Silicon to be Replaced by Proteins?

I’m revamping my Molecular Biology course and have stumbled upon a few interesting nanotechnology topics that might be of interest to some people…

A few years ago, I attended a very interesting lecture about the use of biological molecules in building computers. Why, you might ask, would you want to use biological molecules to build computers? The answer is that biological molecules are small – typically on the order of nanoscale (one millionth of a millimeter), whereas most silicon-based chips are at the microscale (one thousands of a millimeter). Thus, if we could use proteins and DNA to build the logic gates and memory circuitry, we could miniaturize computers by at least 1,000 fold. This could have many applications, not the least of which are medical applications. Think of injecting small robots into your bloodstream that are autonomous and can direct themselves to the appropriate location, execute repairs, and leave your body without the intervention of surgeons. It gives a whole new meaning to “take two pills and call me in the morning”.

DNA seems a very likely candidate for building logic gates, and perhaps I’ll discuss them here soon. In the meantime, I just wanted to mention the potential of proteins in serving in memory chips. Proteins are the workhorses in your body. They do everything from digesting bread, to synthesizing fats from ingested sugars, to pigmenting your skin, to making up the bulk of your hair.

One protein in particular, rhodopsin, has attracted a lot of attention for its nanotechnology potential. Rhodopsin is a protein found in your eyes. It is found at the back of the eye and serves as a sensor for light of a specific wavelength (i.e. colour). When light of a specific colour strikes rhodopsin, it causes the protein to change its shape. This change generates a signal that your nervous system interprets as the perception of light or colour. The critical property of this protein is that it can exist in one of two forms, one when it has been hit by light of a certain colour, and another in the absence of light.

Now think of a small cube, maybe 1cm by 1 cm by 1cm that you fill with an ordered array of rhodopsin. You know where each molecule of rhodopsin is in this cube. Each molecule of rhodopsin is tiny – so tiny in fact that we know its atomic composition in great detail. Each molecule lives at a particular place in the cube, and it exists in one of two shapes. Since each rhodopsin lives at a certain fixed physical address, you can shine a laser (i.e. light of a specific wavelength) at that spot and change the shape of one specific rhodopsin molecule in the cube.

Does this start to sound a little bit like the memory of a computer? A memory chip (or a CD or DVD for that matter) is simply a material on which there are several “cells” that live at specific addresses and that exist in one of two states: ON or OFF, or another way of thinking about it is 1 and 0 (the famous binary code). Typically, each of these cells is microscopic.

Hopefully, you see the parallel with the cube of rhodopsin. It’s the same thing, except that the rhodopsin cube encodes the information at a 1,000 fold smaller scale. So for a similar sized disk, you could encode 1 meg of information with silicon technology, or 1 gig of information with biological nanotechnology.

A few issues remain to be worked out. How to “reset” the protein once you have changed its shape, for example. However, this technology is very promising…

Migratory Bird Watch

I know that I said that my next post would be about one of the many topics we discussed in my Molecular Biology course last month, however, something’s come up. Last Wednesday, I played hooky with the two resident ecologists at the University and we went to the George C. Reifel Migratory Bird Sanctuary in Delta, BC, Canada. My colleagues were investigating the area as a potential site for a field trip for their ecology course. My excuse was that I have to oversee everything for the life sciences courses (haha – what a thinly veiled excuse for playing hooky!). The snow geese were said to be in town, and lured by the prospect of a sighting or two (or a thousand), we headed to Delta.

It was a delightful day, not least of which was due to the fantastic weather we enjoyed. This was my third visit to the Reifel Sanctuary. This time, I was accompanied by bird watchers. If you have the opportunity, it’s really worthwhile to visit this site with people who love birds. Not only will they point out where the birds are (you are very likely to miss out if you are not an avid birder), but they will also tell you about the natural history of each species, and (this turned out to be important for my personal safety) which birds have a mean temper and that you should keep a safe distance from…

We saw many bird species. Bald eagles, sand hill cranes, snow geese, mallard ducks, more mallard ducks, still more mallard ducks, wood ducks, other ducks I could not name, blue herons, some other type of heron that was perched on a tree, chickadees, pigeons, coots, hawks, red robins, trumpet swans, and others I could not name. No owls (although we were told they were on site). And most impressive of all, the sky was FILLED with migrating birds. There’s a constant background noise made by the migrating flocks of birds that’s quite soothing.

