Evolution Version 3.01 and The Forest of Life

By Gary Berg-cross
Science is one of those progressive forces that sometimes moves on in surprising ways. Newton’s mechanics was a great accomplishment and remains one of our most useful tools. But Physics has moved on to a grand synthesis of quantum and relativity theories which were not included in Newton’s view. Darwin’s theory grew out of a great deal of evidence which he framed into a a biological theory. When arguing with Creationist, many of us cite Darwin as the authority on the topic with lots of supporting data that the field has added over time.
But most of us know that this theory was only the start. There was a late 1930s synthesis that harmonized the ideas of Darwinian evolutionary theory with Mendelian genetics. It’s a good example of how scientific understanding advances. There was an accumulation of data and additional systemic thinking from several new biological fields, e.g. developmental biology, botany, population genetics, and paleontology. These were used to build a more complete theory. What I’ll call Evolution Version 2 successfully integrated various Darwinian postulates (e.g. the long time needed for species to evolve, the role of individual variation, some variations are selected etc.), and Mendelian genetics into a reformation of evolutionary theory. The new synthesis showed that Mendelian genetics for individuals was consistent with natural selection and gradual macro evolution of species.
But it is not the end of the story. The evolutionary field has accelerated and broadened. With the great deal we have learned in the last 50 years or so it is not surprising that there seems to be a new, and grander evolutionary synthesis that is being discussed and kicked around. As a community that likes progress and sometimes gets into conversations with creationist it’s useful to know the latest thinking. This can be challenging since theories grow complex and their principles more nuances as they do a better job to capturing a broader swath of reality. That’s certainly the case with Newtonian mechanics being superseded by Quantum Mechanics. It is no less likely in the messiness of the Biological realm.

What I’ll call here Version 3.01 of evolution seems to be forming. Like 2.0 it grows out of advances in new areas of biological study – in this case in the last 50 years. A bit part comes from the revolution in understanding DNA, and the comparative genomic analysis it allows. Rapid progress of genomics and systems biology at the end of the 20th century continuing now in the 21st century brings us enormous amounts of new data amenable to modeling and quantitative analysis.The combination of molecular genetics with mathematical modeling this has begun to build a new, much more detailed, complex, and realistic picture of evolution. By 2007 there was enough evidence for Michael Specter to write a New Yorker article on part of the revolution called Darwin’s Surprise:Why are evolutionary biologists bringing back extinct deadly viruses? In the article Specter wrote:

“When the sequence of the human genome was fully mapped, in 2003, researchers also discovered something they had not anticipated: our bodies are littered with the shards of such retroviruses, fragments of the chemical code from which all genetic material is made. It takes less than two per cent of our genome to create all the proteins necessary for us to live. Eight per cent, however, is composed of broken and disabled retroviruses, which, millions of years ago, managed to embed themselves in the DNA of our ancestors.”

This is not exactly the classical hierarchical view of species and inheritance via adaptation. We now understand more complex phylogenetic relationships at the genetic level of human and animal viruses (bird flu?). The data Darwin could use dealt with gross physical features, and the subtleties of the genetic engine of evolution used for Version 2 were invisible to him. Likewise viruses, bacteria or eukaryotes & their relation to species was also outside his theory. But a few years ago there was enough evidence from observation of viruses for Van Blerkom to publish a review article on the Role of viruses in human evolution. He suggested that humans as well as other animals have had to adapt to endogenous retroviruses throughout their evolutionary history because once they infect the DNA of a species they become part of that species and can change the way they function. Over time the number and types have changed but some viruses show evidence of long-standing intimate relationship and co-speciation with hominids. The defense of vertebrates against parasites and other pathogens involves common genes there are extensive and go back 30 million years, being shared by humans, apes. For more see The Tree of Life: Tangled Roots and Sexy Shoots Tracing the genetic pathway from the first Eukaryotes to Homo sapiens.

Data such as these has encouraged new models of what happens in evolution based on more generalized elementary processes similar to those used in statistical physics:

1. domain birth (duplication with divergence),
2. death (inactivation and/or deletion), and
3. innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer such as discussed above).

