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NSF
Conference on Computing
in the Life Sciences
Pomona College - April 25, 1998
The computing revolution continues and its impact
on the life sciences is growing. The conference was designed
to highlight new uses of computing in teaching and research in
the life sciences. A series of short presentations brought focus
and information to inform the discussions. The first discussion
period highlighted the interaction between research and teaching,
asking whether computing was making the interface more permeable.
The second discussion period highlighted needs that were identified
in life sciences computing, especially where NSF might be able
to make an impact.
Introduction: Laura Hoopes, Pomona College and NSF Biology Advisory
Committee: John Fray, NSF
Laura Hoopes welcomed the attendees to the conference and briefly
described the plan of the day. She then introduced John Fray. John
Fray explained that this conference was focused at the leading
edge of NSF's activities for the year. NSF wanted input for planning
its year 200 budget, so it sponsored this conference to listen
to practitioners. He highlighted features of the 1998 and 1999
budgets, especially the Knowledge and distributed Intelligence
(KDI) theme. Biology is seeing this theme in knowledge networking,
learning intelligent systems, and as aspects of such areas as genomics
and life in earth's environments.
A question was raised about NSF's role in the purchase of computers.
John Fray discussed the general theory of NSF that colleges and
universities should supply computers, but told the group that presenting
computers as a tool to solve a problem could now lead to funding
to purchase some computers. Use in the Arabidopsis genome project
was an example he gave. Another question was raised about computational
bioinformatics. For Life in Earth's Environments, the whole scientific
literature needs to be accessed and used, but traditional library
methods are not easily manipulated. does the NSF have any role
in developing new library systems for such work? John told the
conferees that the databases were seen as very important to support
to preserve data. Examples were the results of the Arabidopsis
genome project and data on global changes.
Speakers on the research/teaching interface in life sciences:
Nancy Hamlett, Biology Department, Harvey Mudd College; Newton
Copp, Joint Sciences Department for Claremont McKenna College,
Scripps College, and Pitzer College; Howard Towner, Biology Department,
Loyola Marymount University, Beth Braker, Biology Department, Occidental
College, Elizabeth Rega, Joint Sciences and Stuart Sumida, California
State University at San Bernardino.
Nancy Hamlett described the courses in biology she teaches at
HMC. The pedagogy used in her department de-emphasizes lectures
and examinations and uses critical thinking and synthesis. Computing
enhances the courses in three ways. First, computer techniques
are used by the students in data analysis. Such packages as DNAStar,
PowerPoint, Chart, Spike2, etc. are used to analyze data. Databases
such as GenBank are accessed and used by the students. Second,
demonstrations and simulations that are hard to do in real time
are provided via computers. Examples include evolutionary calculations
and protein purification design. Third, the course uses computing
in teaching techniques. Syllabi and notes are posted on a web page;
reading quizzes are on the web, good links to web resources are
highlighted on the course web page as well. In the introductory
biology class, there are no laboratories but experiences relating
to laboratory work are built into the course. The material relates
to society via group projects on "biology in the news",
in which the students research current topics and provide output
in the form of posters, a web page, or another means they devise.
They must create something that can serve as an educational resource
for the topic.
Nancy has begun to assess the effects of these computer enhancement
to her courses. She now has the results of two student surveys
from the introductory course. Of those who responded (38 students),
95% created a web page. The reasons given were: 68% easy, fast;
22% reaches a wider audience; 13% more effective presentation;
other reasons: wanted to learn HTML, would get better grades. A
few said that they were'sick of web pages.' With regard to the
syllabus, 85% said they preferred it on the web so they would not
lose it. Asked if the projects reinforced the lectures, 40% said
yes, 30% thought they did somewhat, 30% thought not. asked if the
projects related to current issues in society, 66% said yes. Nancy
was asked whether HMC provides assistance to students who are creating
web pages, She said no, they expect them to figure it out, but
she provides assistance if it is clearly needed
Newton Copp described the development of a computer-based course
in Human Physiology. Before the redesign, the course used kymographs
and strip charts to present one to two weeklong laboratories, with
new equipment and experimental systems given every week. The problems
with this system were:
- The students were learning equipment, not biology.
- The students collected data, then went home to prepare the
report. If questions arose, there was no one to ask about data
interpretation.
- Short laboratories gave little chance for students to develop
their scientific abilities to ask and answer questions.
