The Pennsylvania Epidemic

My oldest nephew is seven. The last time I saw him, we spent hours and hours reading Harry Potter together. One of the things I love about this kid is his natural tendency to turn the ordinary into the wonderful and mysterious. For example, when he heard I was moving to Pennsylvania, he paused for a moment and then said,” Hmmmmm. I guess that’s like Transylvania except instead of teeth for fangs the vampires have pencils”. At first I just thought this was very clever and funny ……….. but lately I’ve been looking a little wan and my teeth have been hurting …….. and now I’m concerned that he had a much deeper appreciation of the risks involved in moving to Pennsylvania than I did.

P for possibly plausible?

Last semester Jo led an interesting discussion on significance testing for one of the graduate student meetings.

This week I stumbled upon this article in Nature that elaborates on what was touched upon during the discussion. The more this issue pops up, the more worried I become over understanding even what I consider to be the most basic of statistical concepts. Should I be analyzing my data differently or is it sufficient to acknowledge the limitations of the chosen method of analysis?

Motivatoring?

Recently I’ve been thinking a lot about how much malaria parasites should invest sexual stages that could be transmitted to new hosts versus asexual growth within the host. Even malaria parasites can’t have it all, and this creates a huge conflict for them. They can invest in growing within the host, and that means a lot of future opportunity to invest in transmission, but the length of the infection is uncertain so those future opportunities may never arrive. The tradeoff is akin to the complex problem of when and how much to put aside for retirement, and neither humans nor malaria parasites seem to plan ahead for the future.

My focus is the conceptual problem, but my knee-jerk reaction to motivating the problem is to talk about applied aspects: what parasites put into transmission they can’t put into making the host sick, so understanding optimal transmission investment could tell us why malaria can be so devastating, and how we might be able to trick parasites into making poor decisions. But Stuart Auld makes a compelling argument that we disease ecologists sell ourselves short by playing up the applied aspects of our work when the basic conceptual problems are so important. Something to consider next time you’re stuck in an elevator…

Nothing kills inspiration like a blank page

It might be better to start out a blog post by deleting a block of random letter combinations from the screen, and then typing.

The blank page is a known killer of writing. This phenomenon even has a name: Blank Page Syndrome. With infinite choice of what to write, writing anything at all becomes impossible, or at least much harder.

How to beat it? Lifehack’s website offers 10 suggestions. My favorites of these include starting in the middle, setting small goals such as writing for a set number of minutes, free-writing just anything to get yourself started without regard to whether it is any good or complete garbage (editing is much easier), and changing your physical location.

Other ideas? Having some curly fries at the ‘skellar with lab mates is also inspiring.

Contagious singing

It is February and I am in Maui, Hawaii — land of sunshine, beaches, year-round growing seasons, lush forests and frogfish that are absurdly interesting. But February means one more thing: I came in time for whale watching season.

Between early December and late March, the sounds of the Hawaiian coast change dramatically. Quiet with dolphins, honu’ea (sea turtle) and fish like the ulua, onaga, wahoo and monchong, the summers here are silent under the waves. In the winter, songs migrate in with the humpbacks. Swimming out deep enough and dipping my head underwater, I can hear the slow beats, moans, cries of a whale song. Only male humpbacks sing, and typically, only during breeding season. Each year the song changes, adding new choruses, called “themes,” or deleting other themes of the song from the previous year. Though whales in opposite corners of the ocean vary slightly in their tune, all males within one population sing the same song. To me this is amazing. Every year we see the same phenomenon: a new song is created, different from the previous year, but identical in sound between individuals. Research on whale behavior has yet to understand why whales sing, how they create the sounds or how they learn to mimic each other so exactly. However, the persistence and precise patterning suggests significance for the trait of singing to be maintained, and the energy to be invested in learning a novel song each year.

