The tree of life versus the rhizome of life

Tree by Haeckel (1866). Source wikimedia commons

The metaphor of the tree of life—which illustrates the common descent of all life on Earth—was popularized by Darwin in its Origin of species and later by his contemporary Haeckel, but apparently its roots can be traced back as early as the 18^th century in the writings of various authors (Archibald,2009). On a different line, it also of course echoes the biblical tree of life mentioned in the Genesis.

However, about a decade ago, authors such as W. FordDoolittle (1999) have cast doubt on the tree as a valid representation of the history of living organisms. Since then, articles that question the tree of life have flourished¹. And the debate is far from being settled.

A tree or a rhizome?

Based on the recent development of comparative genomics, the microbiologist Didier Raoult suggested in the journal the Lancet that Darwin’s tree of life should be replaced by a rhizome of life (Raoult, 2010). Raoult sees the rhizome – a complex net of interconnected roots – as a more faithful representation of the history of living organisms.

The Logic of Chance by Eugene Koonin (continuation)

Published by FT Press

In the first part of this post, I insisted on living organisms (viruses, bacteria, eukaryotes) and their evolutionary history. 

Here I want to look at what Koonin writes about the mechanism of evolution.

What drives evolution?

One central idea in Koonin’s book, I think, is to propose an evolutionary outlook that is based on an analogy with the physical world. Central, for instance, is stochasticity, as a force shaping the genomic evolution. Equally important, in Koonin’s view, are the statistical principles that govern the interactions between all genes within a genome (he likens the collection of all genes in a genome to the ideal gas model in physics). Thus, genes are influenced by a number of statistical rules. On this line, even though it is apparently not possible to define “laws of genomics”, certain regularities can be identified, such as the proportion of different functional classes of genes within a given prokaryotic genome.

Koonin writes, p. 405:

“it is remarkable that the advances of genomics and systems biology, while revealing an extremely complex, multifaceted picture of evolution, at the same time allow us to derive powerful and simplifying generalizations. It is tempting to offer yet another version of the famous phrase: Nothing in evolution—and in population genetics—makes sense except in light of statistical physics.”

The Logic of Chance by Eugene Koonin

Published by FT Press

About fifteen years ago, a revolution started in the biological sciences, which goes by the name whole genome sequencing. I don’t have memories of the announcement of the first bacterial genome in 1995 (I was in high school and not really following biology news…), but at the time of the human genome project I was a biology student at the University and I remember very well when the paper describing the human genome came out in 2001 (we had to read it in class!).

Until recently, my feeling about whole genome sequencing was that it was a technical revolution, not a conceptual one. After all, I thought, the sequence information revolution already took place in the seventies, when Carl Woese pioneered the use of 16S ribosomal RNA to construct phylogeny. 

I revised this feeling, thanks in part to the excellent book of Eugene Koonin, The Logic of Chance (2011)—subtitled the nature and origin of biological evolution—and published by Financial Times Press (yes, they do have a science catalog!).

The endosymbiotic theory of Lynn Margulis

Published by Basic Books

Lynn Margulis passed away last November, sadly. She was renowned for the endosymbiotic theory of evolution, which is now part of biology textbooks. She had a wonderful insight: the mitochondria and chloroplasts that are found in eukaryotic cells were, in distant past, free-living bacteria. Thanks to at least two distinct endosymbiosis events, they were incorporated—and not digested—in the eukaryotic ancestor. They became responsible of key functions within the new association, namely respiration and photosynthesis. These symbionts persisted until at some point they were indistinguishable from their host, and all merged to become one new organism, a eukaryotic cell. 

Recently I found a copy of her book Symbiotic Planet (1998) in my usual second-hand bookshop in Davis. It is a short book in which Margulis deals with the scientific idea that has occupied her during most of her career: the serial endosymbiosis theory (or SET). The author sums up the book as follows (p.33):

In short, I believe that most evolutionary novelty arose, and still arises, directly from symbiosis.

The invention of multicellularity

Multicellular yeast cluster. Photo courtesy of William Ratcliff.

In January, William Ratcliff and his colleagues from the University of Minnesota caused quite a stir with their study on the experimental evolution of multicellularity in yeast, published in PNAS. Many media covered the story, including the New York Times, Wired and Scientific American. Briefly, what they did was using artificial selection on unicellular yeast (the baker's yeast Saccharomyces cerevisiae) in order to create an obligate multicellular organism after many generations of selection. What is impressive is that it worked pretty well in all their different test cultures!

Multicellularity was invented several times during the history of life (Rokas, 2008), but since it happened a long time ago it is difficult to reconstruct the exact sequence of events. Experimentation on today's unicellular organisms, however, allows researchers to test mechanisms (and associated mutations) that could lead to a multicellular lifestyle. Of course, this cannot decide for good how the phenomenon occurred many millions years ago – which is not at all the author's claim – but this can prove that such mechanisms can occur, given that an appropriate selection pressure is present.