In 1991, Newton received an ILI grant form NSF to improve these
laboratories. The general design was to introduce a topic, equipment,
experimental design, and possible questions in the first week,
have the students collect data to answer a question in the second
week, and to analyze and interpret the data and draft a report
in the third week. The laboratory and lecture topics were decoupled
to provide long enough blocks for these experiences. Computers
were used to encourage and facilitate exploration, increase the
variety of questions addressed, increase the speed and sophistication
of analysis, better display the results, and stabilize the equipment.
Newton provided examples of exercises that had been done by his
students in this course. he told us that students could address
questions such as signal to noise ratio or alternative displays
to give the clearest interpretation of data. The most positive
outcomes have been increased sizes of samples, increased variety
and speed of analysis, better graphs, and a general shift of focus
to the physiological question being investigated. But, the need
to deal with equipment did not really recede. Students struggle
with how to save files, open windows, and analyze data whole collecting
data. The capabilities of the system are often underutilized by
the students, and the savings realized, amounting to about half
the course budget, were not banked to allow equipment and software
replacement when needed.
Howard Towner teaches an introductory biology class concerning
population biology, evolution, and ecology to about 160 students
each year. In 1994, he received an ILI grant from NSF to create
a laboratory with 11 computers to support their projects, presentations,
and graphing. The students are encouraged to use the simulations
and data analysis packages on their own. Howard described evolution
of the computers and software used by biologists of the 1980's
and 1990's, culminating in web resources available today. In 1998,
he has added information about plants and about the Ballona Wetlands
to the page. He uses a camcorder to capture images of wildlife
for the page. He also recommended other sites, such as the Marine
Biology site run by California Polytechnic University at San Luis
Obispo. To Howard, the great flexibility of access to the web by
people with a variety of platforms is one of its greatest strengths,
compared to the great variety of other computer-based systems he
has used. Howard identified several hurdles for those wishing to
author such sites. It requires access to a server on which the
information can be stored. One must also acquire original materials
or pay attention to copyrights. Material must be put into files
with appropriate formats that are accessible across platforms (for
example GIF files). The author must also spend a good deal of time
to learn about software and hardware, and it is not clear that
his endeavor will be favorable received by faculty personnel committees.
Beth Braker described the use of computers in field work in ecology
and evolution. She told us that students perceive field biology
as a "non--instrumented science" using clipboards and
pencils. Her experience is that data collection is facilitated
a great deal by computers. In ecology, the research efforts depend
on data acquisition, storage, and analysis. These endeavors are
facilitated by the accuracy and efficiency of computer methods.
Beth uses dataloggers for studying the forest canopy, useful in
studying photosynthetic rates and nutrient flow patterns. The GIS
systems available today enable investigators and their students
to create accurate maps of resource placement. Image analysis is
also becoming important in ecology today. It can be used to count
pollen grains on a stigma, obtain population density of animals,
analyze shapes (such as leaf shape as an index of predation), and
measure areas (for example that of fungai blotches on leaves).
Beth described how she and her students used image analysis of
area in a native tropical tree plantation to examine whether or
not such a plantation was more susceptible to herbivores and natural
enemies. they obtain a video image of each leaf and analyze it.
Using four such samples improved the variance of the mean (0.19
for the video analysis compared to 0.7 for the hand analysis).
It also improved the time per sample (8 minutes compared to 20
minutes). Beth gave an example of a local student project asking
how ants affect leaf predation that was accomplished using the
same techniques. Results indicated that ants may remove or negatively
affect herbivores. Some difficulties with the method involve reaching
leaves of interest, keeping the leaves flat, not damaging leaves,
reflection from leaves, analysis of compound leaves, analysis of
very large leaves. In the question period, Beth was asked about
security and backup for the data. She has not totally solved this
problem, but can download data to a laptop or a PC card and back
it up. She was also asked about non-linearity of intensity on videotapes,
and had not addressed this problem. She told us her software was
Imagetool or NIHimage.
Elizabeth Rega and Stuart Sumida discussed enhancing the teaching
and learning of human anatomy via computers. Elizabeth teaches
about 60 students at a time; Stuart teaches about 220 at a time.
They both use images to enhance the laboratory, such as the Virtual
Human. They identify a number of challenges, including inadequate
textbook support (e.g., no color pictures of structures), expense,
student understanding of 2D to 3D conversion of information, and
developing real life motor skills of dissection. They argued that
this subject is not all memorization, but requires a great deal
of three-dimensional visualization, understanding of development
of morphology, and understanding of individual variation. Elizabeth
highly recommended the site http://visembryo.ucsf.edu where embryonic
development can be examined. She uses web lectures with links to
important sites and has virtual office hours on the internet. Stuart
said that Elizabeth had developed a number of these methods and
had shared them with him; he uses them in a different setting.
