Assignments for Today

How does the relationship between observed sequence divergence (p) and substitution events (d) change, when the different bases (or aa) do not occur with the same frequency?
Given a substitution rate of 10^-8 per year and nucleotide, how many substitutions would have occurred in two sequences that had a common ancestor 200 million or 1 billion years ago. Assuming a concentration of 25% per nucleotide, what would you expect for the % sequence identity of the two sequences (ignoring sequence alignment.)

Assignments for Wednesday

Watch video on reconstructing the Tree of Life
What does the term phylogeny mean?
TREE of LIFE overview here, (optional: compare here, here, here and here (especially the discussion is interesting).
Read through Olga's Time-line of the Universe here

Assignments for Friday

Read through file on frequently used formats here
Explore the Genbank Sample file here
Sign up for an account on the bioinformatics cluster at http://bioinformatics.uconn.edu/contact-us/
use 1st pull down menu to sign up for a class account ...

Computer, exam, discussion boards etc.

Slides on Mutual Aid versus(?) Natural Selection here

Feedback loops in GAIA - subsystems can evolve by natural selection

Alternatives to evolution by natural selection?

In biological evolution, what processes might go beyond natural selection?
Do these processes conflict with "Darwinian evolution" or only with the modern synthesis?

Horizontal gene transfer and recombination

Polyploidization (angiosperm and vertebrate evolution) see here and here

Fusion and cooperation of organisms (Kefir, lichen, also the eukaryotic cell)

Evolution of the holobiont (host + symbionts)

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, gene transfer agents

Mutationism, hopeful monsters

Go through coral of life ppt slides.

How old is life on Earth?

The Earth is about 4.6 Ga old, but no crustal rocks has survived from that time. The oldest rocks are no older than 4.0 Ga. But zircon crystals dated to 4.4 billion years BP are found in rocks, are considered evidence for Earth's crust having had formed and being in contact with water already 4.4 billion years BP (here and here)

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, 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.
The amount of carbon in the Issua formation (and its discrimination against agains 13C) is interpreted by Minik Rosing to indicate a highly productive biosphere. (See Minik's presentation at the 2011 ISSOL meeting. Especially slides 6 ff are interesting - the handwritten slides were written with the sedimentary rocks - containing lots of graphite.)
2.7Ga old: probable biomarkers of cyanobacteria and of eukaryotes (Roger Summons, Roger Buick and Jochen Brocks)

See Olga's Timeline of the Universe here

Go through slides on high temperature origin of life and the late heavy bombardment

Goals class 6:

Know the differences between Lamarck's and Darwin's theory, mutationism and the modern synthesis.
Understand the power and the limitations of the tree of life image.
Understand that without selection for function, sequences would have diverged beyond recognition.