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Digital DNA Circuits
TheSync writes "ScienceNews has a story about digital DNA circuits. The circuits use proteins that activate or deactivate genes on the DNA for control. Since an inverter and an AND gate have been created, any digital logic circuit can now be done in DNA. Moreover, evolution can help make circuit elements work better. There is even a "databook" of BioBricks circuit elements and BioSPICE for biocircuit simulation."
I wasn't saying the interface would solve the problem. I was saying that if I designed a cell to respond to an external stimulus with a certain protein production, I'd have a handy interface. Instead of building a cell to light up in the presence of a complex chemical compound, I could then simply have a cell send a protein to a circuit which could then send a signal to a led. Or, vice-versa, I could program a complex series of actions into a processor which would then interface with said S-2-C cell which would produce the proper proteins to achieve the desired effect.
The article certainly goes beyond the idea of having one cell act a certain way. They implied that multiple cells could be chained together like some sort of rube-goldberg contraption. It's the chaining together that seems inefficient to me, when you could use silicon for the complex stuff and an interface cell to make the conversion. Kind of like a digital-to-analog switch, only between silicon and carbon. You still need to hack the cells, but you don't need to create complex machines. That was all I was wondering.
There are applications of this FAR beyond those of silicon. What if you designed a circuit to detect the presents of certain viruses? You could make chemical/biological weapon detectors the size of CELLS! Also, think of what it can give us in a way of examining solutions to problems in our bodies.. you could design circuits to output certain chemicals/protiens when certain chemicals are in our blood stream. We could build cells that help filter out cancerous elements, PRODUCE INSULIN so that people would never need the shot again. This is just the tip of the iceburg on what all is possible with this new technology.
Personally I'de love to sit and tinker with them, a cell program that could provide anti-histimenes when they build up in my system would be really nice, never worry about allergys again. Pipedream maybe, but it looks really sound and possible to me.
"Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
Is right here. Highly suggested reading/listening.
I don't think we'll have serious applications in bioware in the next decade.
The sequencing work done to date is phenomenal. Not trying to sell anyone short. However, the complexity when you move from the genome to the proteome can be fairly described as staggering, so I'm weighing in on the conservative side on this one.
Get thee glass eyes, and, like a scurvy politician, seem to see things thou dost not.--King Lear
What the NPR interviewee said does appear true. However, be aware its not the DNA that's actually performing any operations. Genetic control sequences (called promoters, enhancers, and silencers) are well characterized. It is the product of other genes (i.e. proteins) that perform the operations on DNA and are subject to regulation via these control sequences.
Now what is truly complex is that proteins can bind to other proteins and affect their activity. Lengthy circuits of proteins "touching" one another (called signal transduction pathways) becomes incredibly complex with the exponential level of crosstalk and pathway intersections that can occur. That is where true Bioinformatic power lies....not so much the Folding Projects you see on distributed computing systems.
The design of the "DNA computation" in the original story is contigent upon the aforementioned processes. It does not work on some natural computing power of DNA.
-DD
In the course of her work with Watson and Crick, Rosalind Franklin had to do a serious amount math by hand (Patterson analysis to create Patterson maps). Later, after her work on DNA she was forced to hire a computer (an 18yr old girl) to do the leg work on the data she gathered on the Tobacco Mosaic Virus.
Today I read here http://www.sciencenews.org/20030426/bob11.asp (Computer circuits made of genes may soon program bacteria)
"Silicon circuits perform complex operations using a handful of simple components known as logic gates. Genetic- circuit engineers are now building the same devices inside cells."
I wonder, what she would have thought, to know that very thing she was studying could some day be used to do the math that took up so much of her time.
And while DNA is compact, 2^128 and 2^1000 are really big numbers. 2^128 is about 10^38, and 2^1000 is about 10^300. A pound of hydrogen has about 10^27 atoms, so even if you use one hydrogen atom per key, you need nearly a billion tons of hydrogen just to get 2^128 atoms, let alone a billion DNA molecules.
All this attention from computer scientists to "biocomputing" is mostly hype, and it's probably due to lucrative DARPA grants running out for the old kind of work. There are interesting questions to be asked there and interesting applications to be found, but biologists and mathematicians have been asking those for decades already.