NOTICE: Citizendium is still being set up on its newer server, treat as a beta for now; please see here for more.
Citizendium - a community developing a quality comprehensive compendium of knowledge, online and free. Click here to join and contribute—free
CZ thanks our previous donors. Donate here. Treasurer's Financial Report -- Thanks to our content contributors. --

Origin of life/Bibliography

From Citizendium, the Citizens' Compendium
Jump to: navigation, search
This article is developing and not approved.
Main Article
Talk
Related Articles  [?]
Bibliography  [?]
External Links  [?]
Citable Version  [?]
Gallery [?]
Video [?]
Signed Articles [?]
 
A list of key readings about Origin of life.
Please sort and annotate in a user-friendly manner. For formatting, consider using automated reference wikification.

Books

  • Lane, Nick. The Vital Question: Energy, Evolution, and the Origins of Complex Life (Kindle Locations 4094-4101). W. W. Norton & Company. Kindle Edition.
    • From Amazon: The Earth teems with life: in its oceans, forests, skies and cities. Yet there’s a black hole at the heart of biology. We do not know why complex life is the way it is, or, for that matter, how life first began. In The Vital Question, award-winning author and biochemist Nick Lane radically reframes evolutionary history, putting forward a solution to conundrums that have puzzled generations of scientists. For two and a half billion years, from the very origins of life, single-celled organisms such as bacteria evolved without changing their basic form. Then, on just one occasion in four billion years, they made the jump to complexity. All complex life, from mushrooms to man, shares puzzling features, such as sex, which are unknown in bacteria. How and why did this radical transformation happen? The answer, Lane argues, lies in energy: all life on Earth lives off a voltage with the strength of a lightning bolt. Building on the pillars of evolutionary theory, Lane’s hypothesis draws on cutting-edge research into the link between energy and cell biology, in order to deliver a compelling account of evolution from the very origins of life to the emergence of multicellular organisms, while offering deep insights into our own lives and deaths. Both rigorous and enchanting, The Vital Question provides a solution to life’s vital question: why are we as we are, and indeed, why are we here at all?
  • Oparin AI. (1953) The Origin of Life. New York: Dover Publications.
    • From Amazon: Analyzes three early theories explaining the origins of life on earth and expands his own biochemical explanation of the formation of living substances.
  • Oparin AI, Synge A. (1957) The Origin of Life on the Earth. New York: Academic Press Inc..
  • Cairns-Smith AG. (1990) Seven Clues to the Origin of Life: A Scientific Detective Story. New York: Cambridge University Press, ISBN 13-978-0-521-39828-2; 10-0-521-39828-2.
  • Rosen R. (1991) Life Itself: A Comprehensive Inquiry Into The Nature, Origin, And Fabrication Of Life. New York: Columbia University Press, ISBN 0-231-07565-0.
  • Brack A. (1998) The molecular origins of life: assembling pieces of the puzzle. Cambridge: Cambridge University Press, ISBN 0521564123.
  • Smith JM, Szathmary E. (1999) The Origins of Life: From the Birth of Life to the Origin of Language. New York: Oxford University Press.
  • Kauffman SA. (2000) Investigations. Oxford: Oxford University Press, ISBN 019512104X (cloth : acid-free paper).
  • Ganti T, Griesemer Jc, Szathmary Ec. (2003) The Principles of Life. New York: Oxford University press, ISBN 9780198507260.
  • Hazen RM. (2005) Genesis: The Scientific Quest for Life's Origin. Washington,DC: Joseph Henry Press, ISBN 0309094321.

Journal articles

  • Clémentine Gibard, Subhendu Bhowmik, Megha Karki, Eun-Kyong Kim, Ramanarayanan Krishnamurthy. Phosphorylation, oligomerization and self-assembly in water under potential prebiotic conditions. Nature Chemistry, 2017; DOI: 10.1038/nchem.2878.
    • Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with

subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)—a plausible prebiotic agent produced from trimetaphosphate—efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent. Significantly, higher-order structures (oligonucleotides, peptides and liposomes) are formed under the same phosphorylation reaction conditions. This plausible prebiotic phosphorylation process under similar reaction conditions could enable the systems chemistry of the three classes of (pre)biologically relevant molecules and their oligomers, in a single-pot aqueous environment.


  • Maheen Gull, Mike A. Mojica, Facundo M. Fernández, David A. Gaul, Thomas M. Orlando, Charles L. Liotta, Matthew A. Pasek. Nucleoside phosphorylation by the mineral schreibersite. Scientific Reports, 2015; 5: 17198 DOI:10.1038/srep17198


  • Anja Spang, Jimmy H. Saw, Steffen L. Jørgensen, Katarzyna Zaremba-Niedzwiedzka, Joran Martijn, Anders E. Lind, Roel van Eijk, Christa Schleper, Lionel Guy, Thijs J. G. Ettema. Complex archaea that bridge the gap between prokaryotes and eukaryotes (full-text free). Nature, 2015. DOI:10.1038/nature14447
    • Abstract: The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.


Abstract: Recent developments in microbiology, geophysics and planetary sciences raise the possibility that the planets in our solar system might not be biologically isolated. Hence, the possibility of lithopanspermia (the interplanetary transport of microbial passengers inside rocks) is presently being re-evaluated, with implications for the origin and evolution of life on Earth and within our solar system. Here, I summarize our current understanding of the physics of impacts, space transport of meteorites, and the potentiality of microorganisms to undergo and survive interplanetary transfer.


