I don’t want to use this post to veer into one of my long rants about how we’re all supposed to be trained only as researchers and nobody values teaching quality. All you need to know is: I love teaching, and I am not meant for research.

The THE500 course is taught by several expert guest lecturers who come in to talk about topics such as plagiarism, teaching technology, dealing with classroom disruption, assignment design, making a course outline, etc. On top of that, there are two microteaching sessions, in which you have to teach a 10 minute class for your fellow students (who are all from different departments) and you’re evaluated by a teaching expert. I taught my two mini classes on restriction enzymes and PCR, linking it with forensics.

We also had to write four assignments: The first was a course outline for a proposed course. The second assignment was to write your teaching philosophy as part of your teaching dossier. The third assignment was a group assignment, where you had to pretend you were a hiring committee and prepare a job ad and interview day for potential faculty (I didn’t really like this assignment. I think it was meant to show what the interview process is like, but we had already had a panel discussion with new faculty who explained it in detail).

The fourth assignment was to discuss a paper on any topic related to teaching in higher education, OR you were allowed to substitute this assignment with something else if you had a better idea. I substituted my paper discussion for an article about MIT’s OpenCourseWare program.

Upon reading my article, my course coordinator recommended that I submit it to The Bulletin – UofT’s newspaper for faculty. I did, and they asked me to add a little paragraph to make it UofT-specific, and it was published in the current issue. Pick one up if you’re at UofT! It’s the May 13 issue, and my article takes up the entire back cover.

Alternatively, you can read the original version of the article which I’ve uploaded as a PDF (with a little background info added at the top)
This version does not have the UofT-specific advice at the end, but I figured that if you don’t have access to the newspaper, you’re not at UofT, and you don’t care about that anyway.
The original also has all the references and footnotes that were stripped off the published version.

WOULD YOU RATHER….

a. Spend the money on research that is carried out in institutions that are already at the very front of scientific discovery, to keep up the pace and get the newest information the fastest, but neglecting underfunded countries and institutions.

OR

b. Spend the money on supporting research and science education in second- and third world countries, to give them a chance to catch up, but risking slowing down the top labs, so effectively slowing down the stream of new information (which everyone has access to)

(NB: I am just curious, not actually responsible for the entire world’s science funding. I’d only spend it in coffee shops and bookstores, effectively supporting a whole industry of increasingly wealthy coffee bean farmers and twitchy readers and writers – but we’d soon run out of good science books.)

The title, “Playoff game snack gorging linked to rise in mouth burns”, sounds like there was a study done to suggest this. Maybe two groups of volunteers, one ate vinegar chips every day for a week, the other didn’t, and the first group got mouth burns. A simple experiment that a child could have done for a school science fair.

But once you start reading, it quickly becomes anecdotal, and then descends from there to guesses.

”A Montreal dentist says…”
”We’ve had a couple of cases…”
”...patient really didn’t know what caused it”
”...perhaps the potato chips…”

Yeah. If there were science tabloids this would be on the cover. I’m not saying that there is no way that this could be true. Sure, it’s possible the chips are related to mouth burns. It’s also possible that the celebrities on the covers of the checkout counter magazines are really pregnant and depressed, but it isn’t actual news until their publicist confirms it. With the chips it isn’t actual news until there has been some sort of controlled study. Then we can worry about the chips and about our favourite depressed or pregnant celebrities.

Guys, first of all, I am so sorry about how long-winded this is. This installment only has one step!
Next time I’ll talk about the panel discussion I did at SciBarCamp. I have a problem, though: I have no notes of it, because I was moderating and was very busy with making sure the discussion was happening fairly and interestingly. I didn’t have time to reflect on what people actually said. If you were there and took notes, please send me them.

And now, part 3!

Step 6: Summarizing the poster
After the first day of SciBarCamp I was left with a poster full of individual suggestions for things people thought everyone should know about science, and the promise to hold a session the next day to talk about it. I tried to narrow down the next day’s discussion by grouping somewhat similar statements under more collective sentences, to make it easier to talk about. Unfortunately, it’s really hard to interpret underlying themes from short statements, and when I looked at the list a few days later I saw different ways of grouping everything, which would have changed the whole discussion. Due to the nature of the weekend’s events, I also ended up doing all this at 3 AM after coming home from the pub after a long day of running around. Ideal work conditions? Not so much. But another reason why this part didn’t seem to go so well is that this was the only part of the entire process where I did all the thinking myself. Everything else was collaborative. Had I had more time, in retrospect, I would have preferred to have the grouping done by a large group of people, if at all. I don’t like how this part was very much dependent on just my own middle of the night brain activity.

But just to put everything out there, this is the complete list of everything on the poster and the way I grouped it (Numbers indicate the number of people who agreed if this was more than one. So a sentence with one check mark got marked “x2’, because it was two peoples’ suggestion for something that everyone should know about science.)

