Assignments for Friday's class:
Assignments for Monday's class:
Discuss Homework assignments
Hints on how I envisioned the answers are here, Jukes Cantor spreadsheets are here)
- 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? (aside on probability distributions)
- 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)
Discuss items that go beyond evolution by natural selection.
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 similar but not identical to parents
- More offspring than necessary
- Competition for resources, mates => survival of the
What processes in biological evolution may go beyond inheritance
with variation and selection?
(Many of these conflict with the modern synthesis, NOT with the general definition of natural selection.)
- 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
(links for Beatrix Potter and/or symbiosis fans: http://www.the-scientist.com/?articles.view/articleNo/24954/title/Beatrix-Potter--scientist/ and http://en.wikipedia.org/wiki/Beatrix_Potter and http://www.nytimes.com/books/first/w/wakeford-liaisons.html )
Go through coral of life ppt slides.
How old is life on Earth?
Morphological Fossil Evidence:
- 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
Biological Signature Evidence (examples):
- 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
- 3.2Ga old filamentous fossils, probably of
thermophilic chemotrophic prokaryotes (Rasmussen,
- 1.8Ga old fossils from Gunflint formation:
iron-loving bacteria and cyanobacteria
- 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
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)
See Olga's Timeline of the Universe here
If time slides on high temperature origin of life and the late heavy bombardment