Life after Darwin

Recent genetic discoveries demonstrate that Darwin's 'tree of life' theory of evolution is wrong and it's time to move on, argues Didier Raoult.

Many Greek philosophers perceived the world to be in perpetual motion — a process of constant evolution. In Charles Darwin's world, however, creationism set the rules for science. So, underpinning his theory of evolution is the literal interpretation of the Bible that dominated his era, combined with Aristotle's vision of nature as definitively fixed.

Darwin, together with J. B. Lamarck, promoted a vision of a changing world, while upholding the idea that organisms evolved from a single root — a position held by Adam and Eve in the creationist worldview, and taken over in the modern era by the Last Universal Common Ancestor (LUCA). And from that remnant of the Biblical story of creation sprung the notion of a tree of life, alongside major concepts such as gradualism (the view that speciation does not occur abruptly) and the idea that minor selection pressures can, over time, have a profound effect on improved fitness.

Darwin's vision of the world deeply influenced biology in the 20th century, despite persistent questions posed by factors such as lateral gene transfer, neutral evolution, and chaotic bottlenecks in natural selection. But recent genetic research unequivocally refutes this worldview.

Chimeras

Life is primarily the expression of the information contained in genes. All living organisms appear as mosaics of genetic tissue, or chimeras, suggesting that no two genes have the same evolutionary history. This framework is incompatible with the 'tree of life' representation. Rather, it resembles a rhizome — an underground stem that sends out roots and shoots that develop into new plants.
Indeed, we now know that the proportion of genetic sequences on Earth that belongs to visible organisms is negligible. Furthermore, only 15 per cent of the genetic sequences found in the samples from the environment and from faeces analysed in metagenomic studies belong to the three domains of microbes currently recognised in the tree-of-life framework — bacteria, archaea, and eukaryotes. Viruses contain another 15 to 30 per cent of these genetic sequences.

The unidentified genetic sequences pose a problem, because it is not known whether vehicles other than viruses, bacteria, archaea, and eukaryotes exist. Conversely, we know that new genes, designated ORFans ('orphan genes'), are commonly created by gene duplication, fusion, or other unknown mechanisms. Yet, according to Darwin's tree of life concept, this phenomenon would be impossible.
Human cells comprise genes of eukaryotic, bacterial, archaean, and viral origin. As this chimerism increases, it occasionally integrates genes from microbes that live within the human body — as happens when a human is infected by herpesvirus 6. Once integrated in a person's genome, these genes can be transmitted from parent to child — making microbial genes their 'grandfathers'.
This transfer of genetic sequences from parasites to hosts could involve hundreds of genes for a bacterium in different hosts. For example, if the bacterium Wolbachia's genes are integrated by different hosts, such as spiders, insects, or worms, the hosts' offspring are also descendants of Wolbachia.

Moreover, certain viruses' size and genetic repertoire is comparable with that of bacteria, archaea, or small eukaryotes. Indeed, the life of giant viruses is as complex as that of like-sized microorganisms.

Dogma

But the current classification of the domains of life is based on the ribosome — the production apparatus of proteins — which does not exist in these viruses. Without ribosomes, traditionalists say, viruses cannot be considered biological entities comparable to other microbes. But that is pure dogma; these viruses are akin to the other microbes.

Darwin's theory is further used to support the belief that ancient humans — Neanderthal, Cro-Magnon, and Denisova — did not mix. In fact, based on Darwin's assumptions, most anthropologists claim that modern humans were simply descended from Cro-Magnons, who had exterminated their less-fit adversaries. Given this supposition, a single name (Homo sapiens) is used for both modern humans and the preferred ancestor, Cro-Magnon. But we now know that modern humans are chimeras of these three ancient humans.

This understanding also refutes the legend of 'Mitochondrial Eve', the woman from whom all humans supposedly descend on their mother's side.

Research on the human leukocyte antigen genes, which are involved in the human immune response, shows that such a common ancestor could not have existed; this group of genes derives from those of all three known ancient humans.

Genetic research, in particular, must be free to find new models to explain, and enhance, 21st century scientific discovery. Today, Darwin's theory of evolution is more a hindrance than a help, because it has become a quasi-theological creed that is preventing the benefits of improved research from being fully realised.

About the author:Didier Raoult is director of the Research Unit in Infectious and Tropical Emergent Diseases, collaborating with CNRS (National Center for the Scientific Research), IRD (Research for the Development Institute), and the University of the Méditerranée in Marseille.