Tree of life – or just wood chips?

Having been singularly unenthusiastic about Eugene Koonin’s invocation of the infinite multiverse to lessen the odds for the origin of life, I was a lot more impressed by his 2009 overview  of evolutionary theory in the light of genomics.

It was a comprehensive, thorough (and therefore rather heavy-going for a non-biologist like me) appraisal of the currently understood mechanisms of evolution and their implications for the Neodarwinian synthesis. His broad conclusion is that the time is near (but not quite at hand) for a new theory:

Collectively, the developments in evolutionary genomics and systems biology outlined here seem to suggest that, although at present only isolated elements of a new, “postmodern” synthesis of evolutionary biology are starting to be formulated, such a synthesis is indeed feasible.

Where he stands on the question of whether the Modern Synthesis can accommodate the new elements is obvious from a table examining the status of six primary propositions of Darwin’s original theory, as modified by the synthesis, in which all need to undergo major revision and three are concluded to be simply false.

Here are some things that strike me as significant in the paper.

Firstly, in recognising the repertoire of mechanisms for variation familiar to most of us now – gene, gene region and genome duplication, gene loss, horizontal gene transfer, endosymbiosis, recruitment of gene sequences from “selfish mobile elements” such as viruses, etc – he dismisses Darwin’s “infinitessimally small” changes out of hand.

Gradualism is not the principal regime of evolution.

These same mechanisms also effectively negate the tree of life concept, except as a useful tool for the history of individual genes and small groups of organisms. His preferred metaphor is the “forest of life”, though in his opinion the evidence for common ancestry is still overwhelming. It’s certainly true that, even if we had different original ancestors, the family trees are now thoroughly intermixed.

What is most astonishing to me is just how far natural selection is displaced from the picture.

Natural (positive) selection is an important factor of evolution but is only one of several fundamental forces and is not quantitatively dominant; neutral processes combined with purifying selection dominate evolution.


The majority of the sequences in all genomes evolve under the pressure of purifying selection or, in organisms with the largest genomes, neutrally, with only a small fraction of mutations actually being beneficial and fixed by natural selection as envisioned by Darwin.

I guess the concept of neutral evolution is commonplace now, but the evidence takes Koonin further (based on a population-genetics model formulated by Lynch):

 …the complexity of the genomes of multicellular eukaryotes is interpreted as evolving, primarily, not as an adaptation ensuring organizational and functional complexity but as a “genomic syndrome” caused by inefficient purifying selection in small populations.

Just think what this implies. How often have you heard Neodarwinists protest that evolution is not random because of the wise oversight of natural selection, which step by step takes us up the back of Mount Improbable to a world where each niche is filled with wondrous forms of life closely adapted to their environment? In the Postmodern Synthesis all this is swept away – adaptive selection is a bit-part player. It’s not just that natural selection tends to stabilise rather than innovate, though that’s true. It’s not even that “purifying” natural selection just helps eradicate the deleterious changes that threaten life itself:

The primary driving force of purifying selection might not be the maintenance of a biological function but rather prevention of nonspecic deleterious effects of a misfolded protein.

The biggest changes in complex organisms like ourselves are actually due to the failure of purifying selection to clear up the mess adequately, leaving our genomes chock full of junk from virus attacks and so on, which get somehow co-opted to useful functions like … well, like being a sentient human being.

Darwin’s theory was that tiny chance variations, operated on by an all-wise natural selection, were sufficient to account for the overwhelming appearance of design in nature. In the Postmodern Synthesis – necessitated, remember, by the new knowledge that the Modern Synthesis has downplayed for so long – massive chance variations, operated on by an inadequate clean-up mechanism and, proportionately, hardly at all by adaptive selection, are the sum of how we, and all advanced life, got here.

The simplicity of these universal regularities suggests that they are shaped by equally simple, fundamental evolutionary processes, rather than by selection for specific functions. In some cases, explicit models of such processes have already been developed and shown to fit the data. These models either do not include selection at all or give selection a new interpretation.

Koonin, not surprisingly asks:

Beyond the astonishing, unexpected diversity of genome organization and modes of evolution revealed by comparative genomics, is there any chance to discover underlying general principles? Or, is the only such principle the central role of chance and contingency in evolution, elegantly captured by Jacob in his “evolution as tinkering” formula?

He leaves the question unanswered. If Neodarwinism leaves rather too much too chance for our comfort, the new biology so far offers almost nothing except chance. Small wonder that Koonin, elsewhere, fishes around in the multiverse to lower the odds. It’s hard to believe that even the most naturalistic of naturalists will feel comfortable in an evolutionary world without the loincloth of Darwinian selection. It will be absolutely necessary to find a self-organisational principle within the cell, to explain the presence of order from such genomic chaos. Or, if not, maybe it will once more become plausible, as it did to the Bible writers, that divine reason lies behind randomness itself.

Avatar photo

About Jon Garvey

Training in medicine (which was my career), social psychology and theology. Interests in most things, but especially the science-faith interface. The rest of my time, though, is spent writing, playing and recording music.
This entry was posted in Creation, Science, Theology. Bookmark the permalink.

3 Responses to Tree of life – or just wood chips?

  1. Cal says:

    I liked the last remark. Just because it seems ‘random’ doesn’t mean there isn’t an underlying order to it all

    Thanks for putting this review/summary up


  2. Avatar photo Jon Garvey says:


    If Koonin represents the shape of biology to come, then evolution looks increasingly like Aaron throwing earrings on to the fire until “There came out this calf.” Not so much natural selection as natural alchemy. “Origin of Species” was simple, plausible and largely wrong. The stuff that’s right is horrendously complicated and, as an overall explanation , beggars belief.

Leave a Reply