Observation

I always thought that programming would be like writing instructions, but it's much more like solving puzzles. I see now why so many smart people like it.

No Week 5 in Review

Too busy drowning under midterms. Maybe next week.

In Case There Was Every Any Doubt That a Scientist's Politics and Assumptions Can Invade Their Work

Observe the radically different descriptions of what is essentially the same behaviour in males and females, from Animal Behaviour 8th Ed. by John Alcock, page 369:

Male satin bowerbirds, as we saw in the previous chapter, are capable of copulating with dozens of females in a single breeding season, although they rarely have the good fortune to do so. In other words, males of this species have the capacity to be polygynous. In contrast, most female satin bowerbirds are monogamous, mating with just one male per nesting attempt. But the satin bowerbird's mating system (males potentially polygynous, females mostly monogamous)...

Because girls and boys is different, see...

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

Microbiology
- 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.

Birfday

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.

Rachel Maddow is Awesome. Still.

Week 2 in Review

Animal Physiology
Dropped.

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):
     function
- 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
- K_a = K_eq[H₂O]=[H⁺][A^-]/[HA]
- pK_a = -log(K_a)
- Factors that affect an acid's pK_a:

• 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.

Sinead's Most Excellent Hot Chocolate

I made an adaptation of Sinead's amazing hot chocolate recipe for my family this christmas. It was a big hit. I'll put the recipe I used below. Please bear in mind that everywhere where my recipe is different from Sinead's is because I didn't have the ingredients or equipment available to me.* I make no claim that my modifications are improvements.

I don't have a soy milk maker so I just boiled 2 cups of ground almond in 8 cups of water while I mortar and pestled the spices, which were: 8 cloves, 2-3 tsp anisseed, 1/3 of a cinnamon stick. The almonds and water got extremely foamy and never really got to a rolling boil. I dumped the ground spices in and added one chopped vanilla bean and one dried chili pepper. I cooked this, stirring, for about five minutes and then let it sit about 12 hours in the cold garage. The next day I strained the liquid with cheesecloth and returned it to the pot. I heated it up on the stove while I broke up two bars of Green & Black's 70% and one bar of Terra Nostra's 73%. Then I dissolved about 3 tablespoons of cocoa powder and the chocolate in the liquid. Serve to suspicious relatives, some of whom will turn it down because it's "not healthy" (and never mind the Cinnamon Toast Crunch they have for breakfast).

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*Except the cocoa, which I increased because I was doubling the recipe in my head as I went along and got mixed up.

Do Good and Get Your Money Back

Dave and I have started lending through Kiva, a California-based charity that arranges microloans from private individuals who have money to private individuals who don't.

At the moment they don't charge any interest, so it's not a great place to invest a lot of your money or anything, but it's a great way to be able to keep doing good without going broke.

I heard about it on a fairly recent comments thread on Slacktivist.

What She Said

This whole gleeful hate-on that so many people have for Sarah Palin has really been rubbing me the wrong way lately. Now Flea has explained why.

Thank you

To MSNBC, for calling it this early, so I can get some sleep. And to all you voting Americans out there, for not being *quite* as stupid as you look.

Okay, I'm going to close my computer on MSNBC's 5th straight minute of shots of screaming crowds and get some shut eye before my 8am class tomorrow.

Heh

Heh. "Squirty cream." Heh.

Via.

No One Actually Buys this Shit, Right?

I wasn't going to blog about it, because it isn't even my country, but some of the things McCain said last night were insane. I mean I know a certain amount of insanity is needed to retain the RTC vote, but for the sake of my sanity I refuse to believe that *anyone* could be won over by these gems:

• The idea that nuclear power should be safe is a radical environmentalist position


• The use of airquotes when talking about how late-term abortion bans* shouldn't include exceptions for women's "health"


• The idea that military personal, upon leaving the army, should be fast-tracked into teaching positions in public schools without needing to do any training or pass any certification exams or otherwise show that they, you know, can teach

He also completely cracked me up when claimed that his campaign couldn't be held responsible for Palin's "palling around with terrorists" smear because every rally has its fringe elements.

---

*As an aside, I am very angry at Obama right now for coming out in support of banning late-term abortions, and I don't care if he does think there should be exceptions for the life and health of the mother. These late term abortion arguments are a *huge* red herring in the abortion discussion and he should have called McCain out on that. Women don't up and decide, at 8 months gestation, that they'd rather not be pregnant after all, TYVM, bikini season is coming up so let's go have an abortion.** By including exceptions for life/health of the mother (and one assumes that this includes allowing the termination of fetuses that are dying and/or wouldn't survive out of the womb), the only abortions such a ban would prevent are those of women who have been trying to abort since their first trimester but couldn't because they lacked access, or those being considered by women whose social/economic/whatever situation has just changed dramatically, to the point where they no longer feel they can continue with the pregnancy. In addition, supporting late-term abortion bans while allowing earlier abortions pretty much always requires making what Amp calls the "woman, what woman?" argument. That is unfuckingacceptable and Obama should be ashamed of himself. Here's hoping that his enforced-childbirth support is really just pandering to that seeming majority that believe they support such positions only because they don't actually know much about it.

**Although I personally believe that if they did they should still be allowed to have one, because it's still their damn body.

Rachel Maddow: Full of Win

Amanda Marcotte has up a YouTube video up wherein Rachel Maddow explains what happened to the US banks.

She's so awesome. *sigh*

Dammit!

It's just not fair. All last week I felt like I was fighting off a cold. I got plenty of rest, drank tea, skipped some classes, and just generally took it easy. Last night I finally felt completely better. I even made dinner and did a bunch of dishes and only stayed up a little later than I probably should have. I was all like, yay! No more beginning-of-semester cold!

Then this morning, BAM! DEATH! Well, okay, not death, but big fucking head cold. It's just not fair. And because I skipped all those classes last week trying *not* to get sick, now that I am sick I have to just suck it up and go to class anyway. Goddammit!

Update

For those who are interested:

- Moving into the new apartment went much smoother than I expected it to (and many thanks to those who helped!)
- We're about 90% unpacked, which is good (although that last 10% is always a bitch).
- The new apartment is smaller than the old one, but pretty much everything else about it is much, much better. It's in a complex with a multi-person custodial/managerial staff, all of whom seem to be sober when they're on duty. The attitude towards broken things seems to be to fix them rather than paint over them. The building itself is small enough that it probably isn't supporting a large population of cockroaches. We're in a real neighbourhood, with shops and people who walk and restaurants and *gasp* a subway stop. I could almost cry. The only thing I really don't like is that I'm now much too far from school to bike there. On the other hand, I'm biking distance from other things in the city, which is awesome. And because we're on the subway line, the commute to school by TTC is only about 10-15 minutes longer than it used to be.
- New address will go out to those whose business it is fairly soon. Phone number has not changed.
- Classes start on Monday. There is a >0 chance we'll have finished unpacking by then. Eek.
- After making us wait for the better part of a week, Primus has finally seen fit to provide us with phone and internet service, hence this post.