ECC – Silverton Consulting

I had talked about DNA programming/computing previously (see my DNA computing and the end of natural evolution post) and today we have an example of another step along this journey. A new story in today’s Science News titled DNA used as rewriteable data storage in cells discusses another capability needed for computation, namely information storage.

The new synthetic biology “logic” is able to record, erase and overwrite (DNA) data in an E. coli cell. DNA information storage like this brings us one step closer to a universal biologic Turing machine or computational engine.

Apparently the new process uses enzymes to “flip” a small segment of DNA to read backwards and then with another set of enzymes, flip it back again. With another application of synthetic biology, they were able to have the cell fluoresce in different colors depending on whether the DNA segment was reversed or in its normal orientation.

To top it all off, the DNA data storage device was inheritable. Scientists showed that the data device was still present in the 100th generation of the cell they originally modified. How’s that for persistent storage.

The universal biological Turing machine

Let’s see, my universal Turing machine parts list includes:

Tape or infinite memory device = DNA memory device – Check (todays post, well maybe not infinite, but certainly single bits today, bytes next year, so it’s only a matter of time before it’s KB)
Read head or ability to read out memory information = biological read head – Check (todays post, it can fluoresce, therefore it can be read)
State register = biologic counter – Check (seems to have been discovered in 2009, see Science News article Engineered DNA counts it out, don’t know how I missed that)
State transition table or program = biological programming – Check (previous post plus today’s post, able to compute a new state from a given previous state and current data and write or rewrite data).

As far as I can tell this means we could construct an equivalent to a universal turing machine with today’s synthetic biology. Which of course means we could perform just about any computation ever conceived within a single cell AND all generations of the cell would inherit this ability.

End of natural evolution, …

Gosh the possibilities of this new synthetic biological turing machine are both frightening and astonishing. My original post talked about how adding ECC like functionality plus a ECC codeword to human DNA strand would spell the end of natural evolution for our species.

I suppose the one comforting thought is that flipping DNA segments takes hours rather than nano-seconds which means biological computation will never displace electronic/optronic computation. But biological computation really doesn’t have to. All it has to do is repair DNA mutations over the course of days, weeks and/or years, before it has a chance to propagate in order to end natural evolution.

…, the dawn of un-natural evolution

Of course with such capabilities, “un-natural” or programmed evolution is quite possible but is it entirely desireable. With such capabilities we could readily change a cell’s DNA to whatever we desire it to be.

My real problem is its inheritability. It’s one thing to muck with a persons genome, it’s another thing to muck with their children’s, children’s, children’s, … DNA.

Let’s say you were able to change someone’s DNA to become a super-athelete, super-brain or super-beautiful/handsome person. (Moving from a single cell’s DNA to a whole person’s is a leap, but not outside the realm of possibility). Over time, any such changes would accumulate and could confer an seemingly un-assailable advantage to an individual’s gene line.

There’s probably some time to think these things through and set up some sort of policies, guidelines, and/or regulations environment around the use of the technology before capabilities get out of hand.

In my mind this goes well beyond genetically modified organisms (GMO) organisms that are just static changes to a gene line. Programming gene lines to repair DNA, alter DNA, or even to make better copies, seems to me to be an order of magnitude increase in new capabilities taking us to genetically programmed organisms that has the potential to end evolution itself.

We need to have some serious discussions before it goes that far.

Comments?

Image: E. coli GFP by KitKor

DNA Molecule Arrangement in the Chip (from http://dnacomputing.design.officelive.com)

Read an article the other day in the Economist on how researchers are now performing computation using DNA. The intent is to someday come up with small biologic computers that can be inserted into cells/organisms which can cure or kill cells that are in trouble and leave the rest alone.

Computing soup?!

Research in the area of molecular computing has been going on since 1994, when a scientist created a DNA based solution to compute an answer to a specified traveling salesman problem.

In those days the answer was derived from running a centrifuge on the end-product soup of DNA strings and extracting the answer from the resultant gel matrix.

Molecular computing redefined

Since then, there has been significant improvements in DNA computing. Currently, most are based on DNA strand displacement. Today’s molecular computers consists of free floating DNA or RNA snippets. A logic gate is made up of two strands, one of which is the “computational logic” and the other an “output signal”. In addition to the logic gate there is another DNA/RNA strand which is an “input signal” or almost like input data. Input signals are matched up to a specific logic gate and cause the output signal snippet to be detached creating yet another input signal for other computations cascading down the pipeline.

DNA-RNA based digital logic

By doing all this, researchers have been able to create DNA snippets that perform various logical computing operations such as AND, OR and NOT logic gates and producing the signal pathways to connect them in a computational sequence or “program”.

The molecular automata all looks like elementary electronic circuits made up of base level logic gates logic to me but just as in electronic digital logic it seems to gets the job done. One gets a computation done by adding 1000’s of copies of the logic gates and input sequences together and some how assaying the end result many hours later.

Using these capabilities, they have created DNA programs made up of 74 different DNA strands that could calculate the square roots of 4 digit numbers.

Next, they tied an artificial neuron to fire when input signals hit a certain level together with a soup of 114 different DNA strands to do rudimentary pattern recognition. They used then “programed” their DNA neural net to recognize Yes/No answers provided by different scientists. The report said that the neural net, was able to get the correct answer every time but took 8 hours to perform the calculations.

There are a couple of groups working on a programming language and a simulator tool for DNA or molecular computing called the DNA Strand Displacement (DSD) tool.

The report went on to say how another set of researchers were fabricating synthetic genes which when introduced into cell could be used to trick the cell into producing the cellular computer itself.

The end of natural evolution?

The end game for all this is to create a computational device that can somehow be injected into tissue cells which would identify “sick” cells then cure or destroy them.

A couple of years ago, I was waiting in a doctor’s office for something or another and penned a poem on the end of human evolution involving ECC combined with DNA. (No, you can’t see the poem.)

You see in computers today there is a computational device called an ECC or error correcting code which is a circuit and a special code word that can be appended to a sequence of data that together can then be used to correct for errors in transmission or storage of that data.

Once someone can build digital logic out of DNA-RNA, it’s not a big leap to have build an ECC circuit. Once the circuit is ready, anyone could potentially have their DNA modified to have an appropriate ECC codeword appended to it. With DNA + ECC code word and an active ECC circuit in the cell, it’s quite possible than any single, double, or triple mutation could be detected and fixed inside a cell. Of course ECC can go beyond triple error detection if needed. Also, Reed-Solomon and other erasure codes can even go much beyond that.

After such a device was incorporated into the human genome, it would seem to signal the end to natural evolution, at least for humans.

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