  • Pross, A. (2003), "The driving force for life's emergence: kinetic and thermodynamic considerations", J Theor Biol 220 (3): 393–406, DOI:10.1006/jtbi.2003.3178 [e]
    • Abstract: The principles that govern the emergence of life from non-life remain a subject of intense debate. The evolutionary paradigm built up over the last 50 years, that argues that the evolutionary driving force is the Second Law of Thermodynamics, continues to be promoted by some, while severely criticized by others. If the thermodynamic drive toward ever-increasing entropy is not what drives the evolutionary process, then what does? In this paper, we analyse this long-standing question by building on Eigen's “replication first” model for life's emergence, and propose an alternative theoretical framework for understanding life's evolutionary driving force. Its essence is that life is a kinetic phenomenon that derives from the kinetic consequences of autocatalysis operating on specific biopolymeric systems, and this is demonstrably true at all stages of life's evolution — from primal to advanced life forms. Life's unique characteristics — its complexity, energy-gathering metabolic systems, teleonomic character, as well as its abundance and diversity, derive directly from the proposition that from a chemical perspective the replication reaction is an extreme expression of kinetic control, one in which thermodynamic requirements have evolved to play a supporting, rather than a directing, role. The analysis leads us to propose a new sub-division within chemistry — replicative chemistry. A striking consequence of this kinetic approach is that Darwin's principle of natural selection: that living things replicate, and therefore evolve, may be phrased more generally: that certain replicating things can evolve, and may therefore become living. This more general formulation appears to provide a simple conceptual link between animate and inanimate matter.


  • Meredith Root-Bernstein, Robert Root-Bernstein. 2015 The ribosome as a missing link in the evolution of life. Journal of Theoretical Biology, 2015; 367: 130 DOI: 10.1016/j.jtbi.2014.11.025



    • Abstract:
    • To understand the emergence of Darwinian evolution, it is necessary to identify physical mechanisms that enabled primitive cells to compete with one another.
    • Whereas all modern cell membranes are composed primarily of diacyl or dialkyl glycerol phospholipids, the first cell membranes are thought to have self-assembled from simple, single-chain lipids synthesized in the environment. We asked what selective advantage could have driven the transition from primitive to modern membranes, especially during early stages characterized by low levels of membrane phospholipid.
    • Here we demonstrate that surprisingly low levels of phospholipids can drive protocell membrane growth during competition for single-chain lipids. Growth results from the decreasing fatty acid efflux from membranes with increasing phospholipid content.
    • The ability to synthesize phospholipids from single-chain substrates would have therefore been highly advantageous for early cells competing for a limited supply of lipids.
    • We show that the resulting increase in membrane phospholipid content would have led to a cascade of new selective pressures for the evolution of metabolic and transport machinery to overcome the reduced membrane permeability of diacyl lipid membranes. The evolution of phospholipid membranes could thus have been a deterministic outcome of intrinsic physical processes and a key driving force for early cellular evolution.


  • Hanczyc MM, Toyota T, Ikegami T, Packard N, Sugawara T. (2007) Fatty Acid Chemistry at the Oil-Water Interface: Self-Propelled Oil Droplets. J Am Chem Soc 129:9386-91. | Abstract/Full-Text.
    • Conclusion: We have demonstrated a self-propelled oil droplet system based on fatty acid chemistry. This system exhibits symmetry breaking with four characteristics: directional internal convective flow, directional external water flow, directional product release, and a self-generated pH gradient. The simple ingredients—oil with acid-producing precursor and alkaline water with surfactant—work in concert to produce sustained autonomous motion. The supramolecular structure itself contains the chemistry that fuels its movement. The system produces not only more surfactant but protons resulting in acidification of the environment immediately surrounding the oil droplet. The droplet successfully moves away from this waste product into fresh unmodified alkaline solution and even displays a primitive form of chemotaxis. Although this mechanism of movement is unlike mechanisms of motility employed by natural cellular life, directed motion by convection may be useful in an artificial cell context in the avoidance or delay of chemical equilibrium.
    • See also: In the beginning... was Pac-Man: Simple oil drops show that if you get the conditions right, basic life may emerge almost fully formed. New Scientist 5 March 2011.
  • Tracey A. Lincoln and Gerald F. Joyce, (2009) Self-Sustained Replication of an RNA Enzyme. Science 27 February 2009:ol. 323. no. 5918, pp. 1229 - 1232. DOI: 10.1126/science.1167856



  • Morowitz,H.J.; Srinivasan,V.; Smith,E. (2010) Ligand field theory and the origin of life as an emergent feature of the periodic table of elements. Biological Bulletin 219:1-6.
    • Abstract: The assumption that all biological catalysts are either proteins or ribozymes leads to an outstanding enigma of biogenesis-how to determine the synthetic pathways to the monomers for the efficient formation of catalytic macromolecules in the absence of any such macromolecules. The last 60 years have witnessed chemists developing an understanding of organocatalysis and ligand field theory, both of which give demonstrable low-molecular-weight catalysts. We assume that transition-metal-ligand complexes are likely to have occurred in the deep ocean trenches by the combination of naturally occurring oceanic metals and ligands synthesized from the emergent CO(2), H(2), NH(3), H(2)S, and H(3)PO(4). We are now in a position to investigate experimentally the metal-ligand complexes, their catalytic function, and the reaction networks that could have played a role in the development of metabolism and life itself.
    • See also: Transition metal catalysts could be key to origin of life, scientists report. PhysOrg.com September 3, 2010.

Blogs

News reports related to published research