Ch 15: Evolution of Microbial Life  (start in Biol 205, complete in Biol 206)
creation &? evolution site accepts Fossil record, but not abiogenesis?  = origin of life

BIOL 205
2) Major Episodes in the History of Life:  wiki: used below, wiki: more 
Know fig 2 = table p 282: major events in the evolution of life was in the previous chapter

The oldest fossils are cyanobacteria, 3,500 Mya, fig 3, another Stromatolite site
but the first cells were NOT photosynthetic so where are the fossils of first cells?
3) The Origin of Life (Farabee) or
Kimball: more clearly written,
Wiki also clearly written,
Spontaneous generation is not what happened & of interest to historians
biogenesis in the Hadean (summary, more below) = Primordial soup to prebiotic beach (next)

4) Four stages of the hypothesis for the origin of life on Earth:
The Period is the Hadean
The atmosphere: NH3, H2, CH4, H2O, no O2,
USE: wiki's list of molecules & steps of evolution
This atmosphere is reducing not oxidizing, reducing supports synthesis of larger molecules
1. Abiotic synthesis of organic monomers:
    fig 4, Miller's exp: scroll, produced amino acids, bases (in nucleic acids), & more
    Wiki is easiest to use
    other sources of organic chemicals: Murchison meteorite,  Juan Oro (scroll a bit)
2. Synthesis of polymers (scroll a bit):
    concentrate monomers (by water evaporating),
    & monomers drip onto hot sand/clay e.g./rock (catalyst), forms:
    peptides (short proteins) form from amino acids, &
    nucleic acids, & bits of DNA or RNA, Then what?
3. First self-replicating molecules: 
    movies & resources but "Life's Origins" is not very good,
    The goal is to increase in number = survival of the fittest molecules!
    RNA dominates first? as it can act both as an enzyme & be copied, fig 5, 6a.
    Kimball: an RNA World? &  ribozyme p 302, 
    more RNA World,  Nobel prize,  NYTimes has good discussion,  Berkeley is ok
    But outcome is DNA is primarily used to store code (except RNA virus), while
    proteins, are selected to do almost everything (except be code) as they are endlessly versatile & complex.
4. Formation of pre-cells, how did cell membrane evolve?, getting a cell together?
    Berkeley no answer, fig 6, 7: polypeptide membrane microspheres,
    but lipid-dominant membrane won. 
    More ideas coacaverte,  scroll to rocky start,  middle school ex,  protobiont
5) Mutations & Natural selection affected the pre-cells?,
    refined them & chose the fittest (really?) fugawi
REVIEW p 302
1. Chemical evolution preceeded biological.  What are the sububits of proteins and of nucleic acids?
2. Why cannot life re-evolve today?  How are our polymer molecules protected (answer, food, aging = oxidation)
3. What is a ribozyme?

