Monday, March 24, 2008

Useful things you'll need to know for modern biological research.

A nervous student interested in grad school asked me to elaborate on this since I said most undergrad departments don't teach what you actually need to know to do modern biological research.

I have lots of coy ideas for this post. For example I considered writing simply:

If someone would give me a faculty position, I could just teach it.

But since other helpful commenters have written things like:

No department would ever hire the person who writes this blog

I guess you probably don't want to wait that long to hear what I think. It could be a while.

---

I think most funded biological research now is biomedical. That could be a generalization, but I think most biology that's not even slightly related to medicine is probably underfunded these days.

That said, let's assume the basis of modern biomedical research is molecular and chemical.

Currently, biomedical research includes computational, nanotech, physics, and mathematics of biology.

At least, that's the stuff that gets funded.

Once upon a time, a few decades ago, biology departments did a lot of genetics research. They still do, but maybe not as much. Now it's a lot of stem cells, drug delivery, and signal transduction.

So far as I can tell, lots of departments still teach phylogeny like it's the epitome of biology and the obvious place to start.

Well, it is and it isn't. I personally think you can skip it, or maybe do it later on rather than as an 'introductory' course. It doesn't frame anything, really, so it doesn't make sense to do it first.

---

They still teach a LOT of genetics, and that makes sense to me.

DO take at least one genetics class.

If you want to work with flies or yeast, or make knockout mice, take more genetics. Lots more.

Otherwise, stop there and make sure you got at least 1 good semester of organic chemistry.

I don't mean memorizing and spitting out, I mean DID. YOU. GET. IT.

Do you know the pKa's of the amino acids?

Do you know what a buffer buffers?

Why are some things soluble in water while others aren't? What should you do about it if you need something to dissolve and it doesn't?

How does PCR work?

How long does a PCR primer have to be to make it specifically bind a sequence of DNA?

---

Take statistics.

Take differential equations.

Take a nonlinear dynamics course if you can get into one. It's usually a pretty high level elective.

If you can't do that, read Sync by Stephen Strogatz.

---

Take some history of science. Did you read The Double Helix and The Dark Lady of DNA?

Have you read a biography of Marie Curie? There are several to choose from. How about Barbara McClintock?

---

Did you do optics in your physics class? Do you understand how microscopes work?

What about lasers?

Lots of modern equipment is based on lasers and fluorescent light. Do you understand where fluorescence comes from?

What's the one critical feature that lets us separately detect different colors of fluorescence dyes?

Do you know how modern DNA sequencing works (hint: it uses fluorescence)?

---

How's your computer science? Could you write a program to sort files for you if you knew the file name format? Do you know what symbols are generally frowned upon filenames, and why?

---

Do you know how to use PowerPoint? What about a spreadsheet program? What about Endnote?

Have you ever taken a writing course - of any kind?

Have you ever taken a public speaking course?

Have you ever taken a drawing course?

---

I'm not saying you have to know these things. I'm saying you should make it your business to learn these things.

I could make a much longer list, but I'm kind of tired. I spent the day on an experiment that didn't work.

Oh yeah, I forgot to mention that if you want to do biological research, you need to learn how to deal with failure on an almost daily basis.

I know, they don't teach THAT in college.

I learned it from my extracurriculars. Ever watched America's Best Dance Crew? You should, because dancers are used to getting criticism even on their best work, EVERY DAY. Musicians too. Sports are the same way, if you play semi-seriously, your coach will be on your ass to always be improving.

If you can handle that, and be your own coach, you'll do okay.

You have to learn how to pick yourself up and just keep bashing your head against the wall until you make it through.

Most people don't learn that until the end of grad school.

If you already know it going in, you'll probably wonder why everyone else is always complaining.

Labels: ,

25 Comments:

At 10:47 PM, Anonymous Anonymous said...

Figure out how to delegate and remain in control. Feel confident in asking for help. Do these things without feeling too much obligation to the people who you are relying on to assist you.

Take every fair advantage you can. Expend political capital when you must, but make sure that you have some left for a rainy day. Stay in touch with mentors and find an excuse to visit them every few years.

Apply for every source of funding you are eligible for. $$ brings freedom.

Insist on going to at least one meeting a year after your first year in graduate school. Make sure you have done enough work to justify this. Get yourself known outside of your own institution.

