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Palimpsest
Oct. 24th, 2008 10:32 pm" If you look long enough at E.Coli's genome, you will come across hundreds of pseudogenes, instructions with catastrophic typographical errors. You will encounter the genes of viruses that respond to stress by making new viruses and killing their host. Other instructions are mysteriously clumsy, redundant, and roundabout. Still others are cases of outright plagiarism.
Where the metaphor of an instruction manual collapses, other metaphors can take its place. My favorite is an old battered book that sits today in a museum in Baltimore. It was created in Constantinople in the tenth century. A Byzantine scribe copied the original Greek text of two treatises by the ancient mathematician Archimedes onto pages of sheepskin. In 1229, a priest named Johannes Myronas dismantled the book. He washed the old Greek text from the pages with juice or milk, removed the wooden boards, and cut the binding strings on the spine. Myronas then used the sheepskin to write a Christian prayer book. This sort of recycled book is known as a palimpsest.
Despite its new incarnation, The Archimedes palimpsest carried traces of the original text. The prayer book was passed from church to church, scorched in a fire, splashed with candle wax, freshened up with new illuminations, and colonized by purple fungus. In 1907, a Danish scholar named Johan Heiburg discovered that the battered prayer book was in fact the only surviving copy of Archimedes' treatises in their original Greek. But with only a magnifying glass to help him, Heilburg could make out very little of the ancient text. A century later conservationists are making more progress. They are illuminating Archimedes' works with beams of X-rays that light up atoms of iron in the original ink, resurrecting a glowing text of Greek. The palimpsest reveals new depths to the genius of Archimedes, who turns out to have been contemplating calculus and infinity and other concepts that would not be rediscovered for centuries.
E.Coli's genome is not so much a manual as a living palimpsest. E.coli K-12, O157-H7, and all the other strains evolved from a common ancestor that lived dozens of millions of years ago. And that common ancestor itself descended from still older microbes, stretching back over billions of years. The genetic history of E.coli is masked by mutations, duplications, deletions and insertions. Yet traces of the older layers of text survive in E.coli's genome, like vestiges of Archimedes.
Until recently, scientists had only crude toools for reading those hidden layers. They struggled like Heiberg with his magnifying glass. They are now getting a much better look at the palimpsest. Like Archimedes' ancient treatise, they're finding, E.coli's genome is a book of wisdom. It offers hints about how life has evolved over billions of years- how complex networks of genes emerge, how evolution can act like an engineer without an engineer's brain. Nested within E.coli's genomes are clues to the earliest stages of life on Earth, including the world before DNA......"
- from Microcosm: E.coli and the new science of life- by Carl Zimmer
Where the metaphor of an instruction manual collapses, other metaphors can take its place. My favorite is an old battered book that sits today in a museum in Baltimore. It was created in Constantinople in the tenth century. A Byzantine scribe copied the original Greek text of two treatises by the ancient mathematician Archimedes onto pages of sheepskin. In 1229, a priest named Johannes Myronas dismantled the book. He washed the old Greek text from the pages with juice or milk, removed the wooden boards, and cut the binding strings on the spine. Myronas then used the sheepskin to write a Christian prayer book. This sort of recycled book is known as a palimpsest.
Despite its new incarnation, The Archimedes palimpsest carried traces of the original text. The prayer book was passed from church to church, scorched in a fire, splashed with candle wax, freshened up with new illuminations, and colonized by purple fungus. In 1907, a Danish scholar named Johan Heiburg discovered that the battered prayer book was in fact the only surviving copy of Archimedes' treatises in their original Greek. But with only a magnifying glass to help him, Heilburg could make out very little of the ancient text. A century later conservationists are making more progress. They are illuminating Archimedes' works with beams of X-rays that light up atoms of iron in the original ink, resurrecting a glowing text of Greek. The palimpsest reveals new depths to the genius of Archimedes, who turns out to have been contemplating calculus and infinity and other concepts that would not be rediscovered for centuries.
E.Coli's genome is not so much a manual as a living palimpsest. E.coli K-12, O157-H7, and all the other strains evolved from a common ancestor that lived dozens of millions of years ago. And that common ancestor itself descended from still older microbes, stretching back over billions of years. The genetic history of E.coli is masked by mutations, duplications, deletions and insertions. Yet traces of the older layers of text survive in E.coli's genome, like vestiges of Archimedes.
Until recently, scientists had only crude toools for reading those hidden layers. They struggled like Heiberg with his magnifying glass. They are now getting a much better look at the palimpsest. Like Archimedes' ancient treatise, they're finding, E.coli's genome is a book of wisdom. It offers hints about how life has evolved over billions of years- how complex networks of genes emerge, how evolution can act like an engineer without an engineer's brain. Nested within E.coli's genomes are clues to the earliest stages of life on Earth, including the world before DNA......"
- from Microcosm: E.coli and the new science of life- by Carl Zimmer
