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Re: Combined responses 01-Apr-05

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  • Stephen E. Jones
    Group On Thu, 31 Mar 2005 14:53:31 -0000, paulcanagnostopoulos wrote Re: Origins of fx174: [...] ... PA No it isn t. The default option is to do more research.
    Message 1 of 3 , Mar 31, 2005
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      On Thu, 31 Mar 2005 14:53:31 -0000, paulcanagnostopoulos wrote
      Re: Origins of fx174: [...]

      >PK>When prebiotic theories are unable to even theoretically specify
      >>precise forces pushing in the direction of life and why this is so
      >>then randomness is the default option.

      PA>No it isn't. The default option is to do more research.

      So when would Paul A concede that a naturalistic origin if life
      didn't happen?

      If the answer is "never", then does Paul A admit his position is: 1)
      unfalsifiable? and therefore 2) not scientific?

      If the answer to 1) and/or 2) is "yes", then does Paul A admit it is
      hypocritical to reject creationist/ID theories on the grounds that
      they are unfalsifiable and therefore not scientific?

      [...]

      On Thu, 31 Mar 2005 14:52:20 -0000, paulcanagnostopoulos wrote
      Re: Origins of fx174: [...]

      >PK>DNA is ideally suited for its function. Why accept a theory
      >>that substitutes something else in this role when the reason for it is
      >>not the evidence but the need to establish plausibility for a theory?
      >>I thought theories were intended to clarify data. Abiogenesis
      >>supporters seem to fashion data to support theory.

      PA>But there is evidence. You don't know about it because you do not
      >appear to keep abreast of what's going on.

      I agree with Paul *A* here. "DNA" is indeed "ideally suited for its
      function" but it is to mainly do nothing but act as a passive store
      of information:

      "The biological systems in this world have settled on a rather
      complicated way of solving these problems, using several different
      but closely related substances to fulfil the various necessary roles.
      At the core of the system is DNA, a substance which is sufficiently
      inert and unreactive to serve as a reliable memory store. By itself it
      can do almost nothing; it is very inefficient (even if it can operate
      at all) at producing a copy of itself which could be transmitted to
      the next The theory of evolution today generation, even when it is
      provided with all the necessary building blocks. However, it occurs
      in association with protein enzymes, which in the first place enable
      it to be replicated, so that there are copies to pass on to the
      daughter cells, and which also use the information stored in the
      DNA to produce a corresponding RNA and that in turn is used to
      guide the synthesis of a corresponding protein. This whole system
      works extremely efficiently, but as you see it involves separating
      the function of reliability in storing information from that of
      actually using the information as instructions to change the
      surroundings. It is, I suppose, theoretically possible to imagine a
      substance which was both inactive enough to be reliable and active
      enough to have effects in producing a phenotype. Possibly some
      evolving systems on Mars or elsewhere in the universe have
      discovered such a perfect answer to the evolutionary problem, but
      life on this earth has not. It is stuck with a system in which there is
      an inescapable difference between the genotype-what is
      transmitted, the DNA-and the phenotype-what is produced when
      the genotype is used as instructions." (Waddington C.H., "The
      Theory of Evolution Today", in Koestler A. & Smythies J.R., ed.,
      "Beyond Reductionism: New Perspectives in the Life Sciences",
      The Alpbach Symposium, [1969], Radius/Hutchinson: London,
      1972, reprint, pp.362-363)

      The RNA enzymes do most of the work transcribing the information
      stored in DNA into an mRNA transcript which then passes to a ribosome
      comprised of ribosomal RNA (rRNA) *and proteins*, and the ribosome
      then translates the mRNA transcript into proteins by transfer RNA
      (tRNA). So the "evidence" is very strong that RNA was the *core* (but
      not necessarily the whole `apple') of the original living *system*.

      Creationism if it wants to be taken seriously as an alternative to
      Naturalistic Evolution (NE) must *positively* develop, and put on the
      table, its own *comprehensive* general theory/model to explain the
      major facts of the living world, rather than just *negatively* take
      pot-shots at NE, while keeping their own model (assuming they even
      have one) off the table (a la Laurie-who BTW has just unsubscribed).
      I was going to say "creationism/ID," but ID does not claim to be a
      comprehensive general theory or model.