In Lahaina, Maui, the town plays a video on whale songs and humpback migration in the main square. I have already watched the video twice. At one point in the video, there is a world map displayed with highlighted blue dots representing whales. Viewers can watch the blue dots migrate back and forth from their breeding grounds, sometimes seeing the rare stray whale migrate into a different population. This is how new song themes are thought to be introduced, allowing for songs to change each year. A stray whale can spread the song of its “home” population into the “foreign” population, making the song appear contagious. What makes this particularly fascinating is that instead of conforming to the song of the new population, the “outsider” whale instead causes the rest of the population to change their song. The video makes the analogy that this would be like one person who speaks Swahili walking into Paris and instead of the Swahili-speaker learning French, all the Parisians start speaking Swahili. With humans we think of conformity happening to favor the masses. A tourist goes to Maui and picks up a bit of the local culture rather than a tourist going to Maui and Maui picking up the tourist’s culture. With whales ,it seems to be the opposite. It is a bit encouraging to think that a single individual can instigate change. We have all sorts of cliche quotes in English — “Be the change you wish to see…,” “One person can make a difference and every person should try…,” — we seem to need reminders that individuals have power or can exert influence, but in whale culture, individuals change culture all the time. We need look no further than at contagious humpback singing to understand how powerful one individual can be in the sea of an entire population. Pretty inspiring.

 

 

My new pet project

As an American working on malaria, I read a lot of papers reporting the results of field studies in places I’ve never been. I’m usually able to roughly place the country, for example is it in west Africa? East Africa? Coastal or landlocked? But in most cases, I have no idea where the field sites are relative to the boarders of the given country. This bothers me because I want to be able to visualize these locations as real places and not just names and coordinates in a paper.

As an attempt to remedy my ignorance, I’ve recently started mapping papers as I read them. Using Google Maps, every time I read a field study paper, I add a pin on the map. The color of the pin corresponds to the kind of study (e.g. insecticide resistance) and the label of the pin gives the reference and a few key points from each paper. Thus, in addition to showing me where a given study took place, I can also see what other studies were conducted nearby. It’s a work in progress obviously, but I’m excited to see it grow and I would be interested in ideas for how to expand the project.

P. falciparum: my close relative

On Friday night, when I was sitting in the cold for over 30 minutes waiting for a cab, I realized that I wasn’t all that different from a P. falciparum parasite. My chances of success are also influenced by whether or not I operate synchronously with my population. When my cab finally did pull up, I resolved to be an asynchronous organism (at least in the scenarios where asynchrony is beneficial).

Here are some scenarios I’ve identified (through some painful trial and error) that favor asynchrony:

1. Any errand that requires a cab. Don’t do this on a Friday night. My cabbie also suggested avoiding Thursday and Saturday night.

2. Absolutely, under no circumstance, should you attempt to use a laundry mat on a Sunday.

3. For that matter, don’t do any sort of errand that requires sharing a public resource on a Sunday.

4. Avoid the cafeteria between 12pm and 1pm. If you go at 11:45 your lunch will take 20min instead of 50min and you’ll also get first dibs on the salad bar.

I’ve also noticed that in addition to temporal asynchrony it can be beneficial to be spatially asynchronous. For example when you get off a plane, instead of standing in line at the nearest restroom, you should displace yourself from your fellow passengers and use a restroom at a gate where a plane hasn’t just arrived. The benefit of this strategy is highly sex dependent. Men will often lose time walking to a different location since there is always less competition for stalls in a men’s restroom.

I’m a little concerned that this posting will generate a large subpopulation of asynchronous organisms. If this happens, I’ll have to rethink my strategy (Megan can probably help me with that).

“The University of Google Doesn’t Count”

I know it is a Saturday night, and that I just blogged a few days ago. However, I just read this article and I cannot let it pass without a blog post.

Here, in “The Death of Expertise”, author Tom Nichols, a U.S. Foreign Policy analyst and professor at the Naval War College, discusses the meaning of the word “expert” in today’s hyperconnected, information-saturated, “like-share-comment” atmosphere. He makes the point that experts no longer exist, due partially to the fact that the internet and social media allow anyone to find out anything, and anyone to write anything. He does assert that this can often lead to enriching conversation, and true social and political change. However, he points to the danger in everyone’s opinion holding equal weight – the misnomer that democracy has become – leading to real, sometimes terrible, consequences. Pertussis and Playmates, anyone?

Now, I don’t agree with all of his points; a big part of sociopolitical, intellectual movements comes from a small, but motivated group of laypeople speaking up and saying “no, you’re not right, and your degree/experience/position doesn’t give you the right to assume you’re worth more or deserve power over me”. But, this isn’t what’s happening when your friend’s sister’s aunt shares an infographic on facebook about how the government wants to subsidize the murder of your children with GMO corn. Political movements aren’t born out of linking to a Wikipedia page you only bothered to skim. Intellectual dissent doesn’t happen in 140 characters. It happens in a social environment where experts are seen as experts, and their opinions are valued as such – but with an intersection with a public that maintains both general interest and healthy distrust.

