Sunday, September 18, 2011

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 That’s certainly the case with Newtonian mechanics being superseded by Quantum Mechanics.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.


Don Wharton said...

I remember being amazed when I read the book "Endless Forms Most Beautiful." It seems as if there is another wave of new evolutionary insight that I need to read more fully about.

lucette said...

I am getting discouraged. I have just begun to decipher, very very slowly, some of the concepts advanced by Stephen Jay Gould in "The Structure of Evolutionary Theory". How do these compare with the Forest of Life concepts? Is the punctuated equilibrium no longer kosher?

Gary Berg-Cross said...


I'm not versant enough with all aspects of the work, but my opinion is that punctuated equilibrium still applies, but the issue is how important it is and if it needs to be enhanced.
Koonin's (2007) The Biological Big Bang model discussed the major transitions in evolution such as rapid & unexplained appearance of novel characteristics, especially those that count as major transitions in evolution. E.g. origin of cells and the Cambrian explosion.

Koonin has a Biological Big Bang (BBB) model of evolution which proposes that "most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. Then evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on."

Don Wharton said...

Stephen Jay Gould was actually someone who had a negative influence for much of his life within biology. The notiion of punctuated equilibrium is basically just the notion that evolution does not proceed at constant speed. There was never any claim that it did but for much of early Darwinianism there was little research documenting exactly how the speed varied.

The major positive in his last book "The Structure of Evolutionary Theory" is that he ceased to make the false claims that he had made in the past.

For a good while he engaged in a public war with Dennett and Dawkins who he condemned as Ultra-Darwinists. In terms of the factual differences he asserted he was in my opinion wrong on virtually every point.

Gary Berg-Cross said...

I'm not sure that Gould had a negative influence on Biology, but he was such a smooth writer and thinker that he could make a powerful impression on one. He was an aid for the gifted Biologist Ernst Mayr who claimed that Gould took some of his lecture ideas and wrapped them up with a pretty bow as punctuated equilibrium. But there is created due to pushing the issue and clarifying things. Mayr had some many ideas that he couldn't pursue all of them.
I somewhat agree with Dawkins that Gould could play fast and lose with notions on time, just to make his point.

Don Wharton said...

Gary, I remember getting into arguments with biologists at the Washington Ethical Society about who was right in the war between Gould and the so called ultra-Darwinists. One of them was even an editor for a respected Biology journal. Frankly, Gould was wrong on virtually every point in this war and the fact that he did not voice one of his controversial position in his las book somewhat confirms that he knows he was wrong.

Moreover, the Christian creationist took the visible elements of this war and presented the notion that there were holes in Darwinian theory. Gould certainly created the image of deep conflict in the world of biology that was in my opinion totally unnecessary.

In the last couple of years I have had disagreements with people who still seem to think that Gould's notions of group selection have some validity. From what I can tell they don't. The confusion he propagated continues to this day.

Gary Berg-Cross said...

Don, I'll leave it to experts to say how this debate on “group selection,” turned out or if it is still being resolved. I had read that most work was concentrated on the genetic level, but that doesn't mean that Gould was wrong. To me it is always interesting when a few giants contest important issues. If they avoid polemics it usually advances the thinking.

I did read that in 1987, Maynard Smith made what was considered an important concession/clarification:

"There has been some semantic confusion about the phrase 'group selection,' for which I may be partly responsible. For me, the debate about levels of selection was initiated by Wynne-Edwards' book. He argued that there are group-level adaptations…which inform individuals of the size of the population so that they can adjust their breeding for the good of the population. He was clear that such adaptations could evolve only if populations were units of selection…. Perhaps unfortunately, he referred to the process as “group selection.” As a consequence, for me and for many others who engaged in this debate, the phrase cane to imply that groups were sufficiently isolated from one another reproductively to act as units of evolution, and not merely that selection acted on groups.

The importance of this debate lay in the fact that group-adaptationist thinking was at that time widespread among biologists. It was therefore important to establish that there is no reason to expect groups to evolve traits ensuring their own survival unless they are sufficiently isolated for like to beget like….

Smith “Evolutionary Progress and Levels of Selection,” in The Latest on the Best:Essays on Evolution and Optimality, J. Dupre (ed.) 1987, p. 123).

