Assignments for Wednesday's class:
- Start work on take-home exam #1 (due on Friday)
- Review the box below on Evolution through Natural Selection.
- Draw a sketch for the relation between the number substitutions that occurred in evolution and the the percent identity of the two sequences. (I.e. how does the observed similarity change, as more and more substitutions occur?)
- How does this relationship change, if some parts of the sequence are so important that the protein becomes non-functional, if a mutation occurs in these positions (i.e., these parts of the sequence are never observed to undergo any change?
- If substitution were to occur at a rate of 10^-8 per year and per site, how long would it take for two sequences to by less than 20% identical? (do a rough estimate ignoring multiple substitutions and back mutations.)
- If you were to do a realistic calculation and you were to consider a nucleotide sequence, how long would it take to arrive at 20% identity? (tip: how similar are to random sequences that have not been aligned?)
- If protein space is so big, how come that complex functional molecules were assembled?
(If the answer is not obvious, listen to the AMNH round table discussion on Carl Sagan. Link)
Review: ATP synthases
as three cylinder three-cycle engine
Nojiet al (1997) Direct observation of the rotation of F1-ATPase. Nature, 386, 299 - 302 tethered the head group of an ATPase to a cover slip and linked the gamma subunit to an actin filament that was fluorescently labeled:
The resulting movie after ATP addition is here .
What are the different meanings of evolution?
What is needed for natural selection to occur?
What are alternatives to evolution by natural selection?
How does an evolutionary frame work help to
- find genes
- find important non protein coding regions in the genome
- find the function of a hypothetical conserved protein?
In biological evolution, what processes might go beyond natural selection?
Do these processes conflict with "Darwinian evolution" or do only with the modern synthesis?
- gene transfer
- fusion of lineages (e.g., eukaryotes, lichen)
- group selection
- non-random mutations
- directed mutations
- mutationism (big jumps due to mutations, aka Hopeful Monsters)
- genetic drift
- gratuitous complexity / neutral pathways towards complexity
Natural Selection and Evolution
When does "evolution" occur? An
"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
- More offspring than necessary
- Competition for resources, mates => survival of the
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
- 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