Soup vs Mud Chicken vs

What is life? Living organisms have certain properties that are nearly synonymous with the trait of being alive-organization, growth, reproduction, dynamic purposeful activities and (at least in higher organisms) intelligence and consciousness. Life forms that we have come to know are all based on the same type of genetic blueprints (DNA, RNA) and building blocks (proteins), suggesting a common ancestry. That ancestry, life's emergence, is generally viewed as a rearrangement of cosmic matter originally produced in the "Big Bang" which is presumed to have given birth to the universe some 14 billion years ago. Life's molecular emergence can be viewed in the context of two basic questions concerning place of origin ("soup vs mud") and molecular cause and effect ("chicken vs egg").

In the 1920's Russian biochemist A. I. Oparin (1938) and British biologist J. B. S. Haldane (1947) described their concept of a "primordial soup" of organic molecules existing in the earth's oceans a mere 4 billion years ago. Their soup was thought to be a product of geochemical processes and energy sources acting in an atmosphere of unoxidized gases such as methane, ammonia and hydrogen, similar to what exists currently on Jupiter. This primordial atmosphere was the view of eminent chemist Harold Urey (1939), whose graduate student Stanley L. Miller carried out a key experiment in the early 1950's. Miller created a closed environment containing such a primitive atmosphere and passed electric sparks simulating lightning through it. He detected organic molecules relevant to living processes. Fifteen percent of the original methane carbon was found in molecules which included four amino acids, the building blocks of proteins. Miller also found precursors of DNA and ribose sugars from which RNA is formed. Because the most central molecules of life are identical in all organisms on earth, Miller's primordial soup has been considered to represent the conditions from which life emerged. Other research has questioned the hydrogen rich atmosphere upon which Urey and Miller based their experiment and still other work has shown that at least some organic precursors of life can be generated in many types of atmospheres.

There are other candidates for the site of life's origin. Conditions above the thermal vents recently discovered on the ocean floor are believed conducive to the formation of organic compounds, leading some to propose these spots, rather than the traditionally imagined ponds or tidal pools, as the cradle of life ("deep soup"). Thermal vents are home to strange and exotic life forms such as giant tube worms which thrive in the great pressures of the deep ocean. Organic compounds have also been found commonly in intrastellar dust, in comets, and in meteorites that fall to earth. Many believe the supply of organic precursors to life was augmented from space while few admit to believing that primitive cells were transplanted to earth from space.

An alternative explanation has been advanced by A. Graham Cairns-Smith (1982) of Glasgow University, who suggests that early organisms utilized preexisting information templates in the form of wet clay crystals ("mud"). Crystalline inorganic materials appear to have many "life-like" properties such as the ability to store and replicate information in the form of crystal defects, dislocations, twin boundaries, and substitutions. Clay minerals like kaolinite crystallize at ordinary temperatures from aqueous solutions of common rock. Their catalytic surfaces and complex morphology suggested to Cairns-Smith an environment not unlike living material. He observed that defects in crystals could supply multiple, stable alternative configurations which can store and process information much like modern computers. Crystal defects which can move are very similar to primitive cellular automata, dynamic patterns occurring in lattice neighborhoods capable of computing. Cairns-Smith reasoned that certain clays proliferated with their replicating defects (representing information) acting as primordial genetic information and proving useful in alignment of amino acids and protein synthesis. As more efficient organic synthesis developed, Cairns-Smith argues that clay machinery became expendable and was jettisoned in favor of a new biotechnology—DNA and RNA.

Whether or not Cairns-Smith's clay theory is correct, he demonstrates the capacity for information storage in crystal defects. Perfectly ordered crystals which are repetitive and homogeneous have no capacity for information storage but are also extremely rare or do not exist at all. Real crystals have defect structures superimposed. Simply to be finite-to have a shape and size-is a defect, but many other features are almost invariably present. Units are often missing or are replaced by others, and sections of the crystal structure may be misaligned in various ways. While such features can be very small in scale, they provide real crystals with a large potential capacity for information. Certain classes of crystals might have defect structures that replicate as the crystal grows by having the right combination of structural characteristics, growth patterns and cleavage properties. Cairns-Smith (1982) concludes by posing a challenge to discover crystal genes of various materials. He asks:

... Imagine doing experiments with crystals that could evolve, setting them problems-applying selection pressures-and seeing how they cope. This would be an interesting thing to do any way whatever the crystals are made of. We would soon find out whether mineral versions of replicating systems are plausible although we might lose interest in our ultimate ancestors once we had in our hands the first organisms of another kind: the first organisms of our own contriving.