Realize that every day is a job interview. Act accordingly.

Get some industry experience. It doesn't matter where.

Learn how to use one analytical method really well and develop an extension of that approach. It doesn't matter what - sample prep, data analysis, multiplexing, miniaturization, automation.

Realize that without supply side controls on the number of postdoc-trained bioNNNists, you will need to be good and lucky and relevant and funded and sociable and eloquent and well-connected and ... to get an independent academic job.

Don't sacrifice yourself for your job.

[cynic]
Learn to live with yourself after you screw over people around you.
[/cynic]

 
At 12:09 AM, Anonymous Anonymous said...

ok ok, this is your blog, point taken. why are you advising this person to be your clone? sure, you're saying, learn the basics while finding your own interests, but the very fact you have to say this is a bit concerning. shouldn't the undergrad find herself for herself? blah. where is the surprise and joy in finding your own path?

 
At 8:46 AM, Anonymous Anonymous said...

YFS, this is really good. You had another post a while back with some of your ideas about teaching science and I remember also being quite impressed.

Read the NAS 2010 report and I think you will find that "experts agree" with your thinking.

I wouldn't go so far as to say that "most undergrad departments don't teach what you actually need to know". I don't know the stats, but the limited pool I am familiar with does try to teach this stuff. There certainly is a problem, not just in science but across academic disciplines, of balancing some objectively determined programmatic needs with intellectual vanities of the faculty on hand, at least at my place (high ranked small elite university with pretty brick buildings and lots of green space). BUt overall if an undergraduate is a high-performing bioscience major from a decent college/university, the few deficiencies they have upon arriving in grad school can be easily overcome.

Nonetheless, you have provided an incredibly thoughtful post on this subject, for not the first time.

I know you are struggling with the whole faculty position thing, and I certainly understand your desire not to go into industry. I wish you luck in securing a position at an R1, but if that doesn't work out, think about other options in science or science policy or science education or a SLAC. Your thinking on this is exceptionally clear.

 
At 9:42 AM, Blogger Ms.PhD said...

Cynical Anon,

That's great advice. And more or less summarizes a lot of past posts, very succinctly. Thanks!

Anon 12:09,

I guess I meant a few different things by writing this.

These are things I realized after the fact were the most useful to me.

These are things I wish most of our incoming grad students already knew.

Some of them don't know any of it. Most don't know all of it.

These are things that, to me, make the difference between grad student/postdoc/"PI of the future" and technicians who just, for example, send their samples off for sequencing and don't actually know how it works. And don't care.

Anon 8:46,

Thanks!

Every once in a while, I get a comment like this one, and it just warms my heart and makes it worthwhile to have this blog.

Your comment will probably be the highlight of my day.

My only disagreement is that you assume that the grad school is concerned with, and capable of, making up the educational deficiencies of the college curriculum, and I'm not convinced this is always the case.

I'm sure the NAS says the same thing. I usually agree with their reports.

Unfortunately the NAS doesn't have any more power to make sure it happens than I do. They make all kinds of great recommendations, and so far as I can tell, nothing changes.

Then a few years go by, and they issue an updated report, saying more or less the same thing but also pointing out how they said this before.

 
At 10:21 AM, Blogger Hermit, PhD said...

Frightening to see it all laid out at once. I don't think I ever really realized how much of this stuff I've absorbed until I saw that list, went 'holy cow', calmed down and realized 'hey, I know most of this stuff.' Great post!

 
At 11:32 AM, Blogger Dr. Jekyll & Mrs. Hyde said...

Amen to that. I'd expand your last point to emphasize: If your experiment fails, you have not failed. If a series of experiments or workarounds fail, and you have to abandon that line of research, you have still not failed. Sticking it out, past the second or third year when a lot of people can't take this repeated "failure", is what's important. These are hard things to grasp for people accustomed to success.

 
At 11:35 AM, Anonymous Anonymous said...

"These are things I realized after the fact were the most useful to me.

These are things I wish most of our incoming grad students already knew."

These two statements prove that your list is specific to your field only and is not indicative of what students in "modern biological scientists" need to know. Your post is also echoing the disturbing arrogance I hear all too often from scientists (IN ALL FIELDS) about how their sub-field is "the only one that gets funding anymore" (ie the only one that is "important").

It's great to love your field and your work, but try to know a bit more about other fields before you make sweeping statements about "modern biological research".

