sentence has to be one of the most remarkable things ever uttered. It makes no literal sense. Yet because it contains real words, and its syntax and grammar are fine, we can sort of follow along. It’s not quite devoid of meaning.
In the same way, DNA mutations can introduce random amino acid words or phrases, and cells will automatically fold the resulting chain together in perfectly syntactical ways based on physics and chemistry. But any wording changes can change the sentence’s whole shape and meaning, and whether the result still makes sense depends. Sometimes the new protein sentence contains a mere tweak, minor poetic license that the cell can, with work, parse. Sometimes a change (like a frameshift mutation) garbles a sentence until it reads like grawlix—the #$%^&@! swear words of comics characters. The cell suffers and dies. Every so often, though, the cell reads a protein sentence littered with missense or nonsense… and yet, upon reflection, it somehow does make sense. Something wonderful like Lewis Carroll’s “mimsy borogoves” or Edward Lear’s “runcible spoon” emerges, wholly unexpectedly. It’s a rare beneficial mutation, and at these lucky moments, evolution creeps forward. *
Because of the parallels between DNA and language, scientists can even analyze literary texts and genomic “texts” with the same tools. These tools seem especially promising for analyzing disputed texts, whose authorship or biological origin remains doubtful. With literary disputes, experts traditionally compared a piece to others of known provenance and judged whether its tone and style seemed similar. Scholars also sometimes cataloged and counted what words a text used. Neither approach is wholly satisfactory—the first too subjective, the second too sterile. With DNA, comparing disputed genomes often involves matching up a few dozen key genes and searching for small differences. Butthis technique fails with wildly different species because the differences are so extensive, and it’s not clear which differences are important. By focusing exclusively on genes, this technique also ignores the swaths of regulatory DNA that fall outside genes.
To circumvent these problems, scientists at the University of California at Berkeley invented software in 2009 that again slides “windows” along a string of letters in a text and searches for similarities and patterns. As a test, the scientists analyzed the genomes of mammals and the texts of dozens of books like
Peter Pan
, the Book of Mormon, and Plato’s
Republic.
They discovered that the same software could, in one trial run, classify DNA into different genera of mammals, and could also, in another trial run, classify books into different genres of literature with perfect accuracy. In turning to disputed texts, the scientists delved into the contentious world of Shakespeare scholarship, and their software concluded that the Bard did write
The Two Noble Kinsmen—
a play lingering on the margins of acceptance—but didn’t write
Pericles
, another doubtful work. The Berkeley team then studied the genomes of viruses and archaebacteria, the oldest and (to us) most alien life-forms. Their analysis revealed new links between these and other microbes and offered new suggestions for classifying them. Because of the sheer amount of data involved, the analysis of genomes can get intensive; the virus-archaebacteria scan monopolized 320 computers for a year. But genome analysis allows scientists to move beyond simple point-by-point comparisons of a few genes and read the full natural history of a species.
Reading a full genomic history, however, requires more dexterity than reading other texts. Reading DNA requires both left-to-right and right-to-left reading—boustrophedon reading.Otherwise scientists miss crucial palindromes and semordnilaps, phrases that read the same forward and backward (and vice versa).
One of the world’s oldest known palindromes is an amazing
In the same way, DNA mutations can introduce random amino acid words or phrases, and cells will automatically fold the resulting chain together in perfectly syntactical ways based on physics and chemistry. But any wording changes can change the sentence’s whole shape and meaning, and whether the result still makes sense depends. Sometimes the new protein sentence contains a mere tweak, minor poetic license that the cell can, with work, parse. Sometimes a change (like a frameshift mutation) garbles a sentence until it reads like grawlix—the #$%^&@! swear words of comics characters. The cell suffers and dies. Every so often, though, the cell reads a protein sentence littered with missense or nonsense… and yet, upon reflection, it somehow does make sense. Something wonderful like Lewis Carroll’s “mimsy borogoves” or Edward Lear’s “runcible spoon” emerges, wholly unexpectedly. It’s a rare beneficial mutation, and at these lucky moments, evolution creeps forward. *
Because of the parallels between DNA and language, scientists can even analyze literary texts and genomic “texts” with the same tools. These tools seem especially promising for analyzing disputed texts, whose authorship or biological origin remains doubtful. With literary disputes, experts traditionally compared a piece to others of known provenance and judged whether its tone and style seemed similar. Scholars also sometimes cataloged and counted what words a text used. Neither approach is wholly satisfactory—the first too subjective, the second too sterile. With DNA, comparing disputed genomes often involves matching up a few dozen key genes and searching for small differences. Butthis technique fails with wildly different species because the differences are so extensive, and it’s not clear which differences are important. By focusing exclusively on genes, this technique also ignores the swaths of regulatory DNA that fall outside genes.
To circumvent these problems, scientists at the University of California at Berkeley invented software in 2009 that again slides “windows” along a string of letters in a text and searches for similarities and patterns. As a test, the scientists analyzed the genomes of mammals and the texts of dozens of books like
Peter Pan
, the Book of Mormon, and Plato’s
Republic.
They discovered that the same software could, in one trial run, classify DNA into different genera of mammals, and could also, in another trial run, classify books into different genres of literature with perfect accuracy. In turning to disputed texts, the scientists delved into the contentious world of Shakespeare scholarship, and their software concluded that the Bard did write
The Two Noble Kinsmen—
a play lingering on the margins of acceptance—but didn’t write
Pericles
, another doubtful work. The Berkeley team then studied the genomes of viruses and archaebacteria, the oldest and (to us) most alien life-forms. Their analysis revealed new links between these and other microbes and offered new suggestions for classifying them. Because of the sheer amount of data involved, the analysis of genomes can get intensive; the virus-archaebacteria scan monopolized 320 computers for a year. But genome analysis allows scientists to move beyond simple point-by-point comparisons of a few genes and read the full natural history of a species.
Reading a full genomic history, however, requires more dexterity than reading other texts. Reading DNA requires both left-to-right and right-to-left reading—boustrophedon reading.Otherwise scientists miss crucial palindromes and semordnilaps, phrases that read the same forward and backward (and vice versa).
One of the world’s oldest known palindromes is an amazing
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