The Well-Read Biochemist is a collection of supplementary readings - stories, poems, and essays - for an introductory biochemistry course. The readings and my use of them are described in "The Well-Read Biochemist", Journal of Chemical Education, Vol. 73, 732-4 (August, 1996). Here is the reading list, followed by my commentaries on some of the readings.
USM Students:
Find these readings in the red notebook, lower left corner of the bookshelves, Science 153.
A Literary Supplement to Biochemistry: References
Topic: Course introduction; Thinking about scientific (and other kinds of) thinking.
Readings: "Fact, Law, and Theory: Ways of Thinking in Science and Literature," Gale Rhodes and Robert Schaible, Journal of College Science Teaching, XVIII (#4), pp. 228-232, 288, (1989); "The Poetry of Science," John Timpane, Scientific American, July 1991, p. 128.
Topic: DG = DH - TDS, rubber bands, and protein folding.
Reading: "Identity," A. R. Ammons, Collected Poems, 1951-1971, New York: W. W. Norton and Company, 1971, pp. 114-116.
Topic: Comparing protein sequences; phylogenetic trees
Reading: "Worm for a Century, and All Seasons," in Hen's Teeth and Horse's Toes, Stephen Jay Gould, New York: W. W. Norton and Company, 1983, pp. 120-133.
Topic: Myglobin, hemoglobin, and oxygen transport
Reading: "Jerry-Built Forever," Roald Hoffmann, Gaps and Verges, Orlando: Univesity of Central Florida Press, pp. 27-30.
Topic: Mutations and genetic diseases
Reading: "The Wonderful Mistake," Lewis Thomas, The Medusa and the Snail, New York, Bantam New Age Books, pp. 22-24.
Topic: Enzyme kinetics, mathematical models of enzyme action
Reading: "When I Heard the Learned Astronomer," Walt Whitman, collected in Science and the Human Spirit: Contexts for Writing and Learning, Fred D. White, Belmont, CA: Wadsworth Publishing Company, 1989, p. 271.
Topic: Membranes
Readings: "In Need of Mending" and "Corral," Roald Hoffmann, Gaps and Verges, Orlando: Univesity of Central Florida Press, 1990, pp. 27-30.
Topic: Major stages of metabolism
Reading: "Heaven and Earth in Jest," in Pilgrim at Tinker Creek, Annie Dillard, New York: Bantam Books, Inc., pp. 1-14 (or excerpt, pp. 5-10).
Topic: Central metabolic pathways
Reading: "Carbon," in The Periodic Table, Primo Levi, New York: Schocken Books, 1984, pp. 224-233.
Topic: Mitochondrial metabolism
Readings: "Organelles as Organisms," in The Lives of a Cell, Lewis Thomas, New York: Bantam New Age Books, 1974, pp. 81-87; "A Biologist Whose Heresy Redraws the Tree of Life," Jeanne McDermott, Smithsonian, 20 (#5), pp. 192-197, (1989).
Topic: Course conclusion
Reading: "Instruments of Darkness" (excerpt), in The Night Country, Loren Eiseley, New York: Charles Scribner's Sons, 1971, pp. 51-53.
A Literary Supplement to Biochemistry: Commentaries
Order and Accident (A.R. Ammons: "Identity")
The center of a spider's web is the signature of the spider's species, and web after web, the spider recreates its characteristic pattern. But the narrator in Ammons's poem notes that, at the web's boundaries, the spider must connect it to the surroundings. For this reason, the setting of the web determines its nature near and at its periphery. The narrator expresses this trend by use of the thermodynamic term entropy, a measure of disorder.
The scientist speaks of the entropy of systems. A system is simply a part of the world that we choose to isolate and study say, a cornfield, or a flask containing water and some dissolved chemicals. We say that the entropy of a system is high if the system is disordered, that is, if we can see no pattern in the arrangement of its parts. If the parts are neatly arranged in a simple pattern, the entropy is low. To return to the example in the poem, the entropy of the web is lowest the web is most ordered at the center, where it makes a simple spiral, but entropy rises away from the center. At the points of suspension, the spider maps the web onto its surroundings, and the web's entropy is equal to the entropy of the leaf tips, eaves, twigs, or utility wires to which the web is attached, in what appear to be " numerous occasions of accident."
This same trend is apparent in protein identity. Homologous proteins (families of proteins, such as cytochrome c and hemoglobin, that serve the same functions in many different organisms) share the same important residues at their active or functional centers. Moving outward to parts of the protein that simply give it structural integrity or solubility, we find more variation among family members. In the core of the protein, even the substitution of one aromatic side chain for another might disrupt the structure, and thus most internal mutations are not accepted. On the other hand, for many surface residues of water-soluble proteins, which need only allow interaction with randomly moving water molecules that make up the surroundings, almost any polar side chain is acceptable. A diagram of conserved amino acids in homologous proteins shows us which parts that are critical, where the organism can accept no occasions of accident. In this view, the center of the spider web is not so much a mark of identity as an evolutionarily conserved active site, in which most mutations damage the web's effectiveness, and are not successful.
