Assignment for Wednesday:

Read Chapter 3 in the text book. If you are a computer scientist, grab a biochemistry textbook and read the chapter on the properties of amino acids (or check wikipedia). If you are a biologist, refresh your memory on statistical significance (here).
What are type I and type II in case of a data bank search for homologs?
Note: Fig 3.4 seems wrong (no gap penalty, wrong reference cells, but maybe there are different ways to skin a cat). A more accurate decription is here (from a bioinformatics course given at the Univ. of Munich). A very detailed and accurate description is here (it contains more details than you need and probably want to know).
Fig 3.7: Y axis should be probability density.

Go over Quiz #1. (spreadsheed with possible answers to extra credit question is here)

What is needed for evolution to occur?

(Note, this is different from stating that this is all that occurs in evolution)

• Offspring not identical to parents
• More offspring than necessary
• Competition for resources, mates => survival of the fittest.

What processes in biological evolution go beyond inheritance with variation and selection? (We'll discuss many of the following later in the semester.)

• Horizontal gene transfer and recombination
• Polyploidization (botany, vertebrate evolution) see here
• Fusion and cooperation of organisms (Kefir, lichen, also the eukaryotic cell)
• Targeted mutations (?), genetic memory (?) (see Foster's and Hall's reviews on directed/adaptive mutations; see here for a counterpoint)
• Random genetic drift
• Gratuitous complexity
• Selfish genes (who/what is the subject of evolution??)
• Parasitism, altruism, Morons

How old is life on Earth?

• The Earth is about 4.5 Ga old, but no crustal rocks has survived from that time. The oldest rocks are no older than 4.0 Ga.
  
  

Morphological Fossil Evidence:

• For about a decade the oldest microfossils were considered to be about 3.5 Ga old (see here). The fossils (as interpreted by Bill Schopf) look like "modern" Cyanobacteria. Compare the time to to molecular trees of life: Is this a problem? However, recently the evidence for these fossils was questioned.
  
  
• 3.2Ga old filamentous fossils, probably of thermophilic chemotrophic prokaryotes (Rasmussen, 2000)
  
  
• 1.8Ga old fossils from Gunflint formation: iron-loving bacteria and cyanobacteria

Biological Signature Evidence (examples):

• Oldest geological evidence for life - 3.8 Ga ago - is based on ¹³C discrimination (carbon derived from living systems often have lower delta ¹³C values than inorganic carbonates) [here]. The rocks are from Akilia island off the coast of Greenland, and severely altered by metamorphism. However, recently the evidence for that was reassessed.
  
  
• 2.7Ga old: probable biomarkers of cyanobacteria and of eukaryotes (Roger Summons, Roger Buick and Jochen Brocks)

Timeline of the Universe

Recent overview here
Notes on the TREE of LIFE - Powerpoint presentation here