Assignments for Friday's class:
The F1-ATPase as three cylinder three-cycle engine
Nojiet al (1997) Direct observation of the rotation of F1-ATPase. Nature, 386, 299 - 302 tehered the headgroup of an ATPase to a coverslip and linked the gamma subumit to an actin filament that was flurescently labeled:
The resulting movie after ATP addition is here .
What does Bioinformatics have to do with Molecular Evolution?
The following chain although (believed to be) mainly determined by the DNA sequence (plus other components of the cell which in turn are encoded by other parts of the genome) can at present not be simulated in a computer.
DNA sequence ->
Most scientists believe that the principle of reductionism (plus new laws and relations emerging on each level) is true for this chain; however, this is clearly "in principle" only.
At several steps along the way from DNA to function our understanding of the chemical and physical processes involved is so incomplete that prediction of protein function based on only a single DNA sequence is at present impossible (at least for a protein of reasonable size).
Present day proteins evolved through substitution and selection from ancestral proteins. Related proteins have similar sequence AND similar structure AND similar function.
In the above mantra "similar function" can refer to:
The following is based on observation and not on an a priori truth:
THE REVERSE IS NOT TRUE:
In particular, PROTEINS WITH SHARED ANCESTRY DO NOT ALWAYS SHOW SIGNIFICANT SIMILARITY
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)
What processes in biological evolution go beyond inheritance with variation and selection? (We'll discuss many of the following later in the semester.)
Evolution, different meanings, fact vs theory, natural selection -- what else. Is variation gradual?
What is life?
(see Thomas Mann's excerpt from Dr. Faustus)
von Neumann's computers - alive? A-life?
Turing machines and universal computers (Turing's biography)
Cellular automata: A'life; John Conway's game of life. [rules: a cell survives if it has two or three living neighbors. A new cell is created on a "dead" square if it has exactly three living neighbors.] The game was popularized by Martin Gardner in Scientific American in 1970.
"A population of several hundred creatures is created within a supercomputer, and each creature is tested for their ability to perform a given task, such the ability to swim in a simulated water environment. Those that are most successful survive, and their virtual genes containing coded instructions for their growth, are copied, combined, and mutated to make offspring for a new population. The new creatures are again tested, and some may be improvements on their parents. As this cycle of variation and selection continues, creatures with more and more successful behaviors can emerge. The creatures shown are results from many independent simulations in which they were selected for swimming, walking, jumping, following, and competing for control of a green cube."
Genetic Algorithms in engineering: Ingo Rechenberg and others used "natural selection" in the computer to optimize aerodynamic profiles. Biased walk through "sequence" space. Finding optimal solutions. (To avoid local maxima: use demes with limited migration). For more information you can check a comprehensive collection of links on Evolutionary Computation and its application to art and design. It is amazing that GA work fine with rather small populations.
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 lyses 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.
* Lovelock and Watson developped the Daisyworld model (simulation here), in which black and whie 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.