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Re: Living things are designed to evolve.

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  • stewart8724
    James A Shapiro: http://groups.yahoo.com/group/OriginsTalk/message/29246  Cells are built to evolve; they have the ability to alter their hereditary
    Message 1 of 38 , Oct 17, 2012
      James A Shapiro:
      http://groups.yahoo.com/group/OriginsTalk/message/29246%c2%a0 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.

      Charles P:  James A Shapiro is an evolutionist.


      Stewart: James A Shapiro doesn't believe that cells were designed.


      There are 4³ = 64 different codon combinations possible with a triplet
      codon of three nucleotides; all 64 codons are assigned to either an amino
      acid or a stop signal. If, for example, an RNA sequence UUUAAACCC is
      considered and the reading frame starts with the first U (by convention, 5'
      to 3'), there are three codons, namely, UUU, AAA, and CCC, each of which
      specifies one amino acid. Therefore, this 9 base RNA sequence will be
      translated into an amino acid sequence that is three amino acids long.

      Charles P:  The protein created by this purposeful design would begin in
      this example with the sequence: "phenylalanine-lysine- proline" when the
      molecular biologists read the RNA sequence in the direction 5' to 3'.  Here
      are some more DNA digital code information requirements that could not
      possibly have originated by random processes:


      Stewart: Where is the evidence that allows you to stipulate that the protein which is created in this process was a result of "purposeful design"?
      You have taken a scientific understanding and applied without warrant, your own personal beliefs. To provide all this evidence and then add in supplementary and unfounded opinions is tantamount to lying. What you should have done was state separately, that you believe this process is the work of your God. That would be entirely acceptable because it would illustrate that you weren't trying to hide a lie in amongst genuine scientific facts.


      1  The DNA double helix is made up of two phosphate-deoxyribose backbones
      that are "the hardware" for that genome.

      2  The information is not contained in the "hardware" chemical bonds of
      each phosphate-deoxyribose backbone.  The information is in the "software"
      hydrogen bonds.  There must exist a perfect "electromagnetic attractive
      interaction of a hydrogen atom and an electronegative atom, such as
      nitrogen, oxygen or fluorine, that comes from another molecule or chemical
      group. It is not a true chemical bond".  Without the "software" hydrogen
      bonds the two phosphate-deoxyribose backbones would not come together to
      form the double helix.  The translation of the information depends on the
      "software" hydrogen bonds.


      Stewart: We have lots of nitrogen in our atmosphere and hydrogen is the most plentiful element in the universe. Amino-acids can be produced in asteroids, which are very unlikely ever to have had life on them. Here on Earth we have all the conditions necessary to create life. The information you provide explains how life works, nothing on how it was initiated.


      (The "software" hydrogen bonds are between the two "hardware" backbones.  The
      backbone on the left in this diagram is translated from 5' to 3' (top to
      bottom in this example).  The backbone on the right is translated 5' to 3'
      (bottom to top in this example.  The two "hardware" phosphate-deoxyribose
      backbones can only assemble themselves precisely this way -- never
      randomly).


      Stewart: The two phosphate - deoxyribose backbones cannot be assembled at random, but they can be 'precisely assembled' by natural (random) causes.


      6  Scientists can cause chemical reactions to occur in the laboratory with
      non-living molecules to produce amino acids.  The non-living molecules
      always result in a racemic mixture of "left handed and right handed" amino
      acids.  Only living things can produce "left-handed" amino acids naturally.
       The DNA digital code information requires it to be this way.  This can't
      happen by random processes.


      Stewart: So the DNA in living organisms naturally causes amino-acids to be only left handed. Entirely left handed amino-acids do not happen without DNA. This does not imply design or purpose, it simply shows a consequence of amino- acids being produced by DNA.


      Charles P:  All living things can't be adequately described by the laws of
      physics alone.  To be adequately described, all living things must be
      described by: "energy + matter + information".  Biology is an information
      science.


      Stewart: To describe something requires information. All things in existence can be described in material terms, given that we have all the information.


      Leroy Hood:
      http://www.nature.com/nature/journal/v421/n6921/abs/nature01410.html%c2%a0 The
      discovery of the structure of DNA transformed biology profoundly,
      catalysing the sequencing of the human genome and engendering a new view of
      biology as an information science. Two features of DNA structure account
      for much of its remarkable impact on science: its digital nature and its
      complementarity, whereby one strand of the helix binds perfectly with its
      partner. DNA has two types of digital information - the genes that encode
      proteins, which are the molecular machines of life, and the gene regulatory
      networks that specify the behaviour of the genes.


      Charles P:  My purpose for giving this example of technical stuff is to
      assure the average readers on Origins Talk that living things are designed
      to evolve.  None of this evolution could have possibly occurred by random
      processes.  Molecular biologists and the average reader can easily
      recognize the design in these processes.  We know nothing from science
      about what is outside the circle.


      Stewart: Average readers on Origins Talk are well aware of your intentions. None of the information you provided, in any way suggests that living things were designed. That's your take on it.
      Nothing in the information you provided suggests that:- "None of this evolution could have possibly occurred by random processes". That again is your take on it.

      You would do us all a favour if you didn't confuse what science 'states' with what you believe.
      I don't have any objections to your stating your beliefs, neither do I mind that you want to show that science supports your beliefs. What I object to is you interspersing your own descriptions and conclusions in amongst actual scientific evidence, when science falls short of confirming your beliefs.


      ..

