Living on the edge of academia
drmaciver.com
drmaciver.com
This is why it amuses me when people stereotype academic scientists as impractical dreamers -- anyone who has stuck with the process of completing a PhD has demonstrated him or herself to possess a truly super-human tolerance for drudgery.
(Public service announcement: Hire a PhD! They need the work!)
Would you care to shed more light onto doing Comp. Bio research as a graduate student for someone who's seriously considering taking on 6-8 years of indentured servitude into the field?
As far as practical advice for someone contemplating a PhD in bioinformatics, mine would be: don't get a PhD in bioinformatics. There are no jobs, and a PhD is generally just a fantastic waste of time (unless you want to be a professor, and are comfortable with the numerous, well-documented drawbacks of that lifestyle). If you feel that you must explore the field, go far enough to get an MS, then quit.
I realize that's harsh, so I'll add some slightly softer, less-valuable advice: if you must get a PhD in bioinformatics, at least have the good sense to do it in a computer science department, so that you can go back into software when you find there are no jobs in bioinformatics. It's a dangerous mistake to get a PhD in bioinformatics from a biology department (ahem...do as I say, not as I do.)
Failing all of that advice, if you really, really want to be in bioinformatics, despite all good advice to the contrary, then make sure that you spend equal amounts of time at the bench and at the computer. If you want to be respected in the field, you have to have experimental results to back up your computer models, and the best way to do that is to run the experiments yourself. Run away from any program or professor who won't let you work at the bench.
But I appreciate you for also being very adamant about the "dark side" of academia; it would have deterred me if someone else didn't also warn me once about the "dark side" of going corporate (http://news.ycombinator.com/item?id=66390). I appreciate again your advice and will think it over very carefully when I decide as to what exactly I am going to do next.
But don't take my word as proof -- the Science Magazine Career forums are literally filled with sad stories of PhDs and post-docs in the biological sciences who can't get jobs. I wish it had existed when I started my program:
(One more thing: I just read the link to the other comments, and I don't disagree with what they wrote. Most software jobs suck, too. But the key insight here is that most jobs suck -- there is no magic bullet to career happiness. The corollary to that insight is that you need to fail fast; you must quickly work through the things that suck, and find the things that don't.
Because a PhD ties you to one thing for so long, it is almost the antithesis of failing fast. For this reason, I would not recommend a PhD to anyone, unless they explicitly wanted to become a professor, and knew exactly what they were getting themselves into. It's not the kind of decision that rewards indecisiveness.)
Doing biology is the only way to develop biological intuition. Sometimes this means pipetting and killing mice.
Ernst Mayr speaks to this:
"About two years ago, three years ago, for maybe the 20th time I went over the whole business of the species concept. What is a species? I looked at the major figures in the evolutionary synthesis, and I looked at Robzhansky and myself, and Huxley and Stebbins, all of us had reasonable species concepts, and the only person that had a species concept that I thought was quite absurd was the paleontologist G.G. Simpson. And then I said to myself, "Well, he can't have been a naturalist in his youth if he had such a peculiar, unworkable species concept." So I went to Simpson's biography and what did I find? I found that in college he was an English major. He had never been a naturalist as a youngster. He never collected anything, and he discovered geology in his senior year in college, and from there he went to stratigraphy and finally to paleontology. Not surprisingly, not having been a naturalist, he has no idea what a species is and he never had. I argued with him about the species concept year after year, but lacking that background, he was unable to see it, and that is the thing. Being a naturalist -- having had that background of being a naturalist -- gives you a view of nature that cannot be acquired just learning from books."
(Go to bottom of http://www.achievement.org/autodoc/page/may1int-5 for a video of him saying it while sitting next to E. O. Wilson.)
A few years ago, you could count on finding a job at one of the major Pharmas or in a software shop that serves one of them. But many of the pharmas are cash strapped and have been cutting "luxuries" like bioinformatics and software. My experience is that many biotechs are so small and narrowly focused, they often don't benefit from too much bioinformatics work. That leaves academia, but even there, the supply of PHD scientists is way higher than the number of jobs (this is actually a more general problem than in just bioinformatics).
I've often regretted that I didn't just go for a straight CS masters so that I could beef up some of those CS concepts you always avoid when your programming for fun.
I think you need to decide what your ultimate career goal is. If you want to be a PHD scientist getting grants and doing work at a university, then you have to go the PHD route. But if you think you want to work in industry, I would strongly urge a different route, one that doesn't paint you into a corner too much.
I'd like to see more of those papers, especially from industry. But to write such kind of paper, you usually have to devote to a successful project all the way through, which usually takes a few years or more, and then you can write just one paper. Not very efficient way to produce publications, and you might have to write a paper in your spare time, for your employer wants you to write code instead....
Hence, The Journal of Negative Results in Biomedicine (yes, it is actually called that): http://www.jnrbm.com/
Peter Norvig has some great comments on the problem of NOT communicating failed results in his article on interpreting research.
Most of this is findable in Google within 30 seconds. Often when I search for a paper's title, I get a pdf from the author's site before an official ACM or IEEE listing.
They don't advertise this; you have to ask.
Now, what's really annoying is market research. Friggin' Forester and their hundreds of dollars per paper. Hrmf.
Its true, 90% of the stuff doesn't work/isn't applicable and I have spent more money on buying papers than on rent in the past year, and I spend many days working on stuff that often has little or no positive effect. But its still the most cost effective research you can do, after you factor in the value of your time.
Every new idea I develop on my own takes far longer to develop and test, and trying to get better results than everyone else is a lot easier when you're basing your progress on the cutting edge instead of something that is a decade old.
1. http://en.wikipedia.org/wiki/Open_notebook_science 2. http://network.nature.com/groups/harvardpublishingforum/foru...
1) An implementation is not important. We developed an algorithm!
2) Uh... the student who made the program already left and we can't find it.
3) [the student] I can no longer find my notes on which parameters I used to make the figures of the paper.
Very rarely, nearly never, does one encounter a proper software release.
Why? Many reasons--the key point is that only a handful of research institutions have technical staff on board to collect and curate software produced in house.
You find most of the innovation and creativity out in the startups and small businesses.