Origin of life: Difference between revisions

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:*Blackmond 2011<ref name=blackmond2011> Blackmond DG. (2011) [http://dx.doi.org/10.1098/rstb.2011.0130 The origin of biological homochirality]. ''Philos Trans R Soc Lond B Biol Sci'' 366:2878-84.
:*Blackmond 2011<ref name=blackmond2011> Blackmond DG. (2011) [http://dx.doi.org/10.1098/rstb.2011.0130 The origin of biological homochirality]. ''Philos Trans R Soc Lond B Biol Sci'' 366:2878-84.
:**Abstract: The single handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt over 150 years ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. Mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both, are discussed in the context of experimental studies in autocatalysis and in the phase behaviour of chiral molecules</ref>
:**Abstract: The single handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt over 150 years ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. Mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both, are discussed in the context of experimental studies in autocatalysis and in the phase behaviour of chiral molecules</ref>
 
:*[http://www.sciencedaily.com/releases/2012/01/120131175629.htm?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+sciencedaily%2Ffossils_ruins%2Forigin_of_life+%28ScienceDaily%3A+Fossils+%26+Ruins+News+--+Origin+of+Life%29 Scientists Prove Plausibility of New Pathway to Life's Chemical Building Blocks]
:**"ScienceDaily (Jan. 31, 2012) — For decades, chemists considered a chemical pathway known as the formose reaction the only route for producing sugars essential for life to begin, but more recent research has called into question the plausibility of such thinking. Now a group from The Scripps Research Institute has proven an alternative pathway to those sugars called the glyoxylate scenario, which may push the field of pre-life chemistry past the formose reaction hurdle."


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In a scientific context, in order to discuss, much less discover, the origin of life, we must first answer the question, "What is Life?" We can pose that question more coherently by asking, "What essential processes underpin the activity of living?" Knowing the fundamental universal physico-chemical processes that underpin the activity of all living systems gives us a starting point for making observations, generating hypotheses, and performing experiments in the search for life’s origin — for those processes somehow must have given rise to the earliest cells, the basic building blocks and working units of all living things on Earth. We must discover the characteristics of the earliest cells from which all current living things descended.

Because we must look backward to a time nearly four billion years ago, we will find little, but not nothing,[1]  in the way of remains to examine. We can hypothesize, and submit those hypotheses to existing knowledge of earth's early conditions and to experiments attempting to reproduce those conditions. We can narrow our hypotheses and search-paths by dissecting out the most basic and essential physico-chemical processes common to all known living things — the universal biophysics,[2]   biochemistry[3]  and metabolism[4]  of living things — because as conserved core processes they have the greatest probability of embryonic status.

We search for the origin of a system we recognize as living in virtue that it has the informational content and information-processing ability to remain as a spatially compartmentalized far-from-equilibrium near-steady-state self-organized dynamical system of hierarchical robust modular molecular networks, where the networks operate autonomously in their own behalf, to offset responses to perturbations, adapt to changing conditions, and facilitate the system's reproducing itself. We search for the origin of a thermodynamically open system enabled by influx of energy and matter and by a more than compensatory efflux of waste (disorder), which thereby complies with the second law of thermodynamics and permits sustaining and exploiting a dynamically organized state far from the equilibrium state of randomness. Finally, we search for the origin of a system capable, through its self-reproductive ability, of participating in the evolutionary processes[5],[6]  that enable transgenerational evolution of the species to which it belongs, adapting to changing environments.

Scientists do not know the origin of life on Earth. They do have pieces of the puzzle, however. Decades of research have established certain constraints that disallow unbounded speculation. Still, many conflicting plausible scientific scenarios abound.

The history of scientific 'origins of life' thinking

"A quantum recipe for the origin of life"

Theoretical physicist, cosmologist, astrobiologist and science popularizer, Paul Davies,[7] has imagined a "quantum recipe" for the origin of life:[8]

To take up [physicist Erwin] Schrödinger's suggestion [....that quantum mechanics, or some variant of it, would soon solve the riddle of life....],[9] a radical solution to the problem, 'What is life?' could be that quantum mechanics enabled life to emerge directly from the atomic world, without the need for complex intermediate chemistry. Life must have a chemical basis: organic molecules provide the hardware for biology. But what about the software?[8]

The software, Davies argues, resides in quantum information. "....to get life started all you need is to replicate information."[8] He argues that, at the quantum level of reality, information processing can proceed much more rapidly, by comparison presumably with chemical reactions, can achieve gains in information processing performance through such quantum capabilities as tunneling, superposition, and entanglement. He proceeds to conjecture on the replication of the information in an atomic system through a series of interactions, the information in the systems residing possibly in binary form "....making use of the spin orientation of an electron or atom for example."[8] He asserts that quantum mechanics can thus make discrete 'genetic' information.

