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Re: [human-ethology] Re: [evol-psych] Evolutionary innovation through exaptation in metabolic systems - Mr. Kohl falsely sees anti-mutation evidence

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  • james kohl
    If not for the fact that metabolic networks are nutrient-dependent, David Leake might have a point -- although it is difficult to determine what that point
    Message 1 of 8 , Aug 5, 2013
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      If not for the fact that metabolic networks are nutrient-dependent, David Leake might have a point -- although it is difficult to determine what that point might be. If his point is to merely tell me I'm wrong without explaining how mutations contribute to mutation-driven evolution via comparison to what is already known about nutrient-dependent pheromone-controlled adaptive evolution in E. coli, he has gone no further than others who have repeatedly told me I'm wrong -- despite my citations to works like this one: "Predicting the evolution of antibiotic resistance." I'm not sure how others skirt the issues of epistasis when they attempt to discuss mutation-driven evolution, but should not need to beg someone to tell others how mutations lead to epistasis. I only ask that others quit trying to infer I'm wrong and offer a model of adaptive evolution that does not involve nutrient uptake at its start.

       
      James V. Kohl
      Medical laboratory scientist (ASCP)
      Independent researcher
      Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553.
      Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.


      From: David Leake <DWLeake@...>
      To: evolutionary-psychology@yahoogroups.com
      Cc: human-ethology@yahoogroups.com
      Sent: Monday, August 5, 2013 5:53 PM
      Subject: [human-ethology] Re: [evol-psych] Evolutionary innovation through exaptation in metabolic systems - Mr. Kohl falsely sees anti-mutation evidence

       
      As others have noted, Mr. Kohl often seems to provide inaccurate summaries of publications that he claims support his "model" -- in fact, any publication that uses the words "nutrients" "pheromones" "epigenetics" "microRNA" etc may be massaged by him to falsely lend this support

      This latest email is another example, with Mr. Kohl stating: "The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution."

      However an actual reading and comprehension of the article makes it clear that the authors do no such thing. Here are the actual statements they make that include the word "mutation":

      "
      In an organism, a metabolic network can change through mutations. They can lead to addition of new reactions, by way of horizontal gene transfer, or through the evolution of enzymes with novel activities. They can also lead to loss of reactions through loss-of-function mutations in enzyme-coding genes. Natural selection can preserve those changed metabolic networks that are viable in a particular environment. Together, mutational processes and selection may change a metabolic network drastically on a long evolutionary timescale."

      In explaining their experimental procedures for examining metabolic pathway evolution in E. coli, the authors state:
      "Specifically, each mutation step in a random walk involves the addition of a randomly chosen reaction from the reaction universe, followed by the deletion of a randomly chosen metabolic reaction from the metabolic network."

      "The genes encoding them would eventually be lost from a genome. (We note that this loss could still take tens of thousands of years, given known deleterious mutation rates and generation times35, 36, which is enough for some for other genetic or environmental changes to render these reactions functional.)"

      Amazingly, this article appears to be precisely the kind of example that Mr. Kohl himself states (in his email below) would support the mutation view he opposes: "Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'." This article is such an example!

      Cheers,
      Dave Leake

      -----Original Message-----
      From: james kohl <jvkohl@...>
      To: evolutionary-psychology <evolutionary-psychology@yahoogroups.com>
      Cc: human-ethology <human-ethology@yahoogroups.com>
      Sent: Sun, Aug 4, 2013 11:56 pm
      Subject: [evol-psych] Evolutionary innovation through exaptation in metabolic systems

       

      Excerpt: "Many enzymes are capable of using various substrates which can further increase network complexity and the potential for exaptation. The ability to form multiple phenotypes also occurs in regulatory circuits, which can form different patterns of molecular activity, as well as in RNA molecules which can form multiple conformations with different biological functions. Systematic analyses of genotype–phenotype relationships are becoming increasingly possible in such systems."

      My comment: The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution. This makes it seem more likely that sensory input from the environment epigenetically effects adaptive evolution via changes in the microRNA / messenger RNA balance and nutrient changes in everything else downstream from the physiology of metabolism sans mutations theory.

      Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'. Meanwhile, see also a prediction of what will follow from articles like this one:


       
      James V. Kohl
      Medical laboratory scientist (ASCP)
      Independent researcher

      Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.


    • anonymous_9001
      There s a big difference between inferring you re wrong and citing quotes from the article at hand that directly contradict your interpretation of said
      Message 2 of 8 , Aug 5, 2013
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        There's a big difference between inferring you're wrong and citing quotes from the article at hand that directly contradict your interpretation of said article.

        --- In evolutionary-psychology@yahoogroups.com, james kohl <jvkohl@...> wrote:

        I only ask that others quit trying to infer I'm wrong...
      • Edgar Owen
        David, Yes, thanks for once again exposing Kohl s clever use of false citations. In truth I have never seen a single one of the citations referenced actually
        Message 3 of 8 , Aug 6, 2013
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          David,

          Yes, thanks for once again exposing Kohl's clever use of false citations. In truth I have never seen a single one of the citations referenced actually support Kohl's crazy crackpot idea that what organisms eat produce pheromone variations that are the cause of their evolution into different species...

