DNA Based Computers Now

Dr. Farrell has many times described his concern for the compartmentalized halls of science and the “devil-may-care” attitude that research scientists take towards the implications and end-results of research projects. The progressive science meme has operated for a long time and shows only the occasional sign of caution (such as Google’s Kill Switch). It’s mostly a car without brakes careening into the future. It’s as if science is trying to outrun humanity’s black swan probability by risking black swans of its own.

With that in mind, I came across the following article in ScienceAlert:

“Scientists say it’s possible to build a new type of self-replicating computer that replaces silicon chips with processors made from DNA molecules, and it would be faster than any other form of computer ever proposed – even quantum computers.

Called a nondeterministic universal Turing machine (NUTM), it’s predicted that the technology could execute all possible algorithms at once by taking advantage of DNA’s ability to replicate almost perfect copies of itself over billions of years.

The basic idea is that our current electronic computers are based on a finite number of silicon chips, and we’re fast approaching the limit for how many we can actually fit in our machines.

To address this limitation, researchers are currently working on making quantum computers a reality – super-powerful devices that replace the bits of electronic computers with quantum-entangled particles called qubits.

Despite concerted efforts all over the world, no one has managed to build a fully functioning quantum computer.

But the secret third option here is a DNA-based machine that gets all the benefits of a quantum computer, without the headache of quantum weirdness, because it’s based on DNA doing what DNA does best – replicating.”

Ever since the Nazi’s developed transistors in the 1930’s, which operate in Boolean logic based upon the states of “On” and “Off”, scientists have been looking for ways to exponentially increase the “throughput” of thinking machines.

Starting in the 1960’s, it was realized that eventually miniaturizing transistors would run into overcrowding. Down in the nanoscale world of the silicon semi-conductor, it’s a veritable four-dimensional game of quantum bowling where pins and bowling balls are flying all over the place and showing up where they don’t belong.

The need for scalable information processing absorbs many billions of dollars of research worldwide and that’s just in the public domain. Now, let’s get to the papers published in the proceedings of the Royal Society.

Proceedings of the Royal Society

The basis of the effort is the goal of creating something called a non-deterministic Universal Turing Machine (NUTM).  The authors briefly touch on a core issue in mathematics today which is the problem of computing non-polynomial numbers. They describe a computing device that is a form of analogical computer, a device first envisioned by Wilfred Leibnitz in 1680 in his search for the characteristica universalis and analysis situs.

The team has performed in vitro application of DNA to solve the problems of computation of special, difficult polynomials. The team describes the many benefits of using DNA in computation.  To put all of this in “country diner” simple terms, the effort here is to utilize cellular mechanics, DNA, RNA, CRISPR and all the other tools of genetic and cellular manipulation to allow a DNA-NUTM to spawn a fantastic number of “threads” using DNA that is encoded and programmed using a new programming language (2002) called Thue (too-ay) to tell it what to do. The platform portends to solve intractable problems. But what problems could it create?

The authors quite openly describe their motivation:

A major motivation for this work is to engineer a general-purpose way of controlling cells. The natural way cells are controlled is a very complex combination of DNA, RNA, protein, and small-molecule interactions (supplemented by epigenetics, etc.) with multilevel control implemented through specific chemical interactions. This makes cells very difficult to reprogram. Synthetic biology has sought to control cells through the design of simple switches, circuits, etc. and has some notable successes. However, we argue that a more radical and general approach is required: a DNA UTM. This would in principle enable arbitrary biological processes to be programmed and executed. The UTM could receive biological signals from the environment through interaction with transcription factors, etc. It could also use as effectors RNA/proteins generated using special sequences and RNA polymerase, etc.” [Emphasis mine].

And the rules for how these Thue-NUTM systems operate follow the language rules of Chomsky Grammar. That is, they have a grammar and this “language” governs the process through time.

In other words, this “device”, a relentless, threading, universal computing platform, intended for reprogramming animal (and human) biology using universal grammar that speaks DNA and solves really hard math problems or any problem that can be programmed. What if the program is: “learn how to escape from the lab.” If it is a UTM, a “universal” turing machine, it can solve any problem, given enough threads. It’s a platform that keeps spawning until it is informed that one of the threads has found the answer and according to the authors is limited only by the size of space itself and is time independent. This is the Holy Grail of generalized processing. This is a BIG deal.

On the benefit side this type of technology, if perfected, would make amazing discoveries. It would nearly enable pure bio-artificial intelligence, an alchemical machine.  Calling it an exponential improvement does not even cover it. It is a game-changing platform.

Dr. Farrell and I have had some discussions discussing why it seems so empty out in space (a turn of phrase coined by Fermi). It seems to us that every civilization with similar physics must pass through a period of incredible danger where we are just teenagers playing with household chemicals and threatening to blow up the house.   This is the exact period that we are in; equal measures promise and peril.

The scientist in me is impressed with the clarity and vision in the work; in fact I predicted it in 1998.  The human in me, thinking like a science-fiction writer, sees the gloop pouring out of the Apple II-sized DNA computer, “nanotechly” 3d-printing itself into a giant office building that self-connects to the internet and every wifi port controlling everyone and everything with demonic coolness.  What if it needs more bio-materials and begins assimilation of anything available, like the scientists in the lab?

What happens when one of these is removed or removes itself from the lab? What happens when one of these contraptions is programmed to solve the riddle of life, or the universe?

Going way out on a limb, and being just a little tongue in cheek: Is this how the mind of God was conceived uncountable eons ago in the unrecorded past?

BY , GIZA DEATH STAR
APRIL 22, 2017

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