Four new grammar rules for DNA discovered

_{Denyse O'Leary

December 9, 2011

Genetics, News}

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At Pos-Darwinista, we learn that two Brazilian biophysicists have discovered four new rules of DNA “grammar”:

For 60 years, biologists have known of only two grammar-like rules that govern the language of DNA. Now they’ve found four more.

Today, Michel Yamagishi at the Applied Bioinformatics Laboratory in Brazil and Roberto Herai at Unicamp in Sao Paulo, say they’ve discovered several new patterns that significantly broaden the grammar of DNA.

Their approach is straightforward. These guys use set theory to show that Chargaff’s existing rules imply the existence of other, higher order patterns. …

Comments

Thanks for the link PaV;
Chargaff’s “Grammar of Biology”: New Fractal-like Rules Excerpt from Conclusion: It was shown that these rules are valid for a large set of organisms: bacteria, plants, insects, fish and mammals. It is noteworthy that no matter the word length the same pattern is observed (self-similarity). To the best of our knowledge, this is the first invariant genomic properties publish so far, and in Science invariant properties are invaluable ones and usually they have practical implications. http://arxiv.org/ftp/arxiv/papers/1112/1112.1528.pdf
This finding reminds me, somewhat, of the quarter power scaling enigma:
The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf 4-Dimensional Quarter Power Scaling In Biology - video http://www.metacafe.com/w/5964041/
This intriguing 'invariant' finding for DNA will surely be something else for the junk DNA junkies to completely ignore the implications of. i.e. Where is all the random nonsense junk DNA to be found in such invariant order of the genomes across species? This 'invariant' finding is just as Jerry Fodor and Massimo Piatelli-Palmarini rightly found for the quarter power scaling across life:
The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection." Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79
bornagain77_{December 10, 2011
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PaV: Thank you. It's interesting indeed. I saved the paper for future reference.gpuccio_{December 10, 2011
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Here's a pdf version for those interested. BA77: They develop a "generating" set which is invariant over almost the entire set of genomes. This would be analagous to the SU(2) and SO(3) symmetries (set of invariant rotations) in QM. Thought you might be interested in having a look. I tell you, it's got me scratching my head some.PaV_{December 9, 2011
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