I’m sharing this article, because while some of it is a bit egotistical, most of it is an excellently written, albeit hard-to-swallow, look at how feelings =/= facts, but for some reason, we’ve given more weight to emotion than evidence, and disagreement is considered offensive. Yes, in a democratic, “free” society such as the United States, it is expected, and should be protected, that your opinions have the same value as anyone else’s. But you can’t make things up under the guise of equality and expect education, innovation and improvement of society as a whole.

How BS jobs prepared me to be a grad student

I’m of the firm belief that every high school kid, no matter their economic standing, should have to work a part-time bulls**t job. Even if it’s only a few hours a week. I believe this because I worked at a part-time job from when I was 14 through my junior year of college, and I think it’s probably benefited me just as much as any class in college. Here’s why:

1. You’ll have to clean up crap sometimes. My first job was as an usher/concession worker/indentured servant at a movie theatre. I was paid $5 an hour. It was a large multiplex, with 16 auditoriums. Naturally, that means a lot of bathrooms. The odds were forever not in my favor when stuck on bathroom duty, which is what I did for a while when I first started there. This is where I learned, far before pledging a sorority, the concept of “everybody did it, now it’s your turn”. There’s going to be poop on the floor. And overflowing toilets. And your Sunday shift is 8 hours long. Go.

2. Do things quickly, but do them right. This piece of advice comes from my experience in retail. At the end of high school, when my best friends were Robert Smith and Morrissey, I worked at a Hot Topic, peddling packaged punk rock merch to soccer moms. But I had a lot of organization to do. A LOT. We sold band t-shirts by the hundreds, and every quarter, we needed to take stock of every single item in the store for inventory reports. All of my shifts were closing shifts, because I was in school. So when the mall closed at 10, we’d start our clean-up, consisting of folding hundreds of shirts, replacing hangers, exchanging displays, mopping floors, etc. I learned pretty quickly that accurate efficiency was my best friend if I wanted to get home before midnight.

3. Flattery, flattery, flattery. I waitressed. What else can I say?

4. Appreciate those who do “petty jobs”. They’re way less petty and simple than you think. My last job in college was as a pharmacy technician. I went to college in a small rural town, and even though it was small, we were the highest volume pharmacy for not only that town, but the whole county. There are probably a lot of things you do in your life that you think are complicated. Well, being the middleman between a fuming patient and a health insurance company is one of the most complicated things that exists, I am convinced. When people are sick, and drugs are expensive because their insurance doesn’t cover them, they get angry. And sometimes, they get downright nasty with their words. But being in that position, despite the fact I sometimes left for home in tears because of what someone said, or that one time a guy threatened to shoot me, I have a very deep respect for people on the bottom rung who put up with everyone’s crap. Whether it be the janitor who comes in while I’m still here at night or the person who serves me at the drive through. My PhD will never erase the fact that I’ve worked “petty” jobs…and they’re really hard!

Overall, these jobs also taught me that it’s possible to go from “seriously, what am I doing with my life this was the worst decision ever” to “I love this place and my coworkers are awesome!” within a day. And if I’d never cleaned explosive diarrhea off of a wall, worked a Black Friday starting at 4am, or tried to explain insurance benefits to a meth addict at 1am at the pharmacy, I probably would’ve quit by now.

Teacher, Teacher (Episode 1)

This semester, I find myself teaching for the first time. Having had the benefit of an incredible and intimate university experience and not being in the nature of doing things by half measures, I have ambitions to create an understanding of and even a little passion for my subject. That said, I need to ‘Get ‘er (PhD) Done’ and have a passion for my own endeavors. So a tension arises: how can I teach well enough to satisfy The Higher Ups and my slightly megalomaniacal ambitions to inspire a generation, while maintaining a clear focus on research? To solve this tension I did what I always do when presented with a problem – collate the knowledge of others; take their ideas for a ride;  pick holes in them; create a new way, if needed.

So, here’s a two parter. First, all the advice I collated on saving time while remaining an effective teacher and then, at some later date, an insight into what works at PSU and what doesn’t as well as any nuggets of my own. After all, its good to see things through the eyes of one’s students and I hear two-part blogs are all the rage among the undergraduate populus…

The First Day

  • Be authoritative, even strict.
  • Think about what you expectations of students are before teaching, set them out clearly and stick to them for the duration of the semester.
  • Make it clear from Day 1 that no question is a stupid question.

