“Postmodern reassessment of some central propositions of Darwin and Modern Synthesis”
Table 13.1 from The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene V. Koonin.
The accompanying figure likewise gives an excellent contemporary take on Darwin’s ideas — in quantitative terms, natural selection plays second fiddle to neutral evolutionary processes such as genetic drift (allelic variation from random sampling) and draft (where a neutral allele is linked to a beneficial allele).


This figure in the same section illustrates the multiple processes that generate genomic variation, affect its fixation in the evolution of life, and shape the evolution of genomes.
I’m wary of anyone who repeatedly uses the word postmodern and admits only vague understanding or pseudophilosophical engagement. Manuel DeLanda has some quite mind-bogglingly meaningless things to say on the work of (the post-modernist’s bread and butter) Gilles Deleuze and Félix Guattari. I don’t think the “two cultures” ought mix, but you’re free to think what you like.
Thankfully, Koonin compartmentalises some of his less coherent discussion of this subject to an appendix in the book, where he highlights a work I’ve not seen before by Didier Raoult — an established microbiologist with his own Wikipedia page and an overflowing bibliography.
In this lovely little piece, The Post-Darwinist Rhizome of Life, Raoult comes a year late to Darwin’s 200th birthday celebrations, reflecting on the shortcomings of a 19th century theory upheld (and perhaps mythologised) as one of the scientific greats. In part, this may be explicable through the backlash from creationists, leading some to cling to heroes even in light of new developments.
I’ve brought up lateral gene transfer (LGT) before — in this post back in summer on how cancer samples were foumd to be enriched in bacteria‒human LGT. The implications of this finding are still unclear, and as I wrote then, may just be “passenger mutations”.
Raoult in turn points to the work of Doolittle et al in 2007, who discussed this “pattern pluralism” (i.e. the multiple origins of an organism’s genetic information)

The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of single true Tree of Life.

Having been at first wary, I’m now really pleased to see that these effects are being taken seriously by other scientists (these commentaries were published in PNAS and popular medical journal The Lancet). The LGT study I wrote about previously seemed to be a bit of a loner in the literature. Raoult’s piece is accompanied by a rad seemingly quantitative(?) illustration of various mushroom species’ heritage.


Comparative genome analysis shows not only a substantial level of plasticity in the gene repertoire, but also provides evidence that nearly all genes, including ribosomal genes, have been exchanged or recombined at some point in time. Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.
Moreover, there are some genes that do not have a single history, due to the occurrence of intragenic recombinations. Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created through gene fusion, degradation, or other events, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.

On this note, I saw an interesting paper on gene creation the other day, which I’ve not got around to reading in full yet, which found that newly created genes are also often soon lost. The spelling (ORFan vs. orphan) is different but they seem to be on the same topic (the reference Raoult gives doesn’t refer to either by such a name, but does describe how to unearth “unique” ORFS via BLAST, “although this might at present be an artefact of the small number of microbial species studied by whole-genome analysis”). The full paper is over at eLife.

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. Emerging species grow from the rhizome with gene repertoires of various origins that will allow, under favourable environmental conditions, the multiplication and perpetuation of this species. As such, potential new species and new genes are continuously appearing. The success of the species and thus their overall evolution depend mainly on the fitness of the species within their particular environmental conditions at a particular time. The disappearance of a species is not necessarily associated with the disappearance of the genes of its repertoire and each gene can continue along its own history. I suggest we respect the revolutionary mind of Darwin and allow the theory of evolution itself to evolve from a tree to a rhizome.

I can’t really agree with (or even follow with any great certainty) Koonin’s theories on “metanarratives” nor why he “takes exception to the worldview of model-dependent realism”. The rest of the book is brilliant though, particularly his writing on recent developments in viral genetics and metagenomics, something I’ve been wanting to read about for a while.
In light of some further reading into this, it appears that Koonin and Raoult published alongside one another in an issue of Frontiers in Cellular and Infection Microbiology a total of 6 papers between them, and that this was in an effort to “challenge Darwin” as the title puts it.
At first seeing someone take a post-modern/continental philosopher — that is, a subjective approach from sociology — and applying it in genetics seemed novel, and light-hearted. Thinking a bit more critically, it could easily be taken too far, as the editorial to this issue of Frontiers may well do in calling the tree of life phylogeny approach “largely obsolete”.
I don’t have the time or really the academic motivation to form much stronger opinions, but it’s an interesting debate and perhaps in covering it others can come to their own conclusions. Relevant links as usual, are below, last of which is Patrick Forterre, the dissonant voice amidst the rhizome proponents in Frontiers:

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.
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 Scientist” 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.
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.
…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.

࿇  Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press, 2011)
࿇  Raoult (2010) The Post-Darwinist Rhizome of Life. The Lancet, 375(9709) 104-105 
࿇  Robin Tecon, commenting on the work of Raoult and Koonin, feels these opinions are “at the same time a very interesting idea and a very bad idea”. I’m not going to rewrite this post but I do feel Tecon makes strong points here.
࿇  Patrick Forterre (2012) Darwin’s goldmine is still open: variation and selection run the world. Frontiers in Cellular and Infection Microbiology, doi: 10.3389/fcimb.2012.00106s
࿇ …and lastly with thanks to PZ Myers for setting me off on the trail ‒ his post is on neutral molecular evolution, which managed to cause enough controversy without dipping so much as a toe into the pomo side of things, but it’d be ungracious to not credit my source!

