Computers and Biology

Computers have enhance the study of Biology tremendously, as well
discoveries have enhance the progression of computers. Without
computers, Biology would be no where. We would not have the high
tech microscopes. We would not be able to process information at
lighting speeds. Finally, we would have no place to store all the
information that we gathered. Can you imagine all the paper we would
use to record all the information that we gather?
Computers have not only helped us with experimenting; they have
helped us to educate students. There has been tons of software
developed to educate students about science and in particular Biology.
They have allowed students to create experimental 3D models, collect
research and now students can even use computers to dissect “Virtual
Creatures”
Aimed at middle school and high school students, Virtual Creatures is the
creation of a group called SUMMIT (Stanford University Medical Media
and Information Technologies Group). SUMMIT was founded eight
years ago to create computer-based teaching tools for the Stanford
University School of Medicine and has expanded to provide educational
multimedia for medical students and doctors.
This program will allow students to dissect frogs without the scalpels,
probes or formaldehyde. Without touching the frog, you can rotate it to
view it from any angle and study its external anatomy. On command, the
skin turns transparent. You can even zoom through it to view the muscles,
or peel the muscles back to expose the internal organs and skeleton.
The Virtual Creatures team used virtual reality technology to create a rich
environment — called Frog Island — with many opportunities for
interactive learning. After being greeted by a ranger who explains how to
get around the island, students can visit, in any order, a series of huts,
each focusing on a different aspect of frog biology: muscles, organ
systems, bones, nerves, habitat and so on. With this virtual reality model
students don’t have to worry about real-life constraints. For instance,
you can take a frog apart in any sequence. You could start with the
digestive system and then put it back together.
This as you would expect does require a lot of processing power and
high-end graphics. But the speed of innovation in the computer industry
should soon make the necessary technology affordable for many schools.


The SUMMIT team is also looking at ways to transfer most of the
processing work to a central computer, which students and teachers
could access by logging on from a cheaper computer.
This is where biology has actually helped computers develop. Biology
and the study of proteins and molecular biology have helped scientists
develop new ways of building computers. They have helped reduce the
size and cost of creating components for a computer system.
Imagine if we could create a storage medium the size of a sugar cube that
stores a terabyte of information. Imagine if I said that it would not be
based on silicon transistors, but would be based on protein molecules that
change their shape when exposed to light. This enables them to store and
transfer massive amounts of data.
This technology is called Nanotechnology. It is leading to the
development of electronic components at the molecular and atomic
levels. Single bits are going to be represented by single atoms. Chip
sizes have been shrinking at an incredible rate. If they continue at the
current pace now, it will so be more expensive to shrink then it’s worth.
This new technology may provide the answer in protein-based computing.


Researchers are currently studying several molecules to find a possible
“biology standard” for designing computers. The most popular molecule
is a protein called bacteriorhodopsin. Although we are just hearing about
it now, Soviet scientists have been interested in this protein since the early
70’s.
They recognized the potential of the molecule to act as a switch with
on and off positions. This is basically how the silicon transistors work
today. While silicon transistors alter its state when a current of electricity
excites the electrons in it, a protein changes its shape when it absorbs
light. A laser beam is used to control the switching in a matrix of memory
cells.
Bacteriorhodopsin is a complex protein found in most salt-marsh
environments. It contains a light-absorbing component called a
chromophore. When this chromosphore is exposed to light, such as a
laser beam, it absorbs the rays and causes a series of internal processes
to occur with in the bacteriorhodopsin. This changes the electrical
character. Scientists can then translate these resulting electrical changes
into the binary language. This is the language that the computer will
understand.
This experiment has better results when scientists add a second laser.
This creates something called a sequential one-photon architecture. For
long-term memory applications many bacteriorhodopsin devices tend to
create one stable element aside from the natural state, thereby giving you
the requisite 0 and 1. Adding another laser beam also enables engineers
to create a special intermediate state that can branch into two other stable
states. This is especially useful for an application becoming popular not
only in biological circles, but in the holographic community as well; 3D
storage.
The whole goal here is to create a tiny cube that can store vast amounts
of storage. Holographers have another method to reach this goal. They
arrange two sets of laser beams at 90-degree angles. They all face a
bacteriorhodopsin cube. After the first set is fired, a special intermediate
state, which we’ll call A, is created. When the number of A elements
reaches a near-maximum level, scientists then fire the second set of
lasers. This causes the A state to switch to a different short-lived
structure, which we’ll call B. Soon after, structure B changes into a highly
stable format, which we’ll call C. Scientists are really excited about this
format because it can remain stable for years.
When they assign the base state to 0 and the B and C to 1, engineers
have re-created the binary switching technology. The lasers have the
ability to read and write to multiple locations within the bacteriorhodopsin
simultaneously; thus this creates faster parallel operations that can be
implemented. The engineers have estimated that they can perform
operations at a rate of 10MB per second.
There are however some problems with this new technology. Writing is
not a big problem, but reading is. Errors can occur because of noise from
the laser interfering with the read signal. Another problem is the
molecular structure. In order for this to work as high-speed memory
these bacterorhodopsin cubes must be uniformly the same.Any
variation in the structure could change or distort the data. These
problems are being worked and develop by a man named Dr. Robert
Birage of Syracuse University.
Biology and computers have always been intertwined with each other.
Computers are helping teachers teach the subject, and they are helping
researchers to research and make more discoveries at lighting speeds.
Biology is also advancing computer technology. We can see this with the
new nanotechnology. This kind advancement is not going to slow down
anytime soon. Researchers will continue to discover new things in
Biology, and will continue to invent faster ways to push the computer
systems they use.



Computers and Biology
Biology 101
10 wk session
References:
1. Aubrey, David. Progressive proteins. Computer Shopper, April 1996.


Vol 16n4. P563. Online: SearchBank.
2. Levin, Carol. High Protein Computers. PC Magazine. May 30, 1995.


Vol 14 n10. P29. Online: SearchBank.
3. “”Virtual Creatures” Teach Biology Without Dissection,”
http://www.infoseek.com/Content?arn=BW0236-
19980709&qt=biology&lk=noframes&col=NX&kt=A&ak=news1486.