Davies refers to his conjectured quantum information replicator as "atomic Adam" and speculates on the best environments where some such "atomic Adams" might exist. He argues that when a population of such quantum information replicators arises, expect variation in the fidelity of replication because of the quantum uncertainty principle. Given variation, an evolution of the information by means of darwinian-wallacean natural selection, or survival of the fittest replicators, might occur in the prevailing environment. "....and the great darwinian game could begin."[8]

Davies then asks, given the reality of quantum information replicators in a darwinian reproductive-type domain, how 'organic' life arose? He supposes that "At some stage, quantum life could have co-opted large organic molecules for back-up memory." How that 'great leap' might have occurred Davies offers no plausible description, except to say that information in one medium does not preclude translation to other media. Not that the medium of organic chemistry strays far from the underpinnings of its quantum chemical medium.

Once that transfer of information occurs — from quantum to chemical information — expect a loss in rapidity of information processing, but also expect greater stability in the organic molecules, and greater versatility, and greater complexity. Those compensations might ensure the dominance of organic living systems, given natural selection, and its enabling of the exploitation of diverse environments.

Davies seems to worry most about the issue of complexity of quantum life:

How complexity emerges in quantum systems is a subject still in its infancy, but the principles involved could be illuminated by applying algorithmic complexity theory to quantum information theory.[8]

We might ask the question how much complexity must precede the transfer of quantum information to organic molecular information, given the potential for natural selection, and other evolutionary forces — not to mention autopoiesis — to enable the emergence of organic complexity?


Pre-biotic chemistry and the origin of organic molecules

Pre-biotic chemical evolution as prelude to origin of living systems. See, for example:

  • Dyson 1982[10]
  • Eigen and Schuster 1982 [11]
  • Post 1990[12]
  • Davies 2000[13]
  • Galimov 2004[14]
  • Bradley 2004[15]
  • Danchin 2007[16]
  • Sayer 2006[17]
  • Deamer 2006[18]
  • Szathmary 2006[19]
  • Phil Berardelli 2008[20]
  • Robinson R (2005)[21]
  • Protocells: Bridging Nonliving and Living Matter. Edited by Steen Rasmussen, Mark A. Bedau, Liaohai Chen, David Deamer, David C. Krakauer, Norman H. Packard and Peter F. Stadler. ISBN 978-0-262-18268-3.
  • Follmann,H.; Brownson,C. (2009) Darwin's warm little pond revisited - from molecules to the origin of life. Naturwissenschaften 96(11):1265-1292. In this review, we have concentrated on experimental and theoretical research published over the last two decades, which has added a wealth of new details and helped to close gaps in our previous understanding of this multifaceted field.
  • Life did not begin on Earth.[22]
  • Blackmond 2011[23]
  • Scientists Prove Plausibility of New Pathway to Life's Chemical Building Blocks
    • "ScienceDaily (Jan. 31, 2012) — For decades, chemists considered a chemical pathway known as the formose reaction the only route for producing sugars essential for life to begin, but more recent research has called into question the plausibility of such thinking. Now a group from The Scripps Research Institute has proven an alternative pathway to those sugars called the glyoxylate scenario, which may push the field of pre-life chemistry past the formose reaction hurdle."


