Words, Words, Words

by Walt Hearn
PictureA turret of the Troll House, (Hearn residence), Berkeley
"In the beginning was the Word." The logos (Gk. for "word") that John linked to the creation of the world at the beginning of his Gospel, was identified by him as Jesus Christ, who "became flesh and lived among us." God communicated God's love for the world through the "living Word," whom we now meet in the 21st century through the words of Scripture. Clearly, words matter. We use them to communicate feelings and everything we know or think about, including the results of scientific investigations.
 
Of course, words aren't the only way to convey information. Scientific papers also "speak" to readers in non-verbal ways. A book on The Visual Display of Quantitative Information, originally self-published in 1982 by statistician Edward Tufte, continues to make that case. The gist of a paper can sometimes be grasped from a single well-designed illustration. The pertinent equation can be written as P/W =  10^3  (or P = 1000W) where P stands for the communicative value of one picture and W = 1 word’s worth.
 
Scientists go to the text for experimental details, but they have their own routes to get there. I've known physicists who skip the abstract or introductory paragraph to go straight to the equations. A good graph (or photograph) may catch a scientist's eye. As a biochemist fascinated by "natural products," I was often drawn into papers by first poring over any molecular structural formulas they displayed.
           
In my day, biochemists were unraveling the chemical processes by which simple building blocks like amino acids and sugars were synthesized and then linked up to form the proteins and polysaccharides  necessary for life. Nucleotides were other small molecules under investigation but the routes to their polymerization into huge DNA and RNA molecules were not yet clear. Every research lab had a copy of the latest "metabolic chart" hanging on the wall. The charts kept being revised as new reactions were discovered, but the earliest of those "road maps" still had room for the complete structural formulas of each metabolite. The enzymes catalyzing conversions of substrate molecules to their products were usually named for the substrate they acted on (e.g., proteases, glucosidases) or for the type of reaction they catalyzed (phosphorylases, oxidases).
 
The product of one reaction became the substrate for another, often in a pattern of interlocking cycles reminding me of Ezekiel's prophetic vision of "wheels within wheels." On later charts, the names of substrate molecules, rather than their structures, were still linked to their products by arrows (――>), with the name of the enzyme catalyzing each specific reaction written above or below the arrow. Thus the enzyme glucose-6-phosphatase catalyzed the hydrolysis of glucose-6-phosphate into glucose and inorganic phosphate. Enzymes were known to be protein molecules, but back then we had only their "name, rank, and serial number." Eventually the complex chemical structures of enzymes themselves were explored, so my mental picture of metabolism began to change. The complete amino acid sequence of a particular enzyme (pancreatic ribonuclease) was first worked out in 1959.
 
Ribonuclease was very small, as enzymes go, but nevertheless it was composed of 1,876 atoms compared to 24 for glucose (C6H12O6). To visualize in two dimensions how all the atoms in such a macromolecule are connected to each other is not easy. To  write out the sequence of the 124 amino acid sub-units of ribonuclease takes a lot of space, even when each amino acid is represented by only a single letter of the alphabet. And that linear sequence still doesn't show the folded 3-dimensional structure. In biochemical papers today, enzymes are depicted in weird computer-generated drawings of intertwined ribbons and coils, or as big lumpy blobs dwarfing their substrates. My biochemical expertise kept diminishing as the structures of bio-molecules got larger and larger. Today, trying to visualize the structure of DNA molecules, thousands of times larger than glucose, leaves me gasping for breadth.
 
Scientific Vocabulary: A Growth Industry
 
With graphic depictions of molecules getting beyond me, you might think I'd be better off just reading the written text. Alas, the language of many papers even in my own field has become almost undecipherable. Sometimes I have to struggle even with words in the title to figure out what a paper is about. For example, a word ending in "-on" in a title might refer to DNA structural elements (codons, introns, exons), microbiology (prions), or merely charged atoms or molecules (anions, cations). (Once, while teaching an 8 AM elementary course, I tried a gimmick to rouse a sleepy class. I wrote “an-ion [ - ]” and “cat-ion [ + ]” on the blackboard, with “on-ion [   ]” in between. When I asked what charge I should fill in, some students immediately said “zero.” Then I pulled an onion out of my pocket and passed it around to give everybody a whiff. "Now that we're all awake, let's proceed . . .")
 
Atomic physics has multiple -on words. Up to the discovery of the neutrino in my undergraduate days, physicists wrote only of electrons, protons, and neutrons. The last two of those were nucleons, now called baryons (from a Gk. word for "heavy"), each made up of three "quarks." Electrons, which have no quarks, are leptons (from Gk. for "lightweight"). The hadrons (from Gk. for "thick") include not only baryons but also mesons, composed of one quark and one "antiquark." After that it gets complicated. Baryons are called fermions, distinguished from bosons for some reason or other. I think fermions and bosons are named for a couple of famous physicists. Gluons (from the English word "glue") hold quarks together. Muons (from the Gk. letter "μ") are also part of the jargon (from an old French word for "bird chatter"). I think a gnomon has something to do with visible radiation from the sun. Did I get that right? I left out photon, which definitely has to do with light, as does beacon―to be distinguished from bacon (from the sides of hogs). What in the world is a  skyrmion? Maybe some physicist from Wheaton can explain all this to me.
 
Meanwhile, my own biochemical literature is being flooded with "-ome" and "-omic" words, one of the earliest being genome ("a whole haploid set of an organism's chromosomes"), followed, in due course, by epigenome. The -ome of those two words seems to be derived from chromosome (from Gk. χρῶμα, "color" + σῶμα, "body”), part of a cell's nucleus long ago found to be readily stainable by certain dyes. Similar-sounding words can come from totally different roots, such as tome-words from Greek for "cut" (microtome, atomic, appendectomy); nome-words from "law" (metronome, economics); drome-words from "run" (syndrome, palindrome); and nomen-words from Latin for “name” (nomenclature, denomination).   
 