      That is what I will do (if Jesus does not return first! - Mt 24:43;
      1 Thess 5:2; Lk 21:24-28) in my second book, "Progressive Creation:
      A Scientific General Theory of Creation"

      --------------------------------------------------------------------------
      http://members.iinet.net.au/~sejones/pc00summ.html
      Stephen E. Jones
      Projects: Book (Outline): "Progressive Creation:
      A Scientific General Theory of Creation": Contents
      1. What is Progressive Creation?
      2. History of Progressive Creation
      3. Objections to Progressive Creation
      4. Need for Progressive Creation
      5. Creation in the Bible
      6. Creation of the Universe
      7. Creation of the Earth
      8. Creation of life
      9. Creation of plants
      10. Creation of animals
      11. Creation of man
      12. Conclusion
      Bibliography
      --------------------------------------------------------------------------

      PA>The ribosome is a ribozyme.

      As I pointed out, this is misleading (even though some scientists say
      it):

      --------------------------------------------------------------------------
      http://www.hhmi.org/news/steitz.html
      HHMI News August 11, 2000
      High-Resolution Image Illuminates Catalytic Engine of the Ribosome [...]
      The image in the foreground shows the RNA/protein architecture of the
      large ribosomal subunit with the active site highlighted. The background
      shows a schematic diagram of the peptidyl transferase active site of the
      ribosome. Using a high-energy x-ray beam to probe fragile crystals of
      RNA and protein, researchers have obtained the most detailed images ever
      produced of the cellular factory where amino acids are linked into
      chainlike proteins. The studies illuminate the basic structure of the
      ribosome, a protein-making machine found in all cells. These insights
      include the first unequivocal proof that the ribosome is a ribozyme,
      an RNA enzyme.
      --------------------------------------------------------------------------

      The "Catalytic Engine of the Ribosome" may well be "a ribozyme, an
      RNA enzyme", but the "ribosome" *itself* isn't.

      Here are definitions of "ribosome" and "ribozyme" from one of my
      biology dictionaries (cross-referencing asterisks removed for clarity):

      "ribosome A small spherical body within a living cell that is the
      site of protein synthesis. Ribosomes consist of two subunits, one
      large and one small, each of which comprises a type of RNA
      (called ribosomal RNA) and protein. Ribosomes are described in
      terms of their sedimentation coefficients (i.e. their rates of
      sedimentation in an ultracentrifuge), which are measured in
      Svedberg units (symbol S). The prokaryote (70S) ribosome
      comprises a 50S (large) subunit and a 30S (small) subunit; the
      eukaryote (80S) ribosome has large 60S and small 40S subunits.
      Usually there are many ribosomes in a cell, either attached to the
      endoplasmic reticulum or free in the cytoplasm. During protein
      synthesis they are associated with messenger RNA as
      polyribosomes in the process of translation." (Martin E. & Hine
      R.S., eds., "Oxford Dictionary of Biology," [1985], Oxford
      University Press: Oxford UK, Fourth Edition, 2000, pp.521.
      Cross-referencing asterisks removed)

      "ribozyme (catalytic RNA) Any RNA molecule that can catalyse
      changes to its own molecular structure. Self-splicing introns (see
      gene splicing) are examples of ribozymes." (Martin E. & Hine
      R.S., eds., "Oxford Dictionary of Biology," [1985], Oxford
      University Press: Oxford UK, Fourth Edition, 2000, pp.521)

      Note that: 1) a "ribosome" comprises both "RNA (... ribosomal RNA)
      and protein"; while 2) a "ribozyme" is "catalytic RNA," an "*RNA*
      (not RNA and protein) "molecule that can catalyse changes to its own
      molecular structure." I would be interested in any evidence that Paul
      A has that a "ribosome" (i.e. on its own-autocatalytically) can
      "catalyse changes to its own molecular structure" (see quote below
      that says even the *ribozyme* in a ribosome is not autocatalytic).