Such generalized models are part of the picture that Eugene V. Koonin builds in his book, The Logic of Chance: The Nature and Origin of Biological
Evolution (viewable online!!!) which “offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology.”

Some readers may have heard of Koonin before because his arguments have been quoted out of context by Creationsists/Discovery Institute. Koonin does argue that there are problems with Version 2.0 the grand synthesis of 'evolution.' But he is arguing for an extension and not a contraction of the theory. A central part of the story is the underappreciated evolutionary importance of viruses as previously noted. But Koonin covers many other aspects that, taken together, yield a new, much more detailed, complex, and realistic picture of evolution. It’s like supplementing classical mechanics with quantum. This does not mean the traditional paradigm is rejected and abandoned. Instead it is generalized with a more complex set of layers added and richer concepts developed on such things as species and how genes get duplicated and how they get expressed. We are still on Darwin’s path but traveling with an improved vehicle.

Indeed Version 3.01 allows people like Koonin to make an even more compelling case for evolution. What Koonin does in fact is to examine a broad range of topics in evolutionary biology from a modern viewpoint and argues that such concepts as natural selection and adaptation need to be supplemented to explain evolution. Some of the concepts we’ve heard before in fragments such as the horizontal gene transfer. When we give this a more prominent role in evolution one consequence is the need to overhaul the grand “Tree of Life (ToL) concept. That’s the picture of a single starting point that branches simply to produce a new species. A more modern view based on comprehensive comparative analysis of 6901 phylogenetic trees is that the overall pattern of life’s history is more like a Forest, than a single ToL. Koonin analysis of prokaryotic genes revealed evidence for some vertical (tree like) inheritance but this was only particularly strong among a subset of 102 nearly universal trees. The non tree-like topological/inconsistency found in what he call the the Forest of Life was most likely, caused by Horizontal Gene Transfers. A messier story, but it does explain things. Within the Forest Family of Life there remains a core tree like structure dimly aware to Darwin and his data that reflect a significant central trend:



Figure above has two views of life history to replace a single Tree of Life.

(A) The ‘TOL as a central trend’ model. The history of life is represented as a tree, with connecting lines between branches depicting HGT and shaded trapezoids depicting phases of compressed cladogenesis (276). The origin of eukaryotes is depicted according to the archezoan hypothesis whereby the host of the mitochondrial endosymbiont was a proto-eukaryotes (archezoan). A cellular Last Universal Common Ancestor (LUCA) is envisaged. (B) The ‘Big Bang’ model. The history of life is represented as a succession of tree-like phases accompanied by HGT and non-tree-like, Big Bang phases. Connecting lines between tree branches depict HGT and colored trapezoids depict Big Bang phases (151). The origin of eukaryotes is depicted according to the symbiogenesis model whereby the host of the mitochondrial endosymbiont was an archaeon. A pre-cellular Last Universal Common Ancestral State (LUCAS) is envisaged. Ar, archaeon (host of the mitochondrion in b), AZ, archezoan (host of the mitochondrion in a), BB, Big Bang, C, chloroplast, CC, compressed cladogenesis, M, mitochondrion. See “Darwinian evolution in the light of genomics,” Nucleic Acids Research 2009, 1-24.

“Evolutionary genomics effectively demolished the straightforward concept of the ToL by revealing the dynamic, reticulated character of evolution where horizontal gene transfer (HGT), genome fusion, and interaction between genomes of cellular life forms and diverse selfish genetic elements take the central stage. In this dynamic worldview, each genome is a palimpsest, a diverse collection of genes with different evolutionary fates and widely varying likelihoods of being lost, transferred, or duplicated. So the ToL becomes a network, or perhaps, most appropriately, the Forest of Life that consists of trees, bushes, thickets of lianas, and of course, numerous dead trunks and branches. Whether the ToL can be salvaged as central trend in the evolution of multiple conserved genes or this concept should be squarely abandoned for the Forest of Life image remains an open question.”

Version 3.01 may be more technical than a secular layman can across in discussions with evolutionary non-believers but it is interesting to see the continued maturation of scientific thought in this Forest of Life Family we are part of.