      --- In OriginsTalk@yahoogroups.com, Charles Palm <palmcharlesUU@...> wrote:
      >
      > James A Shapiro:
      > http://groups.yahoo.com/group/OriginsTalk/message/29246 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.
      >
      > Charles P: James A Shapiro is an evolutionist.
      >
      > ********************************************************************************
      >
      > Charles P: Gödel's Incompleteness Theorem teaches us that the
      > "recognizable code" can't explain itself without referring to something
      > outside the circle -- something we have to assume but can't prove. Codes
      > are not created by disorder nor disorganization nor random processes.
      >
      > Code: http://www.thefreedictionary.com/code A system of symbols and rules
      > used to represent instructions to a computer; a computer program. Genetics
      > The genetic code.
      >
      > Genetic code: http://en.wikipedia.org/wiki/Genetic_code The genetic code
      > is the set of rules by which information encoded in genetic material (DNA
      > or mRNA sequences) is translated into proteins (amino acid sequences) by
      > living cells.
      >
      > There are 4³ = 64 different codon combinations possible with a triplet
      > codon of three nucleotides; all 64 codons are assigned to either an amino
      > acid or a stop signal. If, for example, an RNA sequence UUUAAACCC is
      > considered and the reading frame starts with the first U (by convention, 5'
      > to 3'), there are three codons, namely, UUU, AAA, and CCC, each of which
      > specifies one amino acid. Therefore, this 9 base RNA sequence will be
      > translated into an amino acid sequence that is three amino acids long.
      >
      > Charles P: The protein created by this purposeful design would begin in
      > this example with the sequence: "phenylalanine-lysine- proline" when the
      > molecular biologists read the RNA sequence in the direction 5' to 3'. Here
      > are some more DNA digital code information requirements that could not
      > possibly have originated by random processes:
      >
      > 1 The DNA double helix is made up of two phosphate-deoxyribose backbones
      > that are "the hardware" for that genome.
      >
      > 2 The information is not contained in the "hardware" chemical bonds of
      > each phosphate-deoxyribose backbone. The information is in the "software"
      > hydrogen bonds. There must exist a perfect "electromagnetic attractive
      > interaction of a hydrogen atom and an electronegative atom, such as
      > nitrogen, oxygen or fluorine, that comes from another molecule or chemical
      > group. It is not a true chemical bond". Without the "software" hydrogen
      > bonds the two phosphate-deoxyribose backbones would not come together to
      > form the double helix. The translation of the information depends on the
      > "software" hydrogen bonds.
      >
      > http://en.wikipedia.org/wiki/Hydrogen_bond
      >
      > http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg (The
      > "software" hydrogen bonds are between the two "hardware" backbones. The
      > backbone on the left in this diagram is translated from 5' to 3' (top to
      > bottom in this example). The backbone on the right is translated 5' to 3'
      > (bottom to top in this example. The two "hardware" phosphate-deoxyribose
      > backbones can only assemble themselves precisely this way -- never
      > randomly).
      >
      > 3 The RNA sequence of UUU-AAA-CCC in this example are not
      > phenylalanine-lysine-proline.
      > They only represent phenylalanine-lysine- proline. This is one of the
      > reasons "why" DNA is a digital code that produces information and this is
      > "how" cells translate the information.
      >
      > 4 The phenylalanine-lysine-proline part of the newly created protein in
      > this example is produced on both backbones.
      >
      > 5 The phenylalanine-lysine-proline found in the newly created protein are
      > "left handed", not a racemic mixture. (chirality). The phenylalanine is
      > "left handed", the lysine is "left handed", and the proline is "left
      > handed".
      >
      > 6 Scientists can cause chemical reactions to occur in the laboratory with
      > non-living molecules to produce amino acids. The non-living molecules
      > always result in a racemic mixture of "left handed and right handed" amino
      > acids. Only living things can produce "left-handed" amino acids naturally.
      > The DNA digital code information requires it to be this way. This can't
      > happen by random processes.
      >
      > http://en.wikipedia.org/wiki/Phenylalanine
      >
      > http://en.wikipedia.org/wiki/Lysine
      >
      > http://en.wikipedia.org/wiki/Proline
      >
      > http://en.wikipedia.org/wiki/DNA_replication
      >
      > http://en.wikipedia.org/wiki/Chirality_(chemistry)
      >
      > Charles P: All non-living things can be adequately described by the laws
      > of physics: "energy + matter".
      >
      > Charles P: All living things can't be adequately described by the laws of
      > physics alone. To be adequately described, all living things must be
      > described by: "energy + matter + information". Biology is an information
      > science.
      >
      > Leroy Hood:
      > http://www.nature.com/nature/journal/v421/n6921/abs/nature01410.html The
      > discovery of the structure of DNA transformed biology profoundly,
      > catalysing the sequencing of the human genome and engendering a new view of
      > biology as an information science. Two features of DNA structure account
      > for much of its remarkable impact on science: its digital nature and its
      > complementarity, whereby one strand of the helix binds perfectly with its
      > partner. DNA has two types of digital information — the genes that encode
      > proteins, which are the molecular machines of life, and the gene regulatory
      > networks that specify the behaviour of the genes.
      >
      > James A Shapiro:
      > http://groups.yahoo.com/group/OriginsTalk/message/29246 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.
      >
      > Charles P: My purpose for giving this example of technical stuff is to
      > assure the average readers on Origins Talk that living things are designed
      > to evolve. None of this evolution could have possibly occurred by random
      > processes. Molecular biologists and the average reader can easily
      > recognize the design in these processes. We know nothing from science
      > about what is outside the circle.
      >
      >
      > [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
        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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