I’d like to send this year out by notifying the group about Andrew’s Big Secret, which I discovered while vacationing in Charleston:
Seems he runs a real estate business directly opposite a bar that serves amazing oyster shots.
Who’d have thunk it.
Happy New Year!
Last week, Katey and Lindsay donned their gowns and got formally Doctored. Katey is my first US PhD graduate; Lindsay was primarily advised by Ottar, but he couldn’t make it. Something to do with being in Perth (the one in Australia). So I escorted them both. After almost two hours of ceremony, we were the last three to go on stage and I was the last to leave it. The applause was raucous. I don’t think I have ever had so many thousands of people so enthusiastic about anything I have ever done before.
This is the best available video on Youtube. I have rewatched George Carlin discuss the fear of germs more times than is still appropriate for me to mention, particularly because even after eight times I still cry from laughing.
The video clip comes in use for many purposes. You can use it to remind roommates, housemates, family members about the hygiene hypothesis. You can force-watch it with friends to preemptively avoid complaints about any of your less than sanitary habits. You can show it to your office mates if they get suspicious about your post-running shower (or lack of one).
My housemate is a very clean person. I made him watch this video shortly after he finished clorox-ing our countertops and he said that he learned more about the immune system than he learned all semester in his nursing courses. Though I am hoping this comment was made with heavy sarcasm, it got me thinking about how to improve the teaching approach. Are teachers in front of a classroom any different than entertainers in front of an audience? I like the idea of thinking of class as a show, a form of educational entertainment with us educators on a stage. A recent article in the Monitor on Psychology put out by the American Psychological Association reported that laughing produces both psychological and physiological changes in the human body that make our brains more receptive to learning. Humor is memorable and could be an untapped method in today’s education system. Think about this: If George Carlin taught immunology, would you ever skip class?
It is customary for infectious disease biologists to open their talks with a quote ascribed to Dr Wiliam H Stewart, who served as Surgeon General of the United States between 1965-69, ‘It is time to close the book on infectious diseases, the war on pestilence is over’. Beginning in this way gives members of the audience, particularly those that study emerging infectious diseases or evolution, the chance to smile knowingly at each other as if to say ‘Ha! How wrong they were!’. Having united the audience in smuggery, the speaker moves on, safe in the knowledge that they’ve established themselves as one of the tribe.
Dr William H Stewart
I decided to open my own bid for membership of this tribe, my thesis proposal, with this quote. To Google, I went. The quote was found, sure, but not a reliable source for it. Then I fell on a letter to Clinical Infectious Diseases by Dr Brad Spellberg. He too had gone after the quote and, after five long years of trying, had found no evidence that Dr Stewart had ever uttered it. Neither had the US Public Health Service. I wasn’t terribly surprised. I often find myself chasing merry go rounds of citations. ‘Author 1’ cites ‘Author 2’ who cited ‘Author 3’, who seems to have decided one morning to state that malaria parasites require a certain nutrient for growth, for example, without performing an appropriate experiment to demonstrate that this is so. Somehow the scientific community picks Author 1’s article as a favorite and it is cited as evidence of the nutrient’s importance, thereafter.
Being in the business of constant questioning, it seems obvious that we should ensure that a cited work actually demonstrates what it is claimed to, if only to prevent us from building ideas on shaky foundations. And, in this verity-pursuing spirit, I would like to join Dr Spellberg in calling for the use of other (confirmed) quotes to illustrate the point that it was once misguidedly believed that the ‘war’ on disease was over. Of the quotes that Spellberg found, I’m backing the use of a statement by Dr Robert Petersdorf, which nicely illustrates the point and might also get a laugh: ‘I cannot conceive of the need for…more [graduating trainees in] infectious diseases…unless they spend their time culturing each other’.
I saw this picture of the brain “Connectivity Matrix” — it is a map of the known connections between parts of the brain — and can’t stop thinking “Wow.” Our brains are so beautiful.
Our culture emphasizes a divide between the sciences and the arts, we have an emergent tendency to divide everything into categories as though math were one thing, music another, biology another. When I see a beautiful figure that comes out of scientific research, I think more and more that knowledge is one big heap, impossible to subcategorize, and it perhaps even loses something when we do.
