Announcement:

CSD is seeking a qualified peer notetaker for this course;

Students who are interested in the position should come to the CSD located in the Wilbur Cross Building, Room 204;
notetakers are hired on a first come, first served basis provided they meet the position qualifications;

Peer notetaker qualifications include: good academic standing (cumulative GPA of 2.5 or higher for undergraduates; 3.0 or higher for graduates); regular class attendance; ability to type and upload comprehensive notes to the CSD notetaking website.

If the content of the notes is not conducive to a typed format (e.g., MATH, CHEM), notetakers may scan and upload legible, hand-written notes. Scanners are available at the CSD;

Compensation is provided - visit http://csd.uconn.edu/notetaking-assistance-3/ for payment information.

Old homework:

• 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 50% 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?)

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

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

Brief comments on what is living and what not (class 4)

Slides on inteins

Is there a definition of life? NASA's working definition of life: "life is a self-sustaining system capable of Darwinian evolution"

Does Darwinian evolution depend on a biopolymer that acts as genetic material?

Gaia hypothesis, levels of selection. Are viruses alive?

Can living systems be divided in smaller sub-systems that are themselves alive? Or, is life a property of the larger system? The ecosystem of the Sargasso sea that includes algae, bacteria and phage (viruses that live on bacteria). The cyanophage play an important role in the system as predators of the primary producers. They lyze the cells allowing for recycling of limiting elements. The phage are part of a living system, but usually are not cindered alive themselves.

The Gaia hypothesis argues that the whole biosphere should be regarded as a single organism, with its own homeostatic feed back loops.
Problems of the hypothesis:

• Earth also includes many feed-forward loops (e.g., melting ice caps lower the albedo, which leads to more warming*). Relying on Gaia's regulatory mechanisms can provide a false sense of safety.
• How does a single organism evolve? With only one Gaia, who would natural selection work? - Natural selection could work with in subsystems, although this often does not work well -> cancer.

* Lovelock and Watson developed the Daisyworld model (simulation here), in which black and white Daisies stabilize the climate of the model planet. The release of DMS heat stressed algae creates a Daisyworld like feed back loop, because it acts as nucleating agent in cloud formation.

Discussion:

Slides on Mutual Aid versus (?) Natural Selection here

What are 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?

• gene transfer
• selfish genetic elements / molecular parasites
• 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

• slides on sequence space here

Goals class 5:

• Appreciate that without selection for function two sequences would have diverged beyond recognition in a few hundred million years.
• Understand the different meanings of the term evolution ("As in evolution of the universe" vs "Nothing in biology makes sense if not considered in the light of evolution".
• Appreciate the power of natural selection
• Understand that other mechanisms in addition to natural selection might be at play in biological evolution