Assignments for Monday's class:

Assignments for next week:


Old homework:

Here is how I envisioned the answers, Jukes Cantor spreadsheets are here)

Jukes Cantor relationship (observed difference p versus number of substitutions d) for nucleotides. (A derivation is here).

Jukes Canot correction

Slides on inteins


Feedback loops in GAIA - subsystems can evolve by natural selection

What are alternatives to evolution by natural selection?

How does an evolutionary frame work help to

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

Natural Selection and Evolution

When does "evolution" occur? An algorithmic approach.

"Darwin's Dangerous Idea" by Daniel C. Dennett, Chapter on Evolution as algorithm is a reading assignment for Monday, Sept. 13. [available through WebCT]

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 (some type of inheritance)
  • More offspring than necessary for replacement
  • 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)
  • 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.

In the unlikely event that we still have time: slides on sequence space here