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Re: [evol-psych] News: Genetic switches play big role in human evolution

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  • james kohl
    Edgar acts as if I cannot explain what he thinks are mutations using my model, when all that s required is to understand the difference between inference of
    Message 1 of 7 , Jun 13, 2013
      Edgar acts as if I cannot explain what he thinks are mutations using my model, when all that's required is to understand the difference between inference of natural selection and evidence of natural selection. Did I not already explain the difference? Is he ignoring the fact that I have done so. Here it is again.

      Excerpt: (with my emphasis) “A new computational method called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), allowed the scientists to integrate these diverse data types and find evidence of natural selection in the regulatory DNA.”
      My comment: If inference was evidence of natural selection there would be no need for other researchers to analyze the role that micro-RNAs play a role in gene regulation, which is suggested below.
      Excerpt: “INSIGHT may now be used by other researchers for analyzing… micro-RNAs, non-coding molecules that also play a role in gene regulation.”
      My comment: Other researches have already analyzed microRNAs in flies. For example,  microRNA-14 acts in neurosecretory cells in the adult brain to control metabolism, and microRNA-124 appears to act in the context of adult brain-directed neuroendocrine control of male pheromone production and behavior. What this means is that instead of the computational inference of natural selection, we now have evidence for the reality of nutrient-dependent pheromone-controlled adaptive evolution (sans mutations theory).
      This evidence shows that
      1) natural selection is for nutrients
      2) microRNAs direct the metabolism of nutrients to pheromones
      Pheromones, which control reproduction in species from microbes to man, signal nutrient-dependent species-specific sex differences in reproductive fitness. That’s how pheromones enable sexual selection for reproduction fitness in flies and mammals.
      Now that we have evidence that natural selection is for nutrients and that sexual selection is for pheromones, it may be time to stop looking at the inference of natural selection as if it were evidence of anything. Clearly natural selection is for nutrients that metabolize to pheromones. This integrates natural selection and sexual selection for pheromones in all organisms that sexually reproduce.
      Does anyone still prefer inference to biologically based evidence of natural selection for nutrients and sexual selection for pheromones? Arguably, I think not everyone can grasp the biological facts, which means that some may always prefer theoretical inferences to evidence of nutrient-dependent pheromone-controlled adaptive evolution.

      I think it's not possible for an antique dealer to understand biological facts, and Edgar exemplifies that fact. He is, however, so incredibly ignorant that I have difficulty being nice to him. A man's got to know his limitations, and Edgar goes far past any I know are mine because his ignorance seems to be unlimited.
       
      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.


      From: Edgar Owen <edgarowen@...>
      To: evolutionary-psychology@yahoogroups.com
      Sent: Thursday, June 13, 2013 8:15 AM
      Subject: Re: [evol-psych] News: Genetic switches play big role in human evolution

       
      Kohl, et al,

      Wonder how Kohl will attempt to explain these mutations? Was it something the proto-humans ate or smelled that produced different pheromones that caused these genetic mutations that resulted in men evolving from apes?

      Perhaps Kohl's snake oil business could come up with a pheromone that causes Creationists to evolve into intelligent objective scientific minded humans?
      :-)

      Edgar


      On Jun 12, 2013, at 9:56 PM, Robert Karl Stonjek wrote:

       


      Genetic switches play big role in human evolution

      June 12th, 2013 in Biology / Biotechnology
      Genetic switches play big role in human evolutionA model of a transcription factor (orange and green) binding to a strand of DNA (light yellow). Transcription factors are proteins which bind to specific sequences of DNA, called binding sites, enabling and controlling the expression of genes. Changes during evolution to the DNA sequence in binding sites can lead to changes in gene expression. Credit: iStockphoto

