Latest in a series of wacky discussions of genome size by physicists,
CLASSIFICATION OF LIFE BY THE MECHANISM OF GENOME SIZE EVOLUTION
DIRSON JIAN LI, SHENGLI ZHANGWe find that the global relationships among species should be of circular phylogeny, which is quite different from common sense based on phylogenetic trees. A domain can be defined by a distinct phylogenetic circle, which is a global and stable characteristic of the living system. The mechanism in genome size evolution has been clarified; hence the main component questions on C-value enigma can be explained. We find the intrinsic relationship between genome size evolution and protein length evolution; that is the genome size and non-coding DNA ratio can be calculated based on protein length distributions.
Can’t access it but dying to know how the C-value enigma has been explained and results in circular phylogeny rather than common sense? Luckily ArXiv has a copy you can check.
I wonder if I could publish a manuscript on genome size in a physics journal that was intentionally utter nonsense, a la Sokal?
It appears they get their “circles” (which look more like blobby scatterplots than circles) by plotting the standard deviation of protein lengths against the number of peaks in the protein-length distribution (which seems statistically shady to me). Even if these plots showed some interesting pattern, they would hardly invalidate the notion of a phylogenetic tree: the abstract doesn’t follow from the paper.
Blake Stacey(Quote)
Hi! I am the author of the papers that you mentioned as nonsense. I respect you because I learned much from your papers and Book. I think that some problems in life science need cooperation of scientists with different academic background. The observations and conclusions in my papers (Ref. 1-3) are based faithfully on the genomic data. I felt excited when I obtained them seriously. So please read my papers carefully before drawing a conclusion. If you feel necessary, I can send the papers that you can’t access. I hope that we can make friends because of the common interests.
The observation of genome size distribution of prokaryotes in your book (Figure 10.12 in Ref. 4) can be explained by my papers (Fig. 4b in Ref. 3 and Fig. 3d and Fig. 4 in Ref. 2).
References:
1. D. J. Li and S. Zhang, Mod. Phys. Lett. B 23 (2009) 3471-3489. arXiv:0811.3164v2.
2. D. J. Li and S. Zhang, Mod. Phys. Lett. B 23 (2009) 3563-3580. arXiv:0811.3164v2.
3. D. J. Li and S. Zhang, accepted by Biochemical and Biophysical Research Communications. arXiv: 0806.0108.
4. T. R. Gregory (ed.), The Evolution of the Genome (Elsevier, Amsterdam, 2005).
Dirson Jian Li(Quote)