He said that the computer makes us better scientists and researchers
and works with the students to develop 2D/3D understanding. He
finds the available resources are better than labeled embryo slides.
He also uses the visible human male project and the visible human
female site, and uses his class web page to point students to those
sites. One of the issues of concern to Stuart is variability between
humans of the same structures. he is not sure that computer based
methods can currently address this issue adequately. Another concern
is that developing such methods is a lot of work, in some ways
resembling producing a text but without royalties or academic recognition.
Third, Stuart reminded us that errors can creep into the best sources,
and presence on the web site for a reliable institution in no guarantee
of absolute accuracy. Fourth, he also finds that 2D/3D mental conversion
is hard for his students, though computer methods do improve this
visualization. Fifth, he shares Elizabeth's concern about development
of motor skills. He felt that these methods make teaching and research
very close together, and pointed to the usefulness of the methods
of his course to paleontologists.
In the question period, Rich Cardullo said the computer-driven
real life motor skills were becoming important too. For example,
students using micromanipulators in his laboratory have benefited
from video game experience. But, this experience does not help
them with phlebotomy. Beth Braker commented that variability is
also an issue in ecology, and that science often prepares an idealized
'the way it is' view that may contrast with individually observed
examples but still reflect an overall tendency. A question about
public web pages elicited the comment that putting up a web page
on a topic with medical implications, such as human anatomy, leads
to a large number of inquires from the public about their medical
problems. It is important to decide how these should be handled.
Elizabeth told us that her virtual office hours software was a
module of Front Page. She has found it very easy, but with a few
bugs
Discussion of whether or not research and
teaching are brought together via computer resources in the life
sciences. T.J. Mueller
commented that increasing student problem solving, which is facilitated
by computer approaches, is much more proximate to research. Nancy
Hamlett commented that there are a number of research areas where
leading edge researchers post their advance class notes on the
web, and these can provide a real current approach to students.
She noted that Norm Pace at UCB has provided such a site. Howard
Towner raised the issue of intellectual property for such sites,
and said that not all researchers are so generous with their new
work. T.J. Mueller noted an upcoming symposium in Claremont on
intellectual property aspects of the web.
Beth Braker said that she found teaching techniques useful in
research was very attractive to students at an undergraduate college.
There was no comparison between student interest in sorting insects
versus downloading video images from a computer. Howard Towner
agreed, saying that his students can digitize sound spectrograms
and use them to analyze research question; this has enlivened classes
as well as research.
Diana Linden raised the question of trouble shooting and student
support for students venturing into new computing areas. T.J. Mueller
said that infrastructure needs to include support staff, but he
has found that the needed level of support is very spotty, especially
for web and multimedia methods. Rich Cardullo commented that the
best peel in these areas are immediately hired by Disney and Warner.
Stuart Sumida said that in introductory biology, he is able to
ease students into web use via asking a question that links the
students to the course web site to prepare for laboratory work,
etc. John Fray commented that this was opening students eyes and
educating them. Newt Copp said that this is also direct preparation
for research; class room computing is being used to develop familiarity
with tools in their classes and projects. He still questions how
to best stimulate curiosity and promote thinking. Web based information
is disorganized, not peer reviewer or moderated, and without feedback
to authors or users. Credit for web-based work is a murky area.
He things more professional societies are beginning to evaluate
and review educational/research resource sites, but such sites
change frequently, so reviews may be out of date.
Nancy Hamlett noted that students can use the computer resources
to get into dialogue with major researchers. In one project in
her introductory class, the students contacted a major research
who was developing DNA-based computers, and he allowed the to e-mail
him 3 questions that he answered via e-mail. Stuart Sumida compared
the impact of computers in the life sciences with that of photography
in movement analysis. One could not know if all four of a horse's
feet left the ground at once until stop motion photography was
developed. computers and their diverse and multiplying methodologies
are having a similar or even greater impact. Howard Towner pointed
out that people depend upon sensory input and that there is no
real substitute for animals and plants; the computer is a preview
and a tool, no a substitute for reality. Diana Linden noted that
the translation from 2D to 3D thinking is helped by computing but
really requires analysis or real organisms. Wayne Steinmetz noted
that once we weighed the peaks from gas chromatograms to integrate
them but now we have much more sophisticated computer methods.
He advised us to expect improvements in computing, not judge what
is possible based on today's technology
Bruce Telzer said that as educators, professors need to provide
on-the-job training in thinking to the students; he finds computers
useful in focusing on thinking rather than repetitive task performance.
In some cases, such as in a graphing program, students may accept
the computer's line when they know it is absurd. he asks students
to make a hand-drawn graph and provide an approximate answer before
leaving the laboratory, in order to combat their lack of trust
in their own observations. Howard Towner said that specific applications
could enhance students critical thinking. In some courses, he uses
a PC generic problem solving program. T.J. Mueller asked Newt Copp
whether his students were thinking more about experimental design
or trying random experiments. Newt said that they can test ideas
quickly, but becoming critical of ideas is hard to obtain from
the students. They tend to stop the analysis as soon as one fit
is obtained, rather than critiquing the fit. Diana Linden described
a program that models the squid giant axon and allows students
to change all the parameters and then get data. This program does
not help, of course, with real axons that give data unlike the
characteristic waveforms. Nancy Hamlett said that it was good to
create experiments in which a large number of students could participate.
She prefers for them to get a real experience rather than a virtual
research experience.
John Fray asked what could be measured in order to see the answer
to the question, does computing bring research and teaching together,
in the past and the present? Does integration of research and teaching
via computing improve education? Will we create long term learners
in this way? Newt Copp said that interdisciplinary work and ability
to work across boundaries could be examined; he aims to produce
undergraduates who can bridge gaps between fields. Wayne Steinmetz
advocated for examination of Nancy Hamlett's teaching methods and
the student outcomes achieved; he believes empowering students
is more important by far than assimilation of ever-larger texts.
Rich Cardullo said that it is a challenge to teach well in spite
of excessive information; achieving depth of learning requires
good designs. We need to assess how well our teaching methods encourage
students to question.
John Fray then asked how long can a professor track a student?
Three years was suggested by Nancy Hamlett, but others thought
some examination of alumni/ae could be possible as well. John suggested
that hands-on learning, moving back and forth between concrete
and abstract, was an important skill to assess, as well as open-endedness
allowing for student initiative and ownership. Several people agreed
with these ideas. Wayne Steinmetz suggested transcripts looking
at types of courses selected before and after certain courses might
be useful. Stuart Sumida brought up the problem of professor evaluation
systems, and thought the kind of intensive teaching strategies
being discussed might result in denial of tenure. John Fray asked
how such perceptions might be changed? Stuart thought one could
cluster junior people so they could support each other, others
suggested tracking tenure processes for creative teachers. They
also suggested assessing for student learning via subsequent selection
of courses, career choices, attitudes towards science, and self-reported
problem solving skills 5-10 years after graduation. John Fray noted
that science literacy is important as well, but it is currently
not tracked. Nancy Hamlett said that since Harvey Mudd established
a biology major very recently, they are able to track all of their
alumni/ae. There are only 5 years of data as yet; alumni/ae are
sent by e-mail a group of open ended questions, and 2/3 respond.
They ask about what in their education served them well or was
important in their careers, strengths, areas to improve, and any
messages they would like to give to prospective students. They
are particularly positive about writing intensive courses and research
experiences so far.
Speakers on infrastructure concerns: Arieh Warshel, University
of Southern California; Steve Mayo, California Institute of Technology;
Fred Lee, Pomona College, Rich Cardullo, University of California,
Riverside; Bruce Telzer, Pomona College; T.J. Mueller, consultant
(formerly Harvey Mudd College); Diana Card Linden, Occidental College
Arieh Warshel began the afternoon session with a talk on understanding
enzyme actions through modeling. The protein structure is able
to tell a scientist where certain things may take place, but not
the energetics or how the reaction works. These features cannot
be understood without computers. Using them the researcher can
approach complexity, build models and check them against known
parameters and thus discern what is happening functionally. He
gave an example of the Ras p21 system and its complex interactions
with GTP and GDP, an important control point for carcinogenesis.
X-ray crystallographic data indicated that gln61 in protein could
possibly act as a base in the attack on GTP to form GDP, but further
analysis using modeling showed that this model was untenable. Additional
examples of the application of this method were given. In the question
period, Arieh told us that he began this type of work on simple
PCs, but has now moved to SGI workstations. Asked how to avoid
the kinds of mistakes in modeling that he had described, he said, "keep
an open mind, model, and aspire to get the actually measured numbers."
