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Author
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Topic: Shannon information in complete genomes
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Itzpapalotl
Member
Member # 623
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posted 05. May 2005 16:37
Chang-Heng Chang1, Li-Ching Hsieh1, Ta-Yuan Chen1, Hong-Da Chen1
Liaofu Luo3 and Hoong-Chien Lee
Abstract
Shannon information in the genomes of all completely
sequenced prokaryotes and eukaryotes are
measured in word lengths of two to ten letters. It is
found that in a scale-dependent way, the Shannon
information in complete genomes are much greater
than that in matching random sequences - thousands
of times greater in the case of short words.
Furthermore, with the exception of the 14 chromosomes
of Plasmodium falciparum, the Shannon information
in all available complete genomes belong
to a universality class given by an extremely simple
formula. The data are consistent with a model
for genome growth composed of two main ingredients:
random segmental duplications that increase
the Shannon information in a scale-independent way,
and random point mutations that preferentially reduces
the larger-scale Shannon information. The
inference drawn from the present study is that the
large-scale and coarse-grained growth of genomes
was selectively neutral and this suggests an independent
corroboration of Kimura’s neutral theory
of evolution.
http://sansan.phy.ncu.edu.tw/~hclee/rpr/Lee_H_Shannon.pdf
see also:
Divergence and Shannon information in genomes http://sansan.phy.ncu.edu.tw/~hclee/rpr/Shan_proofs0504.pdf
"Our analysis of the data combined with computer simulation of genome
growth models suggest a simple coarse-grain representation of genome growth: the ancestors of the
genomes began to grow when they were no greater than 300 b in length via a mechanism whose
main components were neutral stochastic segmental replicative translocations and random small
mutations."
Universality in large-scale structure of complete genomes http://sansan.phy.ncu.edu.tw/~hclee/rpr/Hsieh_gb-2004-5-3-p7.pdf
Complexity,Universality and Growth of Genomes http://www.nchc.org.tw/KING/KING_zh/data1/01.pdf
homepage of H. C. Lee: http://sansan.phy.ncu.edu.tw/~hclee/pub/allpub.html
Is information theory an enemy of ID?
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eswrite
Member
Member # 1672
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posted 07. June 2005 15:43
I get a little lost in the math, but the overall message (see last paragraph) is that information can be added through duplication of genome segments. Of course, there is a large assumption here: that those segments, which presumably are initially neutral are:
a) preserved from generation to generation, so that
b) they can mutate into meaningful coding segments for evolved structures and/or functions.
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