Complex grammar of the genomic language

A new study from Sweden's Karolinska Institutet shows that the 'grammar' of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings, published in the journal Nature, explain why the human genome is so difficult to decipher -- and contribute to the further understanding of how genetic differences affect the risk of developing diseases on an individual level.

...The sequencing of the human genome in the year 2000 revealed how the 3 billion letters of A, C, G and T, that the human genome consists of, are ordered. However, knowing just the order of the letters is not sufficient for translating the genomic discoveries into medical benefits; one also needs to understand what the sequences of letters mean. In other words, it is necessary to identify the 'words' and the 'grammar' of the language of the genome.

...Their analysis reveals that the grammar of the genetic code is much more complex than that of even the most complex human languages. Instead of simply joining two words together by deleting a space, the individual words that are joined together in compound DNA words are altered, leading to a large number of completely new words.

On the Derivation of Ulysses from Don Quixote

I IMAGINE THIS story being told to me by Jorge Luis Borges one evening in a Buenos Aires cafe.

His voice dry and infinitely ironic, the aging, nearly blind literary master observes that "the Ulysses," mistakenly attributed to the Irishman James Joyce, is in fact derived from "the Quixote."

I raise my eyebrows.

Borges pauses to sip discreetly at the bitter coffee our waiter has placed in front of him, guiding his hands to the saucer.

"The details of the remarkable series of events in question may be found at the University of Leiden," he says. "They were conveyed to me by the Freemason Alejandro Ferri in Montevideo."

Borges wipes his thin lips with a linen handkerchief that he has withdrawn from his breast pocket.

"As you know," he continues, "the original handwritten text of the Quixote was given to an order of French Cistercians in the autumn of 1576."

I hold up my hand to signify to our waiter that no further service is needed.

"Curiously enough, for none of the brothers could read Spanish, the Order was charged by the Papal Nuncio, Hoyo dos Monterrey (a man of great refinement and implacable will), with the responsibility for copying the Quixote, the printing press having then gained no currency in the wilderness of what is now known as the department of Auvergne. Unable to speak or read Spanish, a language they not unreasonably detested, the brothers copied the Quixote over and over again, re-creating the text but, of course, compromising it as well, and so inadvertently discovering the true nature of authorship. Thus they created Fernando Lor's Los Hombres d'Estado in 1585 by means of a singular series of copying errors, and then in 1654 Juan Luis Samorza's remarkable epistolary novel Por Favor by the same means, and then in 1685, the errors having accumulated sufficiently to change Spanish into French, Moliere's Le Bourgeois Gentilhomme, their copying continuous and indefatigable, the work handed down from generation to generation as a sacred but secret trust, so that in time the brothers of the monastery, known only to members of the Bourbon house and, rumor has it, the Englishman and psychic Conan Doyle, copied into creation Stendhal's The Red and the Black and Flaubert's Madame Bovary, and then as a result of a particularly significant series of errors, in which French changed into Russian, Tolstoy's The Death of Ivan Ilyich and Anna Karenina. Late in the last decade of the 19th century there suddenly emerged, in English, Oscar Wilde's The Importance of Being Earnest, and then the brothers, their numbers reduced by an infectious disease of mysterious origin, finally copied the Ulysses into creation in 1902, the manuscript lying neglected for almost thirteen years and then mysteriously making its way to Paris in 1915, just months before the British attack on the Somme, a circumstance whose significance remains to be determined."

I sit there, amazed at what Borges has recounted. "Is it your understanding, then," I ask, "that every novel in the West was created in this way?"

"Of course," replies Borges imperturbably. Then he adds: "Although every novel is derived directly from another novel, there is really only one novel, the Quixote."
--- David Berlinski

To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometres in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the portholes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings with find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus of itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell.
We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines. We would notice that the simplest of the functional components of the cell, the protein molecules, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D spatial conformation. We would wonder even more as we watched the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine – that is one single functional protein molecule – would be completely beyond our capacity at present and will probably not be achieved until at least the beginning of the next century. Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.
We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.
What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory which would have one capacity not equalled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.
To gain a more objective grasp of the level of complexity the cell represents, consider the problem of constructing an atomic model. Altogether a typical cell contains about ten million million atoms. Suppose we choose to build an exact replica to a scale one thousand million times that of the cell so that each atom of the model would be the size of a tennis ball. Constructing such a model at the rate of one atom per minute, it would take fifty million years to finish, and the object we would end up with would be the giant factory, described above, some twenty kilometres in diameter, with a volume thousands of times that of the Great Pyramid.
Copying nature, we could speed up the construction of the model by using small molecules such as amino acids and nucleotides rather than individual atoms. Since individual amino acids and nucleotides are made up of between ten and twenty atoms each, this would enable us to finish the project in less than five million years. We could also speed up the project by mass producing those components in the cell which are present in many copies. Perhaps three-quarters of the cell’s mass can be accounted for by such components. But even if we could produce these very quickly we would still be faced with manufacturing a quarter of the cell’s mass which consists largely of components which only occur once or twice and which would have to be constructed, therefore, on an individual basis. The complexity of the cell, like that of any complex machine, cannot be reduced to any sort of simple pattern, nor can its manufacture be reduced to a simple set of algorithms or programmes. Working continually day and night it would still be difficult to finish the model in the space of one million years.
- Michael Denton’s Evolution: A Theory in Crisis (Adler and Adler, 1985)

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And let me add my two cents to this astounding picture. The model that you would complete a million years later would be just that, a lifeless static model. For the cell to do its work this entire twenty kilometer structure and each of its trillions of components must be charged in specific ways, and at the level of the protein molecule, it must have an entire series of positive and negative charges and hydrophobic and hydrophilic parts all precisely shaped (at a level of precision far, far beyond our highest technical abilities) and charged in a whole series of ways: charged in a way to find other molecular components and combine with them; charged in a way to fold into a shape and maintain that most important shape, and charged in a way to be guided by other systems of charges to the precise spot in the cell where that particle must go. The pattern of charges and the movement of energy through the cell is easily as complex as the pattern of the physical particles themselves.
Also, Denton, in his discussion, uses a tennis ball to stand in for an atom. But an atom is not a ball. It is not even a ‘tiny solar system’ of neutrons, protons and electrons’ as we once thought. Rather, it has now been revealed to be an enormously complex lattice of forces connected by a bewildering array of utterly miniscule subatomic particles including hadrons, leptons, bosons, fermions, mesons, baryons, quarks and anti-quarks, up and down quarks, top and bottom quarks, charm quarks, strange quarks, virtual quarks, valence quarks, gluons and sea quarks…
And let me remind you again, that what we are talking about, a living cell, is a microscopic dot and thousands of these entire factories including all the complexity that we discussed above could fit on the head of a pin. Or, going another way, let’s add to this model of twenty square kilometers of breath taking complexity another one hundred trillion equally complex factories all working in perfect synchronous coordination with each other; which would be a model of the one hundred trillion celled human body, your body, that thing that we lug around every day and complain about; that would, spread laterally at the height of one cell at this magnification, blanket the entire surface of the earth four thousand times over, every part of which would contain pumps and coils and conduits and memory banks and processing centers; all working in perfect harmony with each other, all engineered to an unimaginable level of precision and all there to deliver to us our ability to be conscious, to see, to hear, to smell, to taste, and to experience the world as we are so used to experiencing it, that we have taken it and the fantastic mechanisms that make it possible for granted.
My question is, “Why don’t we know this?” What Michael Denton has written and I have added to is a perfectly accurate, easily intelligible, non-hyperbolic view of the cell. Why is this not taught in every introductory biology class in our schools?
- Matt Chait

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