The Hammer Falls...

To anyone outside of the Ivory Tower many of the posts on my blog probably make it seem as though academia is a complete mess. Unfortunately, this is at least partially true - standards of achievement vary wildly among institutes, departments, and even individuals. Ask any number of professors what you should be striving to accomplish as a wannabe professor and they're likely to give you a substantial number of different responses (some aspects, e.g., work hard, publish good papers, etc. tend to be invariant).

A good example of this is the very act of postdoc-ing: What should an interested, newly minted Ph.D. be looking for in a potential postdoc? What should a new postdoc be trying to accomplish during their tenure? On these subjects, as above, I've gotten a few different responses.

One popular answer to the former question is that a postdoc is a time when you should be 'consolidating' your interests into a viable research program. Basically, you should be focusing on publishing some big papers in your field of interest that will get potential employers interested in hiring you to pursue your work with a lab of your own. I've been told that in order to accomplish this goal, you shouldn't enter a postdoc that involves too radical a shift away from the skills you learned during your Ph.D. - that is to say, don't start doing something completely new1.

On the other hand, there have been a few folks who opined that a postdoc is an excellent time to diversify your skills. Also withing the confines of this view, I was told that the postdoc is the best time to be a scientist: You're much more independent (and well-trained) than most graduate students, but you're still free to pursue your own research, free from the later demands of writing grants and running a lab.

While I see some of the wisdom in the second perspective (I have certainly learned a ton of stuff in the ~16 months of postdoc-ing I've done), I have to admit that 'mine' own experiences are probably more in line with the first one. I'm way too busy as a postdoc to spend any significant amount of time improving my skills in areas that are not directly related to my research. I've always got at least 3 projects on the go involving significant time investments, and almost everything I've been doing has clearly defined deadlines - Our lab is involved in the Drosophila ModENCODE Project, which involves a large consortium of labs and thus deadlines are inevitable. When the hammer falls and deadlines loom, the practice of science changes radically: No longer is it the purely intellectual journey of discovery, but rather the focus shifts to determining 'deliverables' and getting s$%t done, ASAP. I'm in one of those periods at the moment, unfortunately.

The funny thing is that, while I'm learning a ton of stuff during my postdoc, I tend to feel that I have less time to reflect and absorb said knowledge than I did during my Ph.D. For instance, during grad school, I began creating text files, wherein I would type summaries of new computational techniques I'd learned that would be useful in subsequent analyses (I had a file on Linux commands, a file on R, a file on PERL, etc.). While I still refer to these files daily, I find it difficult to expand them with the new information I've gained. I'm typically running through analyses so quickly that I don't feel like I have time to explore all of the details of some of the software I use - much to my chagrin2. I've kind-of resolved myself to take a little time here and there to beef up my text files and if I can get them all nice enough, I may even post them here on my site.

Oh well, what else is new, right? I began this post by remarking on how opinions about what I should be doing vary, however, it's pretty clear that the current consensus is somewhere along the lines of 'work your ass off, publish as much as possible, make sure people know who you are.' I'm sure that other people's experiences are different though. If so, I'd love to hear about them!

P.S.: I would like to give a shout out to looniechemist, who runs the blog 'An American postdoc in Canada' and who wrote an interesting post about her early experiences as a postdoc that got me thinking about writing this post.

1For instance, my Ph.D. was a pretty radical departure from the sorts of skills I learned during my undergrad and Masters (I switched from Biochemistry to Evolutionary Biology). This led to me essentially 'burning' a year in order to bring myself up to speed in the field - something I don't regret in the slightest. On the other hand, burning a year as a postdoc is potentially devastating. 

2I think that this has serious implications for the quality of science produced using certain types of software, and I'll expand on this in a future post.

The Myriad Variety of Writing Styles...

I'm often driven to ponder how I'd handle the opportunity to teach or mentor students of my own someday. As many people realize (typically at some point during graduate school), professors are usually never formally taught  how to teach or mentor. I say 'formally taught' in the sense that there are no specific 'classes' that teach effective mentoring skills. In my experience, a large part of learning in science is accomplished via personal observation (e.g., how you or others were mentored) as well as the 'learn-by-doing' philosophy1.