• “Even my six-month old is a scientist”
• “When you go to bed every night you observe that the floor exist. You have a (subconscious?) theory that the floor will be there when you wake up. When you awake and test your theory by stepping out of bed, you have used science”
• “Science doesn’t have to be difficult, complicated, elite, or gendered” (x2)

• “Science-based reasoning should not be the only criteria for determining policy”
• “Science will not save the world”
• “It’s not the only way to truth and understanding” (2x)
• “There is a lot of uncertainty in science, and that is okay” (x2)

• “It’s not science’s job to save the world”
• “Science IS the only way to truth and understanding”
• “Science always wins in the end”

• “Key ingredients of science are intuition and imagination” (x2)
• “Science
  Can be expressed
  As a haiku”
• “Science is a human activity, take from that what you will” (x2)

• “There is nothing as an “objective fact”. We always filter perception by sensors and models”
• “Observations, like opinions, are based on frame of reference”
• “Science is a way of finding things out without (un)intentionally fooling yourself into arriving at false conclusions”

• “That it is falsifiable, and other so-called ways of knowing are not”
• “The appearance of “design” does not necessarily imply design”
• “Science is about evidence”
• “That is based on testable hypotheses and replication” (2x)

• “Evolution” (x3)
• “[everyone should know] Basic proven facts, like the time earth takes to orbit the sun”
• “C = π d “
• “You can’t “escape” gravity” (2x)

• “Scientific knowledge is not isolated. Different scientific theories connect” (3x)
• “Science can be done in several ways. Finding a “valid” one is as much part of the “process” as any other”

• “The words “theory”, “believe”, and “random” are used differently by scientists than by the general public”
• Reply to “science always wins in the end” was “what does that mean?”
• Reply to “Basic proven facts…” was “but when is something “proven”

• I sometimes had a very hard time coming up with the proper description for a group of statements. “The practice of science is independent” is probably the best example of this. I should have said something about “evidence” or “experimental data” there, I guess.
• Some categories might be considered more significant than others, even though they all contain roughly the same number of statements. The entire group about basic scientific facts could be considered a whole different discussion: are we talking about facts people should know, or about the practice of science?
• Some statements could have been in different or in multiple groups, or some groups could have been merged. “Anyone can do science” and “Practicing science is a human activity” are quite similar. And the statement I would much rather have put into a different group was “Science is a way of finding things out without (un)intentionally fooling yourself into arriving at false conclusions”. It should have been in the “independent” rather than the “not independent” group. I ended up crossing it out from the list I brought with me to moderate the panel discussion (more on that later), so nobody knew that I had grouped it wrong and the bigger categories stayed the same, but still…

What I could or should have done was not meddle with the things people wrote down, but pick some of the more popular statements directly from the poster and discuss those. By grouping them and giving the groups new names, I changed what people wrote, and likely influenced the rest of the discussion.

If there had been more time in between having people write on the poster and the discussion afterwards, grouping might have been done as a group. And if I may take a minute to dream about this: The whole list of suggestions could have been posted online, and people could have collectively decided how to summarize it. About a week or two weeks time between poster and discussion would have been enough time for people to digest the poster, and in a perfect world there would be a kind of interactive website where people could first suggest different categories and then a week later the website would show the suggested categories and people could visit again and drag different statements to the different bigger themes – a choice that wouldn’t be visible to other website visitors but would be tallied behind the scenes to ultimately make a list similar to the one I made by myself, but done by a whole bunch of people.

So that was the step I didn’t like. Either this type of discussion should not be done in one weekend, so there is more time to think about this part of the process as a group, or if it has to be in one weekend this step should be entirely left out.

Next time: the panel discussion!

Step 3: Proposing session at SciBarCamp opening night
We started out SciBarCamp with an empty schedule, and on Friday night everyone was free to suggest a topic by filling out a form and putting it up on one of the boards that were spread out across the room. People milled about, talked to each other, read all the proposals, and marked which ones they liked, or left comments and suggestions on the forms.

Looking at proposed talks on Friday night

Because some people had already read my proposal on the wiki, or saw the blog posts about it, they actually asked me about it that night, and I could point them to the appropriate form.
Any votes were only for the sake of scheduling talks in the appropriate rooms, because there was enough room in the schedule to give everyone who wanted to lead a session the chance to do so.

Step 4: Presented introduction on Saturday
I actually wanted to just put up a blank poster on Saturday, and talk about it on Sunday, but found out on Saturday morning that I had an entire big time slot that I didn’t need, so I ended up giving most of my time away and only talked for about ten minutes to introduce what I wanted to do.

Saturday schedule

In this short introduction I mentioned that even though my topic was called “Ten Things Everyone Should Know About Science”, I didn’t actually have a list of these ten things, because I can’t decide that by myself. It’s something that’s easier thought about with a big group of people. I also gave some background on why I thought this was an important topic: I often spend time with people outside of science, and many of these people are very smart, and I tend to assume that they know at least some very basic things, but then find out that many people don’t know what a gene is, or that breeding is a form of genetic manipulation too. So what should everyone know about science? Should they know these facts? Or should they know something about how research is carried out or communicated?
I brought a big blank sheet of paper with the title “What Should Everyone Know About Science?” and invited everyone to contribute to it over the weekend.

Step 5: The poster
On Saturday afternoon, people had a chance to leave their thoughts on the poster, leave a mark at statements they agreed with or counter those they didn’t agree with. It was fun to see people gather round it and read and think together, or wait for people to leave and write something down by themselves.

Poster in progress, with Nature Network Sharpies clipped on

Why did I collect opinions this way? In verbal group discussions (and online as well) not every voice is equally loud. Some people have no problem sharing their views, and others are more subdued. Some people don’t feel like typing a comment on a blog, or don’t like raising their hand in public. Writing one sentence on a poster is a lot less scary, and by giving everyone a chance to write one sentence (or “second” it) it remained somewhat balanced between participants: you can’t see who wrote it, so the quietest person and the loudest person’s statements are of equal value.
People’s backgrounds aren’t taken into account either. You can’t tell by looking at the poster which statements were written by professional scientists and which statement was written by a fifteen-year old. You might say that that’s a bad thing: doesn’t a professional scientist know better? I don’t think so: by rule of thumb the general public has the same level of scientific literacy as someone in grade 9 or 10. Popular science articles are aimed at this level. It’s much easier for a fifteen year old to gauge whether something is at a grade 9 or 10 level than for someone who has been submerged in their own specialty for years. Remember, this is about what everyone should know, and most people haven’t studied science after high school. A large group of SciBarCamp participants were artists with a high interest in science. (Of course they’re interested in science, why else would they even be there?) They also know more about science than the average Joe, because they’re the ones that actually read all those popular science articles that others might line the bird cage with.
Everyone who was at SciBarCamp was more scientifically literate than most people, but not all to the same extent or in the same area of science. This variation is also a benefit: by talking to new people you suddenly find out that they don’t know as much as you thought about a certain topic. That’s eye-opening. That means that there are probably many others who don’t understand it either. I’m a huge fan of scientific outreach for this reason: it’s not just scientists teaching the public, it’s also scientists learning what the public knows or not, and finding out where the knowledge gaps are.

I wanted to use the poster as a foundation for further discussion, so I signed up for a longer time slot on Sunday, and took the poster home to summarize what people wrote on it. In retrospect, that was something I should have done differently, but more on that later.

But today they posted a series of Greenpeace posters about genetic engineering that just don’t make sense at all, and they did not point out that the posters are ridiculous.

The good news is: if you look at the comments they’re full of people who understand what Greenpeace (and Treehugger, unfortunately) did NOT. I still decided to leave my comment as well, just to add to the voices, but I’m glad that the average Treehugger reader is smart enough to recognize crazy genetic fear mongering. The first comment already drives home the point, and everyone else just elaborates.

Of course, this incident reminded me of my SciBarCamp session and prompted me to work on the second part of my write-up for that.

It also reminded me of this xkcd comic :

So, Nalgene drinking bottle contain Bisphenol A, and Bisphenol A is about to be banned in Canada from baby bottles etc.

But forget the water bottles: if you work in a lab you’ll know Nalgene as the company that produces pretty much everything that’s made of plastic in your lab: plastic big beakers, measuring cylinders. There’s a big Nalgene pipette washer behind me as I type this.

If they change the composition of their plastics, won’t that affect someone’s lab results at some point? I mean, those buffers stored for months in Nalgene, for example, won’t they take up way more Bisphenol A than the water that’s in your bottle for half a day? Dialyzing antibodies in a 4-liter Nalgene beaker overnight, would that make a difference with or without Bisphenol A?

Meanwhile, here is a practical tip for cell biologists: don’t book four hours of confocal microscope time right after a visit to the optometrist… Those pupil dilating drops don’t go well with the need to peer through eyepieces and focus on fluorescent cells.

Introduction:
In organizing SciBarCamp one of the things we wanted to do was to get the participants to think about some of the topics they might be interested in before the event itself. On the first night we would give everyone a chance to suggest a session, but we thought it might help people to get their thoughts flowing before they came in. We had a page on the SciBarCamp wiki where everyone could leave their suggestions for topics. A few weeks before the event there wasn’t much there yet, and I wanted to encourage people to leave their suggestions, so as an example I added a topic that I am interested in myself:

On a few recent occasions I found myself explaining things about science in general or about my specific field of Molecular Biology that I thought everyone knew already. I had to explain what a gene is to people who are mere months away from getting a PhD. If they don’t know, how can we expect the general public to understand all these news articles about genetic mutations that make a person more or less susceptible to diseases. And what is a mutation? Mutations are “bad”, right, like the evil mutants in cartoons and video games? Words like “mutation” and “theory” have certain meanings in daily life and other meanings when the same words are used by scientists to talk about their work. Should people be aware of that? What is it that many people may not know about science and really should know?

This is a huge question, and definitely not something I, or anyone, can answer by themselves. I don’t even think a group of just scientists can answer this, because they know too much. They’re too involved, and might overlook things that they find obvious, but which are not necessarily obvious to everyone else. You have to have some feedback from people who can take a step back and who are not “burdened” by too much knowledge of one particular field of science in trying to see a bigger picture.

The SciBarCamp audience was pretty much ideal, because there were some experienced scientists, who know what it’s like to do research, there were graduate students, there were people who work in both science and other fields, and there were a lot of people who weren’t practicing science themselves, but were at least very interested in it and think about science and scientific discoveries and research once in a while. Of course there were only a limited number of people there, so while there was a somewhat large and varied group, you can be even more diverse if you let other people in on the conversation, and that is exactly what happened here.

Step 1: Online Suggestion
In an attempt to get other people thinking about topics they might like to discuss at SciBarCamp, and to get some discussion going, I posted the following on our wiki:
”Since we have some outreach people, writers, artists, bloggers, and other communicators of science I thought we could maybe do some sort of panel discussion about things you think everyone should know about science, or about common misconceptions. (eg. use of the word “theory” in a science context does NOT mean “I don’t know, here’s a wild guess.”, or the discrepancy between science being presented as a list of finished facts/formulas in high school and the dynamics/discovery of actual research)”

Then, to draw people’s attention to the fact that I edited the topics page and that they can do so too if they pleased, I wrote the following on easternblot.net , brainstorming as I typed:
”My idea: find 4 or 5 volunteers from different backgrounds to sit on a 20 minute panel and (with audience feedback) make a list of Ten Things Everyone Should Know About Science. Since we have a wide audience, this hopefully would be a varied list. Actually, maybe we could just put up a large sheet of paper and have people write down what they think should be on the list and get back to it later.”

Step 2: Online Spread
After I posted my suggestions, Michael Nielsen hooked in on the topic with a blog post about what it means to know something and Larry Moran made his personal list of Ten Things Everyone Should Know About Science to which he got several responses in the comments, spreading the conversation further. Chad Orzel, who would not be attending SciBarCamp at all, read Michael’s post and gave his three suggestions for Things Everyone Should Know, generating many more comments on his blog as well.

What happened here is quite interesting: I suggested a topic to discuss at an event that was limited to a certain location, time, and group of participants. Yet here were people starting this very discussion online, and people from all over the world had a chance to participate at their leisure. Of course it happens quite regularly that people are talking online about conferences taking place elsewhere, but what was unique here was that some of the people online were attending the conference, and I was reading everything myself, so the discussion that started online was incorporated into the discussion as a whole, and later referred to.

But I’m getting ahead of myself, we’re not even at SciBarCamp yet. That will be step 3, in a new post, which I haven’t written yet. I just thought I’d give you something to start reading.

Among other things, we accept essays that have previously been written for course assignments and aren’t otherwise used. (Ask course coordinator to check if you can submit to Hypothesis, but it’s fine with us that is was previously course-work)

I’m specifically mentioning this category of possible submissions, because it’s already so very close to the deadline and this is work that has already been written.

We do not accept work that has already been published elsewhere. Check guidelines for anything else. And keep in mind that everything is peer reviewed. For opinion pieces that means you need to not even begin to submit if you don’t cite your sources or use proper argumentation. Our reviewers will jump on that right away.

Anything that comes in after the deadline will automatically move on to the fall issue but will get into the review pipeline as soon as possible. So submit things even if you won’t make it in time for Monday.

P.S. we’re indexed in Google Scholar, everything is open access, and there is a small print run distributed among University of Toronto people, subscribers, and the National Library of Canada.

The assignment I’m writing is on MIT OpenCourseWare first proposed in 2000, announced in 2001, and launched in 2002.
So, yes, it was conceived before Open Access and Wikipedia were known, but this endless fact checking is why everything always takes so long to write…

I’ll be posting photos more regularly over the weekend on easternblot (because I can post directly from Flickr on there)

This why it all takes so long: you have everything all planned out, and nothing can possibly go wrong, but then you have to do more troubleshooting. Grr.

The event covered both a science-inspired dance project and the TV show ReGenesis . Of ReGenesis I said: ”They partnered with the Ontario Genomics Institute to make sure the science on the show is as realistic and probable as possible. Every episode is also accompanied by a science fact sheet for viewers who want to know more.”

The fourth season of ReGenesis just started in Canada, and the fact sheets are back as well, with a small change: for this season the fact sheets are written by me! I was asked to do this after the OGI had found my blog after that post I made in September.

scene from episode 4.01

For the first episode I wrote about extensively drug resistant tuberculosis . Episodes air weekly, so over the next couple of months you can find more fact sheets there.

SciBarCamp is less than two weeks away, and we’re pretty much filled up in terms of participants (We secretly had room for slightly over 100! 112 people are registered as of this moment.)

One of the things we want to do ahead of time is get people thinking about some topics. Even though we will establish the program on Friday night, it helps to come prepared. We have a topics page where so far only two people have written a suggestion. The first suggestion is about science and art, which I’m sure will be covered since we have musicians, poets, and artists attending. The second suggestion is my suggestion: I thought that in a group of scientists, technologists, and artists, we could talk about what the general public really needs to know about science. If you have this conversation with a group of scientists it will tend to get technical (“everyone should know about protein translation!”) but with some balance it could get very interesting.

My original blog post with the topic suggestion
Micheal Nielsen’s response
Chad Orzel’s response

And unrelated to ScibarCamp I also found Chet Raymo’s blog post about what sixth graders should know about science

So tell me, what do you think everyone should know about science?
I’ll bring the contributions of people who are not attending along to SciBarCamp (it’ll be like being there). I want to get a giant piece of paper on which people can write their ideas, and I’ll just print and paste the internet ones.

Are there any other topics in general that you think should be covered at SciBarCamp? Roughly, our participants are working scientists, graduate students, science writers, science bloggers, artists, musicians, technologists, entrepeneurs or multiple of the above.

I have another, simpler, idea. This one was actually so obvious to me that I was sure it had already been done, but Googling gave me nothing:
Rewrite the lyrics of David Bowie’s song Five Years to be about five years of research funding or (even easier) five years of graduate school. You can leave big chunks of the lyrics intact! The song already contains “my brain hurts a lot” and “a girl my age went off her head” and “I had to cram so many things”

If nobody does this, I’ll do it myself at some point.

Make a parody rap music video where the phrase “da hood” does not refer to “neighbourhood” but ”fume hood” or ”tissue culture hood”.

