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MARSEILLE, France--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 world view, and taken over in the modern era by the Last Universal Common Ancestor (LUCA).
And from that remnant of the biblical story of creation sprang 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 world view.
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 percent of the genetic sequences found in the samples from the environment and from feces analyzed in metagenomic studies belong to the three domains of microbes currently recognized in the Tree of Life framework--bacteria, archaea, and eukaryotes. Viruses contain another 15
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, by Darwin's Tree of Life concept, this phenomenon would be impossible.