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I'm a science scout


This is what I've done:

Language Pet Peeve: Sorbet

People who spell it sherbet are wrong. People who pronounce it sor-BAY are wrong and pretentious. People who spell OR pronounce it sherbert should be slapped.

That is all.

Kind of an Awesome Lunch

I haven't food-blogged in a while. Hokay, here's what I'm having for lunch this week:

Start with this recipe. Completely disregard all quantities called for and just use whatever seems right. I didn't even look at the quantities. Replace the canned tomatoes with fresh. Add mushrooms (cut chunky), zucchini, chickpeas, and dandelion greens. Use rotini for the pasta because the spiralliness is excellent.

Right now this sauce is still mostly sauerkraut (which is awesome, but I hear a meal of mostly salt is bad for me), but I bet I could rearrange things so it was just an ingredient and not the main point. Maybe more bitter greens.

The fruitflies from the spider lady's lab are attacking!

I have a friend staying with me this week. Yesterday we had lunch completely independently of each other, miles apart and without communicating. She had falafel and chocolate milk. I had falafel and chocolate soy milk. I think we may be soulmates.

Via @wilw

Via Wil Wheaton's twitter feed, a cool new website that raises awareness about epilepsy: Talk About It.

What He Said

Jesse at Pandagon does a very good job explaining why I don't think civilians should be allowed to carry guns.

Week 9 in Review

Computer Science
- Assignment on files and dictionaries. First assignment where I've actually had some problems getting it right and needed to do a line-by-line debugging in several places.
- SQL requests in Python packages. Still working out the syntax.

Animal Behaviour
- Parental care and evolution of cooperative behaviour.
- Assignment posted: vague instructions, excessive freedom in topic. I am overwhelmed by choice and lack of a place to start. Damn.

Microbiology
- motility: mechanical and biochemical mechanisms, chemotaxis, run/rotate combinations leading to biased random walk
- quorum sensing: bacteria can only perform certain actions (e.g. bioluminscence) if there are a lot of them around. They tell when they've reached critical mass by all secreting a certain molecule. When they sense the concentration of that molecule reaches a threshold level, start action. Physiological mechanisms.

Lab
- Since dropping organic chemistry, I've taken on a bit of responsibility in the lab: I'm trying to keep a half-starved electric eel from dying, and also from killing me. It's fun. This electric eel doesn't like to eat minnows, but will happily eat earthworms. Also, it produces an enormous amount of nitrogenous waste. Tank smells like the tropical forest exhibit at the science centre.
- One of the other undergrads in the lab hit me in the face with her belt buckle. Have an invisible but fairly painful bruise on the side of my nose. She swears it was an accident.

Weeks 6 - 8 in brief Review

So I've missed a few weeks here. Week 6 was right before reading week, and when it ended I was so excited about it being reading week that I forgot to do a review. Then there was reading week, which I spent catching up on Microbiology and Organic Chemistry. Week 7 was a whirlwind of exams and lab prep that ended, Sunday afternoon, with me deciding that, since I'm leaning more and more towards going to graduate school rather than medical school anyway, and since it wasn't required for me to graduate, and since it was just making me completely miserable and taking time away from courses I was actually interested in, that my attitude towards Organic Chemistry was Fuck That Noise. Dropped it. Whew. It wasn't until after I did that that I realized how precariously close I was (and am) to burning out. I spent all of reading week either studying or feeling guilty about not studying and therefore didn't get any real kind of break, and I've been in classes now for 18 months straight because I didn't take last summer off and I'm tired. I think even without org it will be all I can do to keep myself hanging on until the end of the semester. Fortunately I'm not taking any courses next summer, so I can probably get away with having my evenings and weekends largely to myself. *glee*.

Now, however, I have kind of an opposite problem, which is that only taking three courses leaves me with an enormous amount of unstructured time. I was spectacularly unproductive this week. I need to find some way to force some structure on that time. I'm thinking of forcing a four-day week on myself. I know this sounds incredibly spoiled, but it's a real problem. If I tell myself that I'm not allowed to go to campus or do any schoolwork on Tuesdays (when I no longer have class), then I'll have to make myself work the rest of the weekdays in order to get it all done. Which will mean I'll actually do it. Or that's the theory, anyway. Plus, it will give me an extra day off each week, which will help to ward off the burnout. I just need to give myself some structured recreation for Tuesdays, preferably physical activity, so I don't spend the whole day in bed or on the couch. Maybe I'll just spend the entire day at the gym, and when the weather gets warmer start biking around the city. Anyway, I'm open to suggestions for how I can structure my Tuesdays. Maybe I can do some baking.

So finally, this afternoon, the last two months of 5 - 6 hour nights caught up with me. I reached that point where I was so tired I wasn't really in control of my behaviour, and realized this when a friend had to pull me away before I started yelling at a bunch of idiot environmentalist hippies on campus who were making an arts and crafts project out of used coffee cups (because it's less wasteful if you glue your garbage together before throwing it away!). So I got home this evening, had a quick dinner, and went to bed around 7 pm. Which means that now it's 11:30 pm, and even though I'm still tired I can't get back to sleep. Hence, blogging. So now I give you Weeks 7 & 8 in Review:

Computer Science
- while loops
- dictionaries
- building dictionaries from files
- in
- nose

Microbiology
- gram positive vs. gram negative
- gram negative secretion systems: Sec, Tat, Secretion systems I through V. III is a needle that injects stuff into host cells. IV is used for conjugation and is aka "sex pilus".
- gram negative cell wall and outer membrane structure
- gram negative import systems; porins and transporters
- protection systems: capsules, slime, biofilms

Animal Behaviour
- Polygyny. Asked the prof why several systems where both males and females have multiple mates are nonetheless known as polygyny. She said she'd get back to me.
- Parental care. Cost (future reproductive potential) vs. benefit (current reproductive success). Optimize sum of the two curves. Benefit of different amounts of care to different offspring based on their sex: Better to care for the limiting sex (generally female) if you/your offspring are of lower quality. Better to gamble on the non-limiting sex (usually male) if you/your offspring are of higher quality.
- Inclusive fitness, parent-offspring conflict over amount of care, r * b > c
- Tragedy of the commons. Occurs when benefit of an individual using a resource goes entirely to that individual, but cost is distributed among all individuals using that resource. Short-term gain is therefore maximized by selfish behaviour, even at the long-term expense of the resource. One way species can evolve themselves into extinction.

And that's that. Any suggestions for Tuesdays?

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).

---

*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.