stories of and from women in STEM. It's been going for three years now, but of late, contributions have been dropping off. So what is to become of Scientiae? skookumchick writes:

So the question arises: is there still value to having Scientiae? Or should we shut it down as a great community-building tool whose time has come to be let go?

Several bloggers, including myself, would like to see it continue. Among the commenters, there are enough volunteers for hosting to cover almost the entire year. But jokerine comments:

The trouble is, just wanting to read it isn't enough. I want to read it too, but I hardly contribute anymore and I was a horrible host. Hosting isn't any fun if there are no submissions.

Carnivals die without contributions. In response, I have pledged to contribute to the carnival at least seven times in the next year, should it continue. I chose this number because of my blogging frequency and my interest in previous carnival topics. I also want to point out that, even though the focus of the carnival is women in STEM, anyone is invited to contribute. Learn more about the carnival, then voice, er type, your opinion about the fate of Scientiae. Personally I hope we can keep this community carnival going :)

Put on your game face

Bright-eyed and bushy-tailed, most new grad students have a fairly altruistic view of science, even if they hold a more cynical view of the world at large. When you are just starting down that path toward a career in science, you often think only one thing should matter: the science. You are convinced that this is what you'll spend the vast majority of your time doing; that science will be the sole focus of you, your peers, your superiors, your collaborators; that as you advance in your career, you will be evaluated on the quality of that science.

Here's the thing about science: It's done by humans, which means human nature enters into the equation. There are two dicta of human interactions, which complicate things:

• Where two or more people are gathered together, there also shall be disagreement.
• Where four or more people are gathered together, there also shall be factions.

There may be exceptions (but I'm doubtful). In my experience though, anytime you get a group of people together, even if working for a common purpose, politics enter the picture--even in science. chall's post on work politics she's dealing with really got me to thinking about this. The politics don't stop at the lab; they extend into departments, institutes, entire fields of science. How we engage, how we react can impact our careers. It sometimes comes down to how we play the game.

Navigating politics can be a challenge. If you're new to a lab, the dividing line is not always clear, as chall points out. Honestly, this may not be a bad thing; it's easier to stay out of the politics in this situation. Being a veteran in a lab is not always beneficial because the politics can bog you down. They can sap a lot of energy and focus out of you that would be best spent on other things. Trust me. I went there in Bear's lab; it was exhausting and infuriating. There reached a point when things in my life outside of the lab were taking so much energy that I couldn't afford to put any more into frustrated factions. I was far more focused when that happened.

This does not mean we can completely ignore the politics of science and units therein, but we do have to learn the rules of the game and how to choose our battles. Here are a few things I've interpreted from experience and observation during my relatively short time in science (in no particular order):

• If you're at an early career stage, tread carefully, but...
• Occasionally you have to show someone that you will not be his/her doormat.
• You can get by with a lot until you piss off one of these people: the lab manager, the lab admin, or the PI.
• Try not to burn bridges. Any given field of science is a small world after all. You never know when you might be working with/near/for someone you thought you'd never see again.
• You have to be seen. In a meeting with grad students following a seminar at PSU, Ben Cravatt shared one lesson he wished he had learned before starting his independent career. He commented that he thought working hard and doing great science would be enough to get the high profile publications and funding. He realized shortly thereafter that he had to be seen; he needed to go to meetings and present his work, so that he could connect with the people that would be reviewing his manuscripts and grants and begin to establish name recognition. In short, build a network.

To an extent, grad students and postdocs are insulated from the politics of their institutes and fields, which places a definite limitation on the list I provide here. Add to this, that every department and field has its own culture and political climate. The rules of play vary widely, but in academia, those who have successful independent careers learned to navigate the political landscape without falling off a cliff. We have to do good science, but we also have to learn to play the game.