Received: by alpheratz.cpm.aca.mmu.ac.uk id DAA08515 (8.6.9/5.3[ref firstname.lastname@example.org] for cpm.aca.mmu.ac.uk from email@example.com); Tue, 19 Feb 2002 03:12:50 GMT X-Originating-IP: [220.127.116.11] From: "Grant Callaghan" <firstname.lastname@example.org> To: email@example.com Subject: Re: Memes and Emergent Properties Date: Mon, 18 Feb 2002 19:07:20 -0800 Content-Type: text/plain; format=flowed Message-ID: <LAW2-F35swxvR31brPB00003c73@hotmail.com> X-OriginalArrivalTime: 19 Feb 2002 03:07:20.0675 (UTC) FILETIME=[8B992330:01C1B8F2] Sender: firstname.lastname@example.org Precedence: bulk Reply-To: email@example.com
>Subject: Re: Memes and Emergent Properties
>Date: Tue, 19 Feb 2002 10:17:30 +1100
>On Tuesday, February 19, 2002, at 01:50 AM, Grant Callaghan wrote:
>>> > This is, of course, the
>>> >holism versus reductionism debate, and very sterile it is too, IMO. I
>>> >prefer GC Williams' characterisation of reductionism and holism in
>>> >biology as a function of the size of the glassware used.
>>> >John S Wilkins
>>> >Head, Communication Services
>>> >The Walter and Eliza Hall Institute of Medical Research
>>> >Parkville, Victoria, Australia
>>Have you looked at the work going on at the Institute for Systems
>>Biology in Seattle?
>No. Should I (and why :-)?
I think you might get a better view of the holistic approach by a rational
researcher who has done some remarkable things, including inventing machines
that write DNA code and create proteins from scratch. They look at the
whole process within the cell and have invented mathematical models of
complex interactions between cellular components. It's not beaker science
but molecular science. You can check them out very easily at:
Here it is in their own words:
What is Systems Biology?
Technological breakthroughs, including those enabled by the Human Genome
Project, are providing new opportunity to understand the complex systems and
networks responsible for most important biological functions. Systems
biology is a powerful approach to studying genes and proteins made possible
through these technological advances. Unlike traditional biology that has
examined single genes or proteins in isolation, systems biology
simultaneously studies the complex interaction of many levels of biological
information - genomic DNA, mRNA, proteins, functional proteins,
informational pathways and informational networks -to understand how they
Virtually all important biological phenomena, from a cell's utilization of
sugars to the functioning of the human heart, are the result of complex
systems. For decades, biologists have studied individual genes or proteins
in isolation and have made some pivotal discoveries. But this approach has
been limited by the fact that biological systems involve many elements
working together. The Institute's approach focuses on the whole biological
system by creating a detailed description of all the parts and an analysis
of their interrelationships as the biological system performs its functions.
The Human Genome Project initiated new approaches to biology termed
discovery science. This approach focuses on gathering information; that is,
defining all the elements in a system and placing them in a database rather
than seeking to prove or disprove a particular theory. This global
information is then used to inform traditional hypothesis-driven science by
determining how all the elements in a biological system behave when it is
The Institute is developing and refining high-throughput facilities the
combinations of machines and instruments needed for DNA sequencing,
genotyping, DNA arrays, proteomics, cell sorting and a wide variety of
single-cell assays. The Institute's goal is to pioneer information capture
by faster and less costly high-throughput platforms that are fully automated
from sample preparation to final analysis.
The Institute's mathematicians and computer scientists are creating powerful
computational software to understand complex systems. This requires the
analysis of large data sets, the integration of many different types of
biological information, the graphical display of the integrated data and,
finally, the mathematical modeling of biological complexity. These
computational tools constitute one of the grand challenges in biology for
the 21st century.
Collaboration between specialists in biology, chemistry, computer science,
engineering, mathematics and physics is at the core of the Institute's
approach to shaping new biological research methods and technologies. The
challenge is how to educate cross-disciplinary scientists to understand
biology in a deep sense and collaborate effectively in terms of executing
Institute faculty members have played pioneering roles in developing new
machines for and new approaches to genomics, proteomics and high-speed cell
sorting. Technological development is a significant focus of the Institute.
Goals include developing new and refining existing high-throughput platforms
and creating better mathematics approaches for capturing, storing and
distributing biological information.
The Institute focuses considerable research on simple model organisms
(bacteria, yeast, fish, flies, sea urchins and mice). Model organisms can be
perturbed genetically, biologically or environmentally with respect to the
functioning of particular systems and the interrelations of the component
parts can then be studied. The ability to study biological systems of model
organisms provides the Rosetta stones for understanding how these same
systems function in humans.
The Institute currently has partnerships with eight private companies
including the Arctic Region Supercomputing Center at the University of
Alaska, the University of Washington, the Fred Hutchinson Cancer Research
Center, and other universities and institutes.
The Institute's structure, as an independent non-profit collaborating with
the private sector and universities, is unique and provides significant
advantages. Chief among them is a single focus--systems biology an objective
shared by the faculty and staff. In addition, scientists from diverse
disciplines are able to work at the Institute together as teams to attack
specific technology or systems problems. The structure also provides for
efficient administration and the flexibility to move quickly to recruit top
talent and to enter into partnerships or other agreements.
Breakthrough demonstrates principles behind Institute, opens door for
revolutionary approach to medical research
May 10, 2001 - In a research breakthrough, scientists at the Institute for
Systems Biology have demonstrated the power and feasibility of integrating
genomic, proteomic and other biological data types to create a model of the
vast network of molecular interactions that make up a living cell.