If I need to know the Pka of an Amino Acid I can look it up, and a basic understanding of the essentials of O. chem is all I (and most biologists working in genetics, cell biology, evolutionary biology, and organismal biology) need to know.

I'd say that together, these fields make up about 75% of all Biology. On the other hand, if I were a physical biochemist then I should know them by heart. But that's only a tiny percentage of modern biological research.

 
At 6:12 PM, Blogger Ms.PhD said...

Hermit,

Hooray!



Dr.Jekyll & Mrs. Hyde,

Amen to that too! Although I am kind of stuck right now on a failed series of attempts and lack of ideas of how to get around a problem. Hmph.



Anon 11:35,

DISAGREE.

I can't think of a single corner of biology where you wouldn't be affected by not knowing a conservative amino acid mutation from a drastic one.

You don't have to know the actual numbers. That's not the point.

I also can't think of a single corner of biology where you don't use basic biochemistry to understand whether your inhibitors are getting in and whether they're specific or not. Whether your PCR is working and specific or not. Whether your antibody is working and specific or not. Whether your phenotype is affected by nutrition or environmental factors, or not.

Try reading my post again. Do you really think you correctly guessed what field I'm in?

Have you actually been reading this blog? Do you really have the impression that I personally have lots of funding? Or that my field is generally well-funded?

Really?

 
At 9:35 PM, Anonymous Anonymous said...

Amazing!! Kudos, YFS. Ironically, it seems a biophysics or a chemistry major better readies an incoming graduate student for modern biological research than biology itself.

Best wishes on a faculty position someday.

-Sophie

 
At 11:35 PM, Anonymous Anonymous said...

You have a point in that people should have proper background knowledge and an understanding of what they are actually doing when they are pipetting (instead of just following a kit without thinking - or worse - combining random steps from different protocol and still look puzzled when something doesn't work). However, I also think that things will only really truly try to make sense once you start doing actual research. I may have known pKA's and the theory behind a technique - but all that info is useless if you're not actually doing it. So I think the most important piece of advice is: get as much hands-on "wet" training as possible before you get into grad school. And with that I mean full weeks, full days, for a long enough time that you can gain some independence and think for yourself. Know what you are going to get yourself into!

 
At 4:49 AM, Blogger lj said...

Hi all,
I am trying to find out what people feel about their HR departments and would really appreciate your comments on my blog
http://blogs.guardian.co.uk/money/2008/03/what_is_the_future_of.html

I have no experience in the world of science so would be really interested in your thoughs about your career development and opportunities open to you. I was recently at the Met office filming an appied scientist which was really interesting. http://www.youtube.com/watch?v=c4wSLHKgRHA

LJ

 
At 7:13 AM, Anonymous CC said...

On the whole, I think this is a terrific list. But as with your earlier piece on reading the literature, I think there's a lack of recognizing that there's more than one way to skin a cat. You're a big methods person, which is great. I'm happy to be behind the curve a bit on that, and wait for protocols to be worked out. On the other hand, the statistics and programming skills you mention allow me to exploit a niche that most of the lab wizards can't fill.

And despite my wife's repeated attempts to explain it to me, I have never understood how the hell buffers work. I can read the table in Maniatis and make them, and that's always been enough for me. Lasers? When you turn back to the audience, take your finger off the button of the pointer so you don't blind anyone important. That's all I need to know about lasers. 10:47's "Learn how to use one analytical method really well and develop an extension of that approach" is a perfect compromise.

Anyway, as you say, things like creativity, perseverance and good hands and good judgment can't be taught in classes.

 
At 11:23 AM, Blogger Crystal said...

Hi there,
I hope you don't mind, I am planning to re-post this (GREAT) post over at my blog in the next few days. I thought what you had to say was very wise! Thank you for your insight!
Crystal
http://www.goingtohellforthis.blogspot.com

 
At 1:14 PM, Blogger Ms.PhD said...

Crystal,

What do you mean, re-post? Why can't you just use a LINK?

I'll refer you to my Creative Commons Copyright.

 
At 3:02 PM, Anonymous Anonymous said...

this is the same person as Anon 11:35.

I certainly have no idea what sub-field you are in, however given your recommendations it's probably one where you do things like use pKa values and amino acid structures fairly regularly.

