Week 4 in Review

Skipped week 3's review on account of birfday. Not going to try to go back unless absolutely necessary.

Computer Science for the Sciences
- Turned in assignment on creating functions and using if-statements. Felt very clever about two aspects of my assignment. Almost let a float/int error ruin everything.
- Learned about for loops, strings, and lists
- Lab didn't work. Need to redo.

Animal Behaviour
- Sexual selection: Intersexual selection and intrasexual selection
- Alternative strategies:
- Conditional strategies are not hereditary, environmentally determined. All individuals have the capacity for all strategies, use the best one for their given situation (can be behavioural or physiological)
- Distinct strategies are hereditarily determined. Each individual has capacity for only one strategy. Theory says multiple hereditary strategies should only be maintained if they all yield equal fitness. I feel like that's an oversimplification of the situation.

Organic Chemistry
- Studying alkenes:
- IUPAC names for alkenes
- Reactions involving alkenes: addition reactions
- Carbocation intermediates, and stability thereof
- 1,2-hydride or -alkyl shifts
- Bromonium and mercurium ions
- Solubility lab: identifying compounds by solubility and extracting components from mixtures using solubility. Four hours of nonstop stress ruining my whole week. I'm so glad I only have lab every other week.
- Markovnikov and anti-Markovnikov addition, stability of intermediate depends on more than just carbocation stability: steric strain

- History of tree of life: 5 Kingdoms to 8 Kingdoms to 3 Domains and no Kingdoms
- SSU rRNA as universal homologous trait for phylogeny of all living things (except viruses)
- Eucarya more closely related to Archaea than Bacteria, mitochondria and chloroplasts nested within Bacteria, prokaryotes are not living fossils
- Life originated in hydrothermal vents, thermophilia and hyperthermophilia is a less derived trait, not more derived. Cool. (Or, you know, hot).
- Life originated 3.85 bya. Not the most conservative estimate.
- Lab: identifying unknown organism. Gram stain worked perfectly (purple, +ve), acid-fast stain worked well enough to tell acid-fastness (pink, +ve), but smear was clumpy. Need to redo because slides are marked on quality of smear. Practiced endospore staining. Next week check for motility, endospore, and capsule, and redo acid-fast stain. This lab should really be an hour longer than it is.


Two Things

1. Rachel Maddow is amazing. I know I say this at least once a month, but she just keeps topping herself. Her interview with Rod Blagojevich was a thing of beauty; she is completely fearless. I think every politician should be required to be interviewed by her before anyone can vote for or against them. You can watch the interview by clicking here and then clicking on "Previously" and choosing January 27th (it will be available for a week), or you can read the transcript here.

2. After seeing that interview, no politician to whom she is hostile will ever, ever agree to go on her show. Only someone who would still go on her show after she'd called them "coo-coo for cocopuffs" would subject themselves to that, and he already did. It's a damned shame.



Dinner the night before with my family, my name and age spelled out in M&Ms when I woke up, waffles for breakfast, 25 million birthday messages on my facebook page, and loot consisting of a pressure cooker, a kitchen scale, and a mortar and pestle. Being 26 ain't so bad.


Week 2 in Review

Animal Physiology

Computer Science for the Sciences
- booleans don't have xor: and, or, not
- basic structure of a program
- relational operators: <, >, ==, <=, >=, !
- raw_input is always a string
- if statements

Animal Behaviour
- behaviour as adaptation:

  • looking at convergent and divergent evolution to justify hypotheses
  • need for statistical rigour to avoid confirmation bias
  • need for skepticism: just because the evidence doesn't contradict an explanation doesn't mean the explanation is right
- History of study of animal behaviour:
  • instinct only
  • comparative psychology

Organic Chemistry
- IUPAC naming:
  • Parent (longest continuous string of C's):
    • Number of C's: meth-, eth-, prop-, but-, pent-, hex-, hept-, oct-, non-, dec-
    • Shape: if cyclic: cyclo-
  • Suffix:
    • C-C bonds:
      • all single: alkane
      • double: alkene
      • triple: alkyne
    • Functional group:
      • C-X (where X is a halogen): alkyl halide
      • C-OH: alcohol
      • C-NR2: amine
      • C-O-C: ether
      • O=C-OH: aldehyde
      • O=C: ketone
      • O=C-OH: carboxylic acid
      • O=C-O: ester
      • O=C-NR2: amide
  • Prefix (substituents):
    • number carbons to give lowest numbers
    • list substituents alphabetically
- Newman projections: staggered, eclipsed, gauche
- Conformational Stereoisomers: conformers, rotation around C-C bond
- Torsional strain, steric strain
- Energy profiles of conformers
- Cyclocalkanes:
  • angle strain and stability
  • torsional and steric strain, substituents
  • cyclohexane: chair and boat conformations, ring-flip
  • cis-/trans- isomerism
  • diaxial vs. diequatorial isomers

