Genetic Code

See http://www.wikipedia.org/wiki/Genetic_code

This reads like assembly. Do we have a machine that you plug C-code into and that spits out an assembled strand of DNA? Just wondering...

It's called a DNA sequencer. Visit http://used-line.com/cgi-bin/test/used-dna-related.cfm for some good deals on used models. Most of them are from crashed biotech startups. You can be the first kid on your block to create a new life form. But hurry.

Just as important is Protonomics - the amino acids specified by the DNA are assembled into proteins on Ribosomes outside the cell nucleus. How proteins fold, interact and result in functioning cellular structures is the field of Protonomics and determines how cells and MulticellularOrganisms really develop, work and heal. Folding is a very complex problem - supercomputers are needed to solve it. IBM is spending millions of dollars on a variation of "Deep Blue" to do this. How cells signal internally and to each other is also another complex mechanism that determines how cells develop and behave. Like EventDrivenProgramming. The whole stem cell debate is about those early inception cells that have the capability to turn into any kind of cell (once it turns into muscle, skeleton, blood cell, etc., it tends not to change - it continues to replicate as that type). The debate isn't about how they function but about where these should be harvested from. Interestingly, some researchers say how insects' nests develop by insects signalling to each other and constructing is analagous to cells signalling to each other and forming organs. AlanTuring helped develop "CellularAutomaton s" based on what he knew about cells at the time. Also, ScientificAmerican recently had an article discussing the fact that what was thought to be "junk dna" making up large parts of a genome is in fact functional but not understood at all, but has effect when they manipulate it. Sequencing the various organisms' codes is a big first step but there is a long way still to go. You need protenomics design as well as a dna interpreter in order to create a new life form. Actually, it might be possible in the future to design your form in a 3D IDE (Maya?), then it could "compile" the macro structures down to organs, then cells, then proteins/chemicals, then finally the chromosomes and dna needed to "run" the design. I've seen gene "grammars" where people tried to at least specify the "syntax" and "semantics" of dna.

Is it "protonomics" or "protenomics" or "proteonomics" or "proteomics"?

It is "Proteomics". The above paragraph is an adequate sketch of protein folding. That is, however, only the tiniest first step towards "understanding" (if the term even makes sense) how metabolisms work and the role proteins play. Even if the protein folding problem is solved (and some argue it will never be), the result is analogous to predicting the trajectory of an individual molecule in a gas - it might be interesting, but it will not be helpful in predicting the way the gas behaves. Analyzing the ant does not help predict the behavior of the ant-hill.

Understanding micro-level details does help predict macro-level behaviour. There may be EmergentBehavior that make the whole more than the sum of its parts, but certainly knowing underlying mechanisms is valuable. Theories of gas behaviour do try to model individual molecules, even if assumptions are made as to their aggregate interaction, container symmetry and averaged out to come up with pressure on a 6-sided box. Deviations from those simple models ie plasma physics requires analyzing the particles and fields in more detail. Anyone studying ant-hills will of course be interested in analyzing ant development, behaviour and types. Knowing how proteins fold won't magically allow complete understanding of cells, but it will certainly help, as does knowing dna sequences. Lots of work is being done to simulate cell behaviour for example see http://web.sfc.keio.ac.jp/~mt/mt-lab/publications/Paper/ecell/bioinfo99/btc007_gml.html knowledge of protein folding and behaviour will make this more accurate, allow better drugs to be developed as well as pure academic understanding. Many companies business models are predicated on the value of Proteomics. see http://kdpnw.kdp-baptist.louisville.edu/proteomelab/companies.html

The Washington Post article below goes into more detail on Protein Folding, where they say "Such insights almost certainly would have practical effects on the development of drugs, most of which work by stimulating or blocking the action of proteins". http://www.people.virginia.edu/~rjh9u/protfold.html

Further detail from a paper from the researcher mentioned in the article: http://www.pnas.org/cgi/content/full/96/25/14258

Surely Protein Folding is an interesting problem, and great benefit will surely derive from solving it (to the extent that a "solution" is possible). Like sequencing the human genome, however, solving the protein folding problem will not "unlock" the secrets of life in any of our lifetimes. While crucial to the current paradigm for venture capital investment, unfettered hype about the "promise" of such "solutions" burdens the biopharm domain in the same way that similar hype burdened the AI community during the eighties. Those of us who are consumed by the mysteries these molecules present (including yours truly) need to constantly remind ourselves that we are laying the very bottom-most foundation stones of the building that will eventually arise. We are rather more like Lavoisier (who defined a "chemical element" and published the first table of them in 1789) and rather less like Thomas Edison or Henry Ford. I wrote the above paragraph to emphasize the "ant-hill", not to minimize the ants. -- TomStambaugh.

See BlueGene

CategoryBiology