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RE: [OriginsTalk] Re: Origin of Life.

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  • Stanley Sethiadi
    Thank you very much Charles P. I m glad that there is at least one person in this maillist OriginTalk that can think as a mature person who can disinguish
    Message 1 of 12 , Sep 1, 2011
      Thank you very much Charles P. I'm glad that there is at least one person in
      this maillist "OriginTalk" that can think as a mature person who can
      disinguish the difference beween science and faith. In my whole life I study
      and practice science . I studied engineering just to earn a living. My study
      on "the Origin of Life" is my true study, but I cannot earn money from that
      study. Just like Spinoza grinded lenses to earn a living, but his real
      interest was his philosopyy.





      Regards. Stanley.



      From: OriginsTalk@yahoogroups.com [mailto:OriginsTalk@yahoogroups.com] On
      Behalf Of Charles Palm
      Sent: Tuesday, August 30, 2011 2:19 AM
      To: OriginsTalk@yahoogroups.com
      Subject: Re: [OriginsTalk] Re: Origin of Life.





      Stanley Sethiadi: I concluded from this that actually the theory of
      evolution is atheism disguised as science. I have to andmit that the theory
      of creation is theism disguised as science. The theory of origins is not
      science, not true science. It is believe, philosophy or faith. The
      preassumption is believe or unbelieve in the Creator God.

      Charles P: I agree with you, Stanley. Biology is a science of "energy +
      matter + information". Now it is up to us of the scientific disciplines to
      work with the evidence to develop an update to the old "current theory".
      Some of the "current theory" is unscientific wishful speculation. Some of
      the "current theory" has a lot of valuable evidence to help the average
      reader to understand the description of the origin and diversity of life.
      Thank you for your participation on the forum.

      Nature Magazine (Scitable):
      http://www.nature.com/scitable/content/the-digital-code-of-dna-13673 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.

      Understanding Evolution:
      http://evolution.berkeley.edu/evolibrary/article/0_0_0/evodevo_03
      Constraints
      on evolutionary change. A lineage's development may limit the sorts
      of phenotypes that it can evolve. This limitation is called a developmental
      constraint.

      Understanding Evolution:
      http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_02 Biological
      evolution, simply put, is descent with modification.

      Charles P: Maybe one update in the "current theory" would be "Biological
      evolution, simply put, is descent with limited modification"?

      Charles P:
      http://www.nature.com/scitable/blog/labcoat-life/common_ancestry_we_come_fro
      m
      There
      is no evidence that an older ancient extinct fossil species is the ancestor
      of two or more younger ancient extinct fossils species. We learned from
      Khalil
      A. Cassimally that common ancestry has never been tested. My suggestion is
      that scientists direct less resources toward selecting an older ancient
      extinct fossil to be an ancestor of two or more descendants. It seems more
      reasonable to me to investigate what Cassimally said about the identical
      working DNA sequences in different life-forms.
      http://tolweb.org/Palaeognathae/15837 These are flightless birds with no
      common ancestor.
      http://tolweb.org/Neoaves/26305 These are flying birds with no common
      ancestor.

      Charles P: Instead of the "debates" about which dinosaur was the ancestor,
      why not a "discussion" about which working DNA sequences are found in
      flightless birds and which working DNA sequences are found in flying birds?
      A scientific consensus is needed to accept that the only reliable method to
      determine ancestry is DNA evidence. Lacking the necessary DNA evidence from
      fossils, a new scientific consensus could allow the old Darwinism theories
      and the old neo-Darwinism theories to pass into the history books along with
      the old theories of Marx and Freud.

      Charles P: After 150 years of no reliable test for common ancestry and 58
      years of no reliable test for abiogenesis, it is time to update the old
      theories and for scientists to help the students and the average reader to
      understand the description of the diversity of life.

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



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    • Charles Palm
      Stanley Sethiadi: Thank you very much Charles P. I m glad that there is at least one person in this maillist OriginTalk that can think as a mature person
      Message 2 of 12 , Sep 1, 2011
        Stanley Sethiadi: Thank you very much Charles P. I'm glad that there is at
        least one person in this maillist "OriginTalk" that can think as a mature
        person who can disinguish the difference beween science and faith. In my
        whole life I study and practice science . I studied engineering just to earn
        a living. My study on "the Origin of Life" is my true study, but I cannot
        earn money from that study. Just like Spinoza grinded lenses to earn a
        living, but his real interest was his philosopyy.

