I received this from the New England Complex Systems Institute mailing list
and thought it might be of interest to readers of this news group.
David Fell
Dear Colleague:
I am writing to ask if you know anyone who would be an exciting
candidate for a rather unusual position at the University of California,
San Francisco (UCSF). The Physiology department at the University of
California, San Francisco is looking for a faculty member, at assistant,
associate, or full professor level, to join a new inter-departmental group
dedicated to biological systems analysis. This group will attempt to
combine approaches from biology, genomics, physics, chemistry, and
computer
science to create an integrated view of how protein networks in cells
create functional modules, such as signal transduction systems, and how
these networks are appropriately connected to and insulated from each
other
to allow cells to respond to a vast area of perturbations in their
internal
and external environments. All the members of this group would have
interests in both theoretical and experimental approaches to the biology
of
cells, and those who had expertise in both areas would be particularly
attractive to us. Since the community at UCSF is strong in most major
areas of cell biology, we are particularly interested in attracting
candidates who have a strong interest in biology but training and
expertise
in other fields that could contribute to this initiative.
UCSF is a strongly collaborative environment. For this reason, we
are especially interested in candidates who would be interested in forging
connections within this group and the broader UCSF community that would
help to create an enterprise in which the whole would be much more than
the
sum of the parts. We have strong expertise in theoretical work related to
systems neurobiology and protein folding and a new initiative in chemical
biology. There are outstanding graduate programs in Cell Biology,
Neuroscience, Genetics, Molecular Biology, Structural Biology, and
Biophysics, as well as a new graduate program in Chemistry and Chemical
Biology. The Physiology department spans a wide range of these programs,
with faculty working on cell biology, molecular and cellular neurobiology,
and developmental biology.
If you know of anyone who you think would be an outstanding
candidate for this position, could you let me know
(amurray at socrates.ucsf.edu) and also alert them. The job description (
http://keck.ucsf.edu/physio/cellbio.html) and a two page description of
the
Center for Biological Systems Analysis
(http://keck.ucsf.edu/physio/bioprop.html) are on the Web, and I have also
pasted them to the end of this message.
Many thanks
Andrew Murray
Professor of Physiology and Search Committee Chair
INTEGRATIVE CELL BIOLOGY
University of California, San Francisco
The Department of Physiology at UCSF seeks an assistant, associate, or
full
professor working on novel experimental or theoretical approaches to the
biology of cells. Candidates with expertise outside traditional cell
biology, including physics, computer science, evolutionary biology,
mathematics, and chemistry, a particularly encouraged to apply. A
successful applicant will be expected to play an important role in a new
center that will develop integrated approaches to understanding complex
biological systems. She or he will be expected to mount a successful
research program, to participate in graduate and postdoctoral training,
and to teach in graduate and professional school courses.
The search will remain open until an appointment is made, but complete
applications should be received as soon as possible, 1998, to ensure full
consideration.
Please send a CV, a 2-page description of past research and future goals,
and three letters of recommendation to:
Professor Andrew Murray
Chair, Cell Biology Search Committee
Department of Physiology, Box 0444
University of California
San Francisco, CA 94143-0444
--plus current equal opportunity statement--
Biological Systems Analysis: Experimental and Theoretical Approaches to
Bridge the Gap Between Molecules and Cells
As the twentieth century closes, biology faces an opportunity and a
challenge. The opportunity is provided by the rise of genomics, which
yields complete genome sequences and methods for systematically measuring
the levels of every mRNA and protein in populations of cells. The
challenge is to close the gap between chemistry and biology by connecting
the behavior of molecules to the behavior of cells. Even if genome-wide
approaches give us the abundance, distribution, activity states, and
kinetic parameters of every molecule in the cell, we will not understand
how cells work, or how their properties have evolved to allow them to
survive the varied and often harsh environments during the 3.8 billion
years since life evolved. Answering these questions will depend on
developing methods to analyze how networks of proteins are connected to
produce functional modules, such as signaling pathways, and how these
networks interact with each other to control the physiology and behavior
of
cells. The hope is that this analysis will reveal new organizational
("design") principles for biological systems. For example, how can
networks be both robust and evolvable? Robust, in the sense that critical
properties of the network are not affected by environmental,
physiological,
or genetic perturbations. Evolvable in the sense that the properties,
structure, and function of the network can be altered to respond to long
term changes in the external and internal environments of cells.
We believe that answering these questions will require assembling a
small group of scientists who combine a diversity of skills with a
commitment to work closely together to develop new tools for analyzing and
understanding cellular behavior. A Biological Systems Analysis Group
would
integrate theorists and experimentalists and be dedicated to developing
new
approaches to search for general principles that allow cells to survive,
reproduce, and evolve under a wide range of environmental, physiological,
and genetic perturbations. Such a group would include the following
components: cell biologists and chemists who will develop new ways of
monitoring the behavior of living cells and the molecules inside them,
evolutionary biologists who will examine how networks evolve both
historically and during experimental evolution in the laboratory, and
computer scientists and physicists who will model networks and develop
methods for extracting knowledge and recognizing patterns in the enormous
data sets that will be generated by genome-wide analysis methods. A
critical element of a group committed to biological systems analysis will
be a tight interaction between its different components, especially
between
theoretical and experimental approaches. The best ways of ensuring such
an
interaction is to find individuals whose interest and expertise spans more
than one discipline and who use both theoretical and experimental
approaches to scientific problems.
