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.
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:
- 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.
- 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.
- 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.
- 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.
Via Bitch, PhD, we see that anti-choice organization Operation Rescue will holding protests outside abortion clinics all over the US and in a few Canadian cities for 40 days starting /september 23rd. You can check their website to see if a clinic in your area is being targeted, and if so, get in touch with them and ask how you can help.
Please do contact the clinic first, and don't just show up to yell at the protesters. The point here is to help protect the clinic's staff and patients from harassment, not to make life just outside their doors even more noisy and tense.
George Sodini was certainly disturbed. Healthy, well-adjusted people don't go into fitness clubs and shoot up aerobics classes. Nor do they enter universities and shoot students sitting in class and walking in the halls. Marc Lépine was also crazy. But to therefore conclude that nothing about society can be learned from their actions, that nothing can be generalized from their self-stated motivations, is preposterous.
It is possible, even likely, that in a society free of patriarchy, Sodini and Lépine would still have gone on murderous rampages. These two men both felt they had failed in some aspect of their lives. For Sodini it was sex and romance, for Lépine the failure was more general, I think. He was rejected by the army, had difficulty making friends, and generally wasn't happy with his life. It seems likely to me that these failures would still have happened in a patriarchy-free society. Sodini and Lépine both blamed others for their failures, not taking any responsibility on themselves. This strikes me as equally likely to have been true even in a patriarchy-free society.
What strikes me as considerably less likely is that in an egalitarian society, they would have chosen to blame for their failures, and therefore kill, the same groups of people they did.
Even lunatics need context from which to draw their ideas. Sodini didn't shoot up an aerobics class, he shot up a women's aerobics class. Lépine didn't kill students, he killed female students. And the stories they told are familiar as hell. Any woman trying to make headway in a male-dominated field, hell, anyone with regular social contact with a large number of men has heard these stories before. Amanda Marcotte gets it exactly right when she says that women are put down, beaten, or killed for being insufficiently compliant. From refusing to be sexually available to a man to daring to succeed where a man has failed, the crime for which women are continually punished is that of acting like competent, self-reliant, independent adults, and it is exactly this behaviour that George Sodini and Marc Lépine blamed their failures on. It is for these reasons that Sodini and Lépine killed women and not some other group.
Contrary to what Naomi Lakritz seems to think in the above-linked article, I am not blaming men (all men or any particular men, or men as a group) for Sodini and Lépine's behaviour. I don't believe that all men have a little Marc Lépine in them, or that men as a class can be hanged on George Sodini's actions. What I do believe is that the choices these men made were not conceived in a vacuum. Like the choices many other men make, to beat or rape their wives and girlfriends, to mistreat the women in their office, to pass over their female employees for promotion, and to dismiss their female friends in conversation, Sodini and Lépine's choices of who to kill are symptoms of a common cause. Of attitudes prevalent in our society, and many other societies, about how women are or should be versus how men are or should be. These attitudes are held and perpetuated by both men and women and it's less a question of blame than it is one of effect and remedy.
In effect, if not intention, these massacres are acts of terrorism against women. That they were killing women because they were women means that I, and all the other women who weren't in those rooms, am still alive only by an accident of time and place. That knowledge breeds fear. It disinclines women to do things, go places, participate fully in society.
So what's the remedy? I'm not sure. But I would say that, contrary to what Ms. Lakritz would like, the first step is talking about it.
Via Pharyngula, Simon Singh's original supposedly-libelous article:
Some practitioners claim it is a cure-all, but the research suggests chiropractic therapy has mixed results - and can even be lethal, says Simon Singh.
You might be surprised to know that the founder of chiropractic therapy, Daniel David Palmer, wrote that "99% of all diseases are caused by displaced vertebrae". In the 1860s, Palmer began to develop his theory that the spine was involved in almost every illness because the spinal cord connects the brain to the rest of the body. Therefore any misalignment could cause a problem in distant parts of the body.
In fact, Palmer's first chiropractic intervention supposedly cured a man who had been profoundly deaf for 17 years. His second treatment was equally strange, because he claimed that he treated a patient with heart trouble by correcting a displaced vertebra.
You might think that modern chiropractors restrict themselves to treating back problems, but in fact some still possess quite wacky ideas. The fundamentalists argue that they can cure anything, including helping treat children with colic, sleeping and feeding problems, frequent ear infections, asthma and prolonged crying - even though there is not a jot of evidence.