I've been exposed to four different research labs in varying capacities, and one particular aspect of mentoring that has varied considerably for me is how different PIs expect you to write a scientific paper (something that I'm in the process of doing, so it's weighing on my mind). Now, to anyone 'in the know' this isn't particularly surprising - it seems that everyone I talk to has different opinions on which section should be written first, or how it should be laid out, etc. What I've found can be challenging is that I have a particular style that works properly for me, but not necessarily for everyone else.

It's probably because it was my first opportunity to write an actual manuscript, but I've subscribed pretty strongly to the writing philosophy of my M.Sc. supervisor: With the exception of the abstract, a scientific paper should be written in the order that it is presented. So a typical paper is laid out as follows:

ABSTRACT
INTRODUCTION
RESULTS
DISCUSSION
MATERIALS AND METHODS2
REFERENCES

As my M.Sc. supervisor argued, by providing background as to what research has come before, the introduction necessarily establishes how the results should be presented (what should be emphasized? What are the novel contributions that this paper is making?). Similarly, the discussion requires the context of the introduction to interpret the results.

I know that this is not necessarily a popular method of writing. Much more common in my experience is the idea that you should write the results first, then worry about the other sections later. Another variant of this that may be popular with people who come from a genetics background is that you generate the figures before anything else, and then write the entire manuscript around those3. My work is typically fairly computational and there are often many different ways to anazlyze the same data. One of the great 'travesties' of exploratory science is that too often we try to extract all kinds of meaning out of complex data, whereas proper experiments should be designed to test specific questions. Of course, some data are arguably generated in a question-agnostic manner (e.g., large scale gene expression analysis), but the way that you analyze the data is nevertheless contingent on the questions you want to answer. My opinion is that knowing what questions to ask comes from the information contained in the introduction. 

Anyways, in an era of big collaborative manuscripts, writing styles seem destined to clash. Either we get along and modify our approaches, or some privileged few 'pull rank' and lay out the program. And thus we return to the question of mentoring: Is it better to 'teach', and potentially enforce, a particular style, or is it better to encourage a student/postdoc to develop those skills that seem to work for them? Probably a tougher question than I realize, but regardless, I figure it's best to get them while they're young. It's notoriously difficult to teach an old dog new tricks ;-)

1For instance, during my M.Sc. I had a class on effective scientific communication that essentially boiled down to choosing a paper and being marked on your ability to present it. Many students complained that the class didn't include any aspect of actually being taught how to effectively communicate science. Your 'lesson' also happened to be your exam.

2Yes, the position of the M&M section can vary, and it can be written last regardless.

3In certain fields, the figures are the results, but such is not always the case.

Thoughts on Peer-Review...

Peer-review is often touted as one the quintessential reasons for why scientific knowledge is more reliable than that obtained from other mediums: Experts in the field are required to go over submitted manuscripts and vet both the quality of the data and arguments being presented within. But how is peer review performed in practice? Essentially, as a member of a scientific field, you are expected to review manuscripts that are sent to you by editors of scientific publications, pro bono. All in all, I don't think that most scientists would argue that this is not a worthwhile endeavor for the greater good of the field.

This being said however, in some discussions I've had with fellow scientists, I think that many feel that there is a bit of a 'free ride' problem when it comes to peer-review. Though peer-review is designed to weed out those manuscripts whose work and interpretations do not fit the standards of legitimate science, one would expect that most manuscripts will be good enough shape by submission time that the task of the reviewer will involve judging only the content itself. Unfortunately, this is not always the case.

Various factors lead to incomplete manuscripts being submitted. A principle offender is likely the ability to list 'submitted' manuscripts as achievements in grant and scholarship applications. As the deadline for such applications loom, there's a strong pressure to get any 'nearly' complete manuscripts into the hands of a journal. Assuming that such manuscripts are not rejected outright, these greatly increase the amount of work for a reviewer, because in addition to evaluating the science itself, you may now be trying to parse poorly written sentences and incorrectly labeled figures.

Oddly perhaps, there are no 'classes' where you learn how to properly peer-review manuscripts. I suppose it's one of those things that you're supposed to learn from your various mentors - though in my experience, standards for acceptance/rejection vary widely between different people (which is not a bad thing if you value a diversity of opinions). However, I've never encountered a situation where someone thought it was okay to simply reject a manuscript outright because it was incomprehensible as written, thus requiring tedious reading of obscure references and external sources in order to understand what was being argued.

