Re: Memes and Emergent Properties

From: Grant Callaghan (
Date: Tue Feb 19 2002 - 03:07:20 GMT

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    Subject: Re: Memes and Emergent Properties
    Date: Mon, 18 Feb 2002 19:07:20 -0800
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    >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
    work together.

    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
    systems biology.

    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
    state-of-the-art technology:

    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
    biological elements.

    “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 car.

    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


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