Many Greek philosophers perceived the world to be in perpetual motion — a process of constant evolution. However, in Charles Darwin’s world, 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). 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 twentieth century, despite persistent questions posed by factors such as lateral gene transfer, neutral evolution, and chaotic bottlenecks in natural selection. However, recent genetic research unequivocally refutes this worldview.
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 belongs to the three domains of microbes currently recognized in the tree of life framework — bacteria, archaea and eukaryotes. Viruses contain another 15 percent to 30 percent 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 of 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. The life of giant viruses is as complex as that of like-sized microorganisms.