Invasion of the possibly useful jargon

Every time I take a class, I semi-consciously pick up its jargon and use it for all kinds of unrelated things. I'm aware that this is very common among nerds/hackers -- after all, I hang out with lots of them. I, too, speak of "pinging" people in real life, and of the "failure modes" of couches and suchlike. But because I'm a biologist hanging out with mostly non-biologists, it stands out a lot more because everyone else isn't using jargon from their biochemistry classes. I don't know many other people who use words like "inhibit" and "saturation" and "depletion" and "steady state" and "modularity" on a daily-to-hourly basis. (OK, maybe the last two are more widespread than I think, and I just need to hang out with more MechE or EE people.)

The most recent one is "timescale", or "on the timescale of". I picked this one up from my biomechanics class, which analyzes bio-materials of all different sizes from single molecules to whole organs. In order to keep ourselves sane, we have to take into account the size of the object in question when choosing an analysis method. Should we speak of the stresses and strains in a rod made of continuous material, or of the entropy-driven behavior of a randomly meandering chain? Can we ignore thermal motion of molecules, or the transient behavior when you begin applying force? It all depends on the length scale.

I find the word "timescale" very useful in my daily life. It's much easier to say exactly what I mean if I say "on the timescale of weeks" rather than "in the medium-term". I would love to say that it helps other people understand, as well, but unfortunately no one else seems to have picked up on it yet, so I will have to wait and see.

Strangely enough, the jargon-adapting habit seems to be largely involuntary. However, the success or failure of a given word is definitely related to its usefulness, to the usefulness of the metaphor. There's not that much difference between a feedback system in a cafeteria and a piece of complex software, so it makes sense to speak of both of them as having "failure modes". I guess this is what the "seeing-as" theory of intelligence is all about. (Something I read in one of Hofstadter's books... I don't remember which it was, and I don't know what this is all about.)

Addendum: jargon-adapting is also not particularly widespread among people who aren't part of hacker or twinkie social circles. Or, at least, I don't encounter it very much, and I often get laughed at (in a kind way) when I'm hanging out with my friends from Bioengineering and I speak of rainwater "saturating" a drain, thus forming a puddle.

Which tissues are anisotropic?

Today in my biomechanics class we moved out of molecular mechanics and into tissue mechanics. This will involve a lot of stereotypical mech-E stuff like stress and strain and elasticity that all us biologists have never heard of before -- deterministic, bulk properties of continuous solids (or gooey things), rather than stochastic models of single molecules or long chains of molecules being buffeted around by thermal motion.

In this field, as in every other, you have to make simplifying assumptions. Two of the key assumptions we often make about bulk materials are that they are homogeneous and isotropic. That is, they're uniform throughout, and they're the same in every direction. Tissue like muscle (with fibers) or substances like string cheese (also with fibers) are anisotropic (there's your five dollar word for the day). If you're stretching them and you want to find out how they deform, it matters which direction you're pulling. After we learned what all these fancy words meant, we categorized a few tissues:

Isotropic:

• Liver


• Fat


• Blood


• Cartilage

Anisotropic:

• Muscle


• Bone


• Skin


• Ligaments

As I was writing these down, I noticed a pattern. All the isotropic tissues are what I'd call "biochemical tissues". Their main role is to store chemicals or make reactions happen. In contrast, all the isotropic tissues are "mechanical tissues", that make stuff move or stick together. Huh! Insight! But then it occurred to me that this makes total sense. After all, if you're doing a chemical reaction in a test tube, and you pour it into a bowl, the reaction will still happen. Whereas if you suddenly make all the fibers in a muscle run in a different direction, the muscle will do something completely different. If a tissue's job is to apply a force, it needs to apply that force in the right direction. Biochemical tissues are OK being isotropic, because their job is isotropic, and it seems like it ought to be harder for a developing organism to grow an anisotropic tissue, so why bother.

(Cartilage goes under "isotropic tissues", not because it does much in the way of chemical reactions, but because it's basically just a cushiony substance.)

Neat, huh?

Addendum: what about neurons and nerve tissue?

Well, we can throw out "neurons" straight out, because neurons are single cells, and tissues can only be treated as bulk materials if you've got a lot more than single cells. Trying to treat tissues on the tens-of-micrometers scale as bulk materials is like trying to calculate the viscosity of minestrone. It just doesn't apply. The viscosity of chicken broth is way different from the viscosity of beans. It only works if you zoom way, way out so that the effects of all the little bits and bobs become uniform over the entire blob of whatever you're looking at.

