A while back, I stumbled upon an article by Freeman Dyson on Carl Woese. Carl Woese is a long time scientist studying the origins of life and revolutionized thinking around early life, microbiology, and phylogeny.
Freeman Dyson's article is a great overview of the discussions around pre- and post-Darwinian evolution*. Darwinian evolution is what we are used to, a standard "fight for survival" of non-interbreeding species that slowly evolve their fitness to the challenges in the environment.
What really flipped me was Dyson discussing pre-Darwinian evolution, an idea postulated by Carl Woese back in 2004 in an article titled "A New Biology for a New Century." The thought is that early life was a time of promiscuous gene swapping. That, as I see it, an organism was a sack of molecules and genes that worked together to propagate a collection of "features." Then, at some point (Woese suggests at least three) an organism stopped, found a good set of genes, and brought this lateral gene transfer down to a trickle. And there you have a "species."
The three times Woese mentions were the times that gave rise to Archaebacteria, Bacteria, and everyone else. This free mix and match with a sudden stop makes sense of why there are three large groups of cell structures, yet that they are related in some way.
This idea really hit home for me when listening to Penny Chisholm, a microbiologist, talking about Prochlorococcus on Science Friday. This small cyanobacteria might be the most abundant photosynthetic organism, but Chisholm and colleagues only discovered it in the 80s.
What was interesting was her answer about different species of Prochlorococcus: she called them "genomic variants."
This ties back to what Woese was implying about lateral gene transfer and pre-Darwinian evolution and sacks of organisms with a collection of genes. If all organisms are in the possibility-space of all arrangements of genetic elements, then a particular strain of organism would be a peak of variation in that particular area of arrangement of genetic elements (but still part of a continuum of possibility-space).
Micro-organisms still do a lot of gene transfer (witness the spread of antibiotic resistance across species). But I suppose at some level they mix up everything and can have a large amount of variation across a single species. Hence, Chisholm's observation that Prochlorococcus species are best viewed as variants than distinct species. Promiscuous lateral gene transfer across Prochlorococcus "species" deflates the definition of species as non-interbreeding organisms.
As microbial biology has a renaissance due to the rise of synthetic biology (humans effecting lateral gene transfer in micro-organisms at a scale we haven't done before), understanding "speciation" in terms of "genetic variants" will go a long way in understanding how and what genes are to be used.
*Dyson also compares the way cultures laterally transfer as the post-Darwinian era.
Image from If you dream it…
