Is DNA a Fossil of the Origin of Life? (Today’s Most Popular)

31753dna_screen05 "In some sense, the genetic code is a fossil or perhaps an echo of the origin of life, just as the cosmic microwave background is a sort of echo of the Big Bang. And its form points to a process very different from today's Darwinian evolution."

Carl Woese -Microbiologist

What if a process Darwin never wrote about, and never even dreamed ofl, has been controlling the evolution of life throughout most of the Earth's history and altered the evolutionary process itself? What if it turns out that there is a "time machine" that biologists can use to look back towards the origin of life?


Microbiologist Carl Woese and physicist Nigel Goldenfeld both at the University of Illinois at Urbana-Champaign, argue that Darwin's theory of evolution by natural selection applies only to a recent phase of life on Earth; that a process of horizontal evolution led to the rise of the genetic code.

In 1977, Woese took the world of evolutionary biology by storm when his analysis of the genetic machinery involved in gene expression revealed an entirely new limb of the tree of life -the archaea, a group of single-celled microbes as distinct from bacteria genetically as both archaea and bacteria are from eukaryotes. Archaea saw an unprecedented amount of study since Woese’s revolutionary discovery, especially because of their ability to live in extreme habitats. Such “extremophiles” are often found in at deep undersea vents and living in geysers with temperatures frequently rising up to 100 degrees Celsius (212 degrees Fahrenheit) .

Horizontal evolution is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored, which according to Woese and Goldenfeld, are profound. Since micro-organisms represented the majority of life on Earth for the billions of years that life has existed, the most ancient and prevalent form of evolution probably wasn't Darwinian at all.

According to Woese, evolutionary biology took its modern form in the early 20th century with the establishment of the genetic basis of inheritance: Mendel's genetics combined with Darwin's theory of evolution by natural selection. Biologists call this as the "modern synthesis", and it has been the basis for all subsequent developments in molecular biology and genetics.

Woese believes that along the way biologists were seduced into thinking they had found the final truth about all evolution. "Biology built up a facade of mathematics around the juxtaposition of Mendelian genetics with Darwinism. And as a result it neglected to study the most important problem in science – the nature of the evolutionary process."

Woese argues that nothing in the modern synthesis explains how evolution could have produced the genetic code and the basic genetic machinery used by all organisms, especially the enzymes and structures involved in translating genetic information into proteins. Francis Crick, the co-discoverer of the molecular structure of DNA, presumed that the code was just some "frozen accident", inherited by all organisms from an early form of life.  Goldenfeld and Kalin Vetsigian, now at Harvard, however, discovered that it is possible for codes and organisms to evolve together cooperatively, especially effectively through horizontal gene transfer.

As the name suggests, horizontal gene transfer involves cells providing genes with each other, rather than having genes develop in distinct lines unique to each organism.  Present day microbes, and presumably early organisms too, use horizontal gene transfer pervasively, in place of sex to mix genes, thereby creating novel combinations of genes that can generate new functionality.  Now it appears that the genetic code evolved this way, very early on in life's history, even before the root of the tree of life.  In some sense, then, the genetic code is a fossil or perhaps an echo of the origin of life, just as the cosmic microwave background, as Woese points out, is a sort of echo of the Big Bang.

In the past few years, genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world, so an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species.

On the basis of their research, they argue that horizontal gene transfer had to be a dominant factor in the original form of evolution. Evidence for this lies in the genetic code. Though it was discovered in the 1960s, no one had been able to explain how evolution could have made it so exquisitely tuned to resisting errors. Mutations happen in DNA coding all the time, and yet the proteins it produces often remain unaffected by these errors. Darwinian evolution simply cannot explain how such a code could arise. But horizontal gene transfer can, say Woese and Goldenfeld.

"With vertical, Darwinian evolution," says Goldenfeld, "we found that the code evolution gets stuck and does not find the true optimum."

For the researchers the conclusion is inescapable: the genetic code must have arisen in an earlier evolutionary phase dominated by horizontal gene transfer.

"It would have acted as an innovation-sharing protocol," says Goldenfeld, "greatly enhancing the ability of organisms to share genetic innovations that were beneficial." Following this, a second stage of evolution would have involved rampant horizontal gene transfer, made possible by the shared genetic machinery, and leading to a rapid, exponential rise in the complexity of organisms. This, in turn, would eventually have given way to a third stage of evolution in which genetic transfer became mostly vertical, perhaps because the complexity of organisms reached a threshold requiring a more circumscribed flow of genes to preserve correct function.

Woese can't put a date on when the transition to Darwinian evolution happened, but he suspects it occurred at different times in each of the three main branches of the tree of life, with bacteria likely to have changed first.

Early evolution may have proceeded through a series of stages before the Darwinian form emerged. Today, at least in multicellular organisms, Darwinian evolution is dominant but we may still be in for some surprises. "Most of life – the microbial world – is still strongly taking advantage of horizontal gene transfer, but we also know, from studies in the past year, that multicellular organisms do this too," says Goldenfeld.

1994-731.p  As more genomes are sequenced, ever more incongruous sequences of DNA are turning up. Comparisons of the genomes of various species including a frog, lizard, mouse and bushbaby, for example, indicate that one particular chunk of DNA found in each must have been acquired independently by horizontal gene transfer (Proceedings of the National Academy of Sciences, vol 105, p 17023). "The importance of this for evolution has yet to be seriously considered."

How did life on Earth evolve so quickly from  from early geochemistry. What were the key physical processes that led to self-organization of early metabolism and self-reproducing molecules?

In taking this approach to the origin of life, the characteristics of the earliest organisms become very important: do they contain clues about the origin of life that we have not yet teased out?  Astronomers have long understood that by studying the farthest galaxies and stars, they are effectively looking back the beginning of time, receiving photons that have been traveling for billions of years.

If the genetic code has its origins so early on in the evolution of life, then working backwards from the genetic code might make connections with the chemical reactions that must have been important for early life. Many biologists consider the deep sea vents the most plausible location for the origin of life. Furthermore, there is the exciting prospect that similar vents on other worlds, such as the oceans of Jupiter's moon, Europa, may be the host to extra-terrestrial microbial life.

Casey Kazan via material provided by:

The Institute for Genomic Biology at the University of Illinois.

Additional source: http://www.newscientist.com/article/mg20527441.500-horizontal-and-vertical-the-evolution-of-evolution.html?full=true&print=true

http://guava.physics.uiuc.edu/projects/FIBR_overview.html

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