Microbiology: The bacterial cell
- Just history, invention of microscopes, agar plates, Pasteur's flask discovery, germ theory of disease, antiseptic technique, H. pylori,
- really hope I don't have to remember all these dates and names. That would be bullshit.
- Koch's postulates:
  1. suspected pathogen should be present in all cases of disease and absent in all healthy individuals
  2. suspected pathogen should be grown in pure culture
  3. cells from pure culture should cause disease in healthy individual
  4. pathogen should be reisolated and shown to be the same as original

- development of field of immunology, vaccines
- research driven by agriculture and industry, not medicine


Week 1 in Review

Animal Physiology
- Nothing substantive. I'm probably going to drop this course anyway.

Computer Science for the Sciences
- Wow. I know *nothing* about programming. Eep.
- Math in Python: +, -, *, /, %
- Types in Python: str, int, float, long, bool
- Define a function: def function_name(x):
- Define a variable: variable_name=variable quantity
- I'm a clever little logic-problem solver

Organic Chemistry I
- Quick overview of Lewis structures, dipole moments, VSEPR, etc.
- Hybridization: single bonds, double bonds, and lone pairs count as "groups." The number of groups dictates the number of orbitals that hybridize.
- Lewis acids and bases are electron pair acceptors/donors
- Strength of an acid proportional to the stability of its conjugate base
- Ka = Keq[H2O]=[H+][A-]/[HA]
- pKa = -log(Ka)
- Factors that affect an acid's pKa:

  • Electronegativity of atom bonded to the proton (more electronegative, stronger acid)
  • Size of atom bonded to the proton (the larger the atom, the more acidic the compound)
  • Substituents in the molecule (electronegative substituents increase acidity, the closer the substituent is to the proton's bond, the stronger the effect)
  • Electron delocalization (resonance in the conjugate base increases its stability)
  • Hybridization (brings orbitals closer to the nucleus, increasing stability of conjugate base)
- Quite possibly the course from hell.

Animal Behaviour
- Nothing substantive, looks like a lot of fun.
- T.A. is a grad student from the lab next door. Known feminist and all around good person.
- Tutorials will be discussion-based, talking about assigned readings, marks for participation. Wheee!

Microbiology: The Bacterial Cell
- They are going to be strict about the lab rules, wow.
- Light microscopy:
  • Bright field light microscope, image determined by:
    • absorption
    • refraction
    • diffraction
    • spreading
  • Dark field light microscope, image given by reflected and refracted light
  • Phase contrast microscope, image given by refracted light only
  • Fluoresence microscope, image given by light emitted by fluorochromes excited with UV light
- Magnification, basic optics, not even highschool level
- Resolution due to numerical aperture(=amount of light the lens gathers). Physical limitations due to refractive index of air. Use oil to get better resolution. R=λ/2NA
- Confocal microscopy: laser beam reflected off specimen creates image in thin slices, compiled by computer
- Electron microscopy:
  • Transmission electron microscopy: beam of electrons through specimen (dyed with electron-dense material), specimen scatters electrons, electrons that aren't scattered are detected. Optics very similar to bright field light microscopy but with electromagnets instead of lenses.
  • Scanning electron microscopy: beam of electrons reflected off surface (coated with heavy metals)
- Scanning probe microscopy (aka atomic force microscopy, AFM): needle maintains constant distance from speciment, laser reflected off needle detects needle movement.


I *heart* Conservapedia

So much. So much! You just can't make this stuff up. God, I love Conservapedia.

Productive Couple of Weekends

I was sick as a dog last weekend, so all I managed to accomplish was a few loads of laundry, but Dave tidied and vacuumed in the living room and kitchen and did a bunch of dishes. This weekend we managed to:

  • unpack completely from our trip to Montreal and put away the suitcase (I actually did this as soon as we got home!)
  • do meal planning for next week
  • go grocery shopping
  • make lunches for next week
  • make dinners for the next couple days
  • do a bunch more dishes
  • clean out the fridge of old nasty stuff
  • take down the garbage that had been sitting there waiting
  • fold the laundry that we left hanging to dry when we left for Montreal
  • organize some papers in the study
  • empty my binders from last semester and prepare my clipboard with blank lined looseleaf
  • tidy and dust in the bedroom
  • make the bed
  • do another load of laundry
  • vacuum and mop in the bedroom
  • scrub, vacuum, and mop both bathrooms
  • do a bunch of number theory problems (my contribution to that was mostly cheerleading)
Now Dave is doing yet more dishes (they just keep getting dirty again!) and I need to hang up the latest load of laundry, and the study is going to take a few more weekends like this before it's really usable, but I feel like I might be reasonably ready to start the new semester tomorrow.