REVIEW
Ch 13: How Populations Evolve = microevolution: evolution in real time
Box: Persistent Pests: is an example of microevolution, so is MRSA
1) Charles Darwin & The Origin of Species
Darwin established the ideas of evolution & natural selection in his 1859 book   
Darwin's Cultural & Scientific Context:
During his voyage around the world Darwin observed the adaptations of organisms that inhabited diverse environments
He was particularly impressed by the adaptations, image of species on the Galapagos Islands
Please review from my chapter page, but also see Process of Science Q & A below
    Descent with Modification, scroll for finches
2) Evidence of Evolution
    The Fossil Record
    Biogeography, image,
    Comparative Anatomy
    Comparative Embryology
    Molecular Biology: DNA differences accumulate like clockwork, calibrate using fossil record
3) Natural Selection
    Darwin's Theory
    Natural Selection in Action
    Does predation drive the evolution of lizard horn length?,  
Texas horned lizard (Texans are tough)
4) Modern Synthesis: Darwinism meets Genetics
    Populations are the units of evolution
A population is all members of one species living in one place. 
It is the smallest unit that can evolve.
Population genetics studies the genetic variation within populations.
    Genetic variation in populations
Polygenic (many gene) inheritance produces traits that vary continuously e.g. skin color
Other traits may be determined by only one gene (pea characters studied by Mendel).
Polymorphic genes determine more than one trait
Mutation & sexual recombination produce genetic variation
    Analyzing gene pools: p + q = 1, p is frequency of S q is frequency of s
            Hardy-Weinberg: p2 + 2pq + q2 = 1, & know assumptions
                                     SS,    Ss      ss,     
Ch 13 Process of Science:
1. Snails: both are preyed on by birds
                              Striped          Unstriped       Totals
        living                264        +       296    =         560    
        broken/eaten     486                 377    =         863
         totals               750       +        673    =       1423
a)   Which are more subject to predation:
       486/750 = 0.648, or 377/673 = 0.560?    
       The striped  
      Over time what may happen?
       The striped all die
b)    If striped (S) is dominant to unstriped (s),
      what is the frequency of each allele in those alive?
Let p be frequency (fraction) of S, & q be frequency (fraction) of s
      by definition   p + q = 1,  so  p2 + 2pq + q2 = 1
       Which do you know:  p2,  2pq,  or  q2 ?
You know q2 because all these snails are unstriped
So q2 = 296/560 = 0.529, take square root, so q = 0.727, therefore  p = 0.273
      Is it ok to use..the HW calculator to figure out how many are SS and Ss?
Probably, I really don't know
      Are birds really selecting one type over the other,
      or could the difference be due to chance?  5% rule
In biology 5% variation is not a significant difference,
as the difference between 0.648 & 0.560 is greater than 5%
the birds are probably selecting/seeing the striped more easily
    Population genetics and health science:
          cannot eliminate recessive bad allele as it seldom meets itself, & new mutation brings it back
    Microevolution as change in a gene pool: what happens:
           fitness makes some gene allele frequencies rise & others fall
5) Mechanisms of Microevolution (software resource)
    Genetic Drift: chance, includes bottleneck effect, & founder effect
Why do bottlenecks change allele frequencies of a gene in a population?
Compare population of 50 with 250: in smaller population one allele becomes fixed more often
In a population what contribution do non-breeders make to natural selection?
In humans it could be complex, in other species, maybe not much
Which is more likely to loose an allele?
       if the population = 20, & p = q = 0.5, or p = 0.9, q = 0.1: the latter
SKIP
Can use software on I:\Wilkin, double click DRIFT,  source
Can do 10 Trials (not one), 10 Generations (least available), & correct Population.
A DOS program on my I drive, alelle, includes mutation
Harder to use: evolve is on my I drive in EvolGenius folder .using. this software covers all evolution mechanisms.
Costs of low genetic diversity? inbred dogs, wiki, NYTimes, death & disease  
    Gene Flow: migration
    Mutation: bad alleles remain in populations due to new mutations replacing those removed
    Natural Selection: A Closer Look: directional selection, disruptive selection, stabilizing selection
6) Population genetics of the sickle cell allele
        is stabilizing selection?
Ch 14: How Biological Diversity Evolves
Box: One troublesome species or two?
Macroevolution & the diversity of life
The origin of species
Ch 14 Process of Science
1. Theory vs hypothesis, skip
2. Two populations of mice on opposite sides of a river:
a) same species or not, how do you decide? collect & breed them     
b) how to decide without "disturbing" them? build bridge to connect them
Tree of Life, trees of life over time,  make the new tree larger, taxonomy lab. Kingdoms..

Ends BIOL 205 Review,  Prokaryotes (next) & Protists are in Biology 206

1) BOX: Biology & Society (Biol 206): 
Bacteria & viruses as agents of bioterrorism. 
Not made/kept in USA since Nixon

Fig 2: oldest fossil prokaryotes 3.5 billion years ago, but eukaryotes only 1.6 billion years ago
CHECK: p 298, put in order:
1) diversification of animals (Cambrian explosion)
2) evolution of eukaryotic cells
3) first humans
4) colonization of land by plants & fungi
5) origin of prokaryotes
6) evolution of land animals
7) evolution of multicellular organisms

Microbe Zoo, K-12 & topics.  Microbial Ecology Resources,  wiki's Prokaryotes,  another but no images,
Microbiology also includes eukaryotes: mostly protists & fungi: Microbiology course,  another course/textbook: 
  1. prokaryotes are everywhere & the most abundant life: Farabee: general resource,
  2. they affect humans & ecosystems, NOTE: some listed here are not prokaryotes!
  3. Two groups of prokaryotes: bacteria & archaea.  Wiki: prokaryotes: = bacteria & archaea
  4. compare three domains (includes eukaryotes):  list of links,  
  5. Kimball: eukaryotes evolved from archaea, & added bacteria as organelles, wiki's comparison
  6. Archaea: 3 groups: 1) halophiles (sea/salt), fig 9, 2) thermophiles (hot), & 3) methanogens (anaerobes/guts),
    7. Kimball's SIX: includes some like it: cold, really hot, & very acidic or very basic
  7. Extreme pH South Chicago "hydrogen oxidizer", & antarctic is cold.

