Saturday, March 24, 2012

The current apex of human cleverness

may be these unremarkable-looking machines, which are Illumina gene sequencers. The other day I had the pleasure and privilege of getting a tour of the DOE Joint Genome Institute in Walnut Creek, which has 8 of these babies. With these and the other sequencing machines, they sequence well over 100 gigabases of DNA a day.

Something about these machines intrigues me, the way they combine the accumulated cleverness of chemistry, optics, lasers, robotics, computation, microfluidics, all in service of gathering even more knowledge. The way they have literally black-boxed these techniques so that the entire astonishingly complex process can be treated conceptually as just one thing (sort of). The way they unite academia, industry, and government efforts, and blur the lines between them. The way all these forces are concentrated serially on the base pairs of a strand of DNA, one little atomic-scale bit at a time, until it's all read. How many people contributed to this concentrated ingenuity in one form or another? It gave me a little burst of the technological sublime.

Apparently the hot thing in genomics now is the ability to read the genomes of individual cells (single-cell genomics). Another little room had the physical device that makes this possible, which takes a drop of cell-containing water and physically breaks it into into tiny droplets with ultrasound, some small fraction of which contain cells, and then plops each of the desirable droplets into wells on a plate through manipulation of electric fields. Then each cell can be separately amplified and sequenced. Before this technique, genomes could only be sequenced from cultured cells, and most organisms can't be cultured.

The good news for me is that while the technology for producing biological data is getting more powerful at faster-than-Moore's-law rates, the ability to interpret it is lagging, which means plenty of opportunity for the software to manage, analyze, interpret, and navigate the deluge.

No comments: