No Offense

Recently a girl in my new lab said to me, "you can tell me if you find my jokes offensive. I know I tend to joke about a lot of crazy stuff, so you should tell me if it bothers you." She had just made a slightly off-colour (and not very funny) joke. Doesn't matter what it was.

I smiled blandly at her and returned to the actual conversation. At the time I thought that I was deciding not to say anything about her somewhat offensive joke because I didn't want to take the time to explain that the reason I found the joke offensive was not the reason she thought someone might find it offensive. Like explaining to someone that when they call your shirt "gay" you aren't offended because they didn't like your shirt. It wasn't that, but it was somewhat analogous. And I just didn't want to get into it.

I mean, it's true. I didn't want to get into that with her. But as I let more and more stupid little things from her slide, and I had absolutely no interest in mentioning any of them, I realized there was more going on. So here's the thing.

It's not about my feelings. First of all, my feelings don't get particularly hurt when someone makes derogatory remarks about a group I'm a member of. It's pretty simple: if someone is that much of a bigot then their opinion doesn't matter to me, and if their opinion doesn't matter, then nothing they say can hurt me. Really. My primary emotional response is boredom. But that's an aside, and here's the more important point: when it comes to my relationships, I don't want someone to refrain from making certain jokes or using certain language because I find it offensive. I want them to refrain from doing those things because *they* find it offensive. I want them to have thought critically about the assumptions that underlie their jokes and about the effect their language has on others. And if they are someone who does not do that kind of thinking, well, I want them to wear that fact on their sleeve.

Just one thing I do have to get off my chest, though: If you want to have a career studying sexually transmitted infections, then by the time you're in grad school you should be able to talk about sex without needing to crack terrible jokes to assuage your discomfort. Seriously.

Damn Buggers

Spent less than two hours at the Centre for Vector Biology yesterday, so of course I now have a mosquito bite in the middle of February.

My time is measured in assignments

For all that I've been in school basically my whole life, I've never really measured time like this. Certainly for the past three years of doing this biology degree I measured my time in the normal units: days, weeks, months, occasionally semesters. But now that I'm in my last semester I find my time is measured in assignments:

Am I done being an undergrad yet? No, I still have that presentation for Maydianne's class.

Will I be done after that? No, then I have two presentations for Mark's class.

So, if I do that can I stop? No, then I have to write a paper for the Plagues course.

And then will I be done? Uh uh, then I have to write mock grant proposals for both Maydianne and Mark.

Oh, well will I be done after that? Nope, I have to write up my research project.

And then I'll be done? Well, no I still have to present my research project.

And then? Well, then I'll be done with classes, but don't get too excited because I still have to spend four months hauling ass out to my stupid horrible no good very bad suburban campus for a research project. Pretend it's still undergrad or I won't be able to make myself do it.

And then? And then I'm done.

I have no idea what week it is

Seriously. Between funding applications, grad school applications, actual school work, and stressing about the fact that I'm not doing anything to prepare for the GRE's (yes, plural, general and subject), blogging just isn't happening. Maybe next semester. Or next summer. Or once I've finished my Ph.D., found a job, got tenure, and am nearing retirement. Bah.

Fall '09: Week 1 in Review

Week 1 was a short week. Technically classes started on Thursday, but I went in Wednesday to talk to my new supervisor about what my research project was going to be about, and do various other administrative things.

So, here's the review:

Supervised study

• Read the grant proposal for the project I'll be working on (invasion mechanisms of Salmonella
• Found out which aspect I'll be working on
• Signed and turned in all necessary forms and got approved for the course
• Got a look at the confocal microscope I'll be working on. Confocal microscopes are really cool. You take a cell that has some proteins that have been marked with fluorescent markers, and it uses a laser to excite the markers in thin slices covering the whole cell, and then it uses the slices to build a 3-D image that you can then look at. *Very* exciting.
• Was given two papers to read. Read the first and most of the second.