Two days ago I met someone who works part time as an artist’s model. She sits for paintings that he then sells at art fairs and festivals and things. It seems like an antiquated idea that people still hire live models outside of art school, I always imagined “sitting for a painting” to be an activity of the last century. The model said that the artist has tried to teach her how to paint multiple times on the premise that everyone can learn to do art; though he is an artist, painting was a learned skill just like reading and writing. We don’t only teach “talented” people to read, we teach everyone. He argues the same should be true for art. I agree that it is odd that everyone in America is required to read and write but no one is required to learn how to paint. In my experience the emphasis on learning art is lost in many education systems because of our aversion to subjectivity in the grading system or perhaps the lack of more concrete teaching methods on how to foster creativity. How do we teach creativity?
Not only do we categorize knowledge as being art, science, math, etc., we also categorize people as being artsy, science-y, math-y. Musicians rely on math to maintain rhythms, artists rely on the scientific proportions found in nature to capture realistic images in their works and as a scientist, I appreciate the beauty of a simple figure depicting a thousand words I would have otherwise had to write. With all this emphasis on inter-disciplinary learning we should teach a class on the beauty of scientific figures. I want to be an artist in addition to a scientist so I can make images that exude excitement and creativity, like the human brain diagram does for me.
Also: go to the “gallery” tab on the Human Connectome Project page and stare at a few more “wow”-inducing photos. The diffusion in the brain video is also wildly exciting.
Every now and then I think about how much better I would be at grad school if I could do it all over again. But since I have no desire to go through grad school twice, I think it might be better to just send some advice back in time. After some consideration, I’ve decided that the two pieces of advice I would give myself are:
1. There are no perfect experiments.
2. You’re rarely, if ever, going to come up with a truly great idea but you can definitely come up with some publishable ideas. It’s the published ideas that do the most for your career.
These two pieces of advice are both based on the most valuable thing I learned in grad school, which is how to recognize and manage limitations. Unfortunately for everyone, this is something I could only really learn through experience. While I have no single gem of wisdom, an informal poll of the PhDs in my life did reveal that most people have some bit of advice that they would send back in time. This advice includes:
1. Read the [censored]-ing student handbook.
2. Take up a hobby, preferably a contact sport. And get a cat.
3. However bad it gets, don’t be tempted to get a cat.
4. A list of all failed experiments.
5. Get on with it.
6. You’re not as smart as you think you are.
7. Just relax, you’ll finish.
8. You will become better friends with alcohol.
9. Be nicer to your advisor.
10. Never graduate.
As a researcher who works in the Center for Infectious Disease Dynamics, do I have a professional obligation to take advantage of preventative measures to stop the spread of disease, like getting an annual flu shot?
I have to confess, I never got the flu shot before starting at CIDD. I wasn’t in a high-risk group (not very young, nor very old) and never gave it too much thought. Last year I got the shot, and felt like I had done my academic duty.
Since vaccines are available I plan to get it this year too.
The VAX game (developed at CIDD) shows how important vaccines can be to stop the spread of disease. Since CIDD is its own social network, we are in essence protecting each other by getting the flu shot (and washing our hands, practicing good hygiene etc). So, is it just altruistic to get the shot to protect our friends? Are vaccines wasted on our generally healthy population? If everyone got the flu shot in CIDD would productivity increase measurably? Curious to hear your thoughts.
The delicious, though expired, morning beverage.
This morning I woke up and had the best cup of coffee I have ever had in my life. Angels descended from the heavens, the coffee gods and goddesses were smiling over my kitchen, I was drinking Zeus’ ambrosia. (That is the best description I’ve got until we enter the age of internet transmitting smells and tastes — think “scratch n’ sniff” stickers but on a virtual level). If you can imagine coffee, imagine it 150x better than you are expecting it to be and you have replaced the need for a smelling/tasting internet. At first, I thought my year of working as a barista had finally paid off into high quality home brewing skills. Then I reached back into the cupboard to see what beans produced this type of magic and here was the kicker: Chock Full O’ Nuts and the beans were seven months expired. The coffee can was sitting on a shelf above the radiator, hot and musty; this was after they were given to me by my grandmother who gave up coffee five years ago.