      Also, another of my biology dictionaries, says that "Ribosomes" are
      "a complex composed of roughly *equal ratios* of ribosomal RNA (rRNA)
      and *40 or more different types of protein*" (cross-referencing
      capitalisation removed for clarity in this and the next two quotes)"

      "Ribosomes. ribosomes Non-membranous, but often membrane-
      bound, organelles of both prokaryotic and eukaryotic cells, of
      chloroplasts and mitochondria. Sites of protein synthesis, each is a
      complex composed of roughly equal ratios of ribosomal RNA
      (rRNA) and 40 or more different types of protein. " (Thain M. &
      Hickman M., "The Penguin Dictionary of Biology," [1951],
      Penguin Books: London, Tenth Edition, 2000, p.565)

      So since about half a "ribome" is "proteins", it is simply *false* to
      claim "The ribosome *is* a ribozyme" (my emphasis).

      The same dictionary entry continues by saying that even the ribsomal
      RNA "rRNA *includ[es]* at least one ribozyme":

      "Ribosomes are not attached to membranes in prokaryotes,
      chloroplasts and mitochondria, but are commonly membrane-
      bound in eukaryotic cells (esp. actively secreting ones), forming
      rough endoplasmic reticulum, as well as being attached to outer
      surface of outer nuclear membrane. The origin of most eukaryotic
      rRNA is the nucleolus (See RNA Polymerases), a single rRNA
      transcript being cleaved into one each of 18S, 5.85 and 28S rRNA
      subunits. The 18S rRNA molecules form the small ribosomal
      subunit; the 5.85 and 28S tRNAs are joined by a 5S rRNA subunit
      made in the nucleoplasm to form the larger ribosomal subunit, the
      rRNA including at least one ribozyme, a possible remnant of the
      RNA World." (Thain M. & Hickman M., "The Penguin Dictionary
      of Biology," [1951], Penguin Books: London, Tenth Edition, 2000,
      p.565)

      Now "includ[es]" is not the same as *is*. So even the rRNA is not all
      a "ribozyme".

      BTW, the same dictionary under "ribozyme" says that the "ribozyme" in
      "ribosomes" is "almost, but not quite, autocatalytic...":

      "ribozyme Any catalytically active RNA molecule. Their discovery
      in 1981 has widened the extension of the term 'enzyme' beyond
      proteins. Several ribozymes are self-splicing introns (see splicing),
      causing speculation as to their possible roles as intermediates in the
      evolution of biological systems from prebiotic ones. The peptide
      bonds formed on ribosomes are catalysed by a ribozyme-almost,
      but not quite, autocatalytically." (Thain M. & Hickman M., "The
      Penguin Dictionary of Biology," [1951], Penguin Books: London,
      Tenth Edition, 2000, pp.565-566)

      Scientists are trained to be *very* precise in their statements, and
      I assume that those scientists who say "the ribosome is a ribozyme"
      know that it is not literally true. So the best that can be said for
      this claim by scientists who know that "the ribosome is" only *part
      of* "a ribozyme" is that this is the exaggeration of a salesman
      trying to boost up his product in the marketplace with a catchy
      slogan, in order to enhance his own prestige and income.

      [...]

      On Sun, 27 Mar 2005 19:21:28 -0000, paulcanagnostopoulos wrote
      Re: Abiogenesis: Why talk about it at all?, was Re: tRNA synthetases:

      >AC>So SETI is just a waste of money then, looking for non-natural
      >>emanations from the sky. And archaeologists must go back and change
      >>all their discoveries of ancient cities to explain how they got there
      >>by rain and erosion. Or maybe non-human intelligence is acceptable
      >>for an explanation, as long as doesn't fit what the current regime has
      >>decreed to be "religious".

      PA>Human artifacts are naturalistic! Please stop
      >interpreting "naturalistic" to mean "without the involvement of
      >sentient beings."

      As I pointed out, in the case of ID's, the contrast is not between
      supernaturalistic and "naturalistic" causes but between
      "intelligent" and "unintelligent" causes.

      All ID claim is that there is empirical evidence of *real* design in
      nature that is the result of intelligent cause(s) (as opposed to
      Darwinism's claim that it is only *apparent* design that is the result of unintelligent causes.