It would probably be easiest to find a song that already contains the words “da hood” and just work around it. Google suggests the following:
DMX - Where Da Hood At
50 cent – In Da Hood

Do it! Or if it already exists, show me!

And so we did. It’s filling up pretty fast. I love how diverse the particpant list is, and am looking forward to meeting everyone in person!

I wrote a bit more here about the reactions we’ve had, and about my SciBarCamp experiences so far.

The position was introduced in 2004 under a liberal government and is currently being retired under a conservative government.

Radio science show Quirks & Quarks host Bob McDonald said of the decision :
”All science involves uncertainties – that’s the way the system works. But it takes a scientific eye to determine whether those uncertainties are significant or not. Without that perspective, a politician hears conflicting views or biased information that clouds the issue and confuses the public.

That’s where the National Science Adviser comes in. He or she is an independent, expert witness whose job is to provide perspective and education to the people at the top where the decisions are made.

Apparently, that’s no longer going to happen in Canada.”

(sorry for the long quote, I couldn’t trim it down without losing anything significant)

Two days ago, this cartoon ran on PhD Comics, illustrating engineer Jorge Cham’s surprised reaction to learning how cells can be manipulated to produce specific antibodies. The biomedical student replied: ”Yeah, you learn that your first year”.

And today the media are overflowing with news about the first organism with a completely man-made genome. Given that my two examples above show how even highly educated people outside of the field of Biology are not familiar with the things you can do with basic manipulation of DNA, you can imagine the general response of amazement and disbelief that man-made, working DNA would have.

Personally I’m amazed by iPhones and Bluetooth and Google Earth and GPS. Really? They can DO that now? This is because my knowledge about computer science stops somewhere around the concept of Boolean Logic and “Hello World”. I don’t understand how this type of technology works, it all seems very futuristic. Everyone has access to everything from everywhere. Quite 1984, in a way. And yet I don’t panic about it. Most people don’t. It’s just considered new and useful technology.

But when it comes to BIOtechnology everyone is suddenly surprised and shocked by everything. Really, a lot of this is not new and it’s not as shocking as news releases would have you believe. Carl Zimmer explains this to the readers of Wired, so the message hopefully reaches enough of an interested audience, but it really seems like a lot of basic concepts of current molecular biology – the things you can do with it – are not at all understood by many people, and every well-publicized small step forward seems stunningly ridiculous to the public.

Humans can synthesize complex molecules? We can edit DNA and put it into cells? Bacteria can use articifical genes that look like their own?

”Yeah. You learn that your first year.”

I figured out how to check Facebook using my phone – I don’t exactly know how this works, but I know it’s possible and I can use this technology. Now everyone else please learn what biologists can do using DNA - you don’t have to know the molecular details, just know what the technology is capable of and how it is currently used.

To follow up on my previous post, I decided to do my ten minute teaching session on restriction enzymes, using DNA fingerprinting as example. I have lots of ideas, and am only limited by time. (Ten minutes is nothing!)

After that, I want to do two things: write about science and teach science. Research, at least wet lab research, just isn’t something I should be doing for at least some time. I might miss the bench and change my mind, but it’s been nothing but frustration to me these past eight years (MSc work included). Timers beeping, things that need to be done at very specific times in a very specific way, repeating everything a gazillion times – first because it doesn’t work, and then when it finally does work you repeat it another gazillion times for reproducibility. Gah!
I always hoped I would at some point get a lot of great data and feel better about it. I’ve had great data, but the Great Data Induced High only lasted until the next failed experiment. I’ve gotten a lot better at interpreting such situations as (sigh) “learning experiences”, but that doesn’t mean that I like these learning experiences.

What I do like very much is talking about research.

Frankincense

Frankincense and myrrh are tree resins used in incense. They’re collected by “tapping”: slashing the tree bark and letting the resin flow out. Both come from trees indigenous to Africa: Myrrh is collected from Commiphora, and frankincense from Boswellia trees. The tapping of frankincense from Boswellia papyrifera is currently endangering the tree’s survival in Eritrea , so these resins are not just a whimsical hype from a few thousand years ago, they’re still actively being collected.

Other than making incense, what can you do with frankincense and myrrh?

• The ancient Egyptians used charred frankincense as kohl, or eyeliner. Again, not something I would give to a baby.
• Frankincense is also antimicrobial and antifungal . One type of frankincense in particular is able to kill Candida albicans, the yeast we know and hate from yeast infections or thrush. Some diaper rash, when left untreated, can turn into a yeast infection, so at least there is some distant benefit to babies here.
• Myrrh was used in ancient embalming ointments. This is apparently one of the reasons myrrh appears in the biblical nativity story: myrrh was given to symbolize mortality.
• Myrrh is used to treat schistosome infections (parasitic worms) but it’s antiparasitic activities are subject to debate .

Speaking of parasites, and leaving behind the discussion about the suitability of tree resins as baby gifts, there is one parasite that has made it’s way into Christmas traditions in English-speaking countries. No, it’s not the exploitation of the Christmas spirit by retail malls. (Okay, two parasites.) I was referring to mistletoe.

Mistletoe is a parasitic plant growing on trees. Like an unwanted dinner guest it digs it’s roots into the host’s branches to steal nutrients. But classic Christmas movies dictate that even a parasite like mistletoe will eventually learn to give back. And so it does: Lectin isolated from mistletoe is used as an anti-tumor drug because it’s able to induce apoptosis (cell death)
How’s that for a happy christmas story?

