Chapter 16.  The Origins of Life and Precambrian Evolution [To be updated]

• Current origin of life research programs are completely materialistic -- contrast the vitalism pervasive in 19th century thought.  Darwin speaks of the "spark" introduced by the Creator, today "it's all chemistry".
• Some problems and issues:
• What was the environment like when life arose?
• What is life and how is it to be demarcated from non-life?
• How is the first cells arise?
• Immense time spans are involved: earth is about 4 BY old, the first fossils are about 3.5 BY old (but there are geochemical signs of life dated to 3.8BYA).
• The fossil record is incomplete, worsens with age, expected to be non-existent for non-cellular life.
• How many times did life arise?  Are all extant organisms descended from a single ancestor or from a community of ancestors?
• Where did life arise?  On Earth or on other planets?
• The "chicken and the egg" problem:   Nucleic acids contain information for the synthesis of proteins, but nucleic acids require proteins (enzymes) for their replication.  So which came first?
• The RNA World.
• Some RNA molecules have catalytic activity - "ribozymes".
• RNA must be a very ancient molecule - it is universally present in cells, rRNA is one of the the most conserved molecules known, tRNA molecules are universally required adapter molecules.
• ATP and GTP are universal energy-carrying molecules, and these are also components of RNA.
• The RNA World - hypothesis that the first "organisms" were naked RNA molecules with the ability to replicate.  Evidence that this is a plausible hypothesis:
• RNA molecules can evolve - Spiegelman 1967 demonstrated natural selection in populations of Qbeta RNA molecules (Qbeta is a bacteriophage virus).  Provided with pool of nucleotides, Qbeta RNA replicase and ATP, naked RNA molecules evolve toward shorter chain length, faster replication.  They can also evolve resistance to ethidium bromide (poison which binds to RNA, preventing replication).
• Natural selection can increase catalytic activity of ribozymes - Beaudry and Joyce 1992 demonstrated this with the Tetrahymena ribozyme.  Experiment was designed so that RNA molecules with better catalytic activity are more likely to be replicated than those without.  After several "generations" mean catalytic activity of the ribozyme population had increased.  See Figs. 14.4, 15.4.
• Ribozymes can catalyze formation of phosphodiester bonds - Bartel and Szostak (1993).  This would be a critical step in the self-replication of RNA molecules since RNA nucleotides are connected to each other by the formation of phosphodiester bonds.  See Fig. 14.6
• How to get to the RNA world?
• Oparin-Haldane model for the origin of life includes three steps: synthesis of organic molecules from inorganic molecules, polymerization of organic molecules into macromolecules (nucleic acids, proteins, lipids, carbohydrates), assembly of membrane-bound cells.
• Step 1: synthesis of simple organic molecules:
• Miller-Urey experiment (1953) showed that this was not as had as had been thought.  Provided a reducing atmosphere of methane, ammonia and hydrogen and energy in the form of electric sparks, organic molecules (e.g. amino acids form).  Since then, variations of this set-up have produced rich array of organic compounds: nucleotides, sugars, amino acids.  But there are many problems remaining ...
• Was the early atmosphere sufficiently reducing?  An oxidizing atmosphere would have resulted in destruction of newly formed organic molecules.
• Stereoisomerism:  How did it happen that life utilizes L forms of molecules only?  Miller-type synthesis experiment yield L and D forms in about equal proportions.
• Step 2: assembly of polymers:
• This present problems in a "prebiotic soup": molecules collide at random angles so that bond formation occurs rarely, hydrolysis can break newly formed bonds.
• Clay and other mineral surfaces are charged and can catalyze polymerization:  the prebiotic "pizza" rather than "soup".
• Step 3: formation of membranes:
• Polarity of phospholipid molecules encourages formation of membrane-like structures on films of water and on clay surfaces.
• The phylogenetic approach to reconstructing the history of life uses degree of correspondence between genes to decide degree of relatedness between organisms.
• rRNA gene (the one coding for small subunit ribosomal RNA) is a good candidate for this approach: it is present in all organisms, it is highly conserved, it has the same function in all organisms.
• This leads to a completely new view of organic diversity (Fig. 14.16).  There are three "domains": Bacteria, Archaea, Eucarya.  So much for the "Two Kingdom" (animals/plants) or "Five Kingdom" (animals/plants/fungi/protista/monera) systems!
• Contrary to expectation, phylogenies based on different genes are not always congruent (see Fig 14.20).  This suggests that lateral gene transfer occurred early and that extant organisms have multiple common ancestors (this is reflected in the network near the base of the tree in Fig. 14.14).
• When did major branching events occur? Earliest date = 4.4-3.85 BYA, latest date = 3.5-2 BYA.  These dates come from fossils and paleogeochemistry, not molecular data.
• The origin of organelles and the Eucarya
• Margulis (1970) proposed that eukaryotes had evolved via symbiosis -- this is the endosymbiotic theory of origin of mitochondria and chloroplasts.  This has become the standard theory and is supported by multiple lines of evidence:
• Structural similarities between chloroplasts and cyanobacteria, mitochondria and bacteria.
• Organelle genomes (they have them!) contain some of the genes required for organelle assembly and function.
• rRNA phylogenies place chloroplasts and mitochondria with bacteria, not eukaryotes (Fig. 14.24).