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6A COMPUTATIONAL AND ENGINEERING VIEW OF BIOLOGY
Because 21st century biology is very concerned with function, it is helpful to have abstractions
available that characterize the functionality of interest. By doing so, insights derived from study of those
abstractions in other contexts become available for biological use. In addition, because biological sys-
tems are the products of eons of evolutionary history and decision making, viewing them through the
lens of engineering yields insights that are not otherwise available from an analysis that might be based
on first principles.
6.1 Biological Information Processing,
As noted in Chapter 2, biological systems are extraordinarily complex—and partly as a conse-
quence, poorly understood. Yet it is clear that biological systems demonstrate and exemplify function-
ality at different levels.
Artifacts such as computer hardware and software also exhibit functionality and multiple levels. To
facilitate the understanding and construction of such artifacts, computer science has developed infor-
mation abstractions that seek to capture and encapsulate certain kinds of functional behavior in ma-
nipulating and managing information; such abstractions are a primary focus of study of the computer
scientist (Box 6.1).
One key connection to 21st century biology is that many biological problems now require the
simultaneous consideration of phenomena at different scales. For example, biologists can think of
genetics at the level of individual nucleotides, at the level of chromosomes, at the level of genomes, and
at the level of populations. From nucleotide to population is a span of many orders of magnitude, and
it is difficult to conceptualize such a range without moving seamlessly between different levels of
abstraction.
Section 6.1 describes several such abstractions and their specific biological applications already in
use, but the description is not intended to be exhaustive, and there are likely many more such abstrac-
tions capable of providing biological insight, including new or as yet undiscovered techniques or
concepts. As such, this area represents opportunities for both biologists and computer scientists.
(^1) Much of the discussion in Section 6.1 about cells as information-processing devices is adapted from R. Aviv and E. Shapiro,
“Cellular Abstractions: Cells as Computation,” Nature 419:343, 2002.