I never tried to argue that it's irrelavent to get those concepts at a basic level. However, If you were in another sub-field of biology, the emphasis of your list would have been different. I've gotten "the list" from about 5 different faculty members in one form or another, and the only things they've had in common are:

1) "Lab experience"
2) Genetics

 
At 7:44 AM, Anonymous bsci said...

This is a really good post. I could quibble with a few parts being a bit too focused on your own area of biology, but, in general, the list is great.

I think the one area you completely skipped is
Know where the money comes from and how to get it. A modern biologist needs to solid understand of the why and how of funding (i.e. why the public cares more about funding biomedicine than non-medical stuff) and how to get the funding (i.e. writing grants).

You also focused on writing, but not reading. You listed lab skills and classroom knowledge, but applying those skills to reading articles and understanding the limitations of findings is a skill in itself that many don't have.

 
At 11:35 AM, Blogger Crystal said...

will do-

Crystal

 
At 5:19 PM, Blogger EcoGeoFemme said...

It took me a while to decide to comment on this post. My initial reaction was that not all biology is biomed. It may be true, however, that there are more dollars in biomed. Anyway, the post sparked a long conversation between me and ecogeoman about what is biology and what isn't. We think it's the study of life, which means it's much more than biomed, so some of these things might be too specific.

On a related note, many biologists are funded by agencies other than NIH.

Still, it's a good list and good to talk about what people should learn before they start a research career. I think anyone who wants to pursue science (of any kind) should take more math than they think they need. It only helps. Same with writing. But I think the skill that helps the most is outstanding reading comprehension, which not everyone has.

 
At 11:05 AM, Blogger Ms.PhD said...

My bad. Let me clarify: this post was in response to a question from an UNDERGRAD asking what they should do in COLLEGE.

I've ranted AT LENGTH elsewhere on this blog about things that GRAD STUDENTS need to learn, and chief among those is HOW TO READ and how important it is to read lots of scientific literature and learn how to do it with an eye to critical thinking.

I probably should, I know I keep saying I'll do this, collect some of these education-oriented rants into some kind of organized sidebar thing. It is probably time to do that. Soon.

I'd also argue that while it's helpful to learn something about how funding works at a grad level, it's not really going to make much sense to you until maybe the postdoc level, and even then there's not much you can apply for on your own, so you're still stuck nagging your advisor.

And as postdocs we should be TRAINED in how to find and get funding, and right now the only way you'll get that training is if you make a point to find classes where you can learn it. Most PIs seem to gloss right over it, some even view obtaining your own funding as a distraction from your work at the bench.

But absolutely, if you're going into research at the Professor Level, yes, all those things are needed!

Sorry, should have been more explicit up front about the purpose of the post. Been kind of distracted lately, this was kind of an off-the-top-of-my-head post, so I'm surprised and pleased that so many people sent comments on it.

 
At 11:20 AM, Anonymous JaneB said...

I'm curious. Does biology these days have NOTHING AT ALL to do with the whole organism unless it's being used as a walking/growing test tube? I have always thought that biology was the general term - the science of life, as ecogeofemme put it - which encompassed specialities such as botany, zoology and ecology as well as biomed, genetics and biochem. As someone who is a biologist in that my first degree is in a biological discipline, my object of study is the ecosystem or landscape (which certainly includes a lot of life) and my primary and secondary technical skills involve observation and data collection on parts of plants, I consider the label biologist to be reasonable. But I have absolutely NO need to ever know the pKa of an amino acid or basic biochemistry...

I like the basic points you've made, and I strongly agree that students need to think laterally about what skills they acquire on the way through the system, ask more experienced people what they wish they'd learnt earlier etc. But the definition of biology, effectively excluding those who don't look at the inner chemical workings of the individual organism and instead look at what goes on at a larger scale, poked a sore spot for me.

Hope the distractions include some positives as well as the stubbornly uncommunicative experiment!

 
At 3:56 PM, Blogger Ms.PhD said...

Jane,

If you'll accept for the purposes of this discussion my initial premise that the MOST FUNDED biological research these days is bioMEDICAL, then yeah, it's a bit different from ecosystems, which I would consider to be more like geoscience, atmospheres, forestry, agricultural science.... But even there I find it hard to believe that basic biochemistry (photosynthesis anyone?) would not be useful to know, at least vaguely!