It is my impression that the number of papers being published is out pacing the number of new Ph.D.s actively working in academic scientific disciplines. Thus the pool of reviewers per capita is shrinking. I worry that at some point either we're going to have to work hard to make sure that manuscripts are of excellent presentational quality prior to submission, or the hammer is going to have to fall and more papers are going to get rejected outright for even minor 'preparational' offenses. Scientists are generally busy enough already.

Sacrifices of The Academic Life...

As I approach 30 I've begun to think about things that previously didn't bother me. You know, stuff like: What do I want to do with my life? Where do I want to live? Do I ever plan to start a family? I can only imagine that such mental meanderings are typical at this point.

However, I have begun to spend more time thinking about one issue in particular: The large number of sacrifices that one has to make in order to attempt to pursue a career in academia. Two recently published articles, one in The Economist (The Disposable Academic) and a more recent opinion editorial in Science Careers (Falling Off the Ladder), really hit home. The supply of Ph.D.s in most fields vastly exceeds the extremely limited demand, and yet the number of Ph.D.s graduating seems to be perpetually increasing. Thus, competition for a very small pool of 'dream' jobs is extremely fierce, leading to work loads that routinely blow the minds of people outside of the field: You work from 9-7 on weekdays, continue working evenings, and routinely put in full days on weekends?

The defense of such an arrangement is always the same: It doesn't 'feel' like work if you love what you do! For a long time I was able to take comfort in this very mantra (and I must admit that it's still somewhat comforting nowadays as well), but I've really begun to think about whether it's healthy. I love science of course, but surely being economically destitute, and having absolutely no certainty about future job prospects - even to the point of having no good idea when I'll even be able to apply for prospective jobs - does not contribute to life satisfaction and mental well-being.

If I am on a career path towards academia, at least I can say that I'm doing pretty well. I've got a decent number of publications, a fairly robust set of skills, and an idea for a 'niche' that I can carve out for myself in terms of research projects. I guess that as the pressure builds and the duties grow, these types of thoughts eventually must bubble to the surface. There are career options other than those of a lab P.I. (Principle Investigator) - I wonder if many people go through a Ph.D. knowing that they'd rather do something different than academia? Or does everyone want to be a P.I. at first?

Trying Something New...

One of my great pleasures during my Ph.D. was blogging and participating in the community surrounding blog culture - The 'blogosphere' if you will. I managed to post somewhere along the lines of 3 posts per week on average, which I was satisfied with given the demands of school and life. I'd hoped to keep up a similar regimen during my postdoc, but for a while, it just didn't seem like I could pull it off.

So far, I've found postdocing to be far, far more time consuming than doing a Ph.D. This is partially work-related (I generally work from 10-7ish plus weekends, whereas during my Ph.D. I was more 9-5 plus weekends), but also compounded by 'externalities'. I now commute by bike 45 mins each way and try to go to the gym every morning. Thus I leave at 7:30 am and get back at ~8 pm. Factor in getting stuff together for the next day and there's little time left.

All this being said, I'm finding that this work all day followed by vegging out at night is becoming unsatisfying. Between Monday and Friday, I accomplish little in the way of non-work related personal development. Looking back, I know realize that this extracurricular stuff was a major factor in what got me so heavily involved in research in the first place. I read tons of science and humanist related material, which kept me immersed in the culture. I also got to incorporate some of the former into my own research.

Keeping up a website (or blog) is a form of personal development as well. On the rare occasions during which I felt the desire to revisit earlier posts on my former website, I realized how much I've improved at writing down ideas over the years1. My current focus on getting a research program up and running (which seems to be going quite successful so far!) hasn't left much room for writing, and I fear that I've been falling out of practice.

A few months ago on my former blog, I said that I wanted to get back into blogging. I meant it, but did a very poor job of following through with my intentions. There are many reasons for this, but one critical factor hinged on the baggage that my former blog carries. It was written druing a different period of my life, under different circumstances from which I've now moved on. I'm happy with the discussions I had on Musings of the Mad Biologist, but it's time for me to start something new.

All of my future musings will be here. Stay tuned.

1Please don't misconstrue this as tooting my own horn. I'm constantly trying to improve my writing, but it's heartening to see the progress that I've already made.