The book of life

The words we use to describe genetics matter, according to the author of a new book - for instance, "genetic code" should really be "genetic cipher"

By | August 24, 2007

At the announcement of the human genome's near completion in 2000, John Toy, the medical director of the UK's Imperial Cancer Research Fund, said: "We have discovered the human alphabet -- what we now have to do is put the letters in the right order and make a sentence. Only when all of that is done shall we have the book of life to read." Across the pond, Eric Lander, head of the Whitehead Institute at MIT, commented: "I don't know if people realize that we just found the world's greatest history book. We are going to be up every night reading tales from the genome."
We often hear about the "book of life," the "human alphabet," language, script, code, blueprint, software, Holy Grail, and the Rosetta Stone. Such comparisons simplify and make accessible the more complex functioning of DNA, genes, and genomes. But they bring with them ways of thinking, values, and assumptions about the complex phenomena of how DNA operates in heredity and life-processes, and we need to always remember that. Comparing DNA to a word or a gene to a Chicago gangster (such as in Richard Dawkins's Selfish Gene) may seem innocuous, but language itself is never completely neutral. Words and metaphors all have connotations, which can contradict the biological mechanisms they attempt to explain. For example, referring to the genome as an "alphabet" suggests that the genome is a text that can be written, read, translated, re-written, and copyrighted. Texts become someone's property more easily than naturally occurring phenomena, such as trees and stars. Thinking of DNA as letters implies that such DNA letters regularly "spell" genetic "words," or traits in a one-on-one fashion, similar to the way language works. This may help explain why many people continue to adopt the mindset that one gene describes one trait, just as one noun describes one object: There may be a gene for thrill-seeking or criminality or any of a myriad of illnesses. If a genetic word is misplaced or incorrectly spelled, we simply change the word or correct the spelling, a familiar concept that contributed to early optimistic visions of genetic therapies. If only it were that simple. Linguistics have a strong impact on how scientists envision genomics, as well. Even before James Watson and Francis Crick discerned the structure of DNA, physicist Erwin Shrodinger called the mysterious element by which biological structures and life processes are governed a "life-code" in the lectures he gave in Dublin during World War II, published as What Is Life? As Crick commented later, Schrodinger's analogy to Morse code influenced the direction of his and Watson's thinking -- but, he noted, Morse code should have been Morse cipher. Why "cipher," and not "code?" The difference, while seemingly technical, is in fact significant. The word "code" refers to a linguistic operation in which one piece of code (dots and dashes, flags) stands for another in an arbitrary but consistent manner. This is the way language itself works, a word standing conventionally for an object, say a tree, with which it has no intrinsic relation. There's no reason why the word "tree" should stand for the object it describes. The metaphor of the code ultimately implies that, DNA's nucleic acid chains have a consistent but arbitrary relation to the other acids with which they associate, a situation that is not the case at all. DNA is anything but arbitrary, and therefore acts more like a cipher. A cipher has no intrinsic meaning in itself, but operates according to a strict, mathematical set of rules, such as A for adenine, G for guanine, and so forth. As Crick himself reflected at the time of his research, "You understand. I didn't know the difference at the time. 'Code' sounds better, too. 'Genetic cipher' doesn't sound anything like as impressive." Imagine, then, what even more complex metaphors might import. The suggestion that genes function like Chicago gangsters, or act as representatives of the gender psychology of their parental contributors (Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters) smuggle elaborate, psychologically motivated, political narratives of struggle, competition, and bizarre Ozzie and Harriet scenarios of squabbling domesticity into our conceptions of genes. Instead of biochemistry, DNA operates according to our estimations of human psychology and the way the story always goes. Judith Roof is author of The Poetics of DNA, published this year by the University of Minnesota. She is a professor of English and film studies at Michigan State University. Do you see other metaphors in science that you believe don't accurately represent what they describe? Tell us here. Judith Roof Image: University of Minnesota Press. Links within this article: Eric Lander J. Rohn, "Rhyme and reason," The Scientist, August 17, 2007. Richard Dawkins, Selfish Gene M. Wenner, "The war against war metaphors," The Scientist, February 16, 2007. Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters J. Roof, Poetics of DNA


August 24, 2007

The algorithm of life is encoded in the DNA information\n\nThe topic Judith Roof brought into the limelight so eloquently could not be a more acute, burning issue for the nascent science of PostGenetics ("Genomics beyond ENCODE").\n\nIt is excerpted and commented today in the Junk DNA Portal that Genomics is groping for an ?update? of the "definition" of ?gene? - shortly after the untimely death recently of "Junk DNA" (history in less than 35 years). \n\nYes, words carry not only meanings but associations, values, assumptions, metaphors, connotations, frames of mind (and worse; implications that may be scientifically absurd, or even outright ridiculous). Judith Roof duly enumerates the DNA ?book?, ?alphabet?, ?letters?, ?words?, ?script?, ?code? ? and concludes with ?cipher?.\n\nWhile I can hardly wait to read her book (Poetry of DNA), I find it interesting that she does not mention ?information? and ?algorithm?.\n\nTrue, they are less ?poetric? compared with motifs, metaphors or connotations ? but are a bit more helpful on the side of science.\n\nNot that the eternal symbolism of ?in the beginning, there was information? could not be both applicable to the life of the Universe (as in the Bible) as well as to the life of two single-threaded DNA defining together the beginnings of a new life (as for e.g. a human embryo). \n\nThe DNA is nothing but ?information?. Information (although not at all in the probabilistic sense of Shannon, as each A,C,T,G representing ?2 bits?, the negative inverse of binary logarithm of the probability of ¼ chance for any letter to stand in a particular position), but ?information? how to put together molecules found everywhere into a living entity. A ?blueprint?, in the sense of specifying both the raw materials used and the design of how to put them together.\n\nMost respectfully, and not at all on grounds of poetry, I tend to disagree with Judith that the DNA is more of a ?cipher? than a ?code?. ?Cipher? sounds nasty, more than one ways. First, my etymological dictionary says, it originates from the Arabic "zero" or "empty" (that dear DNA could not be, IMHO). Second ?ciphered information? implies to me an intent to hide ? or purposefully make it hard for poor scientists how the DNA works. ?Subtle is the Lord ? but he is not malicious? said Einstein. Independent from any belief system (or gender superiority) my inclination is to go with Einstein on this one.\n\n?Code? may mean more to those who have written quite a bit of ?sets of instructions? for computational purposes, than to easily dismiss for the case of DNA. \n\nI agree that it is not at all the most important (and interesting) task to ?decode? the DNA (let's forget the horrendous oxymoron ? or mixing metaphores - on the frontpage of Nature "Decoding the Blueprint"; see here) . Still, for one, I do believe that the DNA does encode an astounding "information compression" of the algorithm of growth - and therefore, of life.\n\nFinding out the algorithm is a mission for PostGenetics ? and may unfold its poetric side, too. \n\\n
Avatar of: George P. Alcser

