DNA computing and the end of natural evolution

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

2-bit_ALU (from wikimedia.org)
2-bit_ALU (from wikimedia.org)

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.