Biology Reference
In-Depth Information
tersection of computing and biology. Touted—over and over again—as
the embodiment of “Moore's law for biology,” next-gen is literally and
fi guratively connecting the history of semiconductor computer chips to
biological progress. 5 Graphs and charts depicting the logarithmic in-
creases in sequencing speed and decreases in sequencing cost suggest
that biological progress will proceed as inexorably as the increases in
computing power since the 1960s predicted by Moore's law. Jonathan
Rothberg's Ion Torrent Personal Genome Machine makes this connec-
tion directly: this recent piece of next-generation technology uses tiny
pH meters embedded in wells on the surface of a silicon computer chip
to detect the incorporation of a nucleotide. This allows the chip—which
can be manufactured in the same way as any other microchip found in
a desktop computer—to act as the basis for a sequencing machine. 6 Be-
cause it is built on standard computer chip technology, the Ion Torrent
machine hitches biological progress directly to progress in the manufac-
turing of semiconductors (getting more transistors on a chip will allow
more pH meters on a chip, meaning that sequencing can be done faster).
The sequencing pipeline that we encountered in chapter 4 is rapidly be-
ing compressed—in time, space, cost, and complexity. The material and
the digital seem to be moving closer and closer together.
This compression may have several consequences. First, the digital
traces of sequences will come to seem more and more substitutable for
biological samples themselves. If samples or specimens or biological
materials can be rapidly and cheaply digitized, then it becomes even
easier to replace the material with the virtual. We may pay even less
attention to that which is left out of these digital traces, that which is
stripped away in reducing samples to sequence. The constraints and
structures imposed by computer and network tools will become even
less obvious. Bioinformatics itself may be erased: the biological will be-
come the informatic.
But this may be too simplistic (and perhaps too pessimistic) a view.
Next-generation sequencing also opens up possibilities for reversing
some of the trends we have encountered in this topic. The most obvi-
ous possibility is that the organization of biological work may once
again radically shift. As we have seen, the HGP inaugurated massive
changes in the labor and economy of biology—these changes were nec-
essary because the project required large amounts of money, large labs,
interdisciplinary work, and centralized coordination over many years.
But next-generation sequencing could allow genomics to be performed
on a bench top, with a couple of operators, and over a few days or
weeks. Whole genomes could be rapidly sequenced by a single lab, at a
Search WWH ::




Custom Search