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Augmented Reality
With augmented reality, it is possible to superimpose computer
data and graphics onto the video of the physical model. Then
researchers can hold a model in their hands and query the
computer for information—asking what a particular residue
type is, for instance, or looking at how that residue is conserved
across a species.
"The goal is to be able to superimpose any kind of annotation—any
information—on top of the physical model," Olson says.
In his office last week, he demonstrated one application
of this, which he is developing for a high school in Seattle.
He clipped a tiny video camera with a firewire connection
onto his shirt and plugged it into his laptop. Then he turned
on the computer and held a model of HIV protease in front
of the camera. The solid model was captured by the video camera,
and after he adjusted the autofocus and launched the software,
the model appeared on his computer screen.
This model had a little square marker attached to it that
was about the size of a postage stamp and looked like a square
bullseye. The bullseye is key to augmented reality because
it allows the computer to interpret any given frame of the
video image and tell by the shape of the tag what the transformation
of the model is based upon the measured distortion of the
square marker. Knowing the correct transformation in a frame-by-frame
manner allows the computer to track the model in real time
as it is moved in front of the camera.
In his demonstration of this application, Olson first entered
the coordinates for the atoms in the molecule represented
by the physical model he held in his hands. Then he asked
the computer to display all the histidine side chains in the
molecule. There was only one. "OK," he said, "let's display
the phenylalanines, too."
He clicked a few keys, commenting that he is currently working
on integrating voice recognition software with this so that
he could give simple voice commands to the computer. When
he was done, he held up the protein in front of the camera
again, and on the computer screen, the video had added graphics
representing the His and Phe side chains. The graphics moved
as Olson tumbled the protein in his hands.
Then he read in the coordinates for an inhibitor of the
HIV protease and he asked the computer to display this. In
a few seconds, the computer superimposed the inhibitor on
the binding site of the protease. As he turned the model in
his hands, the displayed inhibitor turned as well, keeping
its correct orientation in the binding site.
The technology is still in development, says Olson, and
he is the first to admit that it is primitive. The applications
are not fully automated, the video is low resolution, and
the display is limited to a computer screen or, at best, a
video projector. Someday he envisions integrating augmented
reality with a headset display so that different people could
look at the same object and each see the particular augmented
features they wish to see.
Still, says Olson "It works well enough so that people get
a sense of what we're striving for." He feels that this technology
as it exists could be a powerful tool for creating tangible
interfaces for molecular biology, and he thinks that the application
is only going to get better as technology improves.
"You can buy a digital camera today for $100," says Olson.
"In 10 years, you might be able to buy an HDTV camera for
the same price."
Beauty, Truth, Models, and Everything
Next month, Olson is participating in a forum discussion
at the 30th International Conference on Computer Graphics
and Interactive Techniques, also known as "Siggraph." This
meeting brings together animators and graphics specialists
who work in such diverse areas as basic science and entertainment.
The panel discussion is titled, "Truth Before Beauty: Guiding
Principles for Scientific and Medical Visualization," and
like the rest of the convention it brings together experts
from different areas to discuss a single subject.
"[The panel] is dealing with the issues of visual representation
in the sciences," says Olson. "They invited me to talk about
my work in representing the world you can't see—the molecular
world."
The molecular world is one that is hard to visualize—even
though we see pictures of it on a regular basis. Biology and
chemistry have produced thousands and thousands of glimpses
of this world in the form of structures, and many of these
structures—glossy, full-color, and often quite beautiful—adorn
the covers and pages of the top science journals.
The point of the panel is to ask whether these representations
are true to what the molecular world looks like or if they
sometimes sacrifice truth for the sake of beauty. Olson sees
this as a bit of a straw man.
"[The molecular world] doesn't really look like anything,"
he says.
Since proteins and the other inhabitants of the molecular
world are smaller than the wavelength of visible light, they
are impossible to see. Structural biologists provide models
of molecular structures based on structural data they obtain,
and then they usually abstract these models even more—coloring
particular residues, displaying only the backbone or particular
side chains.
However, proteins have no color as such because color does
not exist at that scale. In fact any picture of a protein
is not entirely accurate because electron distributions and
other dynamic features of proteins do not readily translate
into static images. But this is just splitting hairs.
"All representations of the molecular world are models,"
he says. "None of them are true per se."
The measure of a molecular representation, says Olson, is
how well it conveys information. As such, it is often enlightening
to show a model that displays less information. If you look
at a backbone model of a protein, for instance, you can easily
follow the snaking amino acid chain with your eye. Backbone
representations have less to do with how the proteins fill
space than how they fold up.
Beauty, says Olson, is another question. "Truth and beauty
are not really along the same axis."
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