Wednesday 20 January 2016

Encoding the secrets

In 2010, Craig Venter "created life": he made a sequence of DNA by wholly artificial means and inserted it into the geneless husk of a bacterium and the resulting chimera hummed and thrummed and came to life by starting to replicate. Like god or evolution he didn't put a random string of the DNA 'bases' together but a series of modules that coded for genes that molecular biology had shown to be functional.  One of the giant-shoulders on which the project was bases was investigation into a 'minimal genome': the smallest collection of genes that was demonstrably self-sufficient.  It's a lot smaller than the genome of lab pack-horse Escherichia coli which contains about 4000 protein-coding genes.  Which is turn is smaller than, say, Pseudomonas fluorescens which is about 6500 genes in size.  Why the difference?

Well, in Yr3 F&F aka Food&Ferm aka Food and Fermentation Microbiology, we're currently isolating and characterising LABs - lactic acid bacteria - on which so much of the interest in food lies.  Without LABs no cheese, no yoghurt, no kefir, no koumiss, no sauerkraut, no kimchi, no sourdough bread . . . and no silage for winter feeding of the dairy-cows that produce the milk that allows the LABs to work their milky magicin the dairy industry.  One of the peculiarities of LABs is that they are "fastidious" - or fussy or selective.  They won't grow well on regular 'nutrient agar'; they need some supplements. And if you add even 0.5% yeast extract, by supplying a cocktail of amino acids, vitamins and goodies, then the LABs will grow.  They make tiny pin-point colonies on a Petri dish as opposed to the big gobs of snot that Pseudomonas will develop, but they do grow and multiply.
Q. Why are they fastidious?
A. Because they lack the biochemical capability to make a rake of essential nutrients.
Q. Why do they lack that capability?
A. Because they have a reduced-instruction-set for a genome: typically only 2000-2500 genes in size.

Is 2000 genes the smallest possible? No: Venter and Co. used Mycoplasma mycoides as a template for their computer generated life-form.  It manages quite well, thank-you, with  only 1000 protein coding genes. One interesting thing about The Venter Genome which I addressed in an earlier trib is that the development team inserted 4 'watermarks' into their artificial genome, which contained encoded information.  This info included a list of the authors, an encrypted key to the code, and some deep quotes to show that they were Renaissance Chaps.  The code wasn't designed to be unbreakable and me and my smarter pal Kevin were able to crack it - albeit using two rather different methodologies. Wanna go? The watermarks are still on line.  Encoding in DNA, hmmm?  Maybe we can write something more meaningful than a list of Venter's employees and collaborators and a quote from James Joyce. If we need 1000 genes = 1 million bases to encode the replication machinery and essential metabolic systems, then we can write a lot more than a tweet of information in another 'payload' million-bases.  You'll need 3 bases for each letter in English or кириллица, so 1 million bases can make a text of about 50,000 words. You can say a lot in 50,000 words.

Dr. Christian Bök, a Canadian poet has been obsessing about the idea of writing something for all time rather than the ephemeral triumphs of getting a paper in Science. He's not piffling about with Escherichia coli either: that's far too likely to snuff out if, for example, Earth gets too hot for all the mammals. No: Deinococcus radiodurans is your only man for immortality. It is a really remarkable organism: the radiodurans means withstanding radioactivity: if zapped with sufficient X-rays you and me and Escherichia coli will roll over and die because ionizing radiation will destroy DNA. Deinococcus OTOH has developed ways of restoring its genetic material after it has been fragmented in this way.  The point is that if you have a message for all time and all space and wanted to send it out there to share: Deinococcus radiodurans might be the ideal space-ship.  If the question is "What's the message?" the answer might be "42".  That's a cheap shot.  I really don't know what humanity knows that we really should share with little green men from Planet Zorg.  Do read the piece about Christian Bök: it's a more thoughtful explanation of the technical issues of cosmic communication than I can manage.

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