I’m taking a few weeks off blogging, so I’ll be back in 2008. Happy holidays!

Sixty-three years later, this tree is still standing, but very sick. It’s being attacked by a fungus and a moth, and if it should fall over it would likely damage neighbouring buildings.

Any other tree in this situation would be immediately cut down.

But this is not any other tree. The quote above is a quote from Anne Frank’s diary, and the chestnut tree stands in the backyard of the house behind the Anne Frank House. The tree is mentioned in several of Anne’s diary entries, as it was a huge part of the tiny fragment of outside world that she saw day in and day out.

The museum has proposed taking the tree down and replacing it with a graft of the original tree. A clone, in other words.
But many people were not happy with the idea of a tree-clone, and would rather try to save the original, dying, tree. Tree experts have been called, and a recent court hearing gave them a few weeks to find out if there was a safe way for the tree to remain standing without posing a threat to the surrounding buildings. The argument of those opposed to felling the tree is that the graft would not be the original tree that Anne saw from her window. The museum argues that the dying ugly tree isn’t what Anne saw from her window either—she saw a healthy tree.

What happens to other famous trees? The apple tree that is thought to have inspired Newton is long dead, but clones of the tree are still in existence. Redwoods are being cloned , and the oldest tree in the world has been cloned”. Several grafts of the Anne Frank tree have already been made. One was given to actress Emma Thompson when she launched the tree’s website last year. Yes, the tree has a website, that’s how famous it is.

It’s not the cloning of the tree itself that people oppose, but the idea of replacing the original with a genetically identical one. The second tree is NOT the first tree. The tree has been given a personality, and that’s not in its genes. The grafts are linked to the original, and people associate them with the famous tree, but it’s not the same tree. It’s somehow inferior.

This often happens during only one talk of a two-talk seminar hour, and not necessarily the second talk, so it’s not just my lack of sleep. It’s also not entirely attributable to the topic, because I’ve been fully awake and interested during talks about things I know nothing about. Someone in my department gave a talk about the 4th dimension last year. I still don’t quite understand the science/maths behind it, but it was a great talk and I listened all the way through.

This slideshow about how to give good slide show presentations is not specifically aimed at scientists (no, really, we need those data slides once in a while) but it does have some good advice.

I’d just like to add: please, please, please address the audience and not the screen! Honestly, I’ve attended talks where the speaker was with her back to the audience for 20 minutes. I don’t even know what she looked like!

I used to also advocate not memorizing everything word for word, but some people with terrible presentation-stage-fright told me that they sometimes black out during the talk and can only get through it if they have everything memorized literally. That allows them to keep talking on autopilot when they’re having a moment of panic. I guess that’s okay. But then don’t memorize your jokes, because they’re not funny if you’re on autopilot, and you’ll just get even more nervous if nobody laughs. Only sparingly add jokes if you’re confident about your presentation skills and your (and the audience’s) sense of humour.

My picks:
Proteic portrait by Marta de Menezes.
Marta spelled out her entire name in one letter amino acid codes, and engineered the corresponding peptide.

Pigeon Blog by Beatriz da Costa
” PigeonBlog enlists homing pigeons to participate in a grassroots scientific data gathering initiative designed to collect and distribute information about air quality conditions to the general public.”

Streptomyces by Linda Čihařová
Linda subjects photographs of a bioinformatics lab to the same algorithms as the lab’s researchers use on their data.

Dangerous Liaisons
This documentary screens three times at enter3 this weekend. It follows a Transgenic Pheasant Embryology Art and Science Lab as part of an honours biological arts course in Leiden.

I wish I could be in Prague this weekend to see all this!

The last two days of the program consist of free public lectures by past winners. The speakers and talks are in such high regard that my supervisor even cancels our regular Friday labmeeting to allow us to attend the Gairdners. Really, that’s saying something. This year’s theme is Cancer. Unfortunately, the Gairdners hit Toronto at the same time as a nasty cold virus, and I only just recovered enough to allow myself into a full lecture hall in time for the last talk, by Dr. Richard Peto of the Clinical Trial Service Unit & Epidemiological Studies Unit at the University of Oxford. He won the Gairdner Award in 1992.

A live-blogged summary of his talk on cancer mortality in relation to smoking is below. They’re notes, so the grammar is…non-existent.

”Expression Patterns”, as a play on “Gene Expression Patterns” but with the double meaning of “expression”. After all, this is a place to express myself, and I write a lot about science and art/culture (other people’s expressions)

I have three pages full of word associations, and only very few usable things came out. (Monkey, typewriter—you know the story)
My runner-up choice was “Neighbour Joining”, a method of creating phylogenetic trees, but I felt a blog wasn’t really about “joining neighbours”. I still think it’s a great name for a Bioinformatics forum or group, so feel free to use it if you have such a thing and are in need of a name.

I also have the obscure “Arty PCR” starred on my pages of babble. You know, like “RT PCR”. Too far fetched, that’s why I didn’t use it.

Finally I tried to find something using the word “domain” (protein domain, web domain) but didn’t get anywhere with that.