The research, featured in the May 4 edition of Science Magazine, represents
a major advance supporting the concept of systems biology by demonstrating
the feasibility of creating models for accurately predicting molecular
interactions within cells.
“This accomplishment is at the core of the Institute’s scientific mission in
its successful integration of biological data types that have largely
remained disconnected from each other,” said Trey Ideker, principal author.
“It represents a major milestone and a proof of principle for the systems
approach. Our success gives us confidence that we’ll be able to decipher
increasingly complex informational networks within cells and organisms.”
“Ultimately, the modeling approach we used promises to revolutionize the
study of disease and illness by generating information needed to develop new
medical treatments in a much shorter timeframe,” Ideker said.
In an unprecedented integration of methods and technologies spawned by the
Human Genome Project, the research team gathered huge amounts of data from
genes, proteins, and molecular interactions within the cell. These data were
generated by exposing the pathway of galactose utilization in yeast to a
battery of test conditions in which known genes and other molecular
components were removed one by one. For each test condition, responses were
recorded at several different levels of biological information utilizing
DNA microarrays gathered genomic information revealing which genes were
turned on or off under each condition.
Proteomics techniques pioneered by the Institute’s Dr. Ruedi Aebersold
measured the types and quantities of the proteins produced by each expressed
Existing biological databases were mined to identify molecules known to
interact in each condition, including data on interactions among proteins as
well as between proteins and DNA.
The diverse data types were then integrated using the Institute for Systems
Biology’s high-throughput computational facilities. The research is of
particular significance because in less than a year, it succeeded in
verifying a large body of prior findings — findings that took more than 20
years to accumulate through traditional research involving very few elements
at a time. The research also succeeded in identifying a number of new
interactions not previously documented through traditional research methods,
opening whole new fields of study.
“While systems biology is still in its infancy, the findings of this study
highlight the promise of future gains that will dramatically impact the
treatment of human disease and illness,” Ideker said.
“This research is the essence of what the Institute for Systems Biology is
all about,” said co-founder and President Dr. Leroy Hood. “It is clear that
you cannot learn about systems by studying one gene or protein at a time. It
is also clear that the information from genes and proteins must be
integrated if we are to understand systems. The Institute’s capacity for
advancing integration is one of its most unique and important features.”
The Institute for Systems Biology is formed around the realization that
advancing biology in the 21st Century will rely on using advanced biological
and computational technologies to generate and correlate many different
levels and types of biological information. Unlike traditional scientific
approaches that examine single genes or proteins, systems biology focuses on
simultaneously studying the complex interaction of vast numbers of
“The Institute is unique in its collection of technologies and talent for
advancing systems biology,” Hood said. “We’re very excited about the growing
momentum behind the systems approach. It is integrative methods like this,
harnessing the power of proteomics and other emerging fields, that will take
biology to the next level.”
For Ideker, a good analogy for the systems approach would be trying to
figure out how a car works. Biologists in the past would specialize, a few
studying only the wheels, others studying only the transmission. And
biologists working on different subjects frequently wouldn’t talk with each
other. The systems approach focuses on defining all the components of the
car and recording their relationships to one another as the car actually
functions. By integrating different types of information, a mathematical
model can ultimately be constructed describing the structure and behavior of
The authors of the research include Ideker, Dr. Vesteinn Thorsson, Dr.
Jeffrey Ranish, Rowan Christmas, Jeremy Buhler, Jimmy K. Eng, Dr. David R.
Goodlett, Dr. Aebersold and Dr. Hood of the Institute for Systems Biology
and Dr. Roger Bumgarner of the University of Washington. The research was
made possible by contributions from diverse backgrounds. Ideker, for
instance, was originally a computer engineer who joined Hood’s lab to train
in molecular biology. Other authors provided expertise from backgrounds
including physics (Thorsson) and protein chemistry (Aebersold and Ranish).
The Institute for Systems Biology was founded in January 2000 by Hood,
Aebersold and Dr. Alan Aderem as a public research institute devoted to
systems biology, an emerging field made possible by rapid advancements in
genomic, proteomic and computer technologies. The Institute, which has grown
to more than 160 staff, is also committed to pioneering new approaches to
science education and increasing public awareness of biotechnology issues.
Hood, who co-developed the automated genetic sequencing technology that
enabled the Human Genome Project, was among a small group of scientists who
first advocated for the international effort in 1985. Aebersold, who is
widely recognized for his work in analytical protein biochemistry and
proteomics, leads a research group at the ISB that is focused on developing
new methods and technologies for understanding the structure, function and
control of complex biological systems. Aderem, a prominent immunologist and
cell biologist and pioneer in the study of innate immunity, has provided
scientists with fundamental insights into the functioning of the macrophage.
They are working to apply the systems approach to a variety of model systems
as well as human cells.
Other members of the Institute’s interdisciplinary faculty include Dr. Ger
van den Engh, engineering and cell sorting; Dr. George Lake, advanced
computational methods; Dr. John Aitchison, yeast cell biology; and Dr.
Timothy Galitski, yeast development.
* * *
On second thought, if this isn't enough to interest you, I doubt it's
Send and receive Hotmail on your mobile device: http://mobile.msn.com
This was distributed via the memetics list associated with the
Journal of Memetics - Evolutionary Models of Information Transmission
For information about the journal and the list (e.g. unsubscribing)
This archive was generated by hypermail 2b29 : Tue Feb 19 2002 - 03:24:27 GMT