There is a subtle and interesting connection between entropy and description. An ordered, low-entropy system is easy to describe: "The corn is planted at intervals of 2 feet in rows three feet apart." This description might tell us precisely the locations of thousands of cornstalks. But if the corn is planted at random, a high-entropy system, and we want the same precise description of the whereabouts of every stalk, we must describe each and every location, requiring far more words. In like manner, it takes many words to describe the web's points of contact: "One suspending line is connected to the left end of the fluorescent light above the sink. Another runs to the right window frame 2.4 feet above the sill. The third drops from the left center of the web to the top of a small pestle that sits in a mortar on the sill. The three main supporting strands meet to from a triangle with the following sides and angles: ." But we can describe the heart of the web succinctly: "It's a garden cross spider web, 5.5 inches in diameter." A short description means low entropy. Think about it: you need 40 Ramachandran angles to describe the conformation of 20 residues of polypeptide in high-entropy random coil, but you can describe any length of low-entropy alpha helix with only two angles.
Returning to the poem, notice that when the narrator generalizes beyond the specific example of the web, the tone and language of the poem become more mysterious. What is "the underlying that takes no image to itself" and that is "created fully in no particular form"? How is it made manifest in spider webs and moons and bladderweeds, and in those ubiquitous nucleotide-binding domains, for that matter?
The narrator finds it interesting that order (low entropy) prevails at the center, in the midst of the air where the spider could do anything she wishes. In the heart of the web, she is not constrained by having to make connections, yet she slavishly, precisely stamps her identity in the web's active site, its crucial functional center. On the other hand, she must make the entropy of her web rise smoothly toward its boundaries, until the contacts match the disorder of the surroundings. Can you apply this view of the spider's identity, and protein identity, to human identity, and more specifically, to the love expressed by the narrator?
Gale Rhodes
Water Bugs, Metabolism, and Mystery (Annie Dillard: "Heaven and Earth in Jest")
Like the giant water bug, which injects enzymes and reduces the macroscopic and macromolecular organization of its prey to a mixture of building-block molecules (amino acids from proteins, sugars from starches and membrane carbohydrates, fatty acids from membrane lipids and stored fats, salts from bone), many animals perform stage-one catabolism externally. Think of the spider. In fact, think of yourself. Your digestive tract is, topologically speaking, outside your body. A simplified cross-section of a mammalian body is shown below. Note that the digestive tract is continuous with the body's outer surface.
Mammalian Body Plan in Cross Secion (Topologist's View)Because the cell can conserve none of the chemical energy from the Stage-I breakdown of molecules, there is no advantage, and some disadvantage, to bringing all this stuff inside for digestion. So it is hydrolyzed to a relatively small number of building blocks, then drawn into cells, where further oxidative instead of hydrolytic dismantling can occur in a compartment equipped to conserve the abundant energy released. The cell needs fewer transport systems this way, because the myriad molecules of the live organism give way to only 30 or 40 building blocks. The reduction of perhaps 10,000 different proteins to 20 amino acids, which in turn can be absorbed by an even smaller number of transport proteins, strikingly exemplifies the typical converging nature of degradative pathways. (By the way, another advantage is that some of those froggy proteins may be toxic, but the digested building blocks are reliably benign.)
This reduction also points dramatically to our kinship with all of life. If the giant water bug latched onto you or me, the resulting mixture would be indistinguishable from frog soup. In imagining the myriad forms life builds from this soup, we see an essential simplicity beneath the multitude of living forms on the earth. It is when my mind runs back and forth between such simplicity and such complexity that I feel I am blindly touching the hem that Dillard describes.
For all our knowledge of it, this force call it life or nature or God or what you will this extravagant force that pours intricate living forms over the face of the earth, remains purest mystery. As you explore the details of metabolism and learn to follow a little of its logic, it will seem at times that we know so overwhelmingly much. But I hope it will also become clearer how little of the whole endeavor we understand, how halting and partial our attempts to increase our knowledge. Even if there are "bars and doors" set against our knowing it all, it appears that we are nowhere near reaching them; the potential joy of learning still seems boundless. Perhaps the most difficult (and subtle) obstacle is the sheer complexity of life. If so, the limits of our knowledge are not solid barriers at all. Instead they are resilient but persistently entangling webs of ambiguity, indecision, and confusion in the face of nature's profusion.
As an example of that complexity, imagine trying to design a set of digestive enzymes for the water bug. Simple: you just want to hydrolyze everything in sight, right? Not quite: everything except the skin. Why waste the skin? Well, imagine how much of the meal would be lost in the waters of the pond if the enzymes so much as perforated the skin. At first glance, the water bug's approach seems blunt and heavy handed. But those enzymes, bulls in the china shop of froggy macromolecules, handle the proteins and carbohydrates of the skin with kid gloves. Using the impressive specificity of enzyme action, the water bug wastes the skin to save the rest of the meal.