          Edgar



          On Aug 5, 2013, at 5:53 PM, David Leake wrote:

           

          As others have noted, Mr. Kohl often seems to provide inaccurate summaries of publications that he claims support his "model" -- in fact, any publication that uses the words "nutrients" "pheromones" "epigenetics" "microRNA" etc may be massaged by him to falsely lend this support


          This latest email is another example, with Mr. Kohl stating: "The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution."

          However an actual reading and comprehension of the article makes it clear that the authors do no such thing. Here are the actual statements they make that include the word "mutation":

          "
          In an organism, a metabolic network can change through mutations. They can lead to addition of new reactions, by way of horizontal gene transfer, or through the evolution of enzymes with novel activities. They can also lead to loss of reactions through loss-of-function mutations in enzyme-coding genes. Natural selection can preserve those changed metabolic networks that are viable in a particular environment. Together, mutational processes and selection may change a metabolic network drastically on a long evolutionary timescale."

          In explaining their experimental procedures for examining metabolic pathway evolution in E. coli, the authors state:
          "Specifically, each mutation step in a random walk involves the addition of a randomly chosen reaction from the reaction universe, followed by the deletion of a randomly chosen metabolic reaction from the metabolic network."

          "The genes encoding them would eventually be lost from a genome. (We note that this loss could still take tens of thousands of years, given known deleterious mutation rates and generation times35, 36, which is enough for some for other genetic or environmental changes to render these reactions functional.)"

          Amazingly, this article appears to be precisely the kind of example that Mr. Kohl himself states (in his email below) would support the mutation view he opposes: "Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'." This article is such an example!

          Cheers,
          Dave Leake

          -----Original Message-----
          From: james kohl <jvkohl@...>
          To: evolutionary-psychology <evolutionary-psychology@yahoogroups.com>
          Cc: human-ethology <human-ethology@yahoogroups.com>
          Sent: Sun, Aug 4, 2013 11:56 pm
          Subject: [evol-psych] Evolutionary innovation through exaptation in metabolic systems

           

          Excerpt: "Many enzymes are capable of using various substrates which can further increase network complexity and the potential for exaptation. The ability to form multiple phenotypes also occurs in regulatory circuits, which can form different patterns of molecular activity, as well as in RNA molecules which can form multiple conformations with different biological functions. Systematic analyses of genotype–phenotype relationships are becoming increasingly possible in such systems."

          My comment: The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution. This makes it seem more likely that sensory input from the environment epigenetically effects adaptive evolution via changes in the microRNA / messenger RNA balance and nutrient changes in everything else downstream from the physiology of metabolism sans mutations theory.

          Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'. Meanwhile, see also a prediction of what will follow from articles like this one:


           
          James V. Kohl
          Medical laboratory scientist (ASCP)
          Independent researcher

          Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.


        • james kohl
          The quotes simply ignored the fact that the article includes focus on metabolism, which is nutrient dependent, not mutation-driven. When Leake s impression of
          Message 4 of 8 , Aug 6, 2013
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            The quotes simply ignored the fact that the article includes focus on metabolism, which is nutrient dependent, not mutation-driven. When Leake's impression of what I wrote begins with exclusion of the inferred focus on metabolism, and changes the focus to the role of mutations, we are led from biological facts (metabolism is required) to theory (mutations are required).

             
            James V. Kohl
            Medical laboratory scientist (ASCP)
            Independent researcher
            Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553.
            Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.


            From: anonymous_9001 <anonymous_9001@...>
            To: evolutionary-psychology@yahoogroups.com
            Sent: Tuesday, August 6, 2013 1:28 AM
            Subject: [human-ethology] Re: [evol-psych] Evolutionary innovation through exaptation in metabolic systems - Mr. Kohl falsely sees anti-mutation evidence

             
            There's a big difference between inferring you're wrong and citing quotes from the article at hand that directly contradict your interpretation of said article.

            --- In evolutionary-psychology@yahoogroups.com, james kohl <jvkohl@...> wrote:

            I only ask that others quit trying to infer I'm wrong...


          • james kohl
            What kind of idiot states: I have never seen a single one of the citations referenced actually support Kohl s crazy crackpot idea that what organisms eat
            Message 5 of 8 , Aug 6, 2013
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              What kind of idiot states:

              "I have never seen a single one of the citations referenced actually support Kohl's crazy crackpot idea that what organisms eat produce pheromone variations that are the cause of their evolution into different species..."

              when all evidence from every scientific discipline supports my model? That was a rhetorical question. See for example: Physiology is rocking the foundations of evolutionary biology

               
              James V. Kohl
              Medical laboratory scientist (ASCP)
              Independent researcher
              Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553.
              Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.