      (Phys.org) —A Cornell study offers further proof that the divergence of humans from chimpanzees some 4 million to 6 million years ago was profoundly influenced by mutations to DNA sequences that play roles in turning genes on and off.
      The study, published June 9 in Nature Genetics, provides evidence for a 40-year-old hypothesis that regulation of genes must play an important role in evolution since there is little difference between humans and chimps in the proteins produced by genes. Indeed, human and chimpanzee proteins are more than 99 percent identical.
      The researchers showed that the number of evolutionary adaptations to the part of the machinery that regulates genes, called transcription factor binding sites, may be roughly equal to adaptations to the genes themselves.
      "This is the most comprehensive and most direct analysis to date of the evolution of gene regulatory sequences in humans," said senior author Adam Siepel, Cornell associate professor of biological statistics and computational biology.
      "It's taken these 40 years to get a clear picture of what's going on in these sequences because we haven't had the data until very recently," said Leonardo Arbiza, a postdoctoral researcher in Siepel's lab and the paper's lead author.
      Less than 2 percent of the human genome – the complete set of genetic material – contains genes that code for proteins. In cells, these proteins are instrumental in biological pathways that affect an organism's health, appearance and behavior.
      Much less is known about the remaining 98 percent of the genome; however, in the 1960s, scientists recognized that some of the non-protein coding DNA regulates when and where genes are turned on and off and how much protein they produce. The regulatory machinery works when proteins called transcription factors bind to specific short sequences of DNA that flank the gene, called transcription factor binding sites, and by doing so, switch genes on and off.
      Among the findings, the study reports that when compared with protein coding genes, binding site DNA shows close to three times as many "weakly deleterious mutations," that is, mutations that may weaken or make an individual more susceptible to disease, but are generally not severe. Weakly deleterious mutations exist in low frequencies in a population and are eventually weeded out over time. These mutations are responsible for many inherited human diseases.
      While genes generally tend to resist change, a mutation occasionally leads to a favorable trait and increases across a population; this is called positive selection. By contrast, "transcription factor binding sites show considerable amounts of positive selection," said Arbiza, with evidence for adaptation in binding sites that regulate genes controlling blood cells, brain function and immunity, among others.
      "The overall picture shows more evolutionary flexibility in the binding sites than in protein coding genes," said Siepel. "This has important implications for how we think about human evolution and disease."
      This is the one of the first studies to combine recent data that identifies transcription factor binding sites, data on human genetic variation and genome comparisons between humans and apes. A new computational method called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), designed by Ilan Gronau, a postdoctoral researcher in Siepel's lab and a co-author of the study, allowed the scientists to integrate these diverse data types and find evidence of natural selection in the regulatory DNA.
      "Transcription factor binding sites are probably the regulatory elements we know the most about," said Arbiza. "If you want to understand evolution of gene expression regulation, that's a good starting point."
      INSIGHT may now be used by other researchers for analyzing other short regulatory DNA sequences, such as micro-RNAs, non-coding molecules that also play a role in gene regulation.
      More information: INSIGHT
      Provided by Cornell University
      "Genetic switches play big role in human evolution." June 12th, 2013. http://phys.org/news/2013-06-genetic-big-role-human-evolution.html
      Posted by
      Robert Karl Stonjek




    • Edgar Owen
      Kohl, Much of that is just standard evolutionary biology about the influences on selection, much of which you seem unable to understand you ve trashed in
      Message 2 of 7 , Jun 13, 2013
        Kohl,

        Much of that is just standard evolutionary biology about the influences on selection, much of which you seem unable to understand you've trashed in previous posts. The big lacuna in your theory is that there IS NO EXPLANATION AT ALL for how the genetic changes that are selected between originate.

        Of course nutrients and pheromones affect behaviors that are selected among. That's not the point you seem unable to comprehend. Your theory that genetic changes originate in what organisms eat and smell is totally crackpot..

        Edgar



        On Jun 13, 2013, at 3:35 PM, james kohl wrote:

         

        Edgar acts as if I cannot explain what he thinks are mutations using my model, when all that's required is to understand the difference between inference of natural selection and evidence of natural selection. Did I not already explain the difference? Is he ignoring the fact that I have done so. Here it is again.

        Excerpt: (with my emphasis) “A new computational method called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), allowed the scientists to integrate these diverse data types and find evidence of natural selection in the regulatory DNA.”
        My comment: If inference was evidence of natural selection there would be no need for other researchers to analyze the role that micro-RNAs play a role in gene regulation, which is suggested below.
        Excerpt: “INSIGHT may now be used by other researchers for analyzing… micro-RNAs, non-coding molecules that also play a role in gene regulation.”
        My comment: Other researches have already analyzed microRNAs in flies. For example,  microRNA-14 acts in neurosecretory cells in the adult brain to control metabolism, and microRNA-124 appears to act in the context of adult brain-directed neuroendocrine control of male pheromone production and behavior. What this means is that instead of the computational inference of natural selection, we now have evidence for the reality of nutrient-dependent pheromone-controlled adaptive evolution (sans mutations theory).
        This evidence shows that
        1) natural selection is for nutrients
        2) microRNAs direct the metabolism of nutrients to pheromones
        Pheromones, which control reproduction in species from microbes to man, signal nutrient-dependent species-specific sex differences in reproductive fitness. That’s how pheromones enable sexual selection for reproduction fitness in flies and mammals.
        Now that we have evidence that natural selection is for nutrients and that sexual selection is for pheromones, it may be time to stop looking at the inference of natural selection as if it were evidence of anything. Clearly natural selection is for nutrients that metabolize to pheromones. This integrates natural selection and sexual selection for pheromones in all organisms that sexually reproduce.
        Does anyone still prefer inference to biologically based evidence of natural selection for nutrients and sexual selection for pheromones? Arguably, I think not everyone can grasp the biological facts, which means that some may always prefer theoretical inferences to evidence of nutrient-dependent pheromone-controlled adaptive evolution.