Of course, in the end, the skin is not wasted. It too will find its way into other life. It may dart away backwards in a crayfish or rise to the surface in the petals of a pond lily. Or if a hungry nymph munches the skin, what was once earthbound frog may fly far away in the delicate wing of a dragonfly.
Gale Rhodes
Biochemical Windows on the Past (Stephen Jay Gould: "Worm for a Century, and All Seasons")
In this essay, Stephen Jay Gould looks at Darwin's most obscure and specialized books, those that treat corals, orchids, and earthworms, and shows that each exemplifies and recommends a different strategy for studying life's history. The scientist's choice of strategy depends on the nature and adequacy of data:
...if you must work with a single object [orchids], look for imperfections that record historical descent; if several objects are available [coral reefs, barrier reefs, and atolls], try to render them as stages of a single historical process; if processes can be directly observed [accumulation of earthworm castings on top of soil], sum up their effects through time. (Material in brackets added.)
Of course, this description is simplified and idealized, and often in studying the past, our methods partake of one or more of these strategies at the same time.
Biochemistry includes various bodies of evidence that support the theory of evolution by natural selection, and that allow specific evolutionary relationships to be established. For instance, protein chemists construct phylogenetic trees by comparing the sequences of homologous proteins obtained from many organisms. These trees serve as a means of discovering how the organisms evolved from a common ancestor. In this type of reconstruction of the past, is the scientist using one or more of the strategies that Gould describes? If so, which one(s)?
This reading invites us to think about the various means by which biochemists attempt to glimpse the history of life. As you proceed through this course, keep Gould's three strategies in mind: Do they cover the whole range of techniques for studying evolution? Can you describe principles, distinct from Gould's three, that are used in studying the past? If so, can you find examples of these principles in experiments described in your biochemistry text?
Gale Rhodes
Images from Chemistry (Primo Levi: "Carbon")
Levi's poetic fantasy about a carbon atom is filled with images that animate the chemist's world. To a chemist, the molecular world is real, and the invisible events that power the world around us do not go unnoticed. This imaginary world is busy beneath what we see, giving substances their colors, tastes, smells, shapes, and capacities for change.
One of my favorite images in Levi's atomic biography is in the paragraph that ends at the top of page 230, where he describes life as " an inserting itself, a drawing off to its advantage, a parasitizing of the downward course of energy, from its noble solar form to the degraded one of low-temperature heat. In this downward course, which leads to equilibrium and thus death, life draws a bend and nests in it."
Perhaps only a chemist or student of chemistry will feel the full impact of this metaphor. Each time I encounter this passage, I picture a descending reaction-progress curve, that deceptively simple monster of kinetics, with the solar photon as the reactant at the summit of a sharp downward slope, and heat at the base. Then I picture life as a stable intermediate in the midst of this curve, living its metastable existence in a shallow curl ("... life draws a bend and nests in it"), a valley that briefly interrupts the slope. This valley represents, for instance, the conservation of the photon's energy in the form of NADPH, followed by the NADPH-dependent reduction of carbon dioxide to make glucose, and subsequent oxidation of glucose to carbon dioxide, all of them intermediates that cancel out of the overall balanced equation, all of this powering life:
Levi's metaphor reminds us that the unlikely, energy-requiring process of
life and the inevitable, spontaneous decline of the photon's energy are coupled reactions
in the metabolism of the earth.Gale Rhodes
On Whitman's Learn'd Astronomer (Walt Whitman: "When I Heard the Learned Astronomer")
I usually recommend this poem at the end of the last class on enzyme kinetics, because I usually can see that you are sick and tired and hoping we will shortly turn from mathematical concerns, with symbolic E's and S's, to some "real" enzymes, "real" substrates, and some at least visually concrete models of enzyme action. Perhaps, I am guessing, you have had enough, for now, of my reducing all of biology to the Michaelis-Menten equation, and you might well heed the poet's invitation to simply go out and look in wonder at some natural object, and see that the beauty accessible to naive wonder is still there. In my view, it is still there, but now there is more.
I am not content with the common interpretation that the narrator of this poem is completely unreceptive to any analysis of natural processes. Even if tired and sick of the Astronomer's presentation, our narrator must see more in the stars now than before the lecture. To me, part of the beauty of scientific knowledge is that is opens a window on the unseen world, and the seen world no longer looks the same. The world of our immediate senses is not reduced to "nothing but" the analytical model, it is enriched by containing the model within its outer beauty. What we see encompasses the fruits of analysis, and thus is larger, not smaller, for being analyzed. The student can look with new respect at sky, leaf, or insect, recognizing that their outward intricacy is not superficial, but that they are intricate at every level of observation or analysis.
(It has not escaped my notice that the poem can also be taken to advocate active, rather than passive, approaches to learning.)
Commentaries ©1996, Gale Rhodes
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