BIO/CSC295 2009F, Class 05: The Central Dogma (2)

Admin:
* Don't forget to sign up for the Bio picnic!
  * And feel free to contact you BioSEPC members, like David Montgomery,
    if you have questions about biology
  * Friday, Sept. 25, at 5:30 at the Robertson's
* Permission slips!  Whee!  And we don't even get to read them.
* Believe it or not, but we're a little ahead of schedule.  
  We'll see what happens today.
* For Tuesday, you should start reading Chapter 3.  
  Note that there are some spots that are rough going.
* For a week from Tuesday, you should work on the On-your-own project from 
  Section 2.6.  
  * Of course, on-your-own means in a group of two-to-four.
* EC/Support: Watch Ben run at the Les Duke invitational on Saturday.
* EC/Support: Watch Volleyball (see last EBoard or the Calendar for details)
* CS Table tomorrow (noon, PDR A): A Blind Person's Interactions wtih 
  Technology.

Overview:
* Web Exploration, Discussed
* Some more Python
* Guided Project 2.5

Web Exploration:
* Comparing wild type and sickle-cell mutant type HBB gene
* Two strategies for Web exploration
  * Lots of freedom
  * Very explicit
* Responses:
  * Like to start with lots of freedom, and then get explicit instructions
  * Like to learn with explicit instructions, and then explore more on
    your own
  * More open ended questions have a wider variety of correct answers
  * Faculty can even learn something from open-ended questions
  * Open-ended things give you more opportunity for "learning from
    failure"

Discussion of 3', 5', template and coding strands

Algorithms (mostly using the sequence manipulation suite)
* Convert from A, C, G, T to Amino Acids (very convenient)
* Calculated expected number of amino acids given number of nucleotides
  (any calculator should be able to do this)a
* Searching: Finding the first ATG in the strand
* Alignment: Dealing with two sequences that didn't start at the same point
* Matching: Finding the difference between the two strands

* Might have been easier to do as code
  seq1 = read_fasta('hbb-gene.txt')
  seq2 = read_plain_dna('sickle-gene.txt')
  mrna1 = transcribe(seq1)
  mrna2 = transcribe(seq2)
  protein1 = translate(mrna1)
  protein2 = translate(mrna2)
  show_differences(protein1,protein2)

Detour: What is wild type?
* All the genes are homozygous (did I spell that right?)
* Who is the human wild type?
  * The most abundant group: Asian women
* So the reference sequence is not necessarily a wild type.  But, hey,
  biology is messy

Some Python
* Confusion about map

Lab!
* It's long; we'll continue it on Tuesday, which means that the on-your-own
  project will be due a week from Tuesday
* Sam learns that error messages are really a joy limited to anal 
  computer scientists.
  * And worries that sometimes he spends too much effort teaching 
    better coding style

Sam's dumb joke: In six minutes, it will be an amino acid 'Thr'