The RNA World


References

Citations

  1. ↑ Hazen RM. (2005) Genesis: The Scientific Quest for Life's Origin. Washington,DC: Joseph Henry Press. ISBN 0309094321
  2. ↑ Schneider ED, Sagan D (2005) Into the Cool: Energy Flow, Thermodynamics, and Life. Chicago: The University of Chicago Press. ISBN 0-226-73937-6 Chapter Excerpts and Reviews
  3. ↑ The universal nature of biochemistry, by Norman R. Pace
  4. ↑ Smith E., Morowitz HJ. (2004) Universality in intermediary metabolism. Proc Natl Acad Sci U S A 101:13168-13173. PMID 15340153 Full-Text
  5. ↑ Jablonka E, Lamb MJ (2005) Evolution in Four Dimension: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life. Cambridge: The MIT Press
  6. ↑ Reid RGB. (2007) Biological Emergences: Evolution by Natural Experiment. A Bradford Book, Cambridge. ISBN 0-262-18257-2
  7. ↑ Paul Davies Website
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 Davies P. (2005) A Quantum Recipe for Life. Nature 437:819.
    • From Article: [At the time of this article:] Paul Davies is a physicist in the Australian Centre for Astrobiology, Macquarie University, Sydney, and author of The Origin of Life (Penguin, 2003)
  9. ↑ Note: Not a direct quote from Schrodinger's book.
  10. ↑ Dyson F (1982) A model for the origin of life. See Dyson (1982) J Mol Evol 18:344-350
  11. ↑ Eigen M, Schuster P. (1982) Stages of Merging Life: Five Principles of Early Organization.' 'Journal of Molecular Evolution' 19:47-61.
      • Five principles underlie the evolution of the genetic language: the formation of stereo regular heteropolymers, the selection through self-replication, evolution of quasispecies towards optimal structures, regulated cooperation between competitors through catalytic hypercycles and evaluation of translational products through compartmentalization.
  12. ↑ Post RL. (1990) The origin of homeostasis in the early earth. Journal of Molecular Evolution 31:257-64 Summary and Link to Full-Text.
  13. ↑ Davies P. The Fifth Miracle: The Search for the Origin and Meaning of Life (Paperback) Simon & Schuster ISBN-10: 068486309X ISBN-13: 978-0684863092
  14. ↑ Galimov EM. (2004) Phenomenon of life: between equilibrium and non-linearity. Orig.Life Evol Biosph. 34:599-613.
  15. ↑ Bradley WL. (2004) Information, Entropy, and the Origin of Life. In: Dembski WA, Ruse M., editors. Debating Design: From Darwin to DNA. New York: Cambridge University Press. ISBN 0521829496. | Google Books preview, Bradley chapter missing pages.
  16. ↑ Danchin A, Fang G, Noria S. (2007) The extant core bacterial proteome is an archive of the origin of life. Proteomics 7:875-889 PMID 17370266
  17. ↑ Sayer RM. (2006) Self-organizing proto-replicators and the origin of life. Biosystems PMID 17014952
  18. ↑ Deamer D, Singaram S, Rajamani S, Kompanichenko V, Guggenheim S. (2006) Self-assembly processes in the prebiotic environment. Philos Trans R Soc Lond B Biol Sci 61:1809-1818 PMID 17008220
  19. ↑ Szathmary E. (2006) The origin of replicators and reproducers. Philos Trans R Soc Lond B Biol Sci 361:1761-1776 PMID 17008217
  20. ↑ Phil Berardelli (2008) Did Volcanoes Spark Life on Earth? ‘’ScienceNOW Daily News’’, 16 October 2008.
  21. ↑ Robinson R. (2005) Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks. PLoS Biol 3(11): e396 Published: November 15, 2005. Copyright: © 2005 Richard Robinson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  22. ↑ Joseph R, Schild R. (2010) Biological Cosmology and the Origins of Life in the Universe. Journal of Cosmology 5:1040-1090.
      • From Abstract: The confluence of evidence from genetics, microbiology, astrobiology, and astrophysics indicates that life in the Milky Way galaxy began over 10 billion years ago, in nebular clouds. Given the trillions upon trillions of galaxies which exist in this Hubble length (observable) universe, and the trillions of trillions of supernovas which must have taken place in these galaxies collectively, and thus the innumerable stellar and nebular clouds filled with all the ingredients necessary for life, it can be deduced that life would have been created, independently, perhaps in numerous galaxies, including the Milky Way long before our planet was fashioned. The cosmos may be awash with every conceivable form of life. It can be predicted that every planet orbiting a star in every galaxy in the cosmos might have been contaminated with life and that life would flourish, diversify, and then evolve into increasingly complex, sentient and intelligent animals on worlds which orbit within the habitable zone of their sun. This would mean that intelligent beings may have evolved on billions of planets and may have reached our own level of neurological and cognitive development billions of years before Earth became a twinkle in god's eye.
  23. ↑ Blackmond DG. (2011) The origin of biological homochirality. Philos Trans R Soc Lond B Biol Sci 366:2878-84.
      • Abstract: The single handedness of biological molecules has fascinated scientists and laymen alike since Pasteur's first painstaking separation of the enantiomorphic crystals of a tartrate salt over 150 years ago. More recently, a number of theoretical and experimental investigations have helped to delineate models for how one enantiomer might have come to dominate over the other from what presumably was a racemic prebiotic world. Mechanisms for enantioenrichment that include either chemical or physical processes, or a combination of both, are discussed in the context of experimental studies in autocatalysis and in the phase behaviour of chiral molecules
  24. ↑ Koonin EV. An RNA-making reactor for the origin of life. PNAS 2007;104:9105-6
  25. ↑ Baaske P, Weinert FM, Duhr S, Lemke KH, Russell MJ, Braun D. Extreme accumulation of nucleotides in simulated hydrothermal pore systems. PNAS 2007;104:9346-51.

External links

Further reading

  • Forterre P (2006) Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: A hypothesis for the origin of cellular domain PNAS 103:3669-3674
  • Davies P. (2000) The Fifth Miracle: Search for the Origin and Meaning of Life. Simon & Schuster ISBN 978-0684863092
  • From The New York Times Book Review, by Lee Smolin: "If you are going to read only one book on the origin of life, seriously consider this one. From Scientific American: "His thesis is that 'the first terrestrial organisms lived deep underground, entombed within geothermally heated rocks in pressure-cooker conditions.' Davies also looks at the theories that life began by chemical assembly in a watery medium and that it came to the earth from space in the form of already viable microbes--the panspermia hypothesis.

See also

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