        Charles P:
        http://www.nature.com/scitable/content/the-digital-code-of-dna-13673 This
        is where I got the idea of using the terminology of "pre-programmed DNA
        digital code. Leroy Hood and David Galas explain it very well.

        Charles P: http://evolution.berkeley.edu/evolibrary/article/evodevo_01
        Evo-devo or evolutionary developmental biology is the area of research that
        is leading the way in updating the old "current theory" of the last 150
        years.

        Charles P: The "debates" on Origin Talk are based upon each side trying to
        win by proving that they are "right" and that the other side is "wrong". We
        can all win here on the forum by having honest and sincere "discussions" to
        separate scientific consensus from personal philosophy or beliefs or faith.

        Understanding Evolution:
        http://evolution.berkeley.edu/evolibrary/article/nature_06 To ask someone
        to accept ideas purely on faith, even when these ideas are expressed by
        "experts," is unscientific.

        Khalil A. Cassimally:
        http://www.nature.com/scitable/blog/labcoat-life/common_ancestry_we_come_from
        As it turns out though, universal common ancestry has never been properly
        tested before. Instead, it has just been widely assumed as correct by the
        scientific community.

        Wikipedia: http://en.wikipedia.org/wiki/Evo-devo Evolutionary
        developmental biology is not yet a unified discipline, but can be
        distinguished from earlier approaches to evolutionary theory by its focus on
        a few crucial ideas.

        Charles P: Please read the full article by Khalil A. Cassimally. For the
        sake of brevity, this may seem like "dishonest quote mining". In my
        opinion, his ideas make more sense than do the 150 year old "current
        theory".
        1 We share vast sequences of our DNA with chimps; we share some sequences
        with the banana.
        2 Identical sequences in different life-forms may be the only ones that can
        work, so all living organisms would have to have them, no matter what their
        origins.
        3 We do not have to believe that one of our ancestors was a banana. We can
        believe that the pre-programmed DNA digital code found in all living
        organisms has sequences that work for all organisms. We can believe that
        homologous body parts are the result of DNA sequences that work for many
        living species.
        4 We can believe that chickens look like theropods not because of common
        ancestry, but because it is assumed that dinosaurs and birds had common DNA
        sequences. The only reliable method to determine ancestry is DNA evidence.
        5 We do not have to believe in convergent evolution. Cladistics seems
        scientific until scientific conclusions cause some anomalies that are
        unscientifically explained away as "convergent evolution".

        Charles P: I researched the dorsal fins and thermoregulated metabolism of
        ichthyosaurs, sharks, and dolphins.and reported my findings here on the
        forum. It seems more reasonable to me that the same DNA sequences in these
        unrelated species created the similar body parts and the similar body
        functions. There is no logical reason for us to believe that "unrelated
        species" have a "common ancestor".


        [Non-text portions of this message have been removed]
      • Pat Inniss
        Charles, thanks for the links, but I m not exactly sure what to make out of this reference to Cassimally s article. It does seem like you have pulled specific
        Message 3 of 12 , Sep 1, 2011
          Charles, thanks for the links, but I'm not exactly sure what to make out of this reference
          to Cassimally's article. It does seem like you have pulled specific verbiage from the
          nature.com blog to criticize Darwin and the notion that all life on earth stems from a
          common ancestor. However, the actual article is very supportive of universal common origin,
          and in fact discusses a "proof" of such in the form of a statistical analysis of amino acid
          sequences from different species. The complete article can be found at

          http://onlinelibrary.wiley.com/doi/10.1111/j.1740-9713.2011.00472.x/pdf.

          Among the author's conclusions are:

          "Theobald’s models were overwhelmingly in favour of a common ancestry for all extant life forms on Earth,"

          and:

          "What Darwin proposed around 150 years ago, which has steadily become the norm in the scientific world,
          statistics has finally shown to be valid."

          I think these quotes provide a more faithful representation of the gist of the article. I'm not
          enough of a chemist or biologist to evaluate the validity of the underlying assumptions of the
          statistical analysis presented in the article, but the author seems to present a fairly strong
          case for it while also addressing some critics, including one attributing at least some similarity
          in genetics to convergent evolution. While I can see, for instance, the possibility of different
          organisms coming up with similar genetic code to, for instance, metabolize folic acid, I'd guess
          that your example of a highly complex structure like dorsal fins developing independently in
          ichthyosaurs, sharks, and dolphins being reflected in similar DNA sequences would be pretty
          unlikely. I'm sorry I missed that thread but if you'd like to provide msg numbers I wouldn't mind
          going back and reading how you came to that conclusion.

