The Next Three Lectures Will Cover

1
MOLECULAR EVOLUTION MB437 and ADVANCES IN
MOLECULAR EVOLUTION MB537 Marcie McClure, Ph.D.
,mars_at_parvati.msu.montana.edu, 994-7370 Fall,
2006, Tu/Th 1100-1215 Cooley-B2 Lecture 1
8/29/06 Organization Introduction What is
molecular evolution? Lecture 2 8/31/06
The BIG BANG and formation of the elements
necessary for life. Lecture 3 9/5/06
Biogenesis I The primitive earth and the
prebiotic soup. Lecture 4 9/7/06
Biogenesis II Self-assembly, Energetics
and Bioinformational Molecules. Lecture 5
9/12/06 Biogenesis III Protein
or Nucleic Acids first? RNA or DNA? Lecture 6
9/14/06 The RNA world the
three Domains of life and LUCA. Lecture 7
9/19/06 Origin of the Genetic Code and more
on LUCA Lecture 8 9/21/06
Genomes Content and Architecture. Lecture 9
9/26/06 Mutation nucleotide
substitutions and amino acid replacements. Lecture
10 9/28/06 Methods Analyzing sequences
rates/patterns. Lecture 11 10/3/06
open discussion Lecture 12 10/5/06
Molecular Phylogeny I History, terms,
definitions, and limits. Lecture 13 10/10/06.
Molecular Phylogeny II How to determine a
phylogenetic tree. Lecture 14 10/12/06
Molecular Phylogeny III Improvements and
Extensions to Genome Trees. Lecture 15 10/17/06
NEW? Bayesian and HMM Approaches to
plylogenetic reconstruction Lecture 16 10/19/06
Deviation from Tree-like behavior
horizontal transmission of information Lecture 17
10/24/06 open discussion Lecture 18
10/26/06 Convergent Evolution the
antifreeze story. Lecture 19 10/31/06
Evolution of Viruses Lecture 20 11/2/06
Retroid Agents eukaryotic hosts and disease
states. Lecture 21 11/7/06 UNIVERSITY HOLIDAY
Lecture 22 11/9/06 Bioethics of the
Human Genome Project/ Introduction to
Bioinformatics. Lecture 23 11/14/06
Examples of in silico research I the RNA
polymerase story. Lecture 24 11/16/06
Examples of in silico research II the Genome
Parsing Suite finds Retroid Agents. Lecture 25
11/21/06 Protein Disorder predictions
Measles the elegance of in silico and wet
experiments 11/22-24/06 THANKSGIVING
HOLIDAY Lecture 26 11/28/06 Lecture 27
12/30/06 Lecture 28 12/5/06 Lecture 29
12/7/06
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The Next Three Lectures Will Cover

• 1) Speculation and research on the origin of
  life.
• Structure of the arguments
• There are two approaches to the study of the
  origin of life
• From small to large--chemical approach
• From the complex to simple--biological approach
• Geological approach--most recent data
• C) We will cover five stages
• The early earth environment
• Prebiotic chemistry
• Energetics
• Self-assembly processes
• Bioinformational molecules

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The arguments supporting the plausibility of the
occurrence of biogenesis are based on three
principles

• The principle of continuity Models or ideas
  which present a continuous evolutionary pathway
  from proposed origins to the current
  evolutionary life forms are more plausible than
  models that are gapped or discontinuous between
  the origin and the current evolved form.
• 2) The principle of ubiquity Ubiquitous
  conditions are more plausible than specialized
  cases, unless the special case is in some way
  fundamental.
• 3) The principle of robustness Robust models
  should be fairly independent of precise
  environmental conditions.
• Plausible models of biogenesis should include
• 1) the synthetic process
• 2) concentration mechanisms
• 3) degradation mechanisms

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The Hadean period Hell on Earth
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Microfossils from the Apex Chert, North Pole,
Australia. These organisms are Archean in age,
approximately 3.465 billion years old, and
resemble filamentous prokaryotes.
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What was going on during the Archean period?
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Image of Sharks Bay, Australia extant
stromatolites, a cross section of one of these
structures, and a closeup of the cyanobacteria
that make up the bulk of the feature.
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Tiny, tiny Martians? In a Martian meteorite,
patches of carbonate some 50 micrometers across
harbor putative fossils like this half-micrometer
tube-like structural form.
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Basic questions regarding the primitive
environment 1) What was the prebiotic
chemistry? 2) What is the accretion process? 3)
What was the temperature like in the prebiotic
environment? 4) Where did biogenesis take place?
Necessary and sufficient components for
biogenesis 1) nitrogen, hydrogen, carbon, and
a little oxygen 2) reasonable temperature
range 3) some energy 4) a marine environment
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Sugar-Phosphate Bond
Glycosidic Bond
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A Plausible Scenario???
Lets imagine 1) a dilute seawater solution of 2)
the components (aas, carbs, purines, phosphates,
and fatty acids) 3) existed on a lava surface in
an intertidal zone 4) subject to a drying and
wetting cycle 5) then sodium chloride would
precipitate organic anions 6) a variety of
covalent bonds would form between all functional
groups by condensation reactions
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