Friday, February 1, 2013

Weekend Rebel Science Excursion - 14

Scandalously close view of a Tomato Leaf
In this episode we note that Darwin Was Not Infallible, a la "the king can do no wrong" and "the Pope is infallible."

Following up on the previous post in this series, which concerned new scientific thinking about viruses, we look into an emerging hypothesis that may be going in a direction to try to rescue what may now properly be called Darwin's hypothesis.

In his book The Origin of Species, Charles Darwin was honest enough to write that his hypothesis had a problem, which was The Cambrian Explosion:
The Cambrian explosion has generated extensive scientific debate. The seemingly rapid appearance of fossils in the “Primordial Strata” was noted as early as the 1840s, and in 1859 Charles Darwin discussed it as one of the main objections that could be made against his theory of evolution by natural selection.
(Wikipedia, emphasis added; cf. this). As if that was not enough, we now know that there was another, earlier rapid appearance episode prior to the one that troubled Darwin, yes, an earlier event that he was not aware of.

This earlier rapid appearance episode is in addition to two additional associated events, the Great Oxygen Events (GOE), which totals two rapid expansion events and two GOE events:
There is evidence that oxygen levels also rose 1.3 billion years ago and again before the Cambrian Explosion, a rapid proliferation of animal life that began 540 million years ago. Some researchers believe increasing levels of atmospheric oxygen helped trigger the Cambrian Explosion.

Catling says the reason for those rises in atmospheric oxygen “is even more of a mystery than the first one.”

“There were huge ice ages just before the Cambrian Explosion, but also associated with the Great Oxidation Event,” Holland says. “It is important to have a much better understanding of those events and the history of life.”

Kasting, Catling, Des Marais, Hoehler and Holland are members of the NASA Astrobiology Institute so those issues have special relevance for them.
(The Rise of Oxygen, Astrobiology Magazine). The ongoing controversy, not unsurprisingly, has caused infantile feuds which have even ended up in court trials:
The Plausibility of Life ends with a brief critique of intelligent design, suggesting that the concept of facilitated variation will provide a solid argument to rebut creationists. I applaud the authors' intention, as it seems to me that more scientists ought to face the realities of public misunderstanding of science. But their presentation is too brief, and a bit too simplistic. The "controversy" about evolution has nothing to do with the soundness of scientific explanations of the history of life: It's not a scientific controversy, but a social, cultural and political one. Creationism is the result of centuries of anti-intellectualism in the United States, coupled with sometimes cynical exploitation of the issue for political gain. In addition, many scientists have no interest in getting out of the ivory tower to talk to the very same public that pays their salaries and funds their precious research grants. The recent defeat of intelligent design at the trial in Dover, Pennsylvania — at the hand of a conservative judge appointed by George W. Bush — will do much more to promote sanity in public education than any theory about facilitated variation, as scientifically sound as the latter may be.
(Have We Solved Darwin's Dilemma?, emphasis added). Really, where are we when religionists and scientists duke it out in court as a solution to what they both call a cognitive mystery?

The federal case mentioned in the "Have We Solved Darwin's Dilemma?" quote above only determined whether the teaching of "Intelligent Design"  in public schools violated the First Amendment; not in any way did that case even attempt to decide which religious teaching, scientific theory, or hypothesis was the correct one.

Anyway, back to the peaceful discussion of this issue, which is the hypothesis that prions, phages, and viruses evolved prior to cells, thus they could have provided an underlying framework for the transfer of oxygen to the atmosphere:
Several genes coding for key proteins involved in viral replication and morphogenesis as well as the major capsid protein of icosahedral virions are shared by many groups of RNA and DNA viruses but are missing in cellular life forms.

On the basis of this key observation and the data on extensive genetic exchange between diverse viruses, we propose the concept of the ancient virus world. The virus world is construed as a distinct contingent of viral genes that continuously retained its identity throughout the entire history of life. Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes.

Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool.

In this pool, RNA viruses would evolve first, followed by retroid elements, and DNA viruses. The Virus World concept is predicated on a model of early evolution whereby emergence of substantial genetic diversity antedates the advent of full-fledged cells, allowing for extensive gene mixing at this early stage of evolution.

We outline a scenario of the origin of the main classes of viruses in conjunction with a specific model of precellular evolution under which the primordial gene pool dwelled in a network of inorganic compartments. Somewhat paradoxically, under this scenario, we surmise that selfish genetic elements ancestral to viruses evolved prior to typical cells, to become intracellular parasites once bacteria and archaea arrived at the scene.

Selection against excessively aggressive parasites that would kill off the host ensembles of genetic elements would lead to early evolution of temperate virus-like agents and primitive defense mechanisms, possibly, based on the RNA interference principle.

The emergence of the eukaryotic cell is construed as the second melting pot of virus evolution from which the major groups of eukaryotic viruses originated as a result of extensive recombination of genes from various bacteriophages, archaeal viruses, plasmids, and the evolving eukaryotic genomes.

Again, this vision is predicated on a specific model of the emergence of eukaryotic cell under which archaeo-bacterial symbiosis was the starting point of eukaryogenesis, a scenario that appears to be best compatible with the data.
(The ancient Virus World and evolution of cells, 2006, emphasis added). The current theory in vogue in evolutionary biology holds that cells evolved prior to viruses, and thus the controversy.

It takes a lot of work to show that Darwin was infallible, and that work has not been done yet, but the rebels press on in their effort to do so.

The next post in this series is here, the previous post is here.

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