All and all, a very good day, and I recommend it to all… I think Nobi and Mai have decided to bring their students there for their ecology courses in the coming months… I wonder if there’s any way to link this to Molecular Biology somehow? Why should they have all the fun?

Biology to return...soon

... Just posted a new entry on the MacLeans.ca OnCampus Blog , on the merits of using case study pedagogy in the science classroom (image to the left shows some of my students working through a case study).

As I now have some time to update my blogs (having recently finished teaching a Molecular Biology course), you can soon expect some entries in this blog on biological topics... I plan to do a little piece on phage therapy, golden rice, and HIV/AIDS, three topics that generates lots of discussion in my classroom...

Coming soon!

Community Day – The best way to freshen up a course is to cancel class

I was recently invited to contribute to a blog for MacLeans.ca On Campus. This blog, written by a group of 5 university professors, is a place where "A varied group of professors and education researchers come together to discuss their experiences teaching and how to improve the undergraduate experience." Yesterday, I made my first contribution.

Quest University had its first Community Day of the academic year yesterday, and I wanted to write about our experiences. My blog entry is reproduced here, for your reading pleasure...

One day each term, when the students least expect it, all classes are canceled at Quest University Canada. These days are called “Community Days”. We just had a Community Day today.

I would love to claim this was our idea, but it was inspired by a similar event that takes place at the Lester B. Pearson United World College of the Pacific near Victoria BC (an innovative international high school). What’s the goal of this Community Day? It’s threefold.

First, sometimes you just need a break. Quest teaches on the fast-paced block scheduling plan. Students take one course at a time, 3 hrs each day, for 3 ½ weeks. It is an intensive way to learn: students must stay on task and manage their time effectively because assignment due dates come up fast, and before you know it the course is over. You need a breather, a chance to revitalize, interact informally with all students and faculty, not just the ones in your 20-student class.

Second, it promotes student interactions. The morning schedule of a typical Community Day consists of team building and leadership exercises, preferably outdoors. Some of the activities today included trust exercises and the raising of a student-made Quest flag (we first had to dig a hole, then carry a tree log up a hill, then raise the log and stabilize it with ropes once it stood reasonably erect). Oh, I know – a lot of you are probably rolling your eyes, covering your mouth and thinking “and they call this a university? What’s the academic merit of doing that?”. I probably would have been right there with you a few years ago. Sure, it’s unorthodox. But having seen its effects in the classroom first hand, I am now a convert.

Do you know what happens when you set up a situation where students must bond, trust one another, exercise leadership abilities and have fun together? Do you know what happens when you then put them together in a 20-student classroom and ask them to contribute to a class discussion?

You cannot shut them up!

They feel comfortable with one another, they trust that their peers (and their teacher) will accept them, and they do not fear being ridiculed. A non-academic activity goes a long way towards improving the academic quality of my classroom. I’ll sacrifice a day of class any day if it means that the questions and insights that are shared and asked in my classroom are more numerous, more honest, more in-depth, and are contributed by a larger percentage of the students.

Third, the afternoons of a Community Day are generally spent asking for the students’ input on building this university. Quest opened its doors to students a mere 13 months ago. A lot of its policies, practices, and even its identity are currently being developed. The philosophy at Quest is that students wouldn’t be told what to do: study this course and that – they would be active participants in their own education. They are guided through the design of their own degree. They also contribute in building this university. Today, the topics under discussion were student admission, student retention, fundraising (since we are a private non-profit institution), energy-conservation on campus, and student life. It’s amazing what different perspectives students can have on an issue than faculty. It was very refreshing to hear their take on what matters. And they also provided tons of ideas for improving this place.

At the end of the day, when the Community Day is over, you get buy-in. You get the sense that Quest belongs to all of us. That we each have a hand in shaping it. That we are not a number but an important member of a community. That this place is special. It re-infuses energy into all students and faculty and into every classroom. And at the end of the day, we are all reminded that there is no other place we would rather be.

So now you decide – wasn’t a day of “fluff” a valuable part of a student’s education?

