Monday, October 24, 2005

"Damn, that was $#%@#$#@ hard !"

That should be the subtitle of the paper "Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilus 168 genome". The paper reports on the efforts of Japanese scientists to staple together the genomes of two entirely different bacteria and is basically the scientific version of "Pig and Elephant DNA Just Won't Splice" [see here for backstory]: the vast majority of the paper is basically a report of all the stuff they tried and how it failed until it finally worked, 8 years after the project was started. That's quite a contrast to the usual biology paper, in which the "Methods" section [aka "implementation details"], is only a fairly small bit of the paper, and often banished to the very end of the paper, in small font.

One thing that surprises me a bit is that the paper doesn't really get into how the organism with the glued-together genome behaves, other than noting that it only grows in the growth medium needed by one of the bacteria. You'd think that if you created something that chimeric, you'd at least prod it in a few ways to see how it behaves, but there wasn't any of that. Maybe these poor folks just wanted to get this paper out so they could take a breather before actually thinking about what they created.

All that said, though, the effort is an impressive tour-de-force of molecular biology and another example of large-scale genome manipulation [similar to earlier efforts I've mentioned]. We're definitely getting much more ambitious with the length of DNA chunks we're trying to manipulate; once we get truly low-cost, large-scale DNA synthesis, we're going to be in a position to try some really cool stuff, and get results much more quickly than we currently can. It may be a bit like the switch from writing programs on punch cards, submitting your stack of cards to the High Priests Of The Machine and then waiting a day to get your results [which is, I'm told, how it used to be ...] to an interactive programming environment -- when the cost of trying something is lower, you try more stuff and make faster progress.

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