Origins II: Self Assembly to Darwinian Evolution


  1. Self-Assembly

    1. General difficulties

      1. The duality of structure (metabolism, physiology) and information transfer (genetics, reproduction)
      2. Lack of a single organizing natural theory behind this process: we are between the realm of the biological and the physical world
        1. Force vitale problem: there can be no special cases for biological systems. Likewise, the recognition of irreducible complexity in a cellular or biomolecular system does not require divine intervention as a causal explanation.
        2. Physical laws based on the mathematical notion of metric spaces, but biological systems do not all fall into this category. Biolgical structures exist in time, but also in multidimensional, non-metric state space.
        3. Physical laws usually apply independently of the history of the individuals involved (statistical mechanics) but in evolving systems, prior conditions are very important. Life has a history, and prior history is essential to explain any particular state.
        4. Biological evolution is non-deterministic; physical laws are fundamentally about predicting the state of a system in time, i.e. with a deterministic outcome.
      3. There are no homologues of in-between states of "living" in living systems.
      4. Chemists are used to systems in equilibrium or steady state in aqueous solution; biological chemistry involves non-equilibrium chemistry with colloids, sols and gels that are not in simple dilute aqueous solution.


    2. Is there a minimal life system?

      1. Anærobic metabolism can support an entire ecosystem
      2. Heterotrophy comes first if a supply of abiological food exists
      3. Must include a full ecology, be a true ecosystem
      4. Energy flow modeled within terrestrial constraints, i.e. it must be realistic for conditions that exist on Earth


    3. Model systems

      1. Artifical life & cellular automata
      2. Systems theory: An attempt to put together, under one academic roof, a unified collection of thought and understanding of complexity in Nature. Biology, being generally complex, anyway, is one of the more important elements in General Systems Theory.
      3. Protobiont chemical systems
        1. Fox's proteinaceous microspheres
        2. Oparin's coacervates
        3. Lipid micelles


    4. The self-assembly model

      1. Spontaneous assembly of bilipid membranes which form vesicles [based on thermodynamically stable conditions]
      2. Enzymatic activity internally to the vesicle builds a system of chemical activity that is greater inside than out. This leads to the creation pathways that control energy and require "food" molecules from the surrounding environment
      3. Internal physiology generates growth
      4. Independent (?) acquisition of a genetic mechanism to control growth, rebuild the protocell and distribute contents to offspring
      5. Ability to evolve (see below)


    5. Ribozymes and the duality problem

      1. The enzyme paradox: Cells need enzymes to moderate all chemical reactions and allow thermodynamically unfavorable reactions to take place. Enzymes are composed of proteins. These enzymes are necessary for the production of all proteins through the mechanisms of transcription and translation of DNA.
      2. Ribozymes are segments of RNA that can act as an enzyme, i.e. catalyze reactions.
      3. Ribozymes, therefore could pergaps have a dual function in being both an infornation carrier and a reaction moderator.


  2. Darwinian Evolution

  3. In biological evolution, the term "evolution" refers to the processes that generate heritable change. That is the condition whereby changes in the genome are passed on from generation to generation. This of course assumes the preexisting state of an up and running biological ecosystem. There is a fundamental duality to this system in that genotype alternates with phenotype and both are required if evolution is to occur.

    1. The process of Darwinian Evolution

      1. Step 1: generation of heritable variation in the genotype (genetic material, aka DNA).
        1. Mutation
        2. Chromosomal changes
        3. Hybridization (many plants create new species this way)
        4. Symbiosis
      2. Step 2: Natural Selection
        1. Genetic variation is expressed in the phenotype as real changes in morphology, physiology, behavior, etc.
        2. These modified forms are subjected to random elements of survival and the production of offspring within an "environment"
        3. Successive generation of modified offspring results in the establishment on new forms which now have the appearance of "adaptation" to their environment in response to Natural Selection
    2. The Pattern of Evolution: Systematics

      1. By tracing the pattern of relationships, we piece together evolutionary history of speciation events
      2. That pattern is intertwined with Earth history and environmental change as well. The interactive components of change between biology and Earth history is called environmental evolution


Web Resources


Other Resources

  • von Bertalanffy, L. 1968. General systems theory: Foundations, development, applications. New York: Braziller.
  • Whitesides, G.M.1995. Self-assembling Materials. Scientific American, September 1995:146-149.

Update 21 September 2004