      ID does not claim that this was *necessarily* supernatural (see also
      tagline). And as Paul A himself points out above, "`naturalistic'
      [does not] mean `without the involvement of sentient beings.'" So
      what then exactly is Paul A's objection to ID?

      Steve

      --------------------------------------------------------------------------
      "Next Scott and Branch remark, `Most scientists would reply that
      unexplained is not unexplainable, and that 'we don't know yet' is a
      more appropriate response than invoking a cause outside of
      science.' Comment: This is the standard ploy of turning the subject
      matter of ID into a completely different subject matter from that of
      science. Accordingly, there's ID, with its religious invocation of
      supernatural sprites and spirits, and then there's `science' (said
      with a deep voice and plenty of gravitas), which investigates
      `natural causes' (said with the same deep voice and gravitas). But
      in fact, there's only one subject here, namely complex biological
      systems, and the question is whether natural causes, understood
      as unintelligent causes ruled by blind unbroken natural laws, can
      account for them. There are two possibilities: (1) natural causes are
      up to this sort of explanatory work or (2) intelligent causes are
      required as well. To say that if ID is correct, then the phenomena in
      question are `unexplainable' is to define science an enterprise that
      can explain only by natural causes (understood in a reductionist,
      design-excluding way). Scott and Branch are playing a game of
      definitions. Science is a search for the truth underlying natural
      phenomena. Whether an intelligent cause is involved is not
      something that can be excluded on a priori grounds." (Dembski
      W.A., "Commentary on Eugenie Scott and Glenn Branch's `Guest
      Viewpoint: "Intelligent design" Not Accepted by Most Scientists,'"
      ISCID, 2 July, 2002.
      http://www.designinference.com/documents/2002.07.Scott_and_Branch.htm)
      Stephen E. Jones, BSc (Biol). http://members.iinet.net.au/~sejones
      Moderator: http://groups.yahoo.com/group/CreationEvolutionDesign
      & http://groups.yahoo.com/group/ProblemsOfEvolution/ Book: "Problems
      of Evolution" http://members.iinet.net.au/~sejones/PoE/PoE00ToC.html
      & http://members.iinet.net.au/~sejones/pe00cont.html
      --------------------------------------------------------------------------
    • Paul
      ... PK: Until one can demonstrate that a living organism can exist that a)relies solely on RNA for protein encoding and replication functions and b) is able to
      Message 2 of 3 , Apr 1, 2005
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        SJ:
        > The RNA enzymes do most of the work transcribing
        > the information
        > stored in DNA into an mRNA transcript which then
        > passes to a ribosome
        > comprised of ribosomal RNA (rRNA) *and proteins*,
        > and the ribosome
        > then translates the mRNA transcript into proteins
        > by transfer RNA
        > (tRNA). So the "evidence" is very strong that RNA
        > was the *core* (but
        > not necessarily the whole `apple') of the original
        > living *system*.

        PK: Until one can demonstrate that a living organism
        can exist that a)relies solely on RNA for protein
        encoding and replication functions and b) is able to
        evolve to such a state in primordial conditions devoid
        of life, regarding RNA as core or even evidence at all
        for a natural cause of the original living system is a
        matter of speculation rather than confirming empirical
        evidence.
      • paulcanagnostopoulos
        ... specify ... so ... When one of the following occurs: 1. Evidence appears for the existence of a supernatural designer who clearly had a hand in the origin
        Message 3 of 3 , Apr 1, 2005
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          --- In CreationEvolutionDesign@yahoogroups.com, "Stephen E. Jones"
          <sejones@i...> wrote:
          > >PK>When prebiotic theories are unable to even theoretically
          specify
          > >>precise forces pushing in the direction of life and why this is
          so
          > >>then randomness is the default option.
          >
          > PA>No it isn't. The default option is to do more research.
          >
          > So when would Paul A concede that a naturalistic origin if life
          > didn't happen?

          When one of the following occurs:

          1. Evidence appears for the existence of a supernatural designer who
          clearly had a hand in the origin of life.

          2. A few hundred or a thousand years go by without any compelling
          progress in abiogenesis research.

          > If the answer is "never", then does Paul A admit his position is:
          1)
          > unfalsifiable? and therefore 2) not scientific?

          Never say never.

          ~~ Paul
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