George P. Alcser

Posts: 1

August 25, 2007

In an otherwise clear and pointed commentary on how linguistic connotations steer, if not control, our popular approach to the new genetics, Dr. Roof seems to appropriate Dr. Frances (sic!) Crick to the feminine with the mere slip of an "e" and thus unintentionally, yet amusingly, illustrates her thesis.
Avatar of: Noah Er

Noah Er

Posts: 1

August 27, 2007

I have often been intrigued by this topic of genetics. One particular point arises from the Bible's statement in Psalms 139:16. I am sure I'll read more about this in the forthcoming new book.
Avatar of: Alison McCook

Alison McCook

Posts: 68

August 27, 2007

The above commenter is correct -- when originally posted, the story misspelled Francis Crick's first name. The error has been corrected. Thanks for letting us know!\n\nAlison McCook\nSenior editor

August 28, 2007

My comment does not refer exactly to imperfect metaphors in science. After all, metaphors can never be 100% adequate or they would no longer be metaphors. They are to depict just an aspect of reality. Everybody understands it, I believe. However, there a words in science or at the interface of science and everyday life, that annoy me really quite profoundly. I would call them obvious misnomers and classify them into two categories: \n1.) cases of word inflation, products of scientists’ (or their sponsors) lust for fame or money or appreciation; exaggerated to the limits of absurdity (examples: A. astronaut – meaning formally a person travelling to the stars, although there is no doubt that if ever such a travel should be undertaken, the person’s outfit would have to be completely different from the present day ‘astronaut’s’ ; “cosmonaut” sounds way more appropriate, but is not used in the West, probably for political/historical reasons (though in this case ‘reason’ sounds rather inappropriate, too); B. asteroid vs. planetoid – see above; C. ‘post-genomic era’ – just a few complex genomes have been sequenced so far, probably less than half of any of them understood; the genomic era has just passed or begun? D. a plague of ‘omic’ sciences meaning just that the scientists studying molecules different form nucleic acids and proteins have their ambitions too; E. epigenetics – most likely an unappreciated region of genetics\n2.) crude simplifications, products of scientists’ assumption that the wide public is very dumb, lazy and will buy only the simplest stories, and it is important it should buy some stories; my favourite example: ‘genetically modified organisms’ – are these the only organisms whose genomes have been genetically modified? most obviously no.\nOn a positive note, I appreciate the trend in scientific English to use simple words to accurately deliver complex ideas, e.g. ‘know-how’ compared to methodology, ‘boxes’ as conserved DNA sequence elements etc. I regret this trend is more and more abandoned in my native language. Many of my fellow countryman are too busy or too lazy to interpret foreign notions, so we just borrow words, dump them freely into a completely incompatible language and it begins to evolve into an illogical, messy dialect of English.\n

August 29, 2007

One must sympathize with Dariusz Michalczyk complaining about misnomers, particularly in what is "Genetics beyond ENCODE" (i.e. "Genetics beyond Genes, JunkDNA and Central Axiom).\n\nAs elaborated elsewhere the maddeing confusion in what is the "PostModern" (Post-ENCODE) Genomics, all three of the most fundamental axioms have proven to be wrong ("Junk DNA" is anything but 98.7% of the human DNA to be discarded, definition of "Genes" is obsolete as is, and even Crick's "Central Dogma" is false).\n\nThe general public, however, should not listen too closely to the embarrassing turmoil when (some) leading Genomists openly confess that their science strayed into a blind alley (a rapidly diminishing minority still holds onto the remnants of the "establishment").\n\nLaypeople, on the other hand, should take it utterly seriously that their tax-dollars for decades have not been appropriately focused on finding the causes of their hereditary diseases; including Alzheimer's, Parkinson's, Fragile X, etc that are most likely *not* caused by "genes" but in the 98.7% of human DNA that was "framed" to be "junk".\n\nThe primary challenge to the new science of PostGenetics ("Genomics beyond Genes") is *NOT* its terminology. \n\nThe primary challenge is to focus the awareness of the public that resources must be re-allocated to try to save hundreds of millions suffering from (or to be diagnosed with) "Junk DNA diseases".\n\
Avatar of: mtraven


Posts: 1

September 3, 2007

Actually the DNA code is more like a code than a cipher. Translation of DNA to amino acids is done not by an algorithm but by a "code book" comprised of the set of tRNAs and aminacyl-tRNA synthetases, which are enzymes that link amino acids to tRNAs. These of course are coded for in the genome, so the genome is best described as a code that contains its own decoder.

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