Of course I’m just one of those people involved in both science and art, and at this forum discussion I definitely wasn’t the only one. The panel consisted of Christina Jennings (producer of the Canadian science TV drama ReGenesis), Peter Outerbridge (actor in ReGenesis), Liz Lerman (creator of “Ferocious Beauty: Genome”, a dance inspired by the human genome), Elizabeth Johnson (dancer in Ferocious Genome), and Jeff Nisker (physiologist and playwright) who also brought along Martha Zimmerman (actress in Nisker’s play “Sarah’s Daughters”).

Christina Jennings, Peter Outerbridge, Liz Lerman, Elizabeth Johnson, Jeff Nisker, Martha Zimmerman, and James Friesen

In “Some Popular Fallacies About Vivisection” Carroll takes several statements used by 19th century pro-vivisectionists and argues against them. Interestingly, he starts out by saying that the golden mean is somewhere between the statement that vivisection is justifiable and the statement that it is never okay. So already he admits to not being entirely opposed to animal research. What he takes issue with is purposely inflicting pain on animals, not so much killing itself. He gives some examples of cases which he considers over the top examples of avoiding animal deaths, and the first example nicely illustrates how far animal rights have come in the past century. Carroll, who was obviously a fervent supporter of animal rights, believed in 1875 that it was a bit over the top to not kill some puppies if the litter is too big:

”Never may we destroy, for our convenience, some of a litter of puppies—or open a score of oysters when nineteen would have sufficed—or light a candle in a summer evening for mere pleasure, lest some hapless moth should rush to an untimely end! Nay, we must not even take a walk, with the certainty of crushing many an insect in our path, unless for really important business ! Surely all this is childish.”

Several fallacies that Carroll argues against involve the morality of the scientists doing the research. He points out that while they say that it’s necessary to use animals to advance medical research, many scientists actually just do the research to satisfy their own curiosity.

”As one who has himself devoted much time and labour to scientific investigations, I desire to offer the strongest possible protest against this falsely coloured picture [that science is unselfish]. I believe that any branch of science, when taken up by one who has a natural turn for it, will soon become as fascinating as sport to the most ardent sportsman, or as any form of pleasure to the most refined sensualist. ”

He does have a point here: curing diseases might be the goal of the research, or at least that is what you write in your grant application, but in the end scientists do the work because they want to do research. But Carroll extends this to wanting to hurt animals, and that’s not the same thing. Maybe “doing research” is a goal in itself rather than a means for the goal of “curing diseases”, but “animal experimentation” is still only a means for the goals of “doing research” or “curing diseases” and not a pursuable goal in itself. Carroll would probably agree that if a scientist had a choice between animal research and non-animal research resulting in the same information, they should choose the option without animals. He also mentions that, despite not supporting vivisection, he is not opposed to legislating it either. (”(...) the risk of legislation increasing the evil is not enough to make all legislation undesirable.”)

If Carroll knew that more than a century later scientists have to go through rigorously monitored procedures to get permission to do anything involving animals, that there are alternatives involving cell cultures, fake animals, or computer modelling to reduce the need for animals in research or teaching to the absolute minumum, that any animals used are better cared for than many pets, and not purposely hurt, would he approve?
I think he would. I think all of his concerns are dealt with, and what’s more: nobody would even dare kill part of litter of puppies for convenience!

The Explore-At-Bristol science centre in Bristol (UK) is currently hosting an exhibit called Alice Through the Looking Glass. It runs until November, and is mostly meant for children, but I know that if I was anywhere in the UK right now I would personally go and check it out all by my adult self.

The exhibit uses events from both Alice in Wonderland and Alice Through the Looking Glass to explain some basic concepts. The themes seem to be mainly related to perception and physics. (I assume the obvious hallucinogen references (the caterpillar) are left out of this family friendly exhibit.)

If anyone has been here or is planning on going, let me know!

Hogwarts students learn about bezoars in their first year potions class. They’re stones from the stomach of a goat that work as an antidote to most poisons. In book 6, Harry saves Ron’s life by giving him a bezoar after he accidentally drinks poisoned mead in Slughorn’s office.

J.K .Rowling did not make this up: bezoars really exist !. They can be found in the stomach or intestines of various animals (including goats, but also humans , elephants , or llamas [pictured above]), and are composed of undigested hairs (trichobezoar) or nondigestible food material such as cellulose (phytobezoar).

In the 16th century, bezoars (especially from goats and cows) were believed to be universal antidotes. They were also quite rare, and heavily sought after by the rich. King Charles IX of France (1550-1574) was excited when he acquired a bezoar from Spain. He showed it to court physician Ambroise Paré (1510-1590), asking if there was any antidote quite as good as a bezoar like that. Paré told the king that he did not believe there was such a thing as a universal antidote, because there are so many different types of poisons. He suggested an experiment to prove that the bezoar would not work.

Ambroise Paré

Paré asked if there were any prisoners scheduled for hanging. As it happened, a cook was just put on death row for stealing some silverware. The king made the cook a proposition: he could be hanged as planned, a quick and sure death, or he could be poisoned, at which time he would also be given a bezoar. If the bezoar successfully blocked the poison, he would be allowed to keep his life. Naturally, the cook happily took this chance and agreed to be experimented on.

But during book 6 (Harry Potter and the Halfblood Prince) I changed my mind. It wasn’t just Snape’s dubious after-school activities, but my own opinion on what makes good science had changed a bit in the mean time, and two of the books’ characters had developed to fit exactly what I now valued in science: Fred and George Weasley!