I can confidently label these assertions as utter nonsense because I have co-authored a book about alternative medicine with the world's first professor of complementary medicine, Edzard Ernst. He learned chiropractic techniques himself and used them as a doctor. This is when he began to see the need for some critical evaluation. Among other projects, he examined the evidence from 70 trials exploring the benefits of chiropractic therapy in conditions unrelated to the back. He found no evidence to suggest that chiropractors could treat any such conditions.
But what about chiropractic in the context of treating back problems? Manipulating the spine can cure some problems, but results are mixed. To be fair, conventional approaches, such as physiotherapy, also struggle to treat back problems with any consistency. Nevertheless, conventional therapy is still preferable because of the serious dangers associated with chiropractic.
In 2001, a systematic review of five studies revealed that roughly half of all chiropractic patients experience temporary adverse effects, such as pain, numbness, stiffness, dizziness and headaches. These are relatively minor effects, but the frequency is very high, and this has to be weighed against the limited benefit offered by chiropractors.
More worryingly, the hallmark technique of the chiropractor, known as high-velocity, low-amplitude thrust, carries much more significant risks. This involves pushing joints beyond their natural range of motion by applying a short, sharp force. Although this is a safe procedure for most patients, others can suffer dislocations and fractures.
Worse still, manipulation of the neck can damage the vertebral arteries, which supply blood to the brain. So-called vertebral dissection can ultimately cut off the blood supply, which in turn can lead to a stroke and even death. Because there is usually a delay between the vertebral dissection and the blockage of blood to the brain, the link between chiropractic and strokes went unnoticed for many years. Recently, however, it has been possible to identify cases where spinal manipulation has certainly been the cause of vertebral dissection.
Laurie Mathiason was a 20-year-old Canadian waitress who visited a chiropractor 21 times between 1997 and 1998 to relieve her low-back pain. On her penultimate visit she complained of stiffness in her neck. That evening she began dropping plates at the restaurant, so she returned to the chiropractor. As the chiropractor manipulated her neck, Mathiason began to cry, her eyes started to roll, she foamed at the mouth and her body began to convulse. She was rushed to hospital, slipped into a coma and died three days later. At the inquest, the coroner declared: "Laurie died of a ruptured vertebral artery, which occurred in association with a chiropractic manipulation of the neck."
This case is not unique. In Canada alone there have been several other women who have died after receiving chiropractic therapy, and Edzard Ernst has identified about 700 cases of serious complications among the medical literature. This should be a major concern for health officials, particularly as under-reporting will mean that the actual number of cases is much higher.
If spinal manipulation were a drug with such serious adverse effects and so little demonstrable benefit, then it would almost certainly have been taken off the market.
Simon Singh is a science writer in London and the co-author, with Edzard Ernst, of Trick or Treatment? Alternative Medicine on Trial. This is an edited version of an article published in The Guardian for which Singh is being personally sued for libel by the British Chiropractic Association.
You need to opt out of them using your picture in ads. Carl Zimmer explains how:
Facebook lets 3rd party advertisers use your posted photos without your permission. To opt out: Click on SETTINGS (located on top of page in blue bar, next to logout); Select PRIVACY SETTINGS; Select NEWS FEEDS and WALL; Select the TAB that reads Facebook Ads. There will be a drop down box; Select NO ONE. Save your changes & then pass this on. [Thanks to Virginia Postrel]
NB: I use AdBlock Plus and I needed to temporarily disable it in order to see the drop-down menu.
Via Greg Laden
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.
- 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.
- 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.
- 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.
- 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.
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:
- while loops
- building dictionaries from files
- 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
- 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?
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...
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.
- 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.
- 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.
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.
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
- 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
- instinct only
- comparative psychology
- 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-
- 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
- C-C bonds:
- Prefix (substituents):
- number carbons to give lowest numbers
- list substituents alphabetically
- Conformational Stereoisomers: conformers, rotation around C-C bond
- Torsional strain, steric strain
- Energy profiles of conformers
- 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:
- suspected pathogen should be present in all cases of disease and absent in all healthy individuals
- suspected pathogen should be grown in pure culture
- cells from pure culture should cause disease in healthy individual
- 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
- 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)
- 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:
- 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
- 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)
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)