Tuesday, 28 May 2013

The Venter Code

. . .a challenge.
It's three years to the week since J Craig Venter announced the creation of "the first bacterial genome whose parent was a computer".  As any fule kno the genetic code depends on the order in which four bases A T C G are clagged onto a sugar-phosphate-sugar backbone in a double helix.  Nirenberg and Matthaei took the first step in decrypting the biological reality of the code in 1961.  It took fifty years for Craig Venter to be in a position to announce his Genetics-meets-Genesis achievement.  The press conference of the announcement is interesting because JCV is at pains to elaborate on the glitches, hold-ups, and false trails as well as the clever ideas, breakthroughs and ultimate triumph.

Venter has had some really smart ideas over the last 25 years which I'll get round to covering in due course. On this 3rd anniversary I'll note the hubris in the idea that when his people were creating their new bacterial genome from whole cloth (or from four bottles as Venter has it) they chose to write their own names into the sequence . . . in a code, that isn't necessarily the same as the "universal" genetic code
Their artificial genome sequence contains four "watermarks" each of just over a kilobase. The first water mark contains the code for all letters, numerals and punctuation. The others,
 a) the names of 46 people associated with the project. (The Authors of the 2010 paper N=24 are Daniel G. Gibson// John I. Glass// Carole Lartigue// Vladimir N. Noskov// Ray-Yuan Chuang// Mikkel A. Algire// Gwynedd A. Benders// Michael G. Montague// Li Ma// Monzia M. Moodie// Chuck Merryman// Sanjay Vashee// Radha Krishnakumar// Nacyra Assad-Garcia// Cynthia Andrews-Pfannkoch// Evgeniya A. Denisova// Lei Young// Zhi-Qing Qi// Thomas H. Segall-Shapiro// Christopher H. Calvey// Prashanth P. Parmar// Clyde A. Hutchison III// Hamilton O. Smith// J. Craig Venter//) 
b) a website where you can check in when you’ve solved the puzzle and
c) the following meaningful quotes:
* To live, to err, to fall, to triumph and to recreate life out of life. Joyce
* See things not as they are, but as they might be. Oppenheimer
* What I cannot build, I cannot understand. Feynman

Here’s the data. Your task is to crack the code. When this-all hit the news-stands 3 years ago, I put this task to the smartest young(er) people I knew and only got one "begob I'll give it a lash" response.
Interestingly my technique and his were quite different although the solution was the same. That feller has just landed a lectureship in a different university and I suggest that these two 1000-day-separated events are not unrelated. Solving this puzzle requires a crucial creative insight or two and some grunt work to see the task through to completion.

That's a pretty good summary of what makes a successful scientist.  So hats off to Kevin Byrne!  (I got my lectureship too - hence The Blob)

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