Sunday, October 28, 2007

In defense of biology in the classroom

Emblies posted about education in general, and Duff (in his comment) suggested that Biology should be taught in lab and not in class, since largely it does not use a mathematical framework. You should read their posts if you haven't already because they have many interesting things to say. But Duff's comment about biology not being appropriate for class learning piqued my thought and so as not to totally clog Emblies' response page, I'm responding at length here.

Duff says: "In biology, I've long wondered if things would be better served if they did away mostly with lectures, perhaps limited it to once a week for an hour and a half, and the rest of the time was spent working in the lab."

First (and foremost) is that "Biology" is an incredibly broad term. There are some areas of Biology (phylogeny, for instance, or most forms of ecology) which I know less about than I know about physics. Even in a specialty or sub-discipline such as Genetics, there are a huge range of things that people study. The principles may be the same, but the procedures and the questions asked in Harinder's lab (where I work now) are very very different from the procedures and questions asked in Bill's lab (where I worked in high school). I absolutely could not (cannot?) choose a field of genetics, much less a field of biology itself, without classes to introduce me to topics before setting foot in a lab. I know that ecology and phylogeny bore me because I've had to study them for classes at some point and they bored me. I know that molecular biology is interesting because when I read even text book sections for them, I find things that are amusing, interesting, and intriguing. I know that DNA studies interest me more than protein studies because I have taken classes focused on proteins, and I find them less interesting than the classes I have taken focused on DNA. I think that I want to be a molecular geneticist because of experiences that I have had in classes as well as lab. There would have been no feasible way for me to be introduced to as many fields and disciplines as I have been introduced to if I only had class 1.5 hours a week: a year of rotation for a graduate student typically has them visit and do small projects in 3 or 4 labs (as far as I am aware). And one hopes to actually do a substantive project at some of these places, which means that 2 years of rotation needs to be enough to find a lab. But only having interacted with 6 to 8 possible specialties (and that's maximum, with specialty very specifically defined) is certainly not enough to give people an idea of the variety that is biology. So I think that biology classes are a necessary part of training a biologist.

Secondly is the fact that walking into a lab without an understanding of lab principles or procedures is a very very foolish thing to do. My first year, I was in a biology lab class (an advanced introduction, so these were presumably more biologically-inclined people than most classes at the U of C, even for biology majors) in which people did not know (or could not figure out immediately) how to use micropipetters (or, as I like calling them because it's more awesome, pipettemen). They didn't understand sterile technique in the slightest, they got Bacteria everywhere and freaked out instead of swabbing with ethanol and trying again with more finesse, they couldn't load a gel, etcetera. Even in my biochemistry class in my Junior year, there were people who were graduating with a BA in biochemistry and could not load a gel without a guide. My TAs have been consistently impressed with my ability to do things that I consider very simple, such as load and run gels, set up PCR reactions and so forth. All of which tells me that most people are, at base, completely and totally incompetent in lab, and that that incompetence needs must be trained out of them before they set foot near any valuable experiments. I have trouble in lab about keeping everything sterile, pipetting accurately, and getting reactions to work without hitch - so if someone was worse than me at those standard procedures, well, I wouldn't know what to do with them. They would be a waste of time and money. It is ridiculous to expect post-docs and graduate students, who have their own work to do, to also take on training every single biology student who comes through a program. If they were expected to do so, they would never get any of their own work done. So putting people into laboratory situations right away is silly.

Duff goes on to say: "I've always been curious as to what it means to think about biology outside a lab context. That is to say, not that abstract thought about biology cannot be had, but that it must be tied to the laboratory, as biology often does not have a mathematical framework that one can think within."

Admittedly, I laugh about the idea of "theoretical biology" as well, but it does exist. (Harinder is especially good at it, actually.) And there are some principles of biology that can be learned in a classroom very well (and that are actually suited particularly for classroom instruction). Yes, biology is based in observation and experiment rather than theoretical mathematical systems, but that does not mean that it cannot be taught in a classroom. Because there are theoretical underpinnings to much of biology that can be taught, and a worldview that can be exposed, in much the same way that mathematical acumen is necessary to understand and practice physics. I'm trying to think of a really good example and I'm going to go with Dobzhansky's Dictum. Dobzhansky's Dictum is the following: Nothing in Biology makes sense except in light of Evolution. When I first heard it I was dubious. But that's just the point -- it's a theoretical underpinning and a way of looking at the world specific to biology. It forces you to see the connections and relationships between our environment and ourselves, between different parts of our environment, etcetera. It also forces you to see the relationship and interdependence between molecular biology, genetics, and macroscopic biology. Evolution works on all levels, and you can talk about it at the genomic level, at the gene level, at the organismal level, at the systems level, and it's always the same principle. But you have to learn how to look at the world before you start seeing the interconnectedness. You have to hear Dobzhansky's Dictum and think about it for a while, apply it to specific situations, before it makes any sense to you whatsoever.

So the point is that while all kinds of biology don't necessarily have a mathematical framework that one can be taught and can "work within" -- although many kinds of biology do, in fact, have mathematical frameworks that you work within; protein folding problems come to mind -- all kinds of biology do have theoretical frameworks and postulates that you can think about and use to hypothesize. After all, theory != math.