          Regards - Pat Inniss


          -----Original Message-----
          >From: Charles Palm <palmcharlesUU@...>
          >Sent: Sep 1, 2011 8:44 AM
          >To: OriginsTalk@yahoogroups.com
          >Subject: Re: [OriginsTalk] Re: Origin of Life.
          >
          ><snip>
          >Khalil A. Cassimally:
          >http://www.nature.com/scitable/blog/labcoat-life/common_ancestry_we_come_from
          > As it turns out though, universal common ancestry has never been properly
          >tested before. Instead, it has just been widely assumed as correct by the
          >scientific community.
          >
          >Wikipedia: http://en.wikipedia.org/wiki/Evo-devo Evolutionary
          >developmental biology is not yet a unified discipline, but can be
          >distinguished from earlier approaches to evolutionary theory by its focus on
          >a few crucial ideas.
          >
          >Charles P: Please read the full article by Khalil A. Cassimally. For the
          >sake of brevity, this may seem like "dishonest quote mining". In my
          >opinion, his ideas make more sense than do the 150 year old "current
          >theory".
          >1 We share vast sequences of our DNA with chimps; we share some sequences
          >with the banana.
          >2 Identical sequences in different life-forms may be the only ones that can
          >work, so all living organisms would have to have them, no matter what their
          >origins.
          >3 We do not have to believe that one of our ancestors was a banana. We can
          >believe that the pre-programmed DNA digital code found in all living
          >organisms has sequences that work for all organisms. We can believe that
          >homologous body parts are the result of DNA sequences that work for many
          >living species.
          >4 We can believe that chickens look like theropods not because of common
          >ancestry, but because it is assumed that dinosaurs and birds had common DNA
          >sequences. The only reliable method to determine ancestry is DNA evidence.
          >5 We do not have to believe in convergent evolution. Cladistics seems
          >scientific until scientific conclusions cause some anomalies that are
          >unscientifically explained away as "convergent evolution".
          >
          >Charles P: I researched the dorsal fins and thermoregulated metabolism of
          >ichthyosaurs, sharks, and dolphins.and reported my findings here on the
          >forum. It seems more reasonable to me that the same DNA sequences in these
          >unrelated species created the similar body parts and the similar body
          >functions. There is no logical reason for us to believe that "unrelated
          >species" have a "common ancestor".
          >
          >
        • Charles Palm
          Pat Inniss: Charles, thanks for the links, but I m not exactly sure what to make out of this reference to Cassimally s article. It does seem like you have
          Message 4 of 12 , Sep 2, 2011
            Pat Inniss: Charles, thanks for the links, but I'm not exactly sure what to
            make out of this reference to Cassimally's article. It does seem like you
            have pulled specific verbiage from the nature.com blog to criticize Darwin
            and the notion that all life on earth stems from a common ancestor. However,
            the actual article is very supportive of universal common origin, and in
            fact discusses a "proof" of such in the form of a statistical analysis of
            amino acid
            sequences from different species. The complete article can be found at
            http://onlinelibrary.wiley.com/doi/10.1111/j.1740-9713.2011.00472.x/pdf. Among
            the author's conclusions are: "Theobald�s models were overwhelmingly in
            favour of a common ancestry for all extant life forms on Earth," and: "What
            Darwin proposed around 150 years ago, which has steadily become the norm in
            the scientific world, statistics has finally shown to be valid." I think
            these quotes provide a more faithful representation of the gist of the
            article. I'm not enough of a chemist or biologist to evaluate the validity
            of the underlying assumptions of the statistical analysis presented in the
            article, but the author seems to present a fairly strong case for it while
            also addressing some critics, including one attributing at least some
            similarity in genetics to convergent evolution. While I can see, for
            instance, the possibility of different organisms coming up with similar
            genetic code to, for instance, metabolize folic acid, I'd guess that your
            example of a highly complex structure like dorsal fins developing
            independently in ichthyosaurs, sharks, and dolphins being reflected in
            similar DNA sequences would be pretty unlikely. I'm sorry I missed that
            thread but if you'd like to provide msg numbers I wouldn't mind going back
            and reading how you came to that conclusion.