After getting accustomed to genomics, I encountered proteomics, which must deal with the whole protein content of a cell or organism. To my surprise, a European Journal of Proteomics has been published since 2008. Then I heard of glycomics, and no doubt there's a lipidomics, whose meanings I can guess. The journal Metabolomics is published by The Metabolomics Society, founded in 2004. A couple of years ago the American Chemical Society sponsored a "webinar" on the sensametabolome ("all the sensory active compounds giving flavor and aroma to beer, wine, and other food products"). I've come across the connectome ("all the chemical and gap junction synapses in an animal nervous system"), plus phenomics, microbiomics, transcriptomics, and inflammasomics. I've recently seen in Science a definition of the exposome as “the sum of environmental exposures a person experiences from conception until death.” I suppose that includes exposure to neologisms like “exposome.”
 
At Home with Gnomes and Trolls
 
Enough, already. This is giving me a headache, or maybe a stomic ache. The proliferation of new words is getting out of control. Hmmm, the sound of that word "control" reminds me that Ginny and I named our Berkeley home "The Troll House." It has “quirks” (!) and is quaint, so it could have been built by trolls.  The droll trolls we had in mind were mythical forest dwellers, generally with pleasant dispositions. Not so for modern "internet trolls," who take over chat groups or interactive websites and spoil the conversation by hammering away on their own views. Nor for "patent trolls," who buy up patents with the purpose of filing bogus infringement suits.
 
Mythical trolls were somewhat larger than mythical gnomes (pronounced NOMES, not Gene-OMES or Gun-OMES). As a noun, a troll may be less significant in scientific discourse than a gnome (see http://gnomeexperiment.com). Actually, I think that when we christened the Troll House, the name was a play on “Toll House” chocolate-chip cookies. In mythology, trolls were sometimes said to hang out under bridges to exact tolls from anyone crossing the bridge. For awhile we were willing to believe that trolls who had worked under the Golden Gate Bridge had retired and built our house in the Berkeley foothills to keep an eye on their previous place of employment across San Francisco Bay. Then we learned that our house was built in 1922 but the bridge wasn't opened until 1937. Oh, well: another beautiful theory done in by an incontrovertible fact.
 
We meant the word troll to be understood as a verb. To troll means to circulate, as in "Landlord, troll the flowing bowl," or "Troll the ancient yuletide carol." We intended our home to be a place of welcome and conviviality. That's the way I was brought up. My parental home was known as “Hearn Haven.” My Dad's hobby was printing, so while I was away in the Navy in WWII, he designed and printed up for me a “Hearn Haven Chow Pass,” a very official-looking card with our address. I gave the cards to my close buddies, guaranteeing them a meal if they ever got to Houston after the war. Several took me up on it. From the beginning of our marriage in 1966, Ginny and I felt called to a ministry of hospitality—and to working together at it. Since 1972 we've plied that trade at our Berkeley Troll House, though now with waning energy.
 
From the basic idea of circulating comes the definition of trolling as a way to fish, by dragging a line with a baited hook behind a moving boat. In Mark 1:17, Jesus told some Galilean fishermen that he would train them to fish for people. They'd been using nets, but casting a big net (as in modern televangelism) isn't always the best way to spread the gospel. Our Troll House "turret" where we eat (I told you this house is quaint) is a great venue for one-on-one or two-on-two conversations. With guests at our turret table, the conversation, or merely our practice of holding hands as we "say grace" before a meal, is likely to reveal that we're serious about following Jesus. If anyone "takes the bait" and asks questions or has comments about what faith means to them, we can go from there. The Lord does quite a bit of business in the Troll House turret.
 
Words, words, words. I like that quotation attributed to St. Francis of Assisi (for whom both San Francisco and the current Pope are named): "Preach the gospel always; if necessary, use words."
Walter R. Hearn grew up in Houston and majored in chemistry at Rice University. He received a Ph.D. in biochemistry at the University of Illinois in 1951. After doing research for a year at Yale Medical School and for three years at Baylor College of Medicine, he spent 17 years on the biochemistry faculty at Iowa State University. His research interests included peptide chemistry, hypothalamic hormones, and bacterial pigment biosynthesis.

For five years he was a Visiting Biologist to Colleges for the American Institute of Biological Sciences. He is a Fellow and Life Member of AAAS and an Emeritus member of the American Chemical Society. In 1972 he switched professions and moved to Berkeley to do free-lance editorial work with his wife Virginia. They have edited periodicals and some 200 books, largely for Christian publishers.
 
 Walt joined ASA while he was in grad school and served on the Council in the 1960s. From 1969 to 1993 he edited the ASA newsletter. He was a coauthor of the widely distributed publication, Teaching Science in a Climate of Controversy (ASA, 1986) and author of Being a Christian in Science (IVP, 1997).

He has also contributed chapters to a number of books, the latest being "Creation Matters" in Darwin and the Bible: The Cultural Confrontation (Penguin Academic, 2009), edited by anthropologists Richard Robbins and Mark Cohen. His articles, reviews, and poems have appeared in such publications as Perspectives on Science & Christian Faith and the Berkeley publication Radix, for which Ginny has been copy editor for over 40 years. Walt was once "poetry rejection editor" for Radix magazine. Walt and Ginny have strong IVCF backgrounds, helped to launch New College for Advanced Christian Studies in the 1980s, and are members of Berkeley's First Presbyterian Church.