Eric Schadt's Network
24/03/11 14:55 Filed in: GenomeWeb Daily Scan
Submitted by S. Pelech - Kinexus on Thu, 03/24/2011 - 14:55.
I echo many of Eric Shadt's sentiments that are relayed in the Esquire article by Tom Junod, especially with respect to "networks" and "intelligence." I envision three forms of intelligence: molecular intelligence that operates inside of living cells; cellular intelligence that permits the cells in an organism to communicate with each other and also monitor the external environment; and social intelligence that permits organisms within a group to function together. The same kind of organizing principles are at play at each of these levels despite the vast differences in their scale.
If you want to get a sense of how complex molecular intelligence systems can be with respect to intracellular signal transduction, I invited you to visit www.phosphonet.ca. This open access knowledgebase from Kinexus Bioinformatics features over 93,000 confirmed and ~560,000 putative phosphorylation sites in ~23,000 human proteins. In PhosphoNET, we have also provided evolutionary conservation analyses of each of these phosphosites in 20 other diverse species. With our proprietary algorithms, we further predicted the top 50 out of 500 possible protein kinases that target each of these serine, threonine and tyrosine amino acid residues. Even if only 5% of the human phosphosites, which are highly conserved, are functionally important and each is phosphorylated by only 10 kinases, this indicates an intelligence network with at least a third of a million connections. Layer on the interactions with over 150 phosphatases that dephosphorylate phosphosites and other proteins that can reversibly bind to phosphosites, there is probably over a million critical connections in protein phosphorylation networks. This does not even include gene networks and other types of cellular regulation mechanisms.
Some organisms have far more complex molecular intelligence systems than humans, although we do rate highly in cellular and social intelligence capacity. Plants can have more than twice as many protein kinase genes than mammals, and a lot more genes in total. What they appear to lack in cellular and social intelligence, they more than make up in molecular intelligence.
Link to the original blog post.
I echo many of Eric Shadt's sentiments that are relayed in the Esquire article by Tom Junod, especially with respect to "networks" and "intelligence." I envision three forms of intelligence: molecular intelligence that operates inside of living cells; cellular intelligence that permits the cells in an organism to communicate with each other and also monitor the external environment; and social intelligence that permits organisms within a group to function together. The same kind of organizing principles are at play at each of these levels despite the vast differences in their scale.
If you want to get a sense of how complex molecular intelligence systems can be with respect to intracellular signal transduction, I invited you to visit www.phosphonet.ca. This open access knowledgebase from Kinexus Bioinformatics features over 93,000 confirmed and ~560,000 putative phosphorylation sites in ~23,000 human proteins. In PhosphoNET, we have also provided evolutionary conservation analyses of each of these phosphosites in 20 other diverse species. With our proprietary algorithms, we further predicted the top 50 out of 500 possible protein kinases that target each of these serine, threonine and tyrosine amino acid residues. Even if only 5% of the human phosphosites, which are highly conserved, are functionally important and each is phosphorylated by only 10 kinases, this indicates an intelligence network with at least a third of a million connections. Layer on the interactions with over 150 phosphatases that dephosphorylate phosphosites and other proteins that can reversibly bind to phosphosites, there is probably over a million critical connections in protein phosphorylation networks. This does not even include gene networks and other types of cellular regulation mechanisms.
Some organisms have far more complex molecular intelligence systems than humans, although we do rate highly in cellular and social intelligence capacity. Plants can have more than twice as many protein kinase genes than mammals, and a lot more genes in total. What they appear to lack in cellular and social intelligence, they more than make up in molecular intelligence.
Link to the original blog post.