easternblot.net - it's (not) all about science

Phun is a computer program that lets you build all kinds of things and play around with basic physics concepts (gravity, friction). This is a demonstration video from the creator, Emil Ernerfeldt, who made the program for his MSc degree in computer science at Umeå University in Sweden.

I’m not downloading this right now, because this is exactly the kind of thing I would get addicted to. (Building! Building things that move! On the computer!)

Foldit is a web based computer game that lets you fold proteins, and contribute to science while playing.
From the site:

“Figuring out which of the many, many possible structures is the best one is regarded as one of the hardest problems in biology today and current methods take a lot of money and time, even for computers. Foldit attempts to predict the structure of a protein by taking advantage of humans’ puzzle-solving intuituions and having people play competitively to fold the best proteins.”

Research contributes to global warming.
I’m not surprised. I often feel ridiculous when I make the effort of turning off lights at home while my cells have to grow 24/7 in a 10% CO₂ incubator that’s always running. 10% is not the normal amount of CO₂ - most cells grow at 5% - which means that only my three flasks are in this big incubator all by themselves. Nobody else can use it, they need 5%.

I’m working on a little project that I don’t have time for at all, but it’s about lab waste. I took a bunch of photos of single use items and of different ways we handle trash (without identifying my own lab, because this is all very general. I am thinking of checking Flickr for other contributions - the whole thing will be under a creative commons license anyway). It’s very odd: on the one hand there’s a lot of thought put into how lab waste is handled and I am more confident at the lab about which object goes in which bin than I am at home, where there are confusing objects like paper lined with plastic. And “muffin trays” are not recyclable, according to an info sheet I saved, but I never have muffin trays, so I have to guess which other objects are of the same plastic. Styrofoam? I don’t think it’s recyclable, but one of my previous roommates put it in the blue bin all the time. At the lab it’s much simpler: toxic stuff gets incinerated (red bag), liquid chemicals are sorted in different containers, and pretty much everything else goes in the yellow bags, which are sterilized before being sent to landfill. But there is so much stuff that has to be sterile before it becomes garbage: to make it easier, everything is sealed in individual wrappers and disposable, so you know it’s clean. I only found two wrappers or objects that we could easily replace with something less wasteful. Everything else has become so standard that it’s not even possible to work with anything else.

I’m spoiling my own project. I’m sorry. But it’ll be fun. Meanwhile, if you have photos that show waste processing in your lab that you wouldn’t mind me using (you’ll get proper credit) please drop me a line.

mutagenesis, originally uploaded by irene_c_wang.

This was added to the Flickr group a while ago. This image is one of twelve total (go here to see the rest) and it’s part of Irene Wang’s grade 12 project combining art and biotechnology. She spent a year in a biochemistry lab at KU Medical Center and illustrated all the protocols she used. It was hard to pick a favourite. This mutagenesis one was my favourite to look at, but DNA isolation is probably my favourite to do in the lab, so I liked that too.

If you’re in Toronto this coming weekend, check out Science Rendezvous. Various labs open their doors, and there will be science activities for all ages all throughout the city (and in the ‘burbs)

I keep starring (bookmarking) things in my Google Reader and then never get around to talk about them, so I’ll just list a bunch here and you can read whatever you want:

Something on biomonitoring at Sciencebase. Starred because I did a high school biology project on biomonitors, back when I was still going to study environmental science and save the world. Sorry, world!

“The Love/hate relationship with academia” at Adventures in Ethics and Science, and “Bittersweet Finish” on Lab Life. Starred for reasons summarized in the comments of the latter post.

Top Ten Memory Hacks on Lifehacker. Starred because…because…uhm…what was it again?

“Avoid Boring Watson” on Biomedicine on Display. Starred because I once eagerly attended a talk by James Watson and found him to be extremely boring. He might have been instrumental in discovering things that changed the fields of biology and biochemistry, but he’s a terrible public speaker, not engaging at all. At first I was scared to admit that I found him boring (he’s a living celebrity scientist!), but I’ve since discovered that I’m not the only one that feels that way, and this book review was of interest.

“We need to stop pigeon-holing science” on Biocurious. Starred because I had recently been thinking about this very topic for a thing I’m writing.

At the bottom of the previous post, I mentioned some upcoming (un)conferences in which people who were at SciBarCamp are somehow involved. I had barely hit the “publish” button or I came across another one:
One Big Library Unconference
June 27 at the Centre for Social Innovation (Toronto)
organized in part by SciBarCamp participants John Dupuis and William Denton.
Librarians and those interested in organizing information should attend.

Also, because everyone seems to know the same people in this city, my fellow SciBarCamp organizer Karl Schroeder ended up writing the most recent “Science and Society” pieces for ReGenesis. These pieces are the ones that are always listed next to the Facts Behind the Fiction pieces on the OGI site, but which rotate authors. I’m glad Karl wrote about Silent Spring, because I didn’t really have the space or opportunity to bring up the complicated background behind why DDT was banned in the first place in my piece, but it had to be addressed. The next episode was the most exciting one of the whole season: terrorists held the lab members hostage and forced them to mutate the measles virus. There was a lot of talk about PCR primers in the episode, and the primers formed a major part of the plot, so I did my best to explain what that was about. Karl explained how it is unfortunately unavoidable that someone with bad intentions can access confidential research information. All in all, the creepy thing about that episode was that it was mostly possible. The timeline was technically impossible, though, but there were some fictional “new techniques” written in that made it possible, so even though it wasn’t possible in our reality, it was possible in a fictional world where you can indeed culture and transfect cells in one evening and mutate five locations of a gene at the same time. If only lab work was that fast…