the grammar of the genome?

In my research for "The Library of Life" (a chapter of my project that I'll post about soon) I studied the patterns of a common metaphor used for DNA and genomic research: that the genome is a book, made up of nucleotide base-pairs that are its letters, genes which are words or sentences, all susceptible to being read, copied, or edited.  One good study of the metaphor is "From sequencing to annotating: extending the metaphor of the book of life from genetics to genomics" by Iina Hellsten, in New Genetics and Society (2005). For the theme of Species and Print, the implications of the metaphor are that a specimen's genome is a copy of a species-book, ignoring the fact that organisms of a given species do not share the exact genome-text with others. The first heyday of this was around the time that the Human Genome Project was begun, in 1989-90, although as we'll see it began much earlier.

In the last week I've read two prominent news stories, in the New Yorker for November 16, 2015, and the New York Times Magazine for Nov. 15th, about the recently developed CRISPR technique in genomics, devised by Jennifer Doudna at UC-Berkeley, and Feng Zhang at Harvard (and many others no doubt). These pieces again use the same metaphors of the genome text. What should give us pause is that the insinuations that genetic engineering would be as easy as reading and writing did not come to pass the first time, because the metaphor was not so solid, and so they likely won't happen this time either.

Zhang is quoted in the New Yorker story saying: "Imagine being able to manipulate a specific region of DNA...almost as easily as correcting a typo" and the Times piece echoes this: "Some researchers have compared Crispr to a word processor, capable of effortlessly editing a gene down to the level of a single letter." Note that the sentence ends with "letter" and "typo" not "gene" or "nucleotide" or "GTA or C" as if the metaphor was so widely accepted that the actual DNA stuff need not be described or explained.

The most powerful study of the interrelations between genomics, cybernetics, and information is Who Wrote the Book of Life? (Stanford, UP 1999) by Lily Kay. It's a big tome of which I read only parts so far, but in another interesting paper I found I read of how “Fred Sanger and Walter Gilbert independently invented methods to deduce the sequence of nucleotides in the DNA molecule in 1975-1977”  They hired software specialists, who took the techniques used for early word processing software being invented at this same time. “they were conceiving the sequences as ‘words’ and using the algorithms--programming orders--applied in searches within texts by the word processors” (Chow-White and Garcia-Sancho in Science, Technology, and Human Values 37 [2012]:132). So it appears the origins of this metaphor arose from the coincidence that word-processing software was developed at the same time as genetic engineering. 

The lines from this weekend's articles, and many many others I've read, suggest, as Hellsten puts it, that "one can read off genetic information unambiguously and straightforwardly" and "correct genetic misprints." But this is misunderstanding of what genes are like, and how genomics is done. The vast majority of the genes, and therefore of the nucleotide letters, have an unknown function, or no function at all, in the development and operation of the organism. Genes are switched on or off by other genes or by events in the life and environment of the organism. Some genes block the operation of others. Some portions of the human genome, about 0.5%, are "plagiarized" from bacteria that have elbowed their way into the more noble text of the cells. [see Chris Ponting, "Plagiarized bacterial genes in the human book of life" Trends in Genetics 2001]

And the high-throughput sequencers that "read" these genes do not read like we read books. They blast apart the genome into short sections, and then computers search and match and reassemble the sequence: “Since the chain termination method of DNA sequencing can only be used for fairly short strands (100 to 1000 basepairs), longer sequences must be subdivided into smaller fragments, and subsequently re-assembled to give the overall sequence.” the sequencers produce multiple “reads” of each section of these blasted-apart genomes, and then computers match the overlapping tiles and reassemble the entire sequence. In the “next-generation” shotgun methods, instead of just 10 or 12 copies of each fragment, there may be hundreds. More shotgun cartridges, if you will, requiring far more computing power, but resulting in greater reliability. Still, there are errors." [Chow-White and Garcia-Sancho, p146]. There are errors in sequence readings, and errors in genes themselves. But can we really call them "errors" corrected by an editor?

So although I titled this the grammar of the genome, in truth there is no grammar, and scarcely a syntax, for although there are significant passages, the loss of which can cause mutation or death, these gems of coherence are tiny, lost amid the inchoate gibberish, and pieces of other books. So there is no narrative thread to a genome, no building suspense, and no true beginning or conclusion. There are only fragments. Post-modernists would make much of this, but would not really mean what they say.