Speaking of which, then, what makes physics so much different than biology in its capacity to be theoretical, then? Because Mango, earlier, had the following gem: He had always thought of physics as science and biology as engineering. For Mango that came down to purpose: the purpose of physics was to understand the world, the purpose of biology was to make people's lives better by finding cures and treatments for diseases. Again, physics as a discipline is theoretical and abstract and attempts to understand existence while biology is tied to the day-to-day realities of life and disease.

But it doesn't have to be this way. At least, not in my estimation.

I've sort of lost my train of thought here, so I might come back and clarify/add later. But I think that's enough for now anyway.


Duff said...

Er, I guess I ought to have been more precise in some of my comments. I did not mean to imply that there is no theory in biology just because there is no mathematics. I heartily accept theory != mathematics. What I was trying to get at was what does it mean to make a scientific statement in physics versus biology. Also, I was not (though I don't think you were taking me as doing so) trying to denigrate biology because it doesn't use math as physics does (protein folding is arguably more a domain for physics anyhow, being minimal the minimal energy state of a quantum mechanical/electromagnetic system :P Interesting side note: Carnegie Mellon has recently made a big push into computational biology. Ecology does use some math in its own right though, with predator prey models.)

Example as to how statements can make sense in physics in a way they do not in biology:
I can write and prove specific mathematical facts about physical systems that follow from well established physical principles, yet never hope to actually see these physical situations realized due to other processes in nature that would limit our ability to see the effects. For instances, glueballs in QCD. These probably "exist" in the sense of being a well-defined mathematical feature of quantum chromodynamics. I doubt we will ever observe a glueball, as the dynamics necessary to create one leads to too many interfering effects in our detectors. Namely, the up and down quarks are too light and things easily hadronize at the same energies. Does that mean glueballs are not physical? No, they are, unless you want to deny the basic framework of QCD. But that framework is too well established by other experiments. Hence I can make physically meaningful statements without any direct ties to a laboratory. Other instances would be Poincare's recurrence theorem. In a asymmetrical or dented bowl, a ball rolling without friction will eventually return to a neighborhood of its starting point that is arbitrarily small. Sadly, we do not have balls rolling without friction, but the proof of the theorem follows from Newton's three laws. Conceivably one could build a system with low enough dissipative loss that the effect may be observed, by it would be doubtful. Or if I took a thermally isolated noble gas in a oddly shaped container one would see the gas come arbitrarily close to its initial configuration, if one could measure that configuration. Again, experimental limitations prohibit this, but no one therefore doubts the veracity or scientific nature of these claims, as they follow mathematically from laws well established else where.

So I suppose then that my claim is that one does not see in biology a similar possibility, as biology is more closely tied to empirical observation. But I heartily agree that this does not mean biology has no theory. To make meaningful empirical observation one has to cognize terms and relations that are not directly empirical. Geneticists talk about promoters, enhancers, insulators, etc., but these things are not what they see. These are theoretical terms (but not then invalid) that they have come up with to make sense of complicated molecules undergoing complicated chemical reactions. Just like in physics one does not "see" virtual particles, but are theoretical devices that allow us to describe what we do see.

I guess the difference I am getting at is that biology is mostly concerned about making sense of what we do see. Physics can make meaningful statements about stuff that we may never see.

One may counter that astrobiology is a concerted effort to make the same sort of claims, but I am dubious about the prospects of astrobiology. Namely, they don't produce the same sort of mathematical proofs as physicists when making these claims. Is this being too harsh? I don't think so. Making such claims need some sort of rigorous check to know you are on the right track. In general I see two such checks: empirical and mathematical. Mathematical I will take to be the decided application of formal logic or some sort of calculus with results that follow exactly from the assumptions made.

Duff said...

It seems to me, if I may be somewhat cheeky, that the students who were lost in the lab ought to have spent more time in the lab, not less, in order to fix problems.

Duff said...

Oh, and to clarify something further, the ability to make mathematically sound but untestable claims can get physicists into trouble. String theory I would take to be a prime example: here theorists really are relying on mathematics alone to accomplish their goals, but experimentally string theory is dead before it was fully born.

Elizabeth said...

Wow, Duff! Lots of comments! ^_^

My emphasis on theory was because I feel like a theoretical basis for something can best be taught in a classroom, and so if there is a theoretical basis for biology ergo there are elements of biology which are best taught in a classroom. I realize that that wasn't exactly what you were saying, however.

I certainly didn't take you to be denigrating biology, although I did chastise Mango for doing so (since he's going into biological research he is held to different standards).

In terms of proving things theoretically that can never be seen in real life, well, have you heard of Hardy-Weinberg equilibrium? Basically, if you keep track of the probability of different alleles and have a few postulates, you can define what it means (and what is necessary) for a population to stop evolving. This is a meaningful observation, but it is unlikely (if not impossible) that we will ever actually observe a population that is no longer evolving. The rules that you start out with are derived from observation, but that's true of physics as well unless I am mistaken.

Re: lab-incompetent students - I would posit that they needed to spend more time in a lab class where their foibles and follies wouldn't seriously impede other people's lives.

Alex said...

i have much to say, and yet no time. a CS example why to thoroughly teach in class before moving to computers. In the time it takes me to explain "rm -rf *" someone may very well have destroyed all of their work. the theory, or theoretic knowledge can be priceless, expecially if you are working with any sort of volatile tools (be they acids or command line tools). In sort, i sort of agree with Elizabeth on that point at least.

more later! class is on!