Preparation & Scheduling

  • Spend a maximum of one day preparing – preparation will fill the time you allot to it.
  • Given the above, arrange to teach at the beginning of the week. This will leave the rest of the week free for research.
  • If you have the opportunity (and you may not if you heed the above) watch another more experienced TA teach the material, before you do. This will help you to gauge the timing of the lesson & get a sense for where the students trip up, preventing you from having to explain misunderstandings over email etc.
  • Teaching is exhausting – don’t expect to do anything productive for at least an hour afterward.

Grading

  • You will never want to do grading so just suck it up and do it.
  • Don’t let grading build up, its so much worse when its 3 days worth.
  • Establish your marking technique/rubric and stick to it.
  • If marking a writing assignment read a good selection of your students’ papers (including a known good, average and poor student) to set your rubric and then grade. This will help when trying to justify why you graded in a certain way.
  • Keep grading away from your office, take it home (making sure to make copies before doing so).
  • If you can split your grading with other TA’s, pick a page each and grade just that page from all the students. Less page turning, just one answer to remember.
  • Do not accept complaints about grades for at least 48 hours after the assignment is returned. If a student wishes to contest their grade ask them to explain in writing why. You’ll be amazed how few complain.

Office hours

  • Establish a position on how much you want to help with topics that come up in lectures (assuming that you are only paid to help with the labs) and stick to it.
  • Book a room for office hours near your office.
  • If allowed, make office hours by appointment to save you from spending hours alone in a room that it took you 15mins to get to.

Attitude

  • Be enthusiastic – it will make it more fun for you & your students.
  • You need only be better than one other TA in your cohort.
  • Try not to be lousy.
Terms & Conditions: I will not be taking bets on who recommended the last two.
Please feel free to add your own for the benefit of all future grad students.

What is resistance?

And more to the point, how does it differ from natural variation in susceptibility within a population?

(image from this Nature news piece in 2011).

In the insecticide resistance literature, the World Health Organization defines a population of mosquitoes as resistant to an insecticide if fewer than 80% of them are killed by a one-hour exposure to a given concentration of a chemical.  It’s not a great definition, but at least it is bounded by time and numbers. The WHO categorizes resistance as four types: 1) increased metabolism to non-toxic products 2) decreased target site sensitivity 3) decreased rates of insecticide penetration (thought to be insignificant unless in combination with other mechanisms) 4) increased rates of insecticide excretion (considered uncommon and producing low resistance).

The same WHO document states: “Resistance mechanisms do not necessarily operate throughout all life stages” referring to insecticide resistance testing in mosquitoes. This struck me as similar to malaria where drugs don’t necessarily work on all possible targets (liver stages vs. blood stages for example).

This is just starting fodder for a TBD meeting discussion. Resistance seems poorly defined in many areas of disease prevention and treatment, even when we are looking for it. How does one determine that resistance is a problem? For mosquito control, not all mosquitoes in a population might have resistance to a particular insecticide, and not all “resistant” mosquitoes will survive a dose of chemical, it might depend on how much of it they contact. I’ll be thinking about antibiotics, malaria drugs, and other topics with “resistance” issues – add your two cents here to get a conversation going.

The most money I ever found

Lease renewals in State College happen earlier than probably any other place in the world.  The other day I was required to decide whether to extend my current lease that ends in July.  When I went to the rental office to sign the renewal agreement, I noticed that the rent was $215 per month less than what I was expecting it to be ($2580 over the lifetime of the lease).  How did I react?  I didn’t say anything, signed it, and requested a copy.

Two hours later, I received an email explaining that the rent was listed incorrectly, and requesting that I sign an updated version of the renewal agreement.  The renewal agreement states very clearly that it is a legally binding document.  As such, I’m pretty sure that I’m in the position of power here.  I get to determine what happens moving forward.  I thought about it for a while, and I’ve determined what I’m going to do.  My question for you is, what would you do?  And I don’t mean in the abstract case, I mean in the very real case where the difference is $2580 in your pocket.

For anyone curious, my plan is to let the gods decide.  Go to a casino, and bet it on red.  Re-sign if it hits; everybody wins.  Also, because tone doesn’t always come across in text, that is a joke.  I’m going to sign the stupid thing.  Very reluctantly.