We believe that the problem of how protein networks function and
how they interact with each other should be tackled at the level of the
single cell first, using organisms that combine rapid life cycles with
excellent genetics and powerful tools for genome-wide analysis. Although
this suggests that the initial studies should focus on yeasts and bacteria
and yeasts, general principles that are discovered are likely to have been
conserved during evolution and therefore be directly applicable to the
development of multicellular organisms. One exciting possibility is that
there might be deep similarities between the principles underlying
multiple
biological levels from protein folding through cell biology to
developmental and neurobiology. A Biological Systems Analysis Group would
try and maintain close contacts with scientists working in these other
areas with the aim of looking for organizational principles that apply
across multiple scales in biology.
Components of the Biological Systems Analysis Group
The overall group would be divided into five subgroups:
experimental cell biologists, chemists, genome and evolutionary
scientists,
informatics experts, and theoreticians. These divisions are made solely
for the purpose of structuring the proposal. The principle of the group
would be that all its members were interested in multiple areas and that
its physical and intellectual structure would be designed to encourage
constant interaction between the nominally different groups. Because such
interactions cannot occur successfully beyond a certain size, the entire
Biological Systems Analysis Group would consist of 5-10 group leaders each
running labs of 3-8 scientists.
1: Experimental Cell Biologists and Geneticists
This subgroup would focus on attempting to understand network structure
and
behavior in living cells, by tackling networks that have already been
intensively studied such as bacterial chemotaxis and mating in yeast. The
goal would be to produce an accurate understanding of networks that
included and tested theoretical models that accurately predict the
response
of networks to perturbations as well as revealing the important principles
that underlie their function. This group would have strong connections to
studies on the experimental and theoretical studies on the evolution of
network function, the efforts of theoreticians and computer scientists to
use genome-wide data to predict the existence of new networks in cells,
and
would strongly influence the type of tools developed by the chemistry
group.
2: Chemical and Biochemical Methods for Studying Living Cells
A critical aspect of life that is it is indivisible. One either studies
live cells or biochemical systems prepared from dead cells whose relevance
to the physiology of living cells is always an issue. Although complex
extracts, like those prepared from frog eggs, are a partial solution to
this problem, it is not clear if it will be possible to fractionate and
reconstitute highly complex systems like spindle assembly. An alternative
approach is to develop methods that monitor or perturb individual
networks,
or even individual chemical reactions, with high precision in living
cells. The efforts in this subgroup would have strong and synergistic
interactions with research in the cell biology and theory subgroups.
3: Experimental and Theoretical Evolution
Evolution places strong constraints on the organisms that are alive today.
First, every one of their direct ancestors must have both survived and
reproduced, implying that the ancestors survived and reproduced in a wide
range of environments. Second, they evolved to produce descendants that
could survive and reproduce in novel conditions that the ancestors had
never encountered. Third, most biological inventions were assembled from
existing parts rather than being engineered de novo. One possibility is
that evolutionary constraints mean that cells use only a very tiny
fraction
of the types of networks that could exhibit particular properties such as
switching between states, amplification, etc. This question can be
addressed by comparative analysis of the structures of different existing
networks and by evolutionary experiments that use selective pressure in
the
laboratory to alter the functions of existing networks or produce new
networks with novel functions.
Because the evolutionary history of organisms is encoded in the DNA
of their genomes, there is a strong link between genomics and evolutionary
theory. Both of these subjects are also intimately linked to
understanding
the structure and function of modules that perform tasks in cells:
evolution because its preference for recycling over invention places
strong
constraints on how functional modules work, and genomics because proteins
that function in a network are likely to be regulated in coordinated ways.
The combination of these approaches will play a key role in defining
functional modules inside cells, discovering their evolutionary
relationship to each other, determining how cells integrate and process
information from different pathways, and learning how to recognize
functional modules from genomic information. Work in this subgroup will
have strong connections to all other subgroups, especially the informatics
and theory subgroups.
4: Computer Science and Informatics
The advent of genomics raises a major challenges. How do we extract
knowledge about biology from vast masses of information that come from
genome wide approaches, such as analyzing the pattern of transcription of
every viable gene knock-out in budding yeast? How is such data integrated
with more traditional approaches such as determining the detailed
phenotypes of mutations or in vitro reconstitution of complex reactions.
Hopefully, talented computer scientists who can interact successfully with
experimental and theoretical biologists can play a major role in solving
these problems. Choosing the right group leader(s) in this area will be
critical because the right candidates will need to either have or develop
a
strong feel for biology that will allow their efforts to mesh with those
of
the other subgroups.
5: Theory
As we try to understand more and more complex biological systems, theory
will play a larger and larger role. Although experimental biologists have
traditionally been wary of theory, it will clearly be essential to
understand how complicated biological functions work and to design
experiments that can be used to distinguish between competing
explanations.
A key issue in theory is to try and find ways of framing problems that
minimize the number of variables, maximize the number of constraints, and
suggest simple and direct experimental tests. We believe that scientists
with training in physics and an strong interest in biology can have a
major
impact in this area, especially if they are capable of integrating
theoretical and experimental approaches to biology within their own work.
Although this group would primarily be concerned with problems in cell
biology, we would expect its members to establish interactions with other
groups using similar strategies to attack problems in protein folding,
developmental biology, and systems neurobiology.