Steve Mayo then explained his combinatoric approach to protein
design, a very interdisciplinary field using biology, chemistry,
computer science, and other fields as contributors. he is looking
for insights into protein folding that will facilitate biotechnology
for the next century, enabling scientists to design proteins that
will fold in particular, known ways. First, the backbone position
must be designed; then, the sequence of amino acids must be selected
to get folding and functionality. His method involves consideration
of the hydrophobicity of the core residues; boundary region design
features such as burial of residues, packing, electrostatics; and
surface features such as hydrophilic groups. He uses a design automation
cycle. First, he analyzes, then designs, then simulates the desired
result using computers. Then, he synthesizes the apparently optimal
molecule and examines its real properties. Information from these
experiments forms the basis of the next analysis beginning the
cycle again. He explained the enormously complex system and the
simplifying assumptions he makes for his calculations. Then he
presented results in design of a modified region from a Zinc-finger
Transcription Factor. The design for FSD-1 enabled synthesis of
a domain that folded in close approximation of the real domain
but was not homologous to the original sequence. In the question
period, Steve told us that he is sure that he has found the optimal
solution within the assumptions about rotamer libraries, etc. that
he had made. Another question focused upon thermal stability. Steve
said that hyperthermophilic designs are possible to make.
Fred Lee then discussed bringing to biochemistry and molecular
biology students the use of the interdisciplinary tools of computer
molecular modeling. The connection between structure and properties
is his focus, and his courses are designed based upon the assumption
that the best way to equip students is via hands-on experience.
He builds up their basic skills in Unix and using the internet
formation resources. Then, the students undertake problems that
can be tackled using a Unix cluster and the computational biology
server that are available for student use. He has build web pages
that collect web resources and enhance self-learning on the part
of his students. Tutorials on Unix, protein design editors, compilers,
and on-line help are on his web page. He has the students send
in their papers via FTP. They learn to use visualization software
and to plot phi/psi maps and contact maps for residues. He wants
them to do semicritical/ab initio calculations in solution, not
in gas and to look at protein-ligand interactions, mechanisms,
and computer-based protein design. So far, he has found that the
students need more programming and physical chemical skills in
order to do this successfully. One way this situation could be
improved is to develop a computer science track for biology majors.
Another way is to increase interest of non-biology majors in this
interdisciplinary field. In the question period, Fred was asked
whether his field is an appropriate track for undergraduates in
biology, or whether biology was more to provide a broad training
rather than such a focus. he responded that this direction would
not be for all biology students, but would be for students who
can have completed physical chemistry by junior year. He feels
strongly that students who would want to go on in this area should
have the option available. Fred reminded us that NMR, UV/visible
spectrophotometry, analysis of data, and writing of papers are
all now computer-linked; students are comfortable with many aspects
of computer use. However, computer languages such as Pascal, C,
and Visual Basic would be helpful for today's science students.
Wayne Steinmetz commented that 15 years ago, a task force recommended
that every student take a course with extensive computer methods.
Today, we no longer have this requirement, but students are required
to master statistics and analytical reasoning. Fred thought that
some computer language work could be included in laboratory work
for introductory biology and chemistry students. Chris Rohlman
noted that the liberal arts approach to science has led to students
with all different backgrounds in science courses. Steve Mayo told
us that his graduate students originate from chemistry, physics,
and biology programs and all work together on the same projects.
Rich Cardullo then talked about image processing in cell biology.
He raised the question, How much do we expect students to understand
the black boxes? Rich described the confocal microscopes that optically
section the specimen under study. The uses of computing in image
analysis he classified into two main functions. First, contrast
enhancement can be done via computing. The contrast can be enhanced
temporally using such methods as signal averaging. It can also
be done spatially, suing various filters and convolution kernels.
The second use is in quantitative measurement. Morphometry is one
direction that such studies can take. Another is the study of dynamic
behavior of molecules, for example on cell surfaces. He presented
examples of the analysis of the interaction of the egg zona pellucida
and receptors on the surface of sperm, an interaction that provide
species specificity in fertilization. He also described Xenopus
egg activation. The egg is loaded with a calcium sensitive dye
and observed every thirty seconds. A wave of calcium ion is detected
that moves from the fertilization pole of the egg to the opposite
point on the egg surface over a five-minute period. Stimulation
of the hEGF receptor by adding Epidermal Growth Factor resulted
in pulses of calcium ion release in eggs, rather than waves as
produced by fertilization. Another example Rich gave was of studying
quantitative molecular motions on cells via Fluorescence Recovery
After Photobleaching (FRAP). This techniques uses Nanovid microscopy
and fluorescence correlation spectroscopy. This technique can be
used to follow movement of molecules in three dimensions using
VIFRAP, leading to the conclusion that lipids in membranes have
100% mobility. In the question period, Wayne Steinmetz asked how
one might best prepare undergraduate biology majors to use these
techniques. Rich told us that they are generally ready by junior
year, but that he also finds some physics majors can participate
in these experiments. His groups are composed of students with
different backgrounds, since his work is very interdisciplinary.