            Charles P:
            http://www.nature.com/scitable/blog/labcoat-life/common_ancestry_we_come_from
            Pat, thank you for your guidance in making this a "discussion" rather than
            a debate. As I read it, Cassimally was commenting on Theobald's models. At
            this link, he gives his email address as:
            kacassimally@... . I suggest that you write to him to ask what his
            ideas are. I do not want to speak for someone else.

            Charles P:
            http://onlinelibrary.wiley.com/doi/10.1111/j.1740-9713.2011.00472.x/pdf
            This is what I understood at this link:
            1 Theobald�s letter to Nature reports how an adequate method was finally
            applied to test for UCA. He used statistical tests to give an objective,
            quantified measure of which model � UCA or multiple ancestry � fitted
            the sequence similarities better.
            2 He was in effect testing the two hypotheses against the data. The three
            methods he used � called the Akaike information criterion, log-likelihood
            ratio and log Bayes factor � span statistical philosophies and give a
            quantitative measure � a number, or score � for each of the rival
            hypotheses;
            the Akaike information criterion in particular rewards hypotheses for
            fitting the data well, but penalises them if they are too complex, with too
            many variables and parameters.
            3 Then, it is Kassimally who put in parenthesis: (It is possible to make
            any hypothesis fit any data if you add enough complications to it; the
            Akaike
            information criterion, which is based on measuring comparative entropy or
            information content, penalises such fiddling, and rewards simplicity in the
            model.)

            Charles P: That made me think that Kassimally has a gut feeling (as I do).
            What if nature does not obey human logic? Here is the way that Kassimally
            said it, "My first print article has been published by Significance, the
            statistics popularization magazine of the Royal Statistical Society and
            the American Statistical Association. Titled We come from one I tackle a
            statistical analysis that conclusively point towards a common origin of life
            on Earth rather than multiple ancestors".

            Charles P: Kassimally says that Theobald only explored two possibilities:
            There was one ancestor or there were multiple ancestors to explain life on
            Earth. He did not consider any other possibility. His MATHEMATICS
            concluded that one ancestor is "correct"; multiple ancestors is "wrong".

            Charles P: Here is some algebra logic that I learned in high school:
            (because our forum may not post special characters correctly, "a2" means
            "a*a" or "a squared")
            1. Let a = b
            2. Then a2 = a*b Both sides of the equation are multiplied by "a".
            3. a2 + a2 = a2 + a*b Both sides have added "a2".
            4. 2*a2 = a2 + a*b The left side is simplified.
            5. 2*a2 - 2*a*b = a2 + a*b - 2*a*b Both sides add "-2*a*b".
            6. 2*a2 - 2*a*b = a2 - a*b Right side is simplified.
            7. 2*(a2 - a*b) = 1*(a2 - a*b) Both sides are divided by the same number.
            8. 2 = 1 There is proof that "two equals one".

            Charles P: Yes, I know how the logic fallacy occurred. No, I do not believe
            that 2 = 1. To use the words of Kassimally, "It is possible to make any
            hypothesis fit any data if you add enough complications to it".

            Charles P: Kassimally also said,"As it turns out though, universal common
            ancestry has never been properly tested before. Instead, it has just been
            widely assumed as correct by the scientific community". It seems to me that
            he has some evidence that maybe there is another way to interpret the
            evidence.

            Charles P: Kassimally also said, "Identical sequences in different
            life-forms... may be the only ones that can work, so all living organisms
            would have to have them, no matter what their origins". It seems to me that
            he is considering another way to interpret the evidence. When I was
            researching convergent evolution, I discovered some interesting evidence
            that really solidified this concept for me. It was about the ichthyosaurs,
            sharks, and dolphins with dorsal fins and thermoregulated metabolism in
            common. Maybe the identical DNA sequences in different life-forms is the
            key to the description of the diversity of life on Earth?

            Charles P: My message 25718: DNA sequences: the working parts designed for
            many purposes? The Msx2 gene in the unrelated mole and giant panda is an
            example of Kassimally's idea that inspired me.

            Charles P: My message 25127 Why Don't Common Ancestors Have Tentative
            Names? is just one of 16 messages where I give my interpretation of the
            evidence about ichthyosaurs, sharks, and dolphins that could be used as an
            alternative in a side-by-side comparison with the "current theory" of
            evolution. In my opinion, there are some parts of ToE that need to be
            updated to become scientific.


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