  8. MICROBIAL COMMUNITY FOUND THRIVING IN VERY ALKALINE (PH 12-13) GROUNDWATER

  9. The structure, function, and reproduction of prokaryotes:  resource,  another,
  10. Classification of bacteria: by
    11. a) shape, fig 10: bacilli (rod), or cocci (sphere), or spirilla,
  11. b) cell wall: +/- Gram stain,  neg,  pos,   peptidoglycan: (amino acids & glucose polymer),
    12. c) nutrition: Table 1: nutritional diversity (has SIX categories, movies)
    There are six categories, but know these four: & what is an autotroph that does not use light or inorganic chemicals

    		Energy Source
    		 Carbon Source
    		 Example
    Photoautotroph
    same as plants
    		 sunlight CO2 (inorganic)
    		 cyanobacteria
    Chemoautotroph
    only prokaryotes
         		inorganic compounds
    H2S, NH3
    		 CO2 beta-proteobacteria (scroll),
    vents
    Photoheterotroph
    only prokaryotes
         		sunlight organic compounds purple non-sulfur bacteria
    Chemoheterotroph?
    Heterotroph
    		 organic compounds organic compounds is same as animals & fungi
    d) ability to form spores
  12. e) motility: cell motility bacteria are only organism to invent the wheel in structure, videos.
  13. Reproduction is mostly binary fission: etc,  ? sex,  conjugation: see description & fig
  14. Ecology: the bad: diseases fig 13,14,15: anthrax, bacterial flu (flu usually virus), Lyme disease etc,
  15. the good fig 16,17: sewage treatment & oil spill, digester, fairoaks,  soil bacteria,  bioremediation,
  16. the ugly
REVIEW p 309
1. Differences between Bacteria & Archaea? structural & functional,
    Wiki & Kimball/Archaea, evolution diagram
2. How to distinguish between staph or strep?,  both are gram+,  more,  source
3. classify bacterium: lives in deep damp coal mines, uses methionine only as nutrient for energy and carbon
    answer is on flowchart as this, textbook answer is chemoheterotroph
4. Why are some Archaea referred to as extemeophiles?
5. Why autoclave lab instruments? endospores,  endotoxin or exotoxin,  another,
6. How do bacteria contribute to global warming? 
    Why did the Carboniferous make so much fossil fuel?
    Are any new fossil fuels being made? 
5. Three kinds of bacteria that do not contribute to global warming?
    = 2 kinds of producer & kinds that  promotes producer activity;
6. what pollution do bacteria remove (mostly organics, like oil spills above) &
    what "don't" they remove (very persistent organics, heavy metals)?


First Eukaryotes: Kingdom Protista images, four groups, easy .ppt,  source, (detailed .ppt)
1) protozoa & life cycles,
2) slime molds & life cycles,
3) unicellular algae, & life cycles,
4) multicellular algae = seaweeds,  life cycles, largest: kelp forest
 wiki: has 3 groups: puts all algae together
  1. Origin of Eukaryotic cells (3 things): fig 18 has two
  2. 1) developed system of endomembranes, by plasma membrane infolding?
  3. 2) organelles, probably mitochondria & chloroplast were adopted?
  4. 3) are diploid, by mutation? like polyploidy in plants,  more?

  6. Do mitochondria and chloroplasts have haploid DNA (here): & click mitochondrial Eve QT
    7. primitive eukaryote: giardia, haploid chromosomes of mitochondria & chloroplast: Kimball

  8. protozoans (pre-animals), fig 19: 
  9. flagellates, amoebas, apicomplexans: parasites with device to penetrate host cell, ciliates
  10. slime moulds: wiki, same nutrition as fungi = decomposers:
  11.   either plasmodial fig 20, one cell, many nuclei!,
  12.   or "cellular" fig 21
  13. unicellular algae: (pre-plants) photosynthetic, component of plankton, fig 22, dinoflagellates, diatoms, green algae
  14. multicellular algae fig 23:
  15. seaweeds,    kelp (holdfast) forest,  Sargasso (floating jungle) Sea,  wiki

  17. Protista impact our lives: as food,  culture medium,  carrageen Irish moss,  Red tide, scroll to parasites, lichen
Evolution Connection: The Origin of Multicellular Life 
  1. Unicellular life advantages: quick to reproduce vs
  2. multicellular life: greater complexity - different cell types,
    3. fig 24, early multicellular = spirogyra what is advantage?
    fig 24 colony somehow divided up labor: inside vs outside?
    slime mold cells cooperate to overcome adversity
  3. Lab Exploring Bacterial Endosymbionts and the Organelles of Eukaryotic Cells
Checkpoint p 316
1. Which organelles were probably originally endosymbiotic bacteria?
2. why are protists important in the study of the evolution of life?
3. What three modes of locomotion occur among protozoans
4. Which protozoans are most similar in movement to unicellular stage slime molds
5. What metabolic process separates algae from protozoans?
6. Are seaweeds plants?

1. Which dates furthest into the past, autotrophs or heterotrophs, explain your choice -
what was missing from the atmosphere when cells first appeared?
2. Fossil record: the earliest organisms are haploid, but more recently diploid organisms appeared,
how did this happen, & how can you test your theory?
3. How could sex have evolved - the equal sharing of genes to produce an offspring
4. Biosphere 2 failed because the oxygen ran out, what wasn't allowed for &
how can you test your hypothesis?  Biosphere 1