Blog: Dan E. Linstedt

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DNA Computing & Tic-Tac-Toe

I came across this entry this morning, where DNA computing in enzymes has been activated to play tic-tac-toe. Apparently (the article says) that the system cannot be beat. The article also goes on to discuss how the enzymes affect the DNA strands around it, cutting, splicing, and attaching depending on their choice. In this blog posting I will explore what some of the "possible applications" of this technology might be, a simple thought experiment if you will.

The article can be found here. I've spent a lot of time writing about the nature of convergence, and the fact that I believe "wet-technology" or the mix between natural world models and our electronic models is coming together. Nothing is more evident here. In this particular case we have electronic gates / switches that we normally use to play tic-tac-toe, only they are placed into DNA enzymes. This raises some very interesting questions:

1. How parallel is this DNA computer?
2. If it has so many parallel operations, how fast is it in terms of "operations per second?"
3. What would happen if we took multiples of these tic-tac-toe boards, and tied them together for a game of Othello? If we did this for Chess, what would need to change?

We're always molding our natural world into models that we see to fit our needs, for instance - moving the tubes into a sequence to represent tic-tac-toe. What if instead, we utilized a single strand of folded DNA in three dimensions to represent a tic-tac-toe board? Could the single solution with a single DNA strand play the game on a much smaller level?

This is the type of question that would lead deeper into the Nanohouse abilities. The ability to control a single DNA strand, and utilize a model that already exists to achieve our goals. We would have a much larger scale repeatable model if we could do this.

The thought experiment:
Say for an instant that you had 120 train tracks back to back, and 120 trains (1 on each track). Now say, each train has 120 cars - each one uniquely different, and each trains engine was unique - color, size, shape, horsepower, motor drive, etc.. Now suppose within each train, a series of cars represented a "square" on the tic-tac-toe board. In other words, 20 cars from each train represented one square. Each train represents a different tic-tac-toe board.

Now suppose we released 120 people, told them to go "take" six cars from each train - the only requirement is that they need to all choose a different 6 car set. This might represent the chemical release to a DNA strand, and each of the "people" or incoming chemical mix matches with a specific DNA place in the chain. By repeating this process, and having the "computer" or the "game" choose other car sets, you've effectively re-created a logic gate computing device at the DNA strand level.

The other thing we've done here is suggest that the computations occur in parallel, and that data sets can be different for each "action" - told to attach itself to DNA at different parts of the strand. We've effectively re-created the possibility to play an very large number of finite "games", all in parallel. Very quickly the "winning pattern" will emerge, these may become the rules that are applied to the next engine going forward - in other words, spot the "learning pattern".

Of course, change the game - and we have to start all over again. The learned rules for Tic-Tac-Toe don't necessarily work for checkers or chess.

Some of the other questions still rolling around in my head are:
1. Is DNA Computing (or will it ever be) faster than electron based spin technology?
2. What are the pros and cons of DNA computing versus electron spin technology?
3. What are the recent strides that electron spin technology has made?

It seems to me that electron spin computing has a ways to go, and isn't making advances as fast as DNA computing, but that remains to be seen. It also appears to be a more difficult challenge, as DNA molecules are much larger than electron based control at the atomic level. However - I must ask the question, if we can search 10^8 Terabytes of DNA solution in 3 seconds, how fast (if it ever can be done) will electron spin computing device search 10^8 terabytes? I must also ask, is it really worth the cost or difficulty of overcoming its (electron spin) obstacles to make it happen?

I'd love to hear your thoughts and ideas.

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