The Coming Revolution in Biology

From an interesting article in Nature:

One of the most fundamental patterns of scientific
discovery is the revolution in thought that accompanies a new body of
data. Satellite-based astronomy has, during the past decade, overthrown
our most cherished ideas of cosmology, especially those relating to the
size, dynamics and composition of the Universe.

the convergence of fresh theoretical ideas in evolution and the coming
avalanche of genomic data will profoundly alter our understanding of
the biosphere — and is likely to lead to revision of concepts such as
species, organism and evolution. Here we explain why we foresee such a
dramatic transformation, and why we believe the molecular reductionism
that dominated twentieth-century biology will be superseded by an
interdisciplinary approach that embraces collective phenomena.

The place to start is horizontal gene transfer (HGT),
the non-genealogical transfer of genetic material from one organism to
another — such as from one bacterium to another or from viruses to
bacteria. Among microbes, HGT is pervasive and powerful — for example,
in accelerating the spread of antibiotic resistance. Owing to HGT, it
is not a good approximation to regard microbes as organisms dominated
by individual characteristics. In fact, their communications by genetic
or quorum-sensing channels indicate that microbial behaviour must be
understood as predominantly cooperative.

In the
wild, microbes form communities, invade biochemical niches and partake
in biogeochemical cycles. The available studies strongly indicate that
microbes absorb and discard genes as needed, in response to their
environment. Rather than discrete genomes, we see a continuum of
genomic possibilities, which casts doubt on the validity of the concept
of a ‘species’ when extended into the microbial realm. The uselessness
of the species concept is inherent in the recent forays into
metagenomics — the study of genomes recovered from natural samples as
opposed to clonal cultures. For example, studies of the spatial
distribution of rhodopsin genes in marine microbes suggest such genes
are ‘cosmopolitan’, wandering among bacteria (or archaea) as
environmental pressures dictate.

Equally exciting is
the realization that viruses have a fundamental role in the biosphere,
in both immediate and long-term evolutionary senses. Recent work
suggests that viruses are an important repository and memory of a
community’s genetic information, contributing to the system’s
evolutionary dynamics and stability. This is hinted at, for example, by
prophage induction, in which viruses latent in cells can become
activated by environmental influences. The ensuing destruction of the
cell and viral replication is a potent mechanism for the dispersal of
host and viral genes.