“Postmodern reassessment of some central propositions of Darwin and Modern Synthesis”

Table 13.1 from The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene V. Koonin.

The accompanying figure likewise gives an excellent contemporary take on Darwin’s ideas — in quantitative terms, natural selection plays second fiddle to neutral evolutionary processes such as genetic drift (allelic variation from random sampling) and draft (where a neutral allele is linked to a beneficial allele).

image

This figure in the same section illustrates the multiple processes that generate genomic variation, affect its fixation in the evolution of life, and shape the evolution of genomes.

I’m wary of anyone who repeatedly uses the word postmodern and admits only vague understanding or pseudophilosophical engagement. Manuel DeLanda has some quite mind-bogglingly meaningless things to say on the work of (the post-modernist’s bread and butter) Gilles Deleuze and Félix Guattari. I don’t think the “two cultures” ought mix, but you’re free to think what you like.

Thankfully, Koonin compartmentalises some of his less coherent discussion of this subject to an appendix in the book, where he highlights a work I’ve not seen before by Didier Raoult — an established microbiologist with his own Wikipedia page and an overflowing bibliography.

In this lovely little piece, The Post-Darwinist Rhizome of Life, Raoult comes a year late to Darwin’s 200th birthday celebrations, reflecting on the shortcomings of a 19th century theory upheld (and perhaps mythologised) as one of the scientific greats. In part, this may be explicable through the backlash from creationists, leading some to cling to heroes even in light of new developments.

I’ve brought up lateral gene transfer (LGT) before — in this post back in summer on how cancer samples were foumd to be enriched in bacteria‒human LGT. The implications of this finding are still unclear, and as I wrote then, may just be “passenger mutations”.

Raoult in turn points to the work of Doolittle et al in 2007, who discussed this “pattern pluralism” (i.e. the multiple origins of an organism’s genetic information)

The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of single true Tree of Life.

Having been at first wary, I’m now really pleased to see that these effects are being taken seriously by other scientists (these commentaries were published in PNAS and popular medical journal The Lancet). The LGT study I wrote about previously seemed to be a bit of a loner in the literature. Raoult’s piece is accompanied by a rad seemingly quantitative(?) illustration of various mushroom species’ heritage.

image

Comparative genome analysis shows not only a substantial level of plasticity in the gene repertoire, but also provides evidence that nearly all genes, including ribosomal genes, have been exchanged or recombined at some point in time. Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.

Moreover, there are some genes that do not have a single history, due to the occurrence of intragenic recombinations. Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created through gene fusion, degradation, or other events, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.

On this note, I saw an interesting paper on gene creation the other day, which I’ve not got around to reading in full yet, which found that newly created genes are also often soon lost. The spelling (ORFan vs. orphan) is different but they seem to be on the same topic (the reference Raoult gives doesn’t refer to either by such a name, but does describe how to unearth “unique” ORFS via BLAST, “although this might at present be an artefact of the small number of microbial species studied by whole-genome analysis”). The full paper is over at eLife.

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. Emerging species grow from the rhizome with gene repertoires of various origins that will allow, under favourable environmental conditions, the multiplication and perpetuation of this species. As such, potential new species and new genes are continuously appearing. The success of the species and thus their overall evolution depend mainly on the fitness of the species within their particular environmental conditions at a particular time. The disappearance of a species is not necessarily associated with the disappearance of the genes of its repertoire and each gene can continue along its own history. I suggest we respect the revolutionary mind of Darwin and allow the theory of evolution itself to evolve from a tree to a rhizome.

I can’t really agree with (or even follow with any great certainty) Koonin’s theories on “metanarratives” nor why he “takes exception to the worldview of model-dependent realism”. The rest of the book is brilliant though, particularly his writing on recent developments in viral genetics and metagenomics, something I’ve been wanting to read about for a while.

In light of some further reading into this, it appears that Koonin and Raoult published alongside one another in an issue of Frontiers in Cellular and Infection Microbiology a total of 6 papers between them, and that this was in an effort to “challenge Darwin” as the title puts it.

At first seeing someone take a post-modern/continental philosopher — that is, a subjective approach from sociology — and applying it in genetics seemed novel, and light-hearted. Thinking a bit more critically, it could easily be taken too far, as the editorial to this issue of Frontiers may well do in calling the tree of life phylogeny approach “largely obsolete”.

I don’t have the time or really the academic motivation to form much stronger opinions, but it’s an interesting debate and perhaps in covering it others can come to their own conclusions. Relevant links as usual, are below, last of which is Patrick Forterre, the dissonant voice amidst the rhizome proponents in Frontiers:

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.

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 Scientist” 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.

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.

…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.

࿇  Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press, 2011)

࿇  Raoult (2010) The Post-Darwinist Rhizome of LifeThe Lancet, 375(9709) 104-105 

࿇  Robin Tecon, commenting on the work of Raoult and Koonin, feels these opinions are “at the same time a very interesting idea and a very bad idea”. I’m not going to rewrite this post but I do feel Tecon makes strong points here.

࿇  Patrick Forterre (2012) Darwin’s goldmine is still open: variation and selection run the worldFrontiers in Cellular and Infection Microbiology, doi: 10.3389/fcimb.2012.00106s

࿇ …and lastly with thanks to PZ Myers for setting me off on the trail ‒ his post is on neutral molecular evolution, which managed to cause enough controversy without dipping so much as a toe into the pomo side of things, but it’d be ungracious to not credit my source!

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