Sky Diving - Why Would a Brain Want to Do Such a Thing?

Sky diving was a very cool experience, and I suspect some more may be in my future (and yes, that's me jumping out at 10,000 feet).... But let's ask the question: why would anyone want to jump out of a flying plane, at 10,000 feet of altitude? The answer, of course, is complex. However, we do know something about the brain's reward circuitry. The reward centre of the brain (ventral tegmental area, nucleus accumbens, and others) are a part of the brain that functions to make an individual survive, and reward the person when he or she does something good for survival. Typically, this is sex or food, that kind of thing. Cells in this part of the brain talk to each other by releasing a chemical called dopamine. So whenever you do something good for survival, dopamine gets released in the reward centre, making a person "feel good", and that much more likely to repeat the behaviour that caused the release of dopamine in the first place.

Incidently, novel activities cause the releas of dopamine in that part of the brain. So we enjoy doing things that are new and different. We don't want to overload that system, but novelty is something we appreciate.

Drugs of addiction are addictive because they stimulate that part of the brain: they potentiate (increase) the release of dopamine in the reward centre. So drugs of addiction take over the control of a portion of the brain designed to reward an animal for certain behaviours. It's easy to see how such drugs become addictive: the brain "feels good" each time you take them and makes the person much more likely to repeat the behaviour (i.e. drug taking) that caused the release of dopamine in that part of the brain.

It turns out that some people are less sensitive to dopamine in that area of the brain. Some people have "mutant" D4DR dopamine receptors. By the way, this is not unusual in and of itself: we all have different varieties of different genes in our body - if we didn't, we would all be clones and look identical. However, what has been observed is that people who have the mutat D4DR receptor in the brain tend to score higher on sensation-seeking personality traits (Note: this is not a necessary relationship, it's only a "more likely" type of a relationship). In otherwords, we have noted a correlation between the "adrenaline junky" personality type and havingD4DR receptors in the brain. If you take a moment, you will realize that this makes sense. If you brain is a little insensitive to dopamine, it will take a larger stimulation for your brain to respond to the dopamine release. So a person with a D4DR dopamine receptor needs to experience "stronger sensations" to "fell as good" as a person with the "normal" version of the dopamine receptor to feel.

Incindently, people who score high on the novelty-seeking trait tend to also have a greater likelihood of developing a drug addiction. Part of the reason is that they are simply more likely to try the drug in the first place. Part of the reason is that if they have a brain that is insensitive to dopamine (D4DR receptors) , and they have access to a chemical that is likely to stimulate their brain to levels comparable to what other people experience daily for doing "simple" activities such as eating food and having sex. So in effect, these people are more likely to use drugs of addiction because it allows them to regulate ther dopamine levels and experience "feeling good" to levels comparable to those of controls. That's the theory, anyways.

Based on my past history of SCUBA diving and now sky diving, I suspect I have D4DR receptors in my brain. This is only a guess, based on the noted association between personality trait and dopamine receptor type. I don't know for sure.

If you want to see how you score on this persoanlity trait, you can take this Sensation-Seeking quiz at the BBC website. Obviously, this is not an "official" study of your brain, this is for recreational purposes only.

For those of you out here without this trait, I leave you with this video of my jump... Live vicariously through me!

Soaring like an Eagle...

Ok, so this entry does not have much to do with biology (perhaps a little bit more to do with physics). After exploring the depths of the sea, I decided that it was time to explore the world from an eagle's point of view. I went sky diving along with 14 of my students today. We headed to Pitt Meadows to do our first tandem jump. I think it is safe to say that great fun was had by all. If you get the chance to try it, do. Here are a few shots of my super instructor Rob and myself (thanks to Derek for taking these shots). We dove 10,000 feet. At 5,000, our chute opened. I think the freefall was everyone's favourite. Personally, I really liked the first 5 seconds, when I completely forgot to do everything Rob had told me to do and we were somersaulting out of control. It was very disorienting, and reminded me of when I did gymnastics as a child. The moment the chute opens, the wind stops rushing in your ears, its quiet, and peaceful... and the views! The views! Ahhhh... to be an eagle. I think this sealion may be ready to transform herself into an eagle...