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Friday, April 17, 2015

How Structure Arose in the Primordial Soup

Life’s first epoch saw incredible advances — cells, metabolism and DNA, to name a few. Researchers are resurrecting ancient proteins to illuminate the biological dark ages.
About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. All three of these are essential to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.
“It’s very hard to infer even the relative ordering of evolutionary events before the last common ancestor,” said Greg Fournier, a geobiologist at the Massachusetts Institute of Technology. Cells may have appeared before energy metabolism, or perhaps it was the other way around. Without fossils or DNA preserved from organisms living during this period, scientists have had little data to work from.
Fournier is leading an attempt to reconstruct the history of life in those evolutionary dark ages — the hundreds of millions of years between the time when life first emerged and when it split into what would become the endless tangle of existence.
He is using genomic data from living organisms to infer the DNA sequence of ancient genes as part of a growing field known as paleogenomics. In research published online in March in the Journal of Molecular Evolution, Fournier showed that the last chemical letter added to the code was a molecule called tryptophan — an amino acid most famous for its presence in turkey dinners. The work supports the idea that the genetic code evolved gradually.
Using similar methods, he hopes to decipher the temporal order of more of the code — determining when each letter was added to the genetic alphabet — and to date key events in the origins of life, such as the emergence of cells.
Photo Credits : Olena Shmahalo/Quanta Magazine 

Primordial soup" hypothesis

No new notable research or theory on the subject appeared until 1924, when Alexander Oparin reasoned that atmospheric oxygen prevents the synthesis of certain organic compounds that are necessary building blocks for the evolution of life. In his book The Origin of Life, Oparin proposed that the "spontaneous generation of life" that had been attacked by Louis Pasteur did in fact occur once, but was now impossible because the conditions found on the early Earth had changed, and preexisting organisms would immediately consume any spontaneously generated organism. Oparin argued that a "primeval soup" of organic molecules could be created in an oxygenless atmosphere through the action of sunlight. These would combine in ever more complex ways until they formed coacervate droplets. These droplets would "grow" by fusion with other droplets, and "reproduce" through fission into daughter droplets, and so have a primitive metabolism in which factors that promote "cell integrity" survive, and those that do not become extinct. Many modern theories of the origin of life still take Oparin's ideas as
a starting point.

Robert Shapiro has summarized the "primordial soup" theory of Oparin and Haldane in its "mature form" as follows:

1.The early Earth had a chemically reducing atmosphere.

2.This atmosphere, exposed to energy in various forms, produced simple organic compounds ("monomers").

3.These compounds accumulated in a "soup" that may have concentrated at various locations (shorelines, oceanic vents etc.).

4. By further transformation, more complex organic polymers – and ultimately life – developed in the soup.

Around the same time, J. B. S. Haldane suggested that the Earth's prebiotic oceans—different from their modern counterparts—would have formed a "hot dilute soup" in which organic compounds could have formed. J.D. Bernal, a pioneer in x-ray crystallography, called this idea biopoiesis or biopoesis, the process of living matter evolving from self-replicating but nonliving molecules, and proposed that biopoiesis passes through a number of intermediate stages.

One of the most important pieces of experimental support for the "soup" theory came in 1952. Stanley Miller and Harold Urey, performed an experiment that demonstrated how organic molecules could have spontaneously formed from inorganic precursors, under conditions like those posited by the Oparin-Haldane Hypothesis. The now-famous "Miller–Urey experiment" used a highly reduced mixture of gases—methane, ammonia and hydrogen—to form basic organic monomers, such as amino acids.[63] This provided direct experimental support for the second point of the "soup" theory, and it is around the remaining two points of the theory that much of the debate now centers. In the Miller–Urey experiment, a mixture of water, hydrogen, methane, and ammonia was cycled through an apparatus that delivered electrical sparks to the mixture. After one week, it was found that about 10% to 15% of the carbon in the system was now in the form of a racemic mixture of organic compounds, including amino acids, which are the building blocks of proteins.

Bernal shows that based upon this and subsequent work there is no difficulty in principle in forming most of the molecules we recognise as the basic molecules of life from their inorganic precursors. The underlying hypothesis held by Oparin, Haldane, Bernal, Miller and Urey, for instance, was that multiple conditions on the primeval Earth favored chemical reactions that synthesized the same set of complex organic compounds from such simple precursors. A 2011 reanalysis of the saved vials containing the original extracts that resulted from the Miller and Urey experiments, using current and more advanced analytical equipment and technology, has uncovered more biochemicals than originally discovered in the 1950s. One of the more important findings was 23 amino acids, far more than the five originally found.However Bernal said that "it is not enough to explain the formation of such molecules, what is necessary" he says " a physical-chemical explanation of the origins of these molecules that suggests the presence of suitable sources and sinks for free energy.

Greg Fournier, a geobiologist at MIT, is searching for the origins of the genetic code.