Animal Development

• Going to be looking at morphological and molecular aspects of development
• Prof acts like a teenybopper, anthropomorphises and makes cutesy statements about how chicks are easy model organisms for developments, "but I hope there aren't too many 'easy chicks' in here!"
• Some history of the field
• 250 people in this class, taught in one of the less comfortable auditoriums
• Pretty sure I'm going to drop this one

Molecular Aspects of Plant Development

• Prof is actually a grown-up, and expects us to be
• About 30 people in the class
• Learned about tools to track molecular events in cell at three levels:
  • Gene expression: take the promoter for the gene of interest, put a marker after it instead of the gene, put that complex in a vector and transfect the cell, scan for the marker. Marker is something that will fluoresce, like GFP, or GUS, which has an easy histochemical assay. Need to find out what "histochemical" means.
  • mRNA localization: take tissue, fix it in an RNA-preserving fixative, make labeled probes for the mRNA in question, marinate, wash, scan. Probes show up where the mRNA is.
  • Protein localization: There are two ways to do this.
    1. Immunolocalization: Fix tissue, make antibodies for the protein in question, marinate, wash. Then take other antibodies that bind to the conserved section of teh first antibodies and are tagged. Marinate, wash, scan. The tagged antibodies will show up where the protein is.
    2. Tagging: take the promoter/gene complex for the gene in question, stick the gene for a marker like GFP or GUS after it. Transfect the cell, scan for the marker. The marker will be attached to the protein and will show you where the protein is (unless the marker has interfered with folding or function of the protein).
• Was assigned two papers for next class. Total of 33 pages of reading. Yeep!

And that's all the classes for this week. Because it was a short week I didn't have any classes for Community Ecology and Evolutionary Biology or Intro to Health Studies: Plagues and Peoples. I'll tell you all about it next week.

I'm also devising some good systems for organizing my life. I started a new major knitting project to bring to class with me, and I've realized that I'm going to be doing a buttload of article-reading this semester, and that's just as easy to do on a treadmill as at a desk, so maybe I'll spend less time sitting. We'll see.

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?

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.

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.

Why I Love My Job

Conversation between me and one of the grad students in the lab today:

Me: Why are there fish from the grocery store in the freezer?
Grad Student: This is a fish lab.
m: uh huh...
gs: They're silversides.
m: and...
gs: But they're selling them as smelt, which is not even the same family! And they claim to have caught them in an area where you don't find silversides. So I figured I'd bring them back here, sequence their DNA, and find out what they really are.
m: you know you're the world's biggest geek, right?
gs: No, this is sweet. It's forensic ichthyology!

It Just Seems to Me

Without saying a word against the gentleman who was actually doing the job -- as far as I could tell his behaviour was completely professional and above reproach -- it just seems unlikely to me that the Athletics Department couldn't find a single woman with the skills to install an automatic opener on the door to the women's changeroom. I'm not sayin', just sayin'.

By Jaköbische Decree

All arguments of the following form are hereby banned from use:

1. "No/yeah, cuz I knew this guy once, and he..."

2. "If we had data, I think it would probably show X. In light of X, so-and-so is clearly right/wrong"

All people using arguments of this form shall be sentenced to live in a world such arguments produce.

My Psych Prof Sux

Since I can't send this email to him, I'm posting it here instead. Gotta vent somewhere.

It seems to me someone might want to update the dates and information on the assignments page. I mean, I know the prof is terribly busy, what with having to create a midterm – no wait, the questions are reused from year to year... okay, marking a midterm – no wait, that's done by machine... okay, adjusting the midterm grades – no wait, that's also a job a machine can do... okay, marking our assignments – no, we do that... okay, preparing lectures and slides – nope those are reused year to year too... okay, answering email – nope, three emails I sent this semester went unanswered. Anyway, I'm sure he spent at least an hour writing that screed against cellphone use while driving that we have to respond to, so he's clearly a very busy man, but maybe one of his minions could bother to update the instructions and due dates on the assignment page.

You know, for the assignment that's due on Wednesday? That page.

I Said...

I coulda sworn I posted this, but apparently blogger et it.

The best thing about my Evolution prof: She calls white Americans "European-Americans". Always.

meep

I have four midterms and a major lab report to do before the end of next week. Don't be surprised if you don't hear from me until then. Also, don't be surprised if you find yourselves picking little bits of my brain out of your hair after my head explodes from stress. Anyone want to read and summarize a bunch of articles on sexual selection/prey selection tension in guppies for me? No? Oh well.