              From: Edgar Owen <edgarowen@...>
              To: evolutionary-psychology@yahoogroups.com
              Sent: Tuesday, August 6, 2013 8:22 AM
              Subject: Re: [evol-psych] Evolutionary innovation through exaptation in metabolic systems - Mr. Kohl falsely sees anti-mutation evidence

               
              David,

              Yes, thanks for once again exposing Kohl's clever use of false citations. In truth I have never seen a single one of the citations referenced actually support Kohl's crazy crackpot idea that what organisms eat produce pheromone variations that are the cause of their evolution into different species...

              Edgar



              On Aug 5, 2013, at 5:53 PM, David Leake wrote:

               
              As others have noted, Mr. Kohl often seems to provide inaccurate summaries of publications that he claims support his "model" -- in fact, any publication that uses the words "nutrients" "pheromones" "epigenetics" "microRNA" etc may be massaged by him to falsely lend this support

              This latest email is another example, with Mr. Kohl stating: "The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution."

              However an actual reading and comprehension of the article makes it clear that the authors do no such thing. Here are the actual statements they make that include the word "mutation":

              "
              In an organism, a metabolic network can change through mutations. They can lead to addition of new reactions, by way of horizontal gene transfer, or through the evolution of enzymes with novel activities. They can also lead to loss of reactions through loss-of-function mutations in enzyme-coding genes. Natural selection can preserve those changed metabolic networks that are viable in a particular environment. Together, mutational processes and selection may change a metabolic network drastically on a long evolutionary timescale."

              In explaining their experimental procedures for examining metabolic pathway evolution in E. coli, the authors state:
              "Specifically, each mutation step in a random walk involves the addition of a randomly chosen reaction from the reaction universe, followed by the deletion of a randomly chosen metabolic reaction from the metabolic network."

              "The genes encoding them would eventually be lost from a genome. (We note that this loss could still take tens of thousands of years, given known deleterious mutation rates and generation times35, 36, which is enough for some for other genetic or environmental changes to render these reactions functional.)"

              Amazingly, this article appears to be precisely the kind of example that Mr. Kohl himself states (in his email below) would support the mutation view he opposes: "Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'." This article is such an example!

              Cheers,
              Dave Leake

              -----Original Message-----
              From: james kohl <jvkohl@...>
              To: evolutionary-psychology <evolutionary-psychology@yahoogroups.com>
              Cc: human-ethology <human-ethology@yahoogroups.com>
              Sent: Sun, Aug 4, 2013 11:56 pm
              Subject: [evol-psych] Evolutionary innovation through exaptation in metabolic systems

               

              Excerpt: "Many enzymes are capable of using various substrates which can further increase network complexity and the potential for exaptation. The ability to form multiple phenotypes also occurs in regulatory circuits, which can form different patterns of molecular activity, as well as in RNA molecules which can form multiple conformations with different biological functions. Systematic analyses of genotype–phenotype relationships are becoming increasingly possible in such systems."

              My comment: The authors infer that adaptive evolution is nutrient dependent, which conflicts with stories about mutation-driven evolution. This makes it seem more likely that sensory input from the environment epigenetically effects adaptive evolution via changes in the microRNA / messenger RNA balance and nutrient changes in everything else downstream from the physiology of metabolism sans mutations theory.

              Examples of mutation-driven evolution would help to support that theory, if any could be found that incorporated nutrient-dependent metabolism, which was likely to be one of Darwin's 'conditions of life'. Meanwhile, see also a prediction of what will follow from articles like this one:


               
              James V. Kohl
              Medical laboratory scientist (ASCP)
              Independent researcher

              Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.




            • anonymous_9001
              The kind that recognizes the fact that no matter how many times you explain epigenetic factors involved in transcription control, you still can t address
              Message 6 of 8 , Aug 6, 2013
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                The kind that recognizes the fact that no matter how many times you explain epigenetic factors involved in transcription control, you still can't address observed genomic changes. When asked to describe a mechanism that would make such changes (which is not described in any of your publications), you simply refuse and state that nobody would understand it anyway.

                --- In evolutionary-psychology@yahoogroups.com, james kohl <jvkohl@...> wrote:
                >
                > What kind of idiot states:
                >
                >
                > "I have never seen a single one of the citations referenced actually
                > support Kohl's crazy crackpot idea that what organisms eat produce
                > pheromone variations that are the cause of their evolution into
                > different species..."
                >
                > when all evidence from every scientific discipline supports my model? That was a rhetorical question. See for example:Physiology is rocking the foundations of evolutionary biology
                >
                > Â
                > James V. Kohl
                > Medical laboratory scientist (ASCP)
                > Independent researcher
                > Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553.
                > Kohl, J.V. (2012) Human pheromones and food odors: epigenetic influences on the socioaffective nature of evolved behaviors. Socioaffective Neuroscience & Psychology, 2: 17338.
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