The implications of Cairns-Smith's ideas include the possibility of alternative life forms from propagating crystalline structures and a suggestion that DNA and RNA are not necessarily the only carriers of genetic information. This is in concert with a demystification of life in general. At an international meeting on the origins of life (Eckholm, 1986), Dr. Cyril Ponnamperuma of the University of Maryland suggested "the division between life and nonlife is perhaps an artificial one." He views the animate and inanimate as lying on a continuum both over evolutionary time and among currently existing systems. On such a scale prions, proteinoids, and some viruses would lie near the middle as might some ancient unknown protocell that became the ancestor of life on earth. To speak of advanced chemistry rather than divine creation is certain to disturb religious fundamentalists. Equating life with oscillations in crystals does have an almost biblical resonance, and narrows the conceptual gap between life molecules and technological devices.

Regardless of the precise environment in which life-related molecules emerged, other major questions include whether the carriers of genetic information, DNA and RNA, preceded proteins whose amino acid sequences they determine, or whether proteins, including enzymes and structural elements seemingly necessary for genetic replication, came first. Thus a chicken (DNA, RNA) vs egg (protein) conundrum regarding life's origins has developed. A primary information flow from nucleic acid to protein (chicken before egg) was a "central dogma" in molecular biology. Fox and Dose (1972) challenged this conviction by proposing an alternative evolutionary continuum from the beginning of the material cosmos to the first organisms. In their "egg before chicken" view the sequence of life's organization was from interstellar gases, to amino acids, to polymers, to organized microsystems. As evidence they cite the self organization of amino acids and proteins into "proteinoid" microspheres which can establish communication links and perform other "life-like" functions. Evidence for a "chicken before egg" view has been found by chemist Leslie Orgel and colleagues (Schwarz and Orgel, 1985) of the Salk Institute in La Jolla, California. They recently discovered a 15 nucleotide long DNA-like molecule that had formed spontaneously from much simpler carbon compounds and zinc in the absence of living cells or protein enzymes. Other work has suggested that RNA can function enzymatically to facilitate reactions and the bulk of recent findings leans towards the primacy of nucleic acids.

Manfred Eigen (1971) views this cause/effect problem as a "closed loop" whose original starting point is unimportant. What is important, in Eigen's view, is how molecular self-organization occurs from random events and feedback which lead to macroscopic functional organization, self-reproduction, selection, and evolution: "hypercyles." Eventually, according to Eigen, such systems can escape the prerequisites of their origin and change the environment to their own advantage.

A view of primary nucleic acid (chicken) organization in a primordial aqueous environment (soup) is summarized and elaborated in the writings of biologist Lynn Margulis and Dorion Sagan (1986). They view as logical the facts that RNA and DNA spontaneously formed in the shallow seas of early earth and also became able to self replicate perfect copies of themselves. They liken RNA molecules to half of an open zipper. With the proper complementary ingredients, the missing half forms by using the existing RNA as a template.

Margulis and Sagan (1986) note:

An RNA molecule can do more than copy itself. The sequence of its nucleotides can also serve as a signal for a neighboring strand of RNA to attach the amino acids in its environment, thus forming a portion of a protein which will in turn accelerate the matching of other RNA molecules producing more RNA, more protein like fragments, and so on.

This suggests that at a critical level of evolution, nonlinear accelerations occurred due to the level of associative inter-relationships among evolving molecules. This can help explain how biological systems can produce "order from chaos," and thus apparently violate the second law of thermodynamics which states that ordered systems must dissipate towards disorder.

Margulis and Sagan describe the following scenario for the development of life on earth. RNA formation in the primordial soup led to the evolution of double stranded DNA eons later. This in turn allowed the full variety of life-as manifest in the richness of structures and functions of proteins and other macromolecules. Survivability was enhanced by enclosure of dynamic molecules inside membranes, apparently formed when phospholipid hydrocarbons aligned and, because they were charged on one end, formed spherical droplets which sequestered biomolecules. With the advent of ion channels and other membrane proteins came regulatory voltages and a discrete microcosm: the "prokaryotic" bacterial cell.

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