Now a lot has happened since 1987 so it would be interesting to get a definitive update. I did see something at ... r_2008.pdf a 2007 article in the Journal of Evolutionary Biology which seems to be part of a discussion between David Wilson and a group who disagree with him. Evidently, the group (West, Griffin and Gardner) published a review article on "social semantics", David Wilson published another accusing them of having unfairly dismissed group selection, and the linked article above is the reply to all of that explaining why they think that group selection is almost (but not quite) always a less useful approach than kin selection.

The original review article is: ... _2007a.pdf

and David Wilson's reply is: ... antics.pdf

These articles are difficult, but one person summarized the gist of West, Griffin and Gardner's argument as modern group selection is exactly the same mechanism as kin selection, but it's an approach that causes more confusion than kin selection, so it's not generally used. (By contrast, the older group selection is just sloppy and wrong. This is the idea that organisms evolve to help their groups, or their species. This has been apparently replaced by Hamilton's theory that organisms maximize their inclusive fitness, and modern group selection and kin selection now follow Hamilton's formulation.)

Some say Dawkins also softened his criticism, having perhaps made the larger point and moved on since one heard that "The practical question is whether it happens often enough under natural conditions to explain the observed evolution of group-benefiting behavior, and the answer appears to be "no."

lucette said...

Don wrote:
"One of them was even an editor for a respected Biology journal."
Editors are not always right. They are under all kinds of pressures. I had once to appeal to the Board of Editors of the Journal of Chemical Physics to get a paper accepted in spite of the reviewer and editor's rejections. The mistake was obvious.
The scientific method should not be reduced to the approval or disapproval of an editor. Science is not based on editors' opinions.

lucette said...

Gary, It looks like we could use Occam's razor in the Forest of Evolution. ;(

lucette said...

"The notiion of punctuated equilibrium is basically just the notion that evolution does not proceed at constant speed."

Is it a notion or a possible explanation?

Gary Berg-Cross said...

One popular stance is "We should not regard everything as either supporting punctuated equilibrium or opposing it. It turns out that there's a whole gradation between pure punctuated equilibrium and pure gradualism."

From 3rd Edition of 'Evolution' by English paleontologist Simon Conway Morris (BTW while not supporting creation science he sort of feels that evolution and religion are compatible.

Dawkins and he are compatible on the Science as shown in this interview quote:

Professor Dawkins’s closest intellectual ally on progressive evolution and convergence is Simon Conway Morris (pictured in green shirt), the renowned Cambridge evolutionary paleontologist.

And Professor Morris, as it happens, is an Anglican and a fervent believer in a personal God. He sees convergence as hinting at a teleology, or intelligent architecture, in the universe. (emphasis mine)

Ask Professor Dawkins about his intellectual bedfellow, and his smile thins. “Yes, well, Simon and I have converged on the science,” he says. “I should think in the world there are not two evolutionary scientists who could rival each other in their enthusiasm for convergence.”

As to Professor Morris’s religious faith? “I just don’t get it.”

Anywayhis Science seems good. See for chapters and tutorials

lucette said...

“I should think in the world there are not two evolutionary scientists who could rival each other in their enthusiasm for convergence.”

I am afraid I must be an idiot because I am unable to answer this Dawkins' quote.
Please somebody help me!

Don Wharton said...

Gary, the several links you cite did not work for me. However I did find the critical examination of Wilson titled:

Social semantics: how useful has group selection been?


A couple of cogent quotes from page seven of this document summarize a devastating case against group selection:

“A huge problem in settling the kin selection vs. group
selection debate is that group selection is not properly
defined as a concept. A consequence of this is that there
is no formal theory of group selection. Instead, group
selection theory comprises a number of illustrative models, each of limited generality, with obscure or nonexistent links between approaches and formalisms,
and some models of group selection contradicting others (Okasha, 2006; Gardner & Foster, in press; Wilson & Wilson, 2007).”

“We suggest that these problems do not reflect a failure of the levels-of-selection or contextual-analysis approaches, but rather a failure of the concept of group
selection itself. If there is an idea of group selection, it does not seem possible to capture it mathematically, which would put it beyond the reach of scientific

lucette said...

Don, As the owner of this blog, I guess you are the best person to explain why so many of my comments are followed by a "Delete" icon. I have not seen any "Delete" icon on anybody else comment. Why the special distinction?

Don Wharton said...

@lucette The blog knows that you are the one who posted your comments. It is giving you the option to delete your comments. No one else is given the option to delete your comments from the standard comment display.

lucette said...

Don, I tried to find this information but was not successful. Thanks for your answer.