But we can totally look at nerve tissue this way. Your spinal cord, I would imagine, is a little bit like string cheese or rope. It's a whole bunch of long cellular fibers in parallel. If you pulled on it lengthwise, I would expect it to stretch; if you pulled on it widthwise, I would expect it to fray apart. It's anisotropic.

Gray matter in your cortex, on the other hand, I would call isotropic, or at least closer to isotropic (the cortex does have layers after all). Gray matter is mostly made up of cell bodies arranged more or less randomly, not a bunch of fibers all aligned with each other. Having dissected the odd brain or two, I think the best comparison for gray matter might be a firm jelly. (Exactly how firm it is depends on whether it's been preserved and how.)

So, does nerve tissue fit into the "biochemical" vs. "mechanical" tissue dichotomy? Not very cleanly. Then again, it's an atypical tissue. Its job is to send signals from point A to point B. For spinal cords and nerve bundles, point A and point B are far enough apart that it becomes important, on a macro scale, for the cells to go in the right direction. Gray matter contains mostly cell bodies rather than axons, so it's like a pile of Point As (or Points A, for the Captains Pedantic), whose job is to turn chemical signals into electrical activity.

Ruuuuuuuuuuuuuun!

I was reading my perfectly innocent-looking homework assignment, when all of a sudden I saw this:

Figure 1: Augh!

You know, I figured a biomechanics class (which is, after all, all about the realistic physicality of biology as opposed to magic cartoon enzymes that always work) would feature more realistic estimates of a bacterium's size.

Figure 2: I also figured it would feature less fleeing and primal terror. [Source]

Of course, the answer is that E. coli are measured in μm (micrometers), not meters, and that the micro sign simply failed to render due to some strange failure of MS Word. The lesson is clear: Mistakes in character encodings will kill us all. Go forth boldly, my friends, and godspeed.

Courses for this semester

This semester's coursework has two themes: "Let's Read And Discuss Primary Literature", and "Time To Stop Abstracting Away The Physical Nature Of Biology". Both of my required bioengineering core classes are about cells, molecules, and tissues from a mechanical engineer's perspective. All three of my electives are literature-discussion classes on various topics.

• 20.310 Molecular, Cellular, and Tissue Biomechanics - think introductory mechanics, only all the examples are biological things instead of, you know, steel beams or something. Up till now, I've been accustomed to thinking of DNA as a string of digital (AGCT) information, or maybe as a helical molecule; now it's time to think of DNA as a charged elastic rod, or a randomly-walking polymer. How much force can a motor protein exert to pull a vesicle where it's going? What happens when you push and pull on the cytoskeleton? What's the effect of pressure on cells? How do bones reshape themselves in response to forces?


• 20.330 Fields, Forces, and Flows in Biological Systems - fluids and E&M, only again all the examples are biological things. How do things like diffusion and electrophoresis work? How can you model the cell membrane as an RC circuit? What's the best shape / flow pattern for this sample chamber so that the most protein binds to the sensor on one side?


• 20.385 Advanced Topics in Synthetic Biology - this is paired with a freshman design/seminar course, 20.20, which I took two years ago and which rocked my world so hard. It's a great introduction to synthetic biology. The frosh get to do design projects, and because it's surprisingly hard to do this when you've only had introductory biology, the upperclassmen mentor the frosh teams. And when we're not busy mentoring, we have synthetic biology journal club. I'll be presenting a couple of papers and I'm super pumped.


• 7.25 Biological Regulatory Mechanisms - this just sounds fascinating. All the different ways gene expression or protein action can be controlled. Apart from being cool, this is also highly relevant for synthetic biology. Even apart from that, I'm excited about the lectures. This class involves picking apart the experimental logic of papers in a more rigorous way than I've ever had before, which I'm sure will be good for me as well as being fun. We're focusing on demonstrating results and excluding alternative explanations to an extent that seems to be missing in the modern age of "let's generate a zillion data points and then sift through them". Plus, it's a chance to pick the brains of some aged, sage professors. All in all, it really reminds me of ((my interpretation of) what Raffi said about) learning Talmud.


• 7.346 RNAi: A Revolution in Biology and Therapeutics - yet another paper reading class. I know nothing at all about RNA interference, but it's extremely important both theoretically and (potentially) medically. I'm also interested in using it to make synthetic-biological parts that don't crosstalk as much as protein-based parts do; we'll see if that's feasible.

I plan to blog a lot more about the papers I read in these classes. It probably won't be a full Journal Club post for every paper because I'll be reading about 6-8 papers a week, but I'll at least try to summarize them. (This is partly for your benefit and partly for mine -- I expect that writing paper summaries for the blog will help me read and understand the papers better.) But I will do full Journal Club posts for the papers that I find most interesting, and definitely for the ones I present. I might also write about interesting things that happen in the other two classes.