That is how I arrived on the subject of coffee dates. *Not the kind that happen with people at places (e.g. with Dave and Laura mid-morning), but the kind that are printed on all our bean bags and coffee cans. For that matter how has it come to be that so many things we use and buy come with a set “best by” or “good until” date? I imagine someone sitting in front of heaps of coffee with a timer tasting it at intervals and am guessing no one at Chock Full O’ Nuts ever sat around for seven months or they would have extended the dating. My cynical side says that expiration dates are financial ploys to ensure a steady demand of new product. Does something vacuum sealed or dehydrated self-destruct when it reaches its sellable death day?
When we talk about coffee, the connoisseurs may think that dating is pivotal, but as scientists, what may be even more pivotal is how dating affects our reagents and how drugs may lose efficacy. Nearly everything we use in lab has a date on it but rarely do we know who calculates that date and how one day could change an end result (does the day before the expiration date significantly differ in product content than the day after?).
As law, most pharmaceuticals have to be sold with an expiration date. If you are a drug producer who recognizes that patients take medications with more gravity than I take my coffee, putting an earlier expiration date than is reflective of biological activity has multiple advantages, especially economic ones in addition to erring on the side of safety without stringent testing of later-dating product. Why would any company test the effectiveness of a 10-year old pill vs. a one-month old pill if being good for 10-years would mean your customer only buys product at that frequency? A 2010 story on National Public Radio (NPR) reported that the Food and Drug Administration (FDA) has never had a case of an adverse reaction from expired pharmaceuticals.
A study on the stability of active drug ingredients was put out by Cantrell et al. in the journal Archives of Internal Medicine last November, showing that even after 30 to 40 years on a shelf, the majority of drugs still had 90 percent of the amount of active compound listed, some having even more than the amount listed, by as much as 110 percent. Most drug expiration dates are one year after production date.
When we consider drug treatments for infectious diseases in areas of the world where transportation and distribution are slow and the time from production to receipt could shorten the window before the expiration date encroaches, would it do harm to extend dates? There may be a tremendous amount of waste due solely to the fact that we are throwing out product based on an arbitrary deadline. If dating needs to be reconsidered, who should do it? Currently, it seems like pharmaceutical companies, like coffee companies, food companies and most marketers of perishable goods, are in control of their own expiration dates which leads to high potential for selfish interests to be determining when customers buy new. If an unbiased third-party is needed for expired coffee testing, I volunteer.
Optical illusions are fascinating, because I rely on my visual impressions to be accurate. In fact, that’s how I stay alive as I cross busy streets on my daily walking commute, so I try to pay close attention to the cases where my perception doesn’t line up with reality. Over the Thanksgiving break I caught a few episodes of “Your {Bleeped} Up Brain”, a show that explores how our brains perceive the world and when those impressions are misleading. The show is very good, but I object to the title. My brain isn’t making mistakes, it’s skipping steps–that’s a great time-saver, and it probably saved many of my ancestors from unpleasant death. To take one example from the show, I’ve created my own optical illusion:
Origami dragons: which one is bigger?
Because of the perspective lines, people would describe the origami dragon on the right as larger than the one on the left, but they are the same size. I see this as an example of human brains being pretty well-adapted rather than bleeped-up. Picture if you will two humans, one who’s brain connects the dots and delivers the perception that the right dragon is quite large, and one who’s brain sees instantly that the dragons are the same size. If it were real life, the first human would be off and running, while the second one took each logical step in turn: (1) the two dragons are the same size; (2) one dragon appears to be behind the other; (3) if the first dragon is large, the second must be huge; (4) they’re coming this way; (5) run! One of these humans is much more likely to leave descendants. Thus, there’s a time and a place for logic, and that time is not when being chased by origami dragons.
Rarely does one’s survival depend on seeing through optical illusions and magic tricks, but I concede that the title “Your Generally Well-Adapted But Occasionally-Gullible Brain” doesn’t have the same ring to it.