Blog: Dan E. Linstedt

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Nanotech - genes and computation ability

Genomics, and DNA computing are HOT in nanotechnology. As one researcher has written in US News (March 28th,2005) there are many things we haven't yet considered. Can gene's act as tiny computers? Can they shape the way we move into nanaotechnology? This blog explores this type of thought process.

"Using the powerful tools of molecular biology and comparative genomics, they're finding speciic changes in the DNA that can account for 17,000 species of butterfly or why insects have only six legs instead of a dozen." US News, March 28th, 2005 - "Dances with fruit flies".

While personally I do not agree with evolution as the total story, there are certainly some implications in this article which make genomic computation interesting. The study of nanotechnology includes something called Bio-Informatics, or a crude way to put it: biology that can compute information when manipulated for our purposes. There's also the study of genomics, the manner in which genes interpret how we look, what we like, how much hair we have, and so on.

DNA is a very powerful strand of cells that dictates all of these things. The cells for the genes in the skin are no different than the cells in the genes for the brain. However, different sequencing, and emphasis of these genes allow the body to create different parts and function in a different fashion. Form vs function.

I believe that consistent form is necessary for accurate computation, regardless of where or what the computation is that is taking place. I also believe that the form is a vital key to the success of redundancy of information content, and computational power. In aaddition (if I may be so bold), I believe that computational ability (and information usefulness) is directly proportional to the amount of non-redundant information that is time-keyed.

All that said, the function of the information, at least for genomes appears to be in it's position within the DNA sequence, and whether or not inhibitors limit the functionality according to where the gene is applied (ie: skin, hair, teeth, bone).

Genes can create computation (cells that communicate), otherwise the mind would be a collection of dull grey matter which has no function. The function of those cells is regulated by the enzymes surrounding the cell matter and the location in the body in which these cells exist. Location also has an effect on how the gene is folded - different purposes for the DNA strand cause the DNA to fold in different areas, leading to different results.

Of course if we step back from the DNA form itself and ask the question: what folds the gene? It's an enzyme that does the work. Are they all folded the same way? No. Then how does DNA understand where to fold? First, this is the incorrect question. The correct question is: how does the Enzyme know where to fold the DNA? This is not known today, but let's speak hypothetically for a moment.

Suppose DNA is just the FORM of the data set, suppose the enzyme is the Function (like a program on top of data in a data model - two programs use the same data model for different purposes). Suppose there are three basic (simplistic model) enzymes: one that unzips DNA, one that copies DNA (organizes other molecules into a new copy of the DNA strand), and one that ZIPS it back together again.

Given our simplistic model, where would it make most sense to have some form of rule that says: activate this molecule to fold here when put back together. Would it make sense to have the structure of the DNA actually tell us? How about one of the enzyme engines? In order to answer this question, we'd need a ton of research. However for the purposes of discussion: I'm going to say neither.

I'm going to say that it's hidden in the informational content within the DNA, and that when the DNA is re-combined with other cells (because it's being replicated), the information triggers a chemical reaction at specific spots in the DNA strand that cause it to fold up. In other words, the form and the function are necessary for computation, but it's the content within the form that makes all the difference. I believe there are (as of yet) undiscovered atoms/cells which indicate the informational content of genes.

I think that as we move forward in this age of computation, we will find that the gene itself cannot act as a tiny computer without the enzymes and the correct information. I think however that in the world of "data warehousing and business intelligence" that we must become smarter.

WARNING: CONTROVERSIAL STATEMENT:
We must recognize that there is one way to model information within our systems, one form (today, tomorrow it will evolve) - and that there are thousands of functions of this information, but by building tiny self-contained computational modules on top of the form, larger systems can begin to interpret the information in parallel, and that reduction of redundancy of information is paramount to the evolution of understanding within those systems.

Can gene's act as tiny computers? Yes, but not through form itself. Genes must be combined with enzymes, and information in order to do their jobs properly. Can genes become the ultimate computing device? I think they already are (at least for today and until evolution makes it better). If we can learn to pair up non-invasive information with genetic structures, then we can begin working with informational systems on a level never before seen.

Can DNA computing shape the way we move into nanotechnology? Absolutely, it already has. There are different forms of nanotechnology today, ranging from single atomic layer control to mutli-cell DNA computation. I think DNA computing will become more and more powerful as we begin to understand how to switch on and off different genes in the DNA strand. But it's not just on and off. It's shades of grey, understanding how to inhibit genes to different levels (like gradient colors) can become a huge boon to understanding DNA computing. By the way, DARPA has already done such a thing - in 1999. See one of the nanotech articles on this site for more information.

Love to hear your comments and thoughts, this is a difficult topic with many many opinions, but one thing is certain: We can't test theories that don't exist, and if we don't think outside the box, we can't create the theories to test.

Cheers for now,
Dan L

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