I also don't include in my version of 'biomedical' things like psychology and most cognitive science.

Most human/animal behavioral stuff wouldn't fit unless it also includes something like the effects of drugs (then it's more like neuroscience and physiology). But again, that's the sort of thing you can focus on at the graduate level if you're armed with the right basic skills from college.

I don't know how this devolved into a discussion about what's really biological and what's not. I like ecogeofemme's definition that it has to do with life. But so does theology, if you want to put it that way.

I'm just not at all convinced that coursework about whole organisms, at the college level anyway, is the best way to use up your expensive credit hours.

Seems to me that most biology gets outdated awfully fast, so a lot of things I learned in memorization-oriented biology courses have since changed.

As I've written here many times, I've gotten a lot more use out of basic learning and thinking and analysis skills.

Concepts, not factoids.

Having said that, I have several friends who attended graduate programs where the students take courses with med and vet students the first two years, so they get all the same physiology and pharmacology courses you'd get in those kinds of professional schools.

So I think that's a better way to get organismal biology if you're going into something medically related, rather than taking it at the undergraduate level. And I'm not convinced you need to have seen it at the undergraduate level in order to learn it later! Seems redundant to me!

I'm not so sure about plants. The courses offered related to plants at my school were not so great so I didn't have a lot of options even if I had wanted them.

I would think that students who know early on that they're interested in plants might choose their undergraduate school accordingly, e.g. someplace with an agricultural school or more emphasis on ecology. I'm not sure there are many places to go to learn how to do botanical research, but it probably still exists somewhere, right?

And students who find their calling in college can certainly choose their graduate programs accordingly.

While I would argue that knowing biochemistry can only help you understand plants and ecosystems, right now it's not clear that knowledge of plant biology is necessary for later understanding of biochemistry.

But that might change as pharmacology and drug design move into more biological sources for naturally-occurring drugs.

So I guess we can agree that if you get the basics, whatever those might be for your path, it will give you a lot more flexibility later on because the definition of biology is always changing.

I wrote about biomedical research because that's what I do. For now, anyway.

 
At 2:39 PM, Anonymous JaneB said...

Ah, I see - I didn't make the jump from your (definitely true) statement that the main area of biology with funding is biomed to your use of the word biology thereafter as meaning effectively biomed! Thanks for clarifying. Ecogeofemme's contribution at least makes me feel like I wasn't the only person to read the word slightly aslant of what you meant it to mean.

There is funding - and perhaps more importantly for most of the students I teach, an extensive (if pretty poorly paid!) array of job opportunities across the spectrum from making policy to advising to leading teams to actually doing research outside of the academic, and which are also relatively applied to what feel like real world problems - in the more "eco" side of the discipline. We also relate to the industry or academia debate, the politics, the fighting over money - I guess because so much of what you usually write really resonates with me, the fact that biochemistry is a vital part of your mental furniture whereas organismal taxonomy (even the old-fashioned kind that depends on what you see in the field not on the genetic markers extracted in the lab) is part of mine, and we both regard what we studied as undergraduates of the other's vital furnishing as not terribly relevant, and out of date by noew anyway, was something came as a surprise and therefore I wanted to comment on.

I agree completely with your point that it's the cognitive skills and habits that matter from an undergrad - I'd advise a student not just to read some history of science but to take philosophy of science too, and as much maths as possible, just as you do, because these are the things that gave me the habits of mind that (I hope) make me a competant researcher, scholar and teacher. And if they ever have the chance to take Latin or Greek, it's great mind training, it's fun, AND in every field of science you'll have a much improved chance of understanding, remembering and using the terminology as most of it is essentially classical in derivation.

Sorry, hijacking your comments thread again. A chunk of my thinking time is currently spent trying to pin down some ideas about the tribes we construct for ourselves within disciplines and between academics and practitioners (such a blurry distinction!) - mostly this is an attempt to rationalise some really annoying behaviour in an inter-disciplinary project team without just resorting to labelling the misbehaviours as idiots or saboteurs! The joys of team work, something we definitely all share whatever our discipline!

 
At 7:41 AM, Blogger Crystal said...

Hi there-
I discussed your post on my blog today- I thought you might like to check it out (and let me know what you think). http://goingtohellforthis.blogspot.com/

Also, I'd love to be added to your blogroll, if you'll have me!
Thanks,
Crystal

 
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