Proterozoic and Archaean

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): "The Proterozoic and Archean Eons extend back to more than 3.6 billion years ago and cover the first microfossils and stromatolite fossils. Mikhail Fedonkin, head of the Laboratory of the Precambrian Organisms at the Paleontological Institute in Moscow suggested that a fall of global temperatures and the oxygenation of the biosphere secondary to photosynthesis played a major role in the dramatic change in the availability of heavy metals, which he believes were crucial in the metabolic processes that led to the evolution of complex life. This metal-rich environment served as a catalyst: 'Over 70 percent of known enzymes contain metal ions as a cofactor of an active site. Fast catalyzed reactions segregated life first dynamically and then structurally from the mineral realm.' Once prokaryotes gave rise to eukaryotes through symbiogenesis, life was off and running, exploding in the Cambrian with complex hard-bodied organisms.

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Prokaryote Systematics: The Evolution of a Science

Prokaryote Systematics: The Evolution of a Science: "The "evolutionary clock" (Kimura, 1983) is one of the great discoveries of the 20th century: The fact that in different organisms different (but clearly related) molecular sequences correspond to what appears to be the very same molecular function implies that most of the (net) changes that become fixed over time in any given molecular sequence are selectively neutral; they are of no phenotypic consequence (Kimura, 1983). Such changes must happen more or less randomly in time, and so can be used to measure time in a relative sense. In other words, on the genotypic level a more-or-less steady pace of evolutionary change occurs that is quasi-independent of the sporadic �real� evolutionary changes happening in the overlying phenotype. This independent �evolutionary clock� embedded in the genotype gives the biologist the capacity to infer evolutionary histories and relationships (Woese, 1987); and it has also freed the bacteriologist from the phenotypic quagmire of ill-defined, confusing, or conflicting, and generally phylogenetically uninterpretable morphological and physiological characters."

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Prokaryote Systematics: The Evolution of a Science

Prokaryote Systematics: The Evolution of a Science: "The most useful molecular chronometers actually are molecules like the ribosomal RNAs - molecules with universal, constant, and highly constrained functions that were established at early stages in evolution, functions that are not affected by changes in the organism's environment (except for changes in basic physical parameters such as intracellular pH and temperature). (A strong indicator of the constancy of rRNA function is the near constancy of the molecule's secondary structure within each of the primary kingdoms, and the approximate constancy that holds even between kingdoms [Gutell et al., 1985]). Because rRNAs are large molecules, they contain considerable information; their size also makes them less erratic chronometers than smaller molecules (Woese, 1987). Moreover, rRNAs are easy to isolate in relatively large quantities; they seem not to be subject to lateral gene transfer; and they can be sequenced directly (without resort to gene cloning).

The fact that a precisely functioning molecule such as RNA is under strict functional constraints is both an advantage and a disadvantage. The advantage lies in the constancy of the constraints on the various positions in the sequence and the fact that some positions change far more slowly than others; this last makes the molecule like a clock that includes both a second hand and a calendar—i.e., it can measure a wide range of time intervals. The disadvantage is that the stringent constraints lead to more (local) sequence convergence than otherwise, and the vast differential in rates at which positions change makes analysis more problematic than it would be for a uniform rate situation. (Another of its advantages would appear to be that RNA is a “nonlinear” chronometer and so is potentially capable of distinguishing rapidly vs. slowly evolving lineages, and, therefore, localizing the root of a tree without the need to resort to the use of outgroup sequences [Woese, 1987]).

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Full text | A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

BioMed Central Full text A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land: "A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land"

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Why I'm Happy I Evolved - New York Times

Why I'm Happy I Evolved - New York Times: "Some people want to think of humans as the product of a special creation, separate from other living things. I am not among them; I am glad it is not so. I am proud to be part of the riot of nature, to know that the same forces that produced me also produced bees, giant ferns and microbes that live at the bottom of the sea."

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EVOLUTION: ON PLACOZOA -- THE SIMPLEST KNOWN ANIMAL

EVOLUTION: ON PLACOZOA -- THE SIMPLEST KNOWN ANIMAL: "Often described as the simplest known animal, the unassuming marine placozoan Trichoplax adhaerens is one of a handful of 'lower' metazoans that have so far defied being pigeonholed. "

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New cellular evolution theory rejects single cell beginning

New cellular evolution theory rejects single cell beginning: "In the late 1970s Woese identified the Archaea, a group of microorganisms that thrive primarily in extremely harsh environments, as a separate life form from the planet�s two long-accepted lines � the typical bacteria and the eukaryotes (creatures like animals, plants, fungi and certain unicellular organisms, whose cells have a visible nucleus). His discovery eventually led to a revision of biology books around the world.

The three primary divisions of life now comprise the familiar bacteria and eukaryotes, along with the Archaea. Woese argues that these three life forms evolved separately but exchanged genes, which he refers to as inventions, along the way. He rejects the widely held notion that endosymbiosis (which led to chloroplasts and mitochondria) was the driving force in the evolution of the eukaryotic cell itself or that it was a determining factor in cellular evolution, because that approach assumes a beginning with fully evolved cells.

"The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different," Woese wrote in his introduction. "As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance."Woese calls this critical point in a cell’s evolutionary course the Darwinian Threshold, a time when a genealogical trail, or the origin of a species, begins. From this point forward, only relatively minor changes can occur in the evolution of the organization of a given type of cell.To understand cellular evolution, one must go back beyond the Darwinian Threshold, Woese said.His argument is built around evidence "from the three main cellular information processing systems" – translation, transcription and replication – and he suggests that cellular evolution progressed in that order, with translation leading the way.The pivotal development in the evolution of modern protein-based cells, Woese said, was the invention of symbolic representation on the molecular level – that is, the capacity to "translate" nucleic acid sequence into amino acid sequence.

The advent of translation, he said, caused various archaic nucleic-based entities to begin changing into proteinaceous ones, emerging as forerunners of modern cells as genes and other individual components were exchanged among them. The three modern types of cellular organization represent a mosaic of relationships: In some ways one pair of them will appear highly similar; in others a different pair will.This, Woese said, is exactly what would be expected had they individually begun as distinct entities, but during their subsequent evolutions they had engaged in genetic cross-talk – they had indulged in a commerce of genes."

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