Biocurious

/ a biophysics blog

Science Rendezvous 2008

Posted 8 May 2008 by PhilipJ under

If you find yourself in Toronto this Saturday, May 10, you should check out the wide variety of events going on under the Science Rendezvous umbrella, everything from science demos at universities or malls to lectures by one of Canada’s own Nobel laureates, John Polanyi.

I’ll be presenting optics demos with the Institute for Optical Sciences in the McLennan Physics building at the St. George campus of the University of Toronto, and there will be all kinds of other interesting things happening in the immediate vicinity of the physics and chemistry buildings — click here to see them all.

If you need any further convincing, you can see some of the neat experiments we’ll be demonstrating in this video – my Ph.D. advisor’s enthusiasm is catching.

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We need to stop pigeon-holing science

Posted 4 May 2008 by PhilipJ under &

My brief anxiety over what kind of scientist I am was initially posted as a bit of a joke. As the resident wet lab junkie (scary!) in what is primarily an ultrafast optics group, having spent at least as twice as much time on sample prep over the past 8 months as I have on aligning lasers to do fancy nonlinear optics, it gets harder and harder to say things like “I’m a physicist“ with the same kind of certainty that I once would.

And you know what? That’s okay. The more I play in other sandboxes (or as the case has been, dark rooms*), the more I realise my own sandbox of physics is no “better” than anyone else’s. We’re just asking, and trying to answer, different questions.

This is all coming to mind because we just finished holding the annual Chemical Biophysics Symposium again, and on the first evening of every symposium there is a panel discussion on some interesting topic. Something that keeps coming up at these kinds of discussions is the “us” versus “them” comments, wherein “us” is invariably physicists (or physical chemists), who are the majority of the audience at the symposium, and “them” are those nebulous biologists who never seem to be around to offer a biologists viewpoint on science.

I have news for physicists who have woken up to find lots of fun problems in biology: most of us are solving physics problems in biological systems. We are nowhere near addressing most biological problems. It is flashier and more exciting to say we’re working on cancer, or drug deliver, or what have you, but in most cases we really aren’t working with biologists to help solve biological problems, despite claims that we are now starting to study biology the “right way”.

It is useful to recall Bob Austin’s take on the interesting problems in biology:

I want to do the big problems: I want to understand energy flow in biomolecules; I want to understand how genes are turned on and off; I want to understand the collective processes in cell growth; I want to understand how the brain works; I want to understand the origins of consciousness. […]

Nowhere above does he say “the physics of …”. It is great that physicists are turning to biology for new problems to solve, but I grow a little tired of the physics vs biology mentality. If we truly want to make great strides in understanding biological phenomena, we need to stop pigeon-holing disciplines. There is no “us” or “them”, “they” aren’t doing things incorrectly, we’re all simply using the tools we were trained to use to solve the problems we find interesting. What we really need to do is find better ways to share ideas, so that everyone understands exactly what they can contribute. We can’t be afraid to learn from each other, and in the case of biology, it is most certainly a two way street.

* More on this soon.

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Molecule of the Month: Prions

Posted 3 May 2008 by PhilipJ under

prions

Prions are proteins that can adopt two different forms, a normal form and a misfolded form. This may not seem unusual, since many proteins are flexible and adopt different shapes. However, prions have another unusual characteristic: the misfolded form of the prion can force normal prions to change into the misfolded shape. In this way, a few misfolded prions can corrupt a whole population of normal prions, converting them one-by-one into the misfolded shape. This can have deadly consequences, as the levels of misfolded proteins build up. For instance, misfolding of the PrP prion causes fatal neural diseases in humans and other mammals. To make things worse, misfolded prions are infectious, so a small dose of misfolded prions can infect and corrupt an entire organism.

The normal form of the prion protein PrP (shown here) is found on the surface of nerve cells, but when it changes into its misfolded form, it aggregates into long fibrils that clog up the normal functioning of the brain. Infection occurs when a little bit of the misfolded protein is eaten or accidentally gets into the blood through an injury. A devastating example occurred in a native population in Papua New Guinea, where ritual cannibalism was part of funeral ceremonies. The epidemic probably started when one person developed the disease spontaneously (PrP occasionally adopts the misfolded state all by itself, causing very rare sporadic cases of the disease). Then the misfolded prions spread through the community when the infected person was eaten. More recently, there has been concern that the prions that cause mad cow disease could spread to humans by eating infected meat. The cow PrP protein is very similar to human PrP, and several cases of this type of infection have been seen.

Read the rest at David’s homepage, here.

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New Perspective on Blood Clot Mechanics

Posted 25 April 2008 by Andre under

My collaborator John Weisel has just published a nice Perspective article in Science describing some of the recent progress that has been made in elucidating the mechanical properties of blood clots.

It’s a fascinating subject in part because of its relevance to health. As John puts it:

[A]lthough clotting is vital to the preservation of life, blood clots that impede the flow of blood in vivo—called thrombi—are responsible for most heart attacks and strokes and complicate other pathological conditions, including many types of cancer and peripheral vascular disease.

clot and fiber

But clots are also interesting purely from the materials perspective. In this context, they are a wonderful programmable material. A single protein monomer—fibrin—encodes the entire hierarchical structure of clots. A solution of fibrin will spontaneously self-assemble into a beautiful branched meshwork that fills a test tube but is still more than 99% water. To accomplish this feat, fibrin is more complex than some of the proteins that make up other networks like those found in the cellular cytoskeleton like actin and tubulin. This complexity makes studying fibrin both a challenge and a thrill. The challenge is to devise experiments that are sufficiently well controlled to interpret, as we tried to do in our single molecule pulling paper from last year (paper [free on Pubmed Central]; post at Biocurious). The thrill comes from the enormous variety of factors that modulate clot structure and function. Fibrin forms a smart material: it responds to external chemical cues found in blood that can cause it to grow or dissolve or to become stiffer and more impervious to mechanical insult. In fact, there are dozens of factors responsible for regulating the formation and degradation of blood clots in humans and these can be leveraged to perform useful experiments or to develop variations on biological clots with new properties.

All of these things are possible, and are indeed already happening, but we still don’t know in detail how the structure and properties of fibrin give rise to its macroscopic properties and that means that we still can’t be as clever as we would like in treating mechanical diseases involving fibrin and in designing new materials inspired by its properties.

But this too is starting to change, so stay tuned…

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Identity crisis

Posted 17 April 2008 by PhilipJ under

I just used ChemDraw for the first time! What does this mean???

Also, I’m studying for a biological chemistry final. It could hardly be more different than studying for a physics course. Blurring the line between the sciences in research is awesome, taking the other side of the line’s courses can be… tricky. Biology isn’t harder than physics, it’s just different.

Come on May 1st.

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Philosophical Saturday: George Wald

Posted 5 April 2008 by PhilipJ under &

George Wald made considerable progress in our understanding of the chemistry and physiology of vision (which just so happens to be the area I find myself in now). He won the Nobel Prize (physiology or medicine) in 1967, and his lecture in Stockholm opened with a beautiful description of experimental science:

I have often had cause to feel that my hands are cleverer than my head. That is a crude way of characterizing the dialectics of experimentation. When it is going well, it is like a quiet conversation with Nature. One asks a question and gets an answer; then one asks the next question, and gets the next answer. An experiment is a device to make Nature speak intelligibly. After that one has only to listen.

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