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The Nine Basic Principles of Natural Genetic Engineering

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  • Charles Palm
    James A Shapiro: http://www.ftpress.com/store/product.aspx?isbn=0132780933 Evolution: A View from the 21st Century (Loc 1026 on my Kindle) Over the last 60
    Message 1 of 2 , Aug 11, 2012
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      James A Shapiro: http://www.ftpress.com/store/product.aspx?isbn=0132780933
      Evolution: A View from the 21st Century (Loc 1026 on my Kindle) Over the
      last 60 years, DNA has proven to be an extremely complex and malleable
      information storage medium. Virtually all cells possess the basic
      biochemical tools for modifying DNA:

      1 proteins that cut DNA stands.

      2 proteins that unwind DNA stands.

      3 proteins that polymerize DNA strands.

      4 proteins that anneal (strengthen or harden) DNA stands.

      5 proteins that spice DNA strands.

      The generic operations that living cells have been shown to carry out on
      their genomic molecules indicate that any rearrangement is possible as long
      as the product is compatible with the basic rules of DNA structure (see
      Table II.3).

      ********************************************************************************
      Charles P: This is what I have noticed so far in in Evolution: A View from
      the 21st Century:

      1 The first tenet of classical Darwinian evolution is now refuted.
      Beneficial mutations are not random, DNA seems to be designed to change in
      order to adapt to environment pressure. Hereditary variation arises from
      the non-random action of built-in biochemical systems that mobilize DNA and
      carry out natural genetic engineering.

      2 I counted 1,162 references and also many tables to illustrate and
      support the conclusions that are open to scrutiny by believers and
      non-believers. Any statements made by me are also open to scrutiny by
      believers and non-believers.

      ********************************************************************************
      Book Description:
      http://www.amazon.com/Evolution-Century-Press-Science-ebook/dp/B0054KOKZ2/ref=dp_kinw_strp_1


      1 James A. Shapiro proposes an important new paradigm for understanding
      biological evolution, the core organizing principle of biology. Shapiro
      introduces crucial new molecular evidence that tests the conventional
      scientific view of evolution based on the neo-Darwinian synthesis, shows
      why this view is inadequate to today's evidence, and presents a compelling
      alternative view of the evolutionary process that reflects the shift in
      life sciences towards a more information- and systems-based approach in
      Evolution: A View from the 21st Century.

      2 Shapiro integrates advances in symbiogenesis, epigenetics, and
      saltationism into a unified approach that views evolutionary change as an
      active cell process, regulated epigenetically and capable of making rapid
      large changes by horizontal DNA transfer, inter-specific hybridization,
      whole genome doubling, symbiogenesis, or massive genome restructuring.

      3 Evolution marshals extensive evidence in support of a fundamental
      reinterpretation of evolutionary processes, including more than 1,100
      references to the scientific literature. Shapiro's work will generate
      extensive discussion throughout the biological community, and may
      significantly change your own thinking about how life has evolved. It also
      has major implications for evolutionary computation, information science,
      and the growing synthesis of the physical and biological sciences.

      ********************************************************************************

      James A Shapiro: (Loc 2614 in my Kindle) Using this 21st Century
      scientific perspective, we can articulate a more interactive and
      information-based set of basic evolutionary principles without departing
      from the realm of established empirical observations:

      1 Living cells and organisms are cognitive (sentient) entities that act
      and interact purposefully to ensure survival, growth, and proliferation.
      They possess corresponding sensory, communication, information-processing,
      and decision-making capabilities.

      2 Cells are built to evolve; they have the ability to alter their
      hereditary characteristics rapidly through well-described natural
      genetic engineering and epigenetic processes as well as by cell mergers.

      3 Evolutionary novelty arises from the production of new cell and
      multicellular structures as a result of cellular self-modification
      functions and cell fusions. In many cases, these new structures involve
      the amplification and/or rearrangement of existing functional molecular
      components. In addition, cells (and associated entities such as viruses)
      have the capacity to generate entirely new nucleic acid, protein, and other
      molecular components that can subsequently be integrated into functional
      cell or multicellular systems. As discussed previously, it remains to be
      thoroughly investigated to what degree cell sensing, information
      processing, and genome targeting can heuristically accelerate the
      production of useful novelties. A priori, functionally relevant guidance
      for natural genetic engineering would appear to enhance the probability of
      success in generating useful novelities. This supposition requires
      rigorous testing.

      4 Natural genetic engineering and other evolutionarily innovative
      processes respond to stimuli that place the core organism objectives of
      survival, growth, and proliferation in peril. These dangerous challenges
      are most likely to occur at times of major ecological disruption.

      5 Active hereditary variation and evolutionary innovation will continue as
      long as ecological disruptions and challenges to core vital objectives
      persist.

      6 The role of selection is to eliminate evolutionary novelties that prove
      to be non-functional and interfere with adaptive needs. Selection operates
      as a purifying but not creative force.

      7 Evolutionary inventions that survive purifying selection and prove
      useful are subject to microevolutionary refinement, perhaps by the kind of
      processes envisaged in conventional theories.

      8 Successful evolutionary inventions are subject to amplification, reuse,
      and adaptation to new functions in response to successive ecological
      challenges.

      9 Taxonomically specific characters become established as the functional
      integration of past evolutionary novelties increasingly places constraints
      on the kinds of additional inventions that will prove functional.

