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.

What are Raoult’s arguments? We find, first, the understanding that lateral gene transfer is an essential motor of evolution. Secondly, and it derives from the first observation, the impossibility to draw a unique phylogenetic tree for all the genes in one organism; gene-trees disagree with each other. Finally, we can observe the creation of new genes that don’t belong to any phylogenetic tree. Raoult writes:

  “A post-Darwinist concept of the living species can be proposed, to integrate the theories of multiplicity and de-novo creation. In accordance with the theory on the evolution of human societies proposed by Deleuze and Guattari, I believe that the evolution of species looks much more like a rhizome (or a mycelium) […]. Consequently, this view of evolution resembles a clump of roots that considers the occurrence of multiplicities.”

I think that Raoult’s proposition is at the same time a very interesting idea and a very bad idea.

Now it is true that our view of the evolution of bacteria has changed profoundly since we know that lateral (horizontal) gene transfer is a very important process that shapes bacterial genomes. Does it apply to eukaryotes? For sure important gene transfers have occurred (endosymbiosis of mitochondria and chloroplasts, for instance), but during most historical time it probably remained a side phenomenon in eukaryotes. Hence, I don’t see how it could invalidate the tree of life concept.

  

The multiplicity of phylogenetic trees that can be drawn for each gene in one organism is another interesting problem raised by Raoult. Eugene Koonin, in his book The logic of chance, notes the incongruence between gene-trees in one given organism. But interestingly he writes (p.165):

“However, notwithstanding the newly discovered web-like character of evolution, Darwin’s metaphor reflects a deeper truth: Trees remain the natural representation of the histories of individual genes, given the fundamentally bifurcating character of gene replication and the substantially low frequency of intragenic recombination compared to intergenic recombination at long evolutionary distances”

Koonin further suggests to replace the tree of life by a forest of life, a collection of all gene-trees.  I think both the rhizome and the forest are unnecessary complications. After all, the tree of life doesn’t have to be reduced to a phylogenetic tree. If we speak of the tree of life as a model, it still stands very well (as Koonin emphasizes, there is something intrinsically “tree-like” in the evolutionary process). And a model is not the exact depiction of reality (or it wouldn’t be a model anymore!) .

As to the last argument of Raoult – the de novo formation of genes –, I simply don’t understand what he means, since present genes have all evolved from ancestor genes!

Maybe more important: when we compare the merits of the tree and the rhizome as a metaphor for the history of life, the tree wins flat out. One great achievement of the tree of life was to illustrate how all creatures originated through common descent and variation, therefore undermining the belief in the immutability of species (the creationist view). It is difficult to find another image that would strike the mind with such beauty and power. Sorry, but most non-scientists don’t know what a rhizome is in the first place! If we were to exchange the tree metaphor for the rhizome, I believe we would muddle up things, not clarify them.

Promoting the rhizome

But the battle still rages on. The open-access journal Frontiers has a new collection (“Research topic”) edited by Didier Raoult and Eugene Koonin, which is mostly dedicated to the defense of the rhizome of life concept.  (Curiously it was published in Frontiers in cellular and infection microbiology, not in its sister journal Frontiers in evolutionary and population genetics). 

The collection consists of fourteen articles (five of which are co-authored by Raoult, one by Koonin), and its provocative title is “Microbial genomics challengeDarwin” (awful title in my opinion; I explain why later). I didn’t read everything (far from it), but basically they discuss how modern knowledge undermines the “dogma” of Darwinism, and thus they ask for a “post-modern” theory of evolution seen as a “paradigm shift”. The editors write, in their editorial, that “pervasive horizontal gene transfer makes the original concept of the Tree of Life largely obsolete.” 

Among the choir of voices supporting the rhizome, there is a dissonant one: Patrick Forterre. Fortunately, Forterre brings a formidable counterpoint in an article entitled "Darwin's goldmine is still open: variation and selection run the world", and the editors should be praised for having invited a contributor who expresses a view so opposed to theirs. Forterre writes, for instance:

“Natural selection is not an “evolutionary force” but the necessary outcome of variation and multiplication. In particular, natural selection cannot be weakened by mechanisms that promote variations (such as epigenetic mechanisms or symbiogenesis), because these processes provide more substrates for selection.”

Leave the old man in peace!

Now something makes me wince, and that is the recent habit to attack Darwin, whenever evolution is discussed, as if he were a present-day scientist. What is the point? It is not as if the theory of evolution had been frozen since Darwin; the great man didn’t even know of genes! What these attackers really challenge in their writings is most often modern synthesis (neo-darwinism), not the view of Charles Darwin. Forterre expresses this very clearly:

“This is a sensitive topic, considering the renewal of creationist thinking in fundamentalist religious circles and the wide publicity given to these “non-orthodox views.” This was best illustrated by the cover of the “New Scientists” issue published in January 2009 showing a tree of life superimposed with the sentence: “Darwin was wrong.” Although the existence of anti-Darwinists in the political arena is certainly not a reason to hide fierce debates between evolutionists over mechanisms and representations of evolution, one can regret to see the name of Darwin used as a foil in these debates. After all, nobody said: “Mendel was wrong” because his concept of the gene was quite different from what we know today (personal quote from Eduardo Rocha).”

And as part of his conclusion:

“At the dawn of the XXI century, some biologists apparently dream to bypass Darwin. For me, this is hopeless, except if we reduce Darwin to some ad hoc version of « Darwinism » or if we consider Darwin as one of our contemporaries, and not a scientist of the XIX century. With the dyad variation/selection, Darwin has provided us with key concepts that are necessary and sufficient to understand the logic of evolution, a goldmine that is still open. All the striking discoveries made in biology during the last 150 years have been extensions of these concepts and recent discoveries in microbial evolution and post-genomic studies are not different.”

Indeed, attacks on Darwin do not come in short supply in “Microbial genomics challenge Darwin”. In the presentation of the research topic by the editors:

“The 200th anniversary of Darwin’s birthday was celebrated in 2009, making the concept of Darwinism even more popular than at the time it was originally proposed, to the extent that it has acquired quasi-religious status.”

We certainly don’t share the same definition of religion. Darwin a prophet? What did I know!

Today’s research on microbial genomics reveals amazing new facts, and it’s important that we discuss how they modify our current knowledge on evolution. But this should be no excuse for a fake controversy with a scientist who died one hundred thirty years ago.

Once more, Patrick Forterre has written exactly the right words:

“whatsoever Darwin’s limitations, I will argue that we still have more to gain standing on his shoulder than tripping him, especially when he cannot reply.”

Very well said, sir!

Notes:

1. See for instance the following collections of articles in the open-access journal Biology Direct: "Evolutionary Biology 150 years after the 'Origin': is a post-modern synthesis in sight?" (2009) and "Beyond the tree of life" (2011).

References:

• Doolittle W. F. (1999). Phylogenetic Classification and the Universal Tree. Science 25;284(5423):2124-9.
• Archibald J. D. (2009). Edward Hitchcock’s Pre-Darwinian (1840) ‘‘Tree of Life’’. Journal of the History of Biology 42:561–592
• Raoult D. (2010). The post-Darwinist rhizome of life. The Lancet, Vol 375, Issue 9709, Pages 104 - 105.
• Koonin E. V. (2011) The Logic of Chance: The Nature and Origin of Biological Evolution. FT Press Science Series. 516 pages.
• Forterre P. (2012). Darwin’s goldmine is still open: variation and selection run the world. Front. Cell. Inf. Microbio. 2:106.