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Re: Living things are designed to evolve.

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  • stewart8724
    Charles P: http://groups.yahoo.com/group/OriginsTalk/message/29246 Quotes from Evolution: A View From The 21st Century , by James A Shapiro: 1 Living cells
    Message 1 of 38 , Oct 14, 2012
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      Charles P: http://groups.yahoo.com/group/OriginsTalk/message/29246 Quotes
      from "Evolution: A View From The 21st Century", by James A Shapiro:

      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.

      Stewart: I find this very difficult to believe. If I cut my finger it will heal, this doesn't require intelligence in my skin cells. Hack at a tree and it'll produce sap to seal the wound, but neither trees nor their cells need to be intelligent or sentient to achieve this.


      James A Shapiro:
      http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html
      In
      other words, the old idea of the genome as a string of genes interspersed
      with unimportant noncoding DNA is no longer tenable. Many eminent
      scientists had opined that the noncoding DNA, much of it repeated at many
      different locations, is nothing more than "junk DNA." ENCODE revealed that
      most (and probably just about all) of this noncoding and repetitive DNA
      contained essential regulatory information. Moreover, much of it was also
      copied into RNA with additional but still unknown functions.

      Stewart: I agree, just as the spaces and punctuation between the characters in your text are essential to give the script meaning.


      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.

      Stewart: Possibly.


      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.

      Stewart: Again possible, but this is not evidence of intelligence in the cell. It's only evidence of another possible mechanism of evolution.


      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.

      Stewart: I don't see how this follows. Wouldn't they offer additional avenues to survival in times of ecological disruption?


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

      Stewart: Probably.


      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.

      Stewart: Selection can't eliminate novelties, it can only fail to select them. The genetic capabilities / novelties remain in the DNA, they're just dormant. Equally selection can't purify because that suggests a contamination, variations or options are not contaminants. If DNA can acquire variations from external sources then the selection process is entirely capable of creative results by utilising these new options.


      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.

      James A Shapiro: 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.

      James A Shapiro: 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.

      Stewart: OK, have you essentially relented Charles? Do you now concede that by the processes described above, evolution can and does happen naturally without the need for an intelligent designer?


      ..

      --- In OriginsTalk@yahoogroups.com, Charles Palm <palmcharlesUU@...> wrote:
      >
      > Charles P: http://groups.yahoo.com/group/OriginsTalk/message/29246 Quotes
      > from "Evolution: A View From The 21st Century", by James A Shapiro:
      >
      > 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.
      >
      > ********************************************************************************
      >
      > Dog Helps Friends In Canoe: http://www.youtube.com/watch?v=0LQOBDImnK8
      >
      > Can You Spot The Cleverly Camouflaged Critters?:
      > http://www.grindtv.com/outdoor/blog/36345/can+you+spot+the+cleverly+camouflaged+critters/
      >
      > James A Shapiro:
      > http://www.huffingtonpost.com/james-a-shapiro/bob-dylan-encode-and-evol_b_1873935.html
      > In
      > other words, the old idea of the genome as a string of genes interspersed
      > with unimportant noncoding DNA is no longer tenable. Many eminent
      > scientists had opined that the noncoding DNA, much of it repeated at many
      > different locations, is nothing more than "junk DNA." ENCODE revealed that
      > most (and probably just about all) of this noncoding and repetitive DNA
      > contained essential regulatory information. Moreover, much of it was also
      > copied into RNA with additional but still unknown functions.
      >
      > ********************************************************************************
      >
      > 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.
      >
      > James A Shapiro: 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.
      >
      > James A Shapiro: 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.
      >
      >
      > [Non-text portions of this message have been removed]
      >
    • Charles Palm
      Tia Ghose: http://www.livescience.com/25190-genetic-roots-vertebrate-intelligence.html Cognitive Big Bang Discovered in Tiny Sea Worm. Several brainy
      Message 38 of 38 , Dec 5, 2012
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        Tia Ghose:
        http://www.livescience.com/25190-genetic-roots-vertebrate-intelligence.html
        'Cognitive Big Bang' Discovered in Tiny Sea Worm. Several "brainy"
        genes
        that were duplicated in a tiny sea creature nearly 550 million years ago
        may have led to the massive expansion in intelligence in vertebrate
        species, two new studies have found.

        James A Shapiro: References #40, #41: Life requires cognition at all
        levels.

        James A Shapiro: References #93 - #95: We can think of this two-level
        proofreading process as equivalent to a quality-control system in human
        manufacturing. Like human quality-control systems, it is based on
        surveillance and correction (cognitive processes) rather than mechanical
        precision. The multistep nature of proofreading is typical of many control
        processes in cells,
        where final precision is achieved by a sequence of two or more interactions
        that are each themselves inherently less precise. In this regard, the most
        applicable cybernetic models are fuzzy logic control systems. In such
        systems, accurate regulation occurs by overlaying multiple imprecise
        (“fuzzy”) feedback controls arranged so that each successive event results
        in greater precision.

        James A Shapiro: In other words, we have numerous precise molecular
        descriptions of cell cognition, which range all the way from bacterial
        nutrition to mammalian cell biology and development. The cognitive,
        informatic view of how living cells operate and utilize their genomes is
        radically different from the genetic determinism perspective articulated
        most succinctly, in the
        last century, by Francis Crick’s famous “Central Dogma of Molecular
        Biology.” So it is appropriate to direct our attention to evaluating the
        validity of Crick’s formulation in light of 21st Century knowledge.

        James A Shapiro: A shift from thinking about gradual selection of
        localized random changes to sudden genome restructuring by sensory
        network-influenced cell systems is a major conceptual change. It replaces
        the “invisible hands” of geological time and natural selection with
        cognitive networks and cellular functions for self-modification. The
        emphasis is systemic rather than atomistic and information-based rather
        than stochastic.

        Stochastic: http://www.thefreedictionary.com/stochastic Involving chance
        or probability.


        [Non-text portions of this message have been removed]
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