Assignment for Friday's class:
Assignment for Monday's class (next week):
Problems accessing huskyCT?
Is it Bioinformatics or not?
windows -> control panel
selection vs display
commands acting on selected aa
neighbors of selected aa
What are the traditional criteria for life? Which of these appears biased?
Would a combination of fewer criteria be sufficient?
Could a virus, if one considers its life cycle, be considered alive?
Claudiu Bandea from the CDC in Atlanta wrote an interesting article on viruses as molecular organisms. Patrick Forterre (here) arrives at a similar conclusion.
Can life be divided in living building blocks (individual cells), or is life a property of a larger assembly? If the latter, what assembly? (the organism, the biofilm, the biosphere)
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