Even as Richard Dawkins informs presidential candidate Rick Perry that “evolution is a fact,” many evolutionary biologists are quietly (or not so quietly) abandoning what Dawkins claims as the central aspect of that fact, namely, the Tree of Life (TOL) hypothesis. In his bestseller The Greatest Show on Earth (2009), Dawkins writes that “today we are pretty certain that all living creatures on this planet are descended from a single ancestor” (p. 408). But this textbook picture, widely accepted since Darwin’s time, is increasingly being dumped by biologists, in favor of very different histories.
You can follow the action by visiting the lively open access journal Biology Direct. This journal is exceptional because it includes the referee reports, along with the authors’ replies to the referees, at the end of each paper. This admirable practice enables the reader to follow the details of scientific debate, usually hidden from public scrutiny.
As an example, check out a paper published this week (still in manuscript form), “The public goods hypothesis for the evolution of life on Earth,” by four European evolutionary biologists (James McInerney, Eric Bapteste, Davide Pisani, and Mary J. O’Connell). McInerney et al. argue that the TOL is “becoming increasingly implausible.” Although the TOL “has been stretched to fit the data” in various ways, “given our knowledge of the data, it seems that the elastic limit of the original hypothesis has been passed.” Time to try a different picture.
To replace the TOL, McInerney et al. favor what they call “the public goods hypothesis.” Borrowing a term from the economics Nobel laureate Paul Samuelson, they argue that many (but not all) genes and proteins are “public goods,” meaning entities that belong to no one in particular. These genes and proteins are thus available for use by all, and their presence in any lineage does not necessarily indicate common ancestry. As they explain,

According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes.

The radical consequences of this hypothesis are easy to imagine — but we leave that as an exercise for the reader.