He pointed out that one problem is the lack of many students arriving
today from high school with biology, chemistry, and physics courses.
He particularly finds almost none with chemistry or physics, and
believes this trend is a real problem.
Bruce Telzer described building a cell biology laboratory around
computer-assisted data acquisition and analysis. His goals are
to introduce image processing. allow universal access to class
data by all students, and to save time. Some examples of his uses
of computers are: capture of EM negatives, light microscopic images,
gels, blots, etc.; developing print images from video images via
software and LaserJet printers; scanning for quantitation of gels
and blots; statistical and graphical analysis, and storing of data
files on servers. He uses a computer with framegrabber, Image1
program, a microscope with video camera allowing high intensity
and low intensity work, power supplies for lamps, fiber optic cables
for high resolution imaging, and an Argus IO image processor. Students
use Image1 and a computer to acquire raw images from microscopy,
from VCR, or from black and white cameras. Bruce told us that students
could look at an axoneme in sperm or cilia and see microtubule
assembly using light microscopy images, although these events are
ten-fold below the resolution of the microscope. also, this type
of analysis takes minutes, not hours and one sees a live image,
as compared to what must be done to observe using an electron microscope.
The image is sent to Argus 10 to subtract background. Then frame
averaging of the image is used to decrease the effects of Brownian
motion. Bruce showed us clear images in which his students had
been able to record assembly of microtubules over time using this
technique. Current students engage in a Five-week analysis of red
blood cell membrane proteins during which he is fairly directive.
Then, he has them select and study a question of their own choice
in cell biology for which he is a resource for the remainder of
the semester. Examples of such projects he give were to purify
microtubules from brain, to recombine dynein and outerfibers, to
reactivated axonemal microtubule sliding. to assess microtubule
protein rations via Western blots or via immunoprecipitation, and
to examine microtubules in cellular cytoskeletons via immunofluorescence.
He recommended the use of laptops with PC cards that enable network
access; his students use them as digital laboratory notebooks and
can also network with other students in the laboratory.
T.J. Mueller (tj@shore.net) described a neurobiology course he
taught in the fall of 1994, involving active, student-driven learning
that he calls "lecture-free learning". He noted that
such methods do not decrease the professor's work load, but do
create a learning environment to engage the students with the subject.
He compared this computer-based course favorably with the neurobiology
course he had taught for 13 years at Harvey Mudd College using
lectures. T.J. put the course material onto multimedia machines
and also let the students put material there. On the first day
of class, T.J. gave an overview of the research issues, methods
what they are used for, etc. The first assignment given was to
look in the newspaper and think of a question you'd like answered
by the class. From this question, a research projects was developed,
then a story was produced, put into multimedia format, and presented
to peers. Examples of such questions were given: Why am I colorblind?
My grandmother has Alzheimer's Disease. What has happened to her
brain? What is motor memory? How does the brain work? The latter
questions was considered too broad; T.J. had to work with some
students to obtain a question that could be addressed by this method.
He gave the students information about library research. After
considering the question each student had raised. T.J. Assigned
the students into groups with related topics, such as the vision
team, the motor team, the memory team, etc. Each team worked together
to develop the understanding necessary to answer their questions.
A first presentation from each team was scheduled in mid semester,
allowing feedback to the teams. They then improved their presentations
for the final peer and instructor evaluation. Class time was used
to follow team progress followed by discussion. After a time, the
students asked for lectures on five particular topics and followed
them with great interest. A problem with the course was the first
generation ILS software used which was very buggy, but the software
for such a course is now much better. In the question period. T.J.
was asked to compare this experience with that of writing a term
paper. It is similar in providing depth rather than breadth, but
real world stories, emphasis on being educational, engaging, and
convincing to peers, use of the more engaging computer/multimedia
materials, and pseudoexperimentation set it apart. There was not
wet laboratory with this course, although, T.J. thought wet lab
would be an asset to such a course. There were 20 students in this
course.
Diane Card Linden described taking a neurobiology course from
a lecture class only to a laboratory course using intracellular
recording. She had an ILI grant in 1990-1992 to develop this course.
