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> They found that not a single gene is shared across all of life. It is definitely a function vs identity. Many mutations of a single gene can perform the sam

by daveguy 10y ago

> They found that not a single gene is shared across all of life. It is definitely a function vs identity. Many mutations of a single gene can perform the same function -- there is a lot of redundancy in genetic code. >If he had done the same set of experiments with a different microbe, he points out, he would have ended up with a different set of genes. This is very interesting. I expect also, that if they proceeded with their knockout in a different order or different sets at one time they would end up with a different set of genes. Maybe they have some massively parallel way to knockout genes, but I doubt they have explored the entire set of knockouts from the original functioning natural organism. They very likely could be at a local minima of genes required (eg no single gene can be knocked out, but no where near the absolute minimum).

djsumdog 10y ago
Years ago I read an interesting paper comparing the types of subsystems found in the Linux kernel with subsystems found in biology (or what we understand of them currently). There is a lot of redundancy in biology, which allows for biological systems to be pretty robust, adaptable and fault tolerant. Of course this also means it's really hard to fix that biological process when things go horribly wrong, such as in many forms of cancer. Paper: “Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.” By Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger Alexander, Mark Gerstein. Proceedings of the National Academy of Sciences, Vol. 107 No. 18, May 4, 2010.
- majkinetor 10y ago
  Thanks for that last paper, epic! Perhaps a good moment to refer to this one: Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148211/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148211/
majkinetor 10y ago
This means that we need first to decide on common environment that minimal synthetics will live on. Then, with this environment fixed, we could try to isolate minimal set of genes for multiple different organisms that are originally viable in this environment. Such environment should also be 'minimal' - i.e. having lowest number of resources required to construct it and lowest amounts of those resouces.

by daveguy 10y ago

djsumdog 10y ago

Years ago I read an interesting paper comparing the types of subsystems found in the Linux kernel with subsystems found in biology (or what we understand of them currently). There is a lot of redundancy in biology, which allows for biological systems to be pretty robust, adaptable and fault tolerant. Of course this also means it's really hard to fix that biological process when things go horribly wrong, such as in many forms of cancer. Paper: “Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks.” By Koon-Kiu Yan, Gang Fang, Nitin Bhardwaj, Roger Alexander, Mark Gerstein. Proceedings of the National Academy of Sciences, Vol. 107 No. 18, May 4, 2010.

majkinetor 10y ago
Thanks for that last paper, epic! Perhaps a good moment to refer to this one: Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148211/ http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3148211/

majkinetor 10y ago

This means that we need first to decide on common environment that minimal synthetics will live on. Then, with this environment fixed, we could try to isolate minimal set of genes for multiple different organisms that are originally viable in this environment. Such environment should also be 'minimal' - i.e. having lowest number of resources required to construct it and lowest amounts of those resouces.