Even though they couldn’t stand the school environment, they’re hard workers and unlike most of the characters they’re creative. They know what they want to make (eg. something that makes you sick just long enough to cut class and then feel better) but they’re open to different ways of reaching their end goal, and they’re willing to adapt their recipes if things don’t work out.

The potions classes have always leaned on following a given recipe exactly, and as a potions teacher, Snape followed the book and never allowed for alternate solutions. However (spoiler alert!) at the end of book 6 we do find that he is far more creative than we’ve ever given him credit for so far. He improved on all the textbook protocols when he was still a student! We’re probably supposed to conclude that he is a much stronger wizard that we’ve ever thought, but it was at that point that I redeemed Snape as a scientist. He did have the mind for it! Unfortunately, he would be most horrible to work with. He would be the kind of person that will never admit that a hypothesis was wrong.

So, in the end, I’m sticking with the Weasley twins as my choice of “Best Scientists”, but Snape is still a very close second.

I asked people for their comments (here and here)

This week Harry Potter and the Order of the Phoenix opens in theatres, and later this month, on July 21st, the final book seven comes out. It’s a hype, but is it really a problem? Millions of kids are anxiously waiting to read a book, why complain? And you can even use the Harry Potter books to teach genetics, as a 2005 Letter to Nature showed. The same idea had previously been mentioned in a British newspaper in 2003, and is explained very well in this powerpoint presentation [ppt].

In brief: Wizarding is a recessive allele. All wizards have the genotype mm (I’m adopting the same notation as the slide show linked above, even though I realize upper and lower case m’s are not the best notation). Muggleness (non-wizardness) is dominant, so Muggles can have either MM or Mm. Pureblood wizards have two wizard parents, so both their parents have mm. Halfblood wizards have one muggle parent, so their muggle parent must have Mm and pass on m. Some wizards, like Hermione or Harry’s mother Lily, are “muggle born”, so both their parents have Mm, and they each pass on m to their wizard child. (As a small aside: Harry’s wizard-hating aunt Petunia (Lily’s sister) is therefore twice as likely to have one copy of the recessive wizard gene than to be a homozygote MM muggle.) Squibs are non-wizard children of wizards. they should have mm, but the theory is that a mutation in one of the m genes would be enough to make them incapable of magic. There are quite a lot of squibs, so it seems the gene is susceptible to mutation.
(See also this post I did for Metafilter two years ago. The cartoon above is by Cathy Wilcox.)

Just recently, another Harry Potter paper came out. This time, Harry has been diagnosed with migraines according to a paper in the journal Headache. The abstract contains the sentence ”Regrettably we are not privy to the Wizard system of classifying headache disorders and are therefore limited to the Muggle method, the International Classification of Headache Disorders, 2nd edition (ICHD-II).” which naturally led me to do a PubMed search for “muggle”. Score! Other than the headche paper, two other articles came up ! Both are from the same group in Singapore, and concern patient treatment in Hogwarts Infirmary and St Mungo’s Hospital for magical maladies. Here is the full text of one of their “studies” in CMAJ. (Be sure to look at the footnote and references.)

Are there more science (or medical) lessons to be extracted from Harry Potter? I think so! For example, I have a very clear idea of which of the characters would make good scientists and why, and will discuss this later this week. Meanwhile, tell me: which of the HP characters do you think would make the best scientist(s)? And who would be terrible?

The discussion was moderated by science writer Clive Thompson , who warmed up the audience by telling the story of how he almost got an automatic poetry generating software program accepted into The League of Canadian Poets .

The panelists came from a variety of backgrounds: Christian Bök , a.rawlings , and Ken Babstock are all poets with a particular interest in science. Lisa Betts , a postdoc in the neuorscience of vision at York University, was the only professional scientist on the panel, but, being married to poet Gregory Betts, she was familiar enough with the other side of the discussion.

From left to right: Clive Thompson, Christian Bök, Ken Babstock, Lisa Betts, a.rawlings

Science and poetry use a different kind of language when communicating, and the panel discussed the merits of both. In a scientific publication, Lisa explained, you need to be very clear because the experiments need to be reproducible. There can be no confusion about what you mean. Poetry uses language for the way it sounds, and a.rawlings is especially fascinated with learning and saying words that are normally reserved for science. In the reading following the panel discussion she read a fragment from Wide Slumber for Lepidopterists that sounded like a protocol for butterfly mounting. But she also recounted that at a recent retreat for sound ecologists, someone mentioned that there are relatively few words to describe sound, and they called on her and the other attending poets to find more words.

I have a blog at easternblot.net about the overlap between science and art or science and daily life. I intended it to be aimed at both non-scientists interested in science, and scientists interested in art. (It’s explained a bit better here ).

I’ll start out here by cross-posting a bit, but eventually I’ll probably put the posts that are geared more towards the scientific community over here.

The blue erlenmeyer flask is a design I originally made for some buttons I’m selling, but later implemented in my site design and use as my online avatar. I don’t look like a flask of bromophenol blue—I look more like this:

(I guess that someone cared about mine, or I wouldn’t be here!)

When I’m not blogging I’m working on my PhD in Biochemistry at the University of Toronto . I moved here in 2002 from Amsterdam, where I did my masters in Chemistry and Pharmacochemistry at the Vrije Universiteit .
I’m entering what is hopefully my final year at UofT this fall, and I am still not sure what I’m doing afterwards. (I guess that’s how people usually end up doing postdocs?)