The goals were to promote students understanding of elusive topics
in biophysics and to have them understand intracellular recording
techniques. Included were early laboratories involving repetition
of tasks so that students learned to setup, trouble shoot, and
carry out experiments on intracellular recording from amphibian
nerves. At the end of the semester, teams carried out projects
that they designed based on the earlier experiences in the laboratory.
the software used was MacLab; at the time, there were few systems
and this was the easiest to use. the intracellular recording apparatus
was hard wired to the modem port for recording potential differences.
The program contains sophisticated routines for analysis of data.
Students maintained their data on a diskette that they could take
home to analyze further via spreadsheets, etc. In addition to collecting
their own data, Diana provides an actin potential program, a sheep
brain program, and a program on neurosimulation on neural networks
for exploration by the students. She gave several examples of projects
the students had performed. One involved physostigmine effects
on spontaneous synaptic potentials. Another examined the effect
of 2mM extracellular Rb+, K+, or Li+ on Vrest*. The system she
uses works reasonably well but the Macintoshes need to be updated
and more memory is needed. Strong points of the laboratory work
included the development of student expertise with both the equipment
and the dissection, the open-ended experiments that students could "own",
and the increased excitement they have about neurobiology. Diana
insists that the students present all of their data in a research
style report. On evaluations, the students say they understand
the concepts and that the best part of the course is the final
project. In the discussion, Karen Parfitt suggested invertebrate
preparations and recommended "the crawdad workshop" at
Cornell University. Diana said that the amphibian preparations
were not very hard to do, and only take five minutes when you are
skilled; they just required the students to practice to develop
their skills. Diana told us she groups the students into pairs
and that the juniors and seniors take this course. She worries
because she is unlikely to gent another ILI to replace her old
equipment, but Occidental does not support or replace Macintoshes.
She is considering applying to ILI to develop laboratories on voltage
clamping.
Discussion of infrastructure needs that arise from increased use
of computing in the life sciences, particularly the role of NSF
in addressing such needs.
T.J. Mueller said that the Mellon grant that is supporting computer
and multimedia based learning at the Claremont Colleges does not
aim to provide basic equipment, but just to allow models and breakthroughs.
He thought NSF is pursuing a similar strategy, and thought NSF
might put pressure on institutions not just to match but to continue
the programs. Others thought that institutions are currently pouring
funds into this area and may be be able to keep up with demand.
Bruce Telzer said that 5 years of life for a computer system is
long, and plans must be made for replacements. T.J. said that personnel
(computer support people) must be increased to allow faculty to
use computing optimally. Asking faculty to add learning multimedia
or computer data acquisition programs to their expertise needs
support; otherwise faculty will not do it. He also suggested that
courses and/or departments should develop a way to bank budget
dollars so that computers and software could be replaced when needed.
Bruce Telzer noted that when a centrifuge is purchased, it last
10-20 years, and one can ask for a replacement on a research grant
or a teaching grant after a long period of use. With the short
lifespan of a computer, replacements may be needed within the time
of one research grant. He thinks the equivalent of a service contract
for an HPLC might be to simply lease computers and always include
the lease cost on every grant proposal. Elizabeth Rega raised the
issue of discrepancies between disciplines. Institutions may replace
computers for science or mathematics but not for English or Art,
leading to resentments. Stuart Sumida said that ways are needed
to integrate curricular, for example through a core program, so
that all can be supported. But, standing budget line items for
computer replacement are needed and are almost never there.
John Fray noted that it would be valuable to NSF to discuss the
short term versus long term approaches to computing. He suggested
that a novel idea might enable people to apply for a new ILI grant,
for example. NSF might also consider developing mechanisms to support
long term, multi-user computer facilities. Stuart Sumida reiterated
the severe lack of support personnel faced by professors at his
institution. He thought perhaps the NSF should not grant equipment
without a guarantee of support personnel from the institution.
A good model for funding would be for NSF to provide or require
as part of the match 1 or 2 years of personnel support and funding
for replacement of the computers in year 5.
John Fray then emphasized that the NSF has moved from its view
that undergraduate institutions focus just on education. They now
see such institutions taking on a major role in the integration
of research and education. The two new review criteria used for
all proposals to the NSF are enabling reviewers to focus on the
issue of whether research results are being disseminated and providing
education in some context. The National Science board, NSF's oversight
body, has recommended that NSF move grant lengths from about three
year to a 4-5 year span on the average. There is a great deal of
new growth in life sciences using computing, for example in genomics,
that John thinks offers an opening for innovative proposals. The
community at this workshop would be a great locus for emphasis
on research/education interfaces as well as life sciences computing.
