Monday, June 7, 2010

Synthetic Life


On May 19. Craig Venter announced that his team at the Venter Institute in La Jolla had succeeded in creating synthetic life. Why has this attracted so little attention?

Venter became famous a decade ago because he was frustrated with the slow progress and high cost of the NIH Human Genome Project, which began in 1990. In 1997 he founded Celera Corporation, which did the job in 3 years at a cost of $300 million. The government-funded effort took 13 years, finishing in 2003, and cost $2.7 billion.

What Venter et al have now done is as follows:

(1) They sequenced the genome of the bacterium Mycoplasma mycoides (which causes lung disease in goats). Its DNA has 1.08 million base pairs.

(2) Starting with the chemicals adenine (A), guanine (G), cytosine (C) and thymine (T) which make up the genetic code, they synthesized stretches of DNA corresponding to segments of the M. mycoides DNA and then managed to get them all to hook up in the right sequence. Thus they constructed from scratch a copy of the bacterium's DNA.

(3) They inserted this synthetic DNA into a different bacterium, M. capricolum, which had had the genes for its restriction enzymes removed (which means that it had no defenses against foreign DNA). The synthetic DNA took over, and the cells started reproducing and behaving just like natural M. mycoides.

A good way of looking at this is that they have taken the cell machinery ("hardware") of M. capricolum and replaced its software (the DNA), which tells it what kind of creature it should be. Having a cell "boot up" with entirely artificial software is an astounding achievement.

There is now a live bacterium in La Jolla whose genetic code was not determined by evolution but by typing it on a computer. This is the first unequivocal example of Intelligent Design – but the Intelligent Designer was Craig Venter, not God.

In my opinion, there have been five major revolutions in human society: the Agricultural Revolution, the Industrial Revolution, the breakout into space, the computer revolution, and now the creation of artificial life. This is HUGE.

In this first test, the team copied natural DNA, but now they can begin exploring variations, perhaps producing wholly new life forms. A major goal is to understand what features of DNA are essential for viable life. Venter's company, Synthetic Genomics Inc., hopes to start producing designer bacteria that can do things like making fuel from algae or cleaning up oil spills.

It is a long way from synthetic bacteria to synthetic differentiated creatures (e.g., living androids), but the way is now open. It will happen sooner than we expect. We need to start thinking about the ethical implications. 

An interesting sidebar is that all DNA has long stretches of base pairs ("junk DNA") with no known function. Although some of it surely does things we don't yet understand, it appears that you can add arbitrary segments without affecting viability. 

There are 256 ways to choose the 4 bases in a stretch of four, so you can use combinations of four base pairs to represent letters, punctuation, etc. Venter & co devised such an alphabet, and included quite a bit of text in their synthetic M. mycoides. The information includes the following quotes: "TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE." - JAMES JOYCE; "SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”- J. ROBERT OPPENHEIMER; "WHAT I CANNOT BUILD, I CANNOT UNDERSTAND." - RICHARD FEYNMAN.

We need an international agreement about the code used to include text in synthetic DNA, and a requirement that it include info about its origin (so that any life that escapes control can be identified).

Incidentally, the human genome has 3.3 billion base pairs, and 96% of it is thought to be junk. This suggests that you could encode the St James Bible four times over in a strand of human DNA, and still have it work to create a human being.

Science fiction story: we find that human junk DNA is not random; we crack the code, and find a long message encoded in our genome. It could be instructions for interstellar communication, left by aliens who created us, or it might be a version of the Bible, in Aramaic…

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