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.
Similarly, 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dramatic transformation, and why we believe the molecular reductionism that dominated twentieth-century biology will be superseded by an interdisciplinary approach that embraces collective phenomena.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.
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