He recommended that proposals to the KDI initiative be seriously
considered. He told the group that computer upgrades could be proposed
in the budget, but institutions would need to identify their potential
effects as a model to other colleges and universities.
Stuart Sumida raised a concern about the development of Internet
II and the commitment of his institution to Internet I. John Fray
said that NSF's support for Internet I was ended; the wave of the
future is Internet II. Wayne Steinmetz noted that access to scientific
library information is very important; soon, paper journals will
be a thing of the past and electronic libraries will be the norm.
John Fray said that proposals relating to this need could be considered
by the Biological Infrastructure Division if a paradigm could be
developed to integrate the proposal with research/education interfacing.
Diana Linden and Wayne Steinmetz told the group that budget cuts
now make electronic approaches to the literature essential for
advanced classes. Elizabeth Rega noted that temporary faculty are
present in large numbers, and often get minimal computer support
John Strauss brought up the pressure from society on higher education
to improve productivity. John Fray suggested that educational institutions
could be transformed via computing into research colleges. Jon
Strauss said that Harvey Mudd and other Claremont Colleges have
no desire to let go of their educational goals; instead, they want
to provide cutting edge research opportunities while still interfacing
research and teaching. John Fray said that great opportunities
exist at NSF for developing uses of computing in life sciences
at the research/teaching interface, and colleges like these must
take the lead in preparing proposals of this kind. Stuart Sumida
noted that consortia are very important; state universities, community
colleges, etc can establish formal or informal linkages to facilitate
such efforts via faculty training and shared resources. He thought
that faculty release time was not as effective as sabbatical support
in getting faculty up to speed on these techniques. T.J. Mueller
suggested a mechanism such as the Mellon grant one, with an umbrella
grant and small subgrants provided to faculty in a consortium.
John Fray told us that this type of mechanism is very hard for
NSF to use.
After dinner lecture: David Laidlaw, California Institute of
Technology. "Impressionistic
Image Analysis".
David Laidlaw described to the group a way to use multilayered
images to provide a great deal of integrated information about
what is going on in a cell or a tissue. His technique uses bio-informatics,
neuroinformatics, and Diffusion Tensor Imaging. His techniques
uses ellipsoids to summarize diffusion information. The images
produced can be viewed in 3-D using special glasses. Rotation of
the structure being studied is followed via video. The images produced
can enable the investigator to view 6 coded values at once in their
different locations within a structure. For example, a view of
the spinal cord showed in 'underpainting' the basic shape with
a grid for the resolution of data. next were ellipses showing anisotropy
or spheres showing isotropy. The orientation of the spheres shows
the direction of the fastest diffusion in the plain. Reddish tint
is used to show extension of the ellipses or spheres out of the
plain. Opacity and striping can be used to indicate other variables.
The results resemble paintings by Van Gogh, but convey an enormous
amount of data. Comparisons of spinal cord of normal people with
those having Multiple Sclerosis revealed a number of changes, for
example much faster diffusion in the diseased areas. There is also
a subtle change in the gray matter structure that can be seen.
David is now applying this technique to mouse mutant strains such
as shiverer, a genetic mutant lacking adequate myelinization of
nerves.
Those in attendance at the NSF Conference on Computing in the
Life Sciences are listed below:
John Fray, NSF
Laura Hoopes, Pomona College
Nancy Hamlett, Harvey Mudd College
Jack Mueller, consultant
Wayne Steinmetz, Pomona College
Howard Towner, Loyola Marymount University
Lynne Mizuno, Glendale College
Richard Cardullo, University of California, Riverside
Bruce Telzer, Pomona College
Elizabeth Braker, Occidental College
Diana Linden, Occidental College
Arieh Warshel, University of Southern California
Chris Rohlman, Pomona College
Stephen Mayo, California Institute of Technology
Julie Archer, California Institute of Technology
T.J. Mueller, consultant, RR1, RFD 317, Little Deer Isle, ME 04650
(formerly Harvey Mudd College)
Eugene Wu, Harvey Mudd College
Jack Strauss, Harvey Mudd College
David Laidlaw, California Institute of Technology
Stuart Sumida, California State University, San Bernardino
Fred Lee, Pomona College
Karen Parfitt, Pomona College
Elizabeth Rega, Joint Sciences for Pitzer, Claremont McKenna,
and Scripps College
Jon Strauss, President, Harvey Mudd College
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