      An evolutionary process that follows these principles will naturally
      display the kind of episodic and abrupt changes found in both the fossil
      and genomic records. Indeed, the punctuated equilibrium pattern of Gould
      and Eldridge should be the default situation, because the stimulating role
      of ecological challenges is unpredictable. When contemporary knowledge of
      natural genetic engineering and horizontal transfer is incorporated into
      the analysis, for example, it has recently been possible to calculate from
      genome databases a striking episode of rapid evolutionary innovation in the
      Archaean eon.

      (Loc 2682 in my Kindle): Evolving life has far exceeded human ingenuity in
      producing immensely complex and reliable self-reproducing entities that
      have repeatedly managed to change, survive, and proliferate despite major
      ecological upheavals. Given the challenges we face as a species, it
      behooves us to find out as much as we can of nature's wisdom in dealing
      with the inescapable trials of life.


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    • Charles Palm
      Charles P: http://groups.yahoo.com/group/OriginsTalk/message/29246 If anyone has empirical and verifiable evidence that can be tested and verified by others
      Message 2 of 2 , Nov 11, 2012
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        Charles P: http://groups.yahoo.com/group/OriginsTalk/message/29246 If
        anyone has empirical and verifiable evidence that can be tested and
        verified by others concerning the nine basic principles of natural genetic
        engineering, please share them with us here on Origins Talk.

        Charles P: Why is it that critics like to debate stuff before they do
        their homework? Why is it that critics like to debate stuff that only
        reflects their personal philosophies while disregarding any empirical and
        verifiable evidence?

        Charles P: http://ncse.com/evolution/science/what-is-science Why is it
        that critics believe that all scientific conclusions are tentative and they
        will be changed if new evidence contradicts previous understanding?
        However, when a scientific writer presents new evidence that contradicts
        that critic's personal philosophies and that critic's previous
        understandings, the critic will debate against the new information without
        doing sufficient homework to verify the empirical evidence? It is OK to
        have a different interpretation of the evidence AFTER doing the necessary
        homework.

        Charles P: Why is it that critics like to debate stuff by pretending that
        they have done their homework and they pretend that they are the only
        science writers who know all of the facts?

        Kathryn Schulz:
        http://www.youtube.com/watch?v=QleRgTBMX88&feature=relmfu Time
        10:00 to 15:55. You think that your beliefs perfectly reflect reality.
        How do you explain it to those who disagree with you? Most of us make a
        series of unfortunate assumptions.

        1 The Ignorance Assumption.

        2 The Idiocy Assumption.

        3 The Evil Assumption.

        Kathryn Schulz: We generate these incredible stories about the world
        around us and then the world turns around and astonishes us.

        ********************************************************************************

        Larry Moran: http://reports.ncse.com/index.php/rncse/article/view/125/135
        It’s
        interesting that none of the 1162 references in his book is to Stephen Jay
        Gould’s contributions to this debate—the absence of a reference to the
        spandrels paper (Gould and Lewontin 1979) is particularly revealing, and
        quite troubling.

        James A Shapiro: Evolution: A View From The 21st Century.

        1 The reading list also includes some newspaper articles and links to
        websites where the works of Darwin and Stephen J. Gould can be accessed.
        The suggested readings are organized according to the book’s contents, and
        citations to them in the printed book appear in bold type to help provide
        well-articulated reference material suitable for the nonprofessional
        reader.

        2 An evolutionary process that follows these principles will naturally
        display the kind of episodic and abrupt changes found in both the fossil
        and genomic records. Indeed, the punctuated equilibrium pattern of Gould
        and Eldridge should be the default situation, because the stimulating role
        of ecological challenges is unpredictable. When contemporary knowledge of
        natural genetic engineering and horizontal transfer is incorporated into
        the analysis, for example, it has recently been possible to calculate
        from genome databases a striking episode of rapid evolutionary
        innovation in the Archaean eon.

        In her 1983 Nobel Prize address, Barbara McClintock made the following
        prediction: “In the future, attention undoubtedly will be centered on the
        genome, with greater appreciation of its significance as a highly sensitive
        organ of the cell that monitors genomic activities and corrects common
        errors, senses unusual and unexpected events, and responds to them, often
        by restructuring the genome”.

        3 Reference #857. Gould, S.B., Waller, R.F. and McFadden, G.I. Plastid
        evolution. Annu Rev Plant Biol 59, 491-517 (2008).

        4 Reference #872. Gould, S.B. et al. Nucleus-to-nucleus gene transfer and
        protein retargeting into a remnant cytoplasm of cryptophytes and diatoms.
        Mol Biol Evol 23, 2413-22 (2006).

        5 Reference #1151. Gould, S.J. The Evolution of Life on Earth. Sci Am 290,
        92-100 (2004).

        6 Reference #1152. Gould, S.J. Punctuated Equilibrium and the Fossil
        Record. Science 219, 439-440 (1983).

        7 Reference #1153. Gould, S.J. and Eldredge, N. Punctuated equilibrium
        comes of age. Nature 366, 223-7 (1993).

        ********************************************************************************
        Charles P: Why is it troubling to Larry Moran that there is no mention
        of a reference to the spandrels paper (Gould and Lewontin 1979)?

        Dr. Sven B Gould: http://www.molevol.de/lab/gould.html

        Steven Jay Gould: http://en.wikipedia.org/wiki/S_J_Gould


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