La Folie, Quo Vadis, Evo-Devo?

達爾文在天國一定會保佑我的, 雖然我知道他一定是被打入地獄, 但這兩篇可以讓他上天堂(完全不知道這三句怎麼來的...XD)

先介紹人物:
E. V. Koonin: NCBI裡面的COGs就是他搞的, 他有多大頭呢? NCBI的FTP有他個人的資料夾(ftp://ftp.ncbi.nih.gov/pub), 還有他自己創一個Biology Direct(http://www.biology-direct.com/), 這Biology Direct有多嗆呢? 月刊, 一期大約十篇以內, 標題都是很聳動的, 比如說"Evolution of complexity in RNA-like replicator systems"(這標題應該只有他敢收吧)
Y. I. Wolf: 除了創立自己的期刊, 其他同上
L. Carmel: Koonin的visting fellow

文章介紹:
Evolutionary systems biology: links between gene evolution and function, Current Opinion in Biotechnology, Volume 17, Issue 5, October 2006, Pages 481-487
Unifying measures of gene function and evolution, Proc. R. Soc. B (2006) 273, 1507–1515, doi:10.1098/rspb.2006.3472

內容:
I.
將九個生物所具有的性質做分類(evolutionary variables and phenomic variables)以及相關性探討
NP:number of paralogs
PPI:number of physical protein–protein interaction partners
GI:number of genetic interactions
EL:expression level
CAI:codon adaptation index
PA:protein abundance
KE:lethal effect of gene knockout
PGL:propensity for gene loss
ER:sequence evolutionary rate
其中ER and PGL為evolutionary variables


II.
在分析上, 利用PCA, data顯示出前三個components, PC1, PC2, PC3, 貢獻了60%的變異
作者將這三個components做出生物意義的解釋
PC1: the "status" or "importance", of a gene in the genomic community, {El, NP, PPI, KE} make "+" contribution; {ER, PGL} make "-" contribution
PC2: "adaptability", the capacity of a gene to respond to changes in the internal or external environment, {NP, GI} make "+" contribution; {KE} make "-" contribution
PC3: a gene's "reactivity", the ability to react to environmental cues. {PGL, EL} make "+" contribution; {GI, RE, PPI} make "-" contribution