jsomers.net | I should have loved biology

I should have loved biology

By James Somers

I should have loved biology but I found it to be a lifeless recitation of names: the Golgi apparatus and the Krebs cycle; mitosis, meiosis; DNA, RNA, mRNA, tRNA.

In the textbooks, astonishing facts were presented without astonishment. Someone probably told me that every cell in my body has the same DNA. But no one shook me by the shoulders, saying how crazy that was. I needed Lewis Thomas, who wrote in The Medusa and the Snail:

For the real amazement, if you wish to be amazed, is this process. You start out as a single cell derived from the coupling of a sperm and an egg; this divides in two, then four, then eight, and so on, and at a certain stage there emerges a single cell which has as all its progeny the human brain. The mere existence of such a cell should be one of the great astonishments of the earth. People ought to be walking around all day, all through their waking hours calling to each other in endless wonderment, talking of nothing except that cell.

I wish my high school biology teacher had asked the class how an embryo could possibly differentiate—and then paused to let us really think about it. The whole subject is in the answer to that question. A chemical gradient in the embryonic fluid is enough of a signal to slightly alter the gene expression program of some cells, not others; now the embryo knows “up” from “down”; cells at one end begin producing different proteins than cells at the other, and these, in turn, release more refined chemical signals; ...; soon, you have brain cells and foot cells.

How come we memorized chemical formulas but didn’t talk about that? It was only in college, when I read Douglas Hofstadter’s Gödel, Escher, Bach, that I came to understand cells as recursively self-modifying programs. The language alone was evocative. It suggested that the embryo—DNA making RNA, RNA making protein, protein regulating the transcription of DNA into RNA—was like a small Lisp program, with macros begetting macros begetting macros, the source code containing within it all of the instructions required for life on Earth. Could anything more interesting be imagined?

Someone should have said this to me:

Imagine a flashy spaceship lands in your backyard. The door opens and you are invited to investigate everything to see what you can learn. The technology is clearly millions of years beyond what we can make.

This is biology.

–Bert Hubert, “Our Amazing Immune System”

In biology class, biology wasn’t presented as a quest for the secrets of life. The textbooks wrung out the questing. We were nowhere acquainted with real biologists, the real questions they had, the real experiments they did to answer them. We were just given their conclusions.

The Roche Biochemical Pathways Poster

Plans for an alien machine, in Contact

For instance I never learned that a man named Oswald Avery, in the 1940s, puzzled over two cultures of Streptococcus bacteria. One had a rough texture when grown in a dish; the other was smooth, and glistened. Avery noticed that when he mixed the smooth strain with the rough strain, every generation after was smooth, too. Heredity in a dish. What made it work? This was one of the most exciting mysteries of the time—in fact of all time.

Most experts thought that protein was somehow responsible, that traits were encoded soupily, via differing concentrations of chemicals. Avery suspected a role for nucleic acid. So, he did an experiment, one we could have replicated on our benches in school. Using just a centrifuge, water, detergent, and acid, he purified nucleic acid from his smooth strep culture. Precipitated with alcohol, it became fibrous. He added a tiny bit of it to the rough culture, and lo, that culture became smooth in the following generations. This fibrous stuff, then, was “the transforming principle”—the long-sought agent of heredity. Avery’s experiment set off a frenzy of work that, a decade later, ended in the discovery of the double helix.

In his “Mathematician’s Lament,” Paul Lockhart describes how school cheapens mathematics by robbing us of the questions. We’re not just asked, hey, how much of the triangle takes up the box?

That’s a puzzle we might delight in. (If you drop a vertical from the top of the triangle, you end up with two rectangles cut in half; you discover that the area inside the triangle is equal to the area outside.) Instead, we’re told that if you ever find yourself wanting the area of a triangle, here’s the procedure:

Biology is like that, but worse because it’s a messier subject. The facts seem extra arbitrary. We’re told to distinguish “lipid bilayers” from “endoplasmic reticula” without understanding why we care about either in the first place.

Enormous subjects are best approached in thin, deep slices. I discovered this when first learning how to program. The textbooks never worked; it all only started to click when I started to do...