Most people use computers most often to write and edit, whether it be novels, scientific papers, school assignments, or, most likely, text messages and social media posts. This revolution in technology has made writing easier, but made the texts more distant from our bodies. Choose what font you may, your writing no longer bears your own hand's print. And the searching and editing features we use can be applied to huge, hidden databases of text, as when we type something into a search engine, or try to find names, titles, or phrases in our computer's drives or our phone's memory. I believe that these ponds and oceans of text have the immensity and mystery of a genome, which may be in our every cell, but is likewise foreign to our consciousness. This is not like rummaging through a shoebox filled with letters from your lover or parent, looking for a memory.



 

Eco-criticism and Biological science

In preparing to write the introduction to my Species in Print book, I finally checked out Practical Ecocriticism: Literature, Biology and the Environment, the book by my emeritus colleague Glen Love, which came out in 2003.

Glen makes a strong case for why literary scholars should study and respect the work of natural scientists. I take that to heart, but I was turned off by much of the argument he uses to advance it.
Love, like others, cites the lecture and book from the 1960s by C. P. Snow, The Two Cultures, which foretold an institutional and methodological split in the university, between humanists and scientists. Unlike others, however, he interprets the lecture as chiding the humanists for not respecting the scientists' values of evidence, hypothesis, experiment, and truth. And Love reprimands other literary scholars for their absorption in post-modern theory, which he claims is solipsisitic and subjective, and denies the existence of nature and wilderness. I'm accustomed to the polemic in eco-criticism between this anti-theory camp, which emerged in the 1990s when the Association for the Study of Literature and Environment was founded, and post-structuralist theory still carried high prestige in literary acedemia. But the polemic is stale now, and suffers from ad hominem attacks and sloppy arguments. One recent exchange in the pages of ISLE, the journal of ASLE, featured S. K. Robisch's exhortation: “Let’s reconfigure our departments toward acknowledgement of the biosphere so passionately denied by the Slavoj Zˇizˇeks of the world who have barely ever stepped from a sidewalk.”

The first problem with Love's chapter on "Ecocriticism and Science" is that he lumps together post-structuralist theory with post-modernism in general, and then extends his animus to the environmental historians who have called attention to the socially-constructed status of "nature" and questioned the definition and heritage influence of "wilderness" in American culture. The influential essay collection Uncommon Ground edited by William Cronon and published in 1995 is accused of a "nature constructionist stance" that plays into the interests of "postmodernist skeptics" who want to destroy natural resources such as tropical rainforests (21-22). The volume has a number of fine essays from various disciplines and viewpoints, and so those lines really surprised me.

The second problem is that Love goes in for sociobiology and literary Darwinism so enthusiastically, and fails to question the assumptions and arguments of this movement. He even condemns Stephen Jay Gould over the use of the phrase "Just-so Stories" to describe the kind of reductionist arguments that sociobiology enjoys so much. To use the phrase taken from Rudyard Kipling's fiction is to imply that the explanations of, to use one common example, why humans like open savanna environments, is to dangerous question the truth of the scientist's views!

One line caught my eye: "the great geneticist Theodosius Dobzhansky said: 'Nothing in biology makes sense except in the light of evolution'" (51). Well, my project aims to show that biology, or natural history as it was more often called back then, certainly did make sense to its practitioners and readers prior to Dawin's theory of evolution. And eco-critics have much to learn from it.

Species in Print


[Gordon M. Sayre is Professor of English and Folklore at the University of Oregon]

My new research project, which I have been pursuing during my sabbatical research leave in Spring, Summer, and Fall 2015, is about species and biodiversity in natural history. This will be the basis for a graduate seminar I will offer at the UO in Spring term 2016, contributing to Oregon's nationally known program in literature and environment.


I've written drafts of several parts of this project for talks at conferences and symposia:

"American Degeneracy: Colonial Science and Environmental Anxiety in the 18^th century" at the Conference on Transatlantic Ecologies, University of California Santa Barbara, Early Modern Center, May 16-17, 2014; and at the Modern Language Association Convention, Vancouver, BC in January 2015.

"The Library of Life" at the

Futures of Environmental Humanities symposium, University of Utah and Brigham Young University, September 24-27, 2015, and at University of Oregon Humanities Center, March 6, 2015

"Misshepeshu and the Walrus: Hybrid French/Anishinaabe Natural History in the 17th-century Art and Writings of Louis Nicolas" at a

UO English department Works-in-progress series talk in April 2015, and at the Association for the Study of Literature and Environment conference in June 2015.