        I think it's not possible for an antique dealer to understand biological facts, and Edgar exemplifies that fact. He is, however, so incredibly ignorant that I have difficulty being nice to him. A man's got to know his limitations, and Edgar goes far past any I know are mine because his ignorance seems to be unlimited.
         
        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.


        From: Edgar Owen <edgarowen@...>
        To: evolutionary-psychology@yahoogroups.com
        Sent: Thursday, June 13, 2013 8:15 AM
        Subject: Re: [evol-psych] News: Genetic switches play big role in human evolution

         
        Kohl, et al,

        Wonder how Kohl will attempt to explain these mutations? Was it something the proto-humans ate or smelled that produced different pheromones that caused these genetic mutations that resulted in men evolving from apes?

        Perhaps Kohl's snake oil business could come up with a pheromone that causes Creationists to evolve into intelligent objective scientific minded humans?
        :-)

        Edgar


        On Jun 12, 2013, at 9:56 PM, Robert Karl Stonjek wrote:

         


        Genetic switches play big role in human evolution

        June 12th, 2013 in Biology / Biotechnology
        Genetic switches play big role in human evolutionA model of a transcription factor (orange and green) binding to a strand of DNA (light yellow). Transcription factors are proteins which bind to specific sequences of DNA, called binding sites, enabling and controlling the expression of genes. Changes during evolution to the DNA sequence in binding sites can lead to changes in gene expression. Credit: iStockphoto

        (Phys.org) —A Cornell study offers further proof that the divergence of humans from chimpanzees some 4 million to 6 million years ago was profoundly influenced by mutations to DNA sequences that play roles in turning genes on and off.
        The study, published June 9 in Nature Genetics, provides evidence for a 40-year-old hypothesis that regulation of genes must play an important role in evolution since there is little difference between humans and chimps in the proteins produced by genes. Indeed, human and chimpanzee proteins are more than 99 percent identical.
        The researchers showed that the number of evolutionary adaptations to the part of the machinery that regulates genes, called transcription factor binding sites, may be roughly equal to adaptations to the genes themselves.
        "This is the most comprehensive and most direct analysis to date of the evolution of gene regulatory sequences in humans," said senior author Adam Siepel, Cornell associate professor of biological statistics and computational biology.
        "It's taken these 40 years to get a clear picture of what's going on in these sequences because we haven't had the data until very recently," said Leonardo Arbiza, a postdoctoral researcher in Siepel's lab and the paper's lead author.
        Less than 2 percent of the human genome – the complete set of genetic material – contains genes that code for proteins. In cells, these proteins are instrumental in biological pathways that affect an organism's health, appearance and behavior.
        Much less is known about the remaining 98 percent of the genome; however, in the 1960s, scientists recognized that some of the non-protein coding DNA regulates when and where genes are turned on and off and how much protein they produce. The regulatory machinery works when proteins called transcription factors bind to specific short sequences of DNA that flank the gene, called transcription factor binding sites, and by doing so, switch genes on and off.
        Among the findings, the study reports that when compared with protein coding genes, binding site DNA shows close to three times as many "weakly deleterious mutations," that is, mutations that may weaken or make an individual more susceptible to disease, but are generally not severe. Weakly deleterious mutations exist in low frequencies in a population and are eventually weeded out over time. These mutations are responsible for many inherited human diseases.
        While genes generally tend to resist change, a mutation occasionally leads to a favorable trait and increases across a population; this is called positive selection. By contrast, "transcription factor binding sites show considerable amounts of positive selection," said Arbiza, with evidence for adaptation in binding sites that regulate genes controlling blood cells, brain function and immunity, among others.
        "The overall picture shows more evolutionary flexibility in the binding sites than in protein coding genes," said Siepel. "This has important implications for how we think about human evolution and disease."
        This is the one of the first studies to combine recent data that identifies transcription factor binding sites, data on human genetic variation and genome comparisons between humans and apes. A new computational method called INSIGHT (Inference of Natural Selection from Interspersed Genomically coHerent elemenTs), designed by Ilan Gronau, a postdoctoral researcher in Siepel's lab and a co-author of the study, allowed the scientists to integrate these diverse data types and find evidence of natural selection in the regulatory DNA.
        "Transcription factor binding sites are probably the regulatory elements we know the most about," said Arbiza. "If you want to understand evolution of gene expression regulation, that's a good starting point."
        INSIGHT may now be used by other researchers for analyzing other short regulatory DNA sequences, such as micro-RNAs, non-coding molecules that also play a role in gene regulation.
        More information: INSIGHT
        Provided by Cornell University
        "Genetic switches play big role in human evolution." June 12th, 2013. http://phys.org/news/2013-06-genetic-big-role-human-evolution.html
        Posted by
        Robert Karl Stonjek






      • anonymous_9001
        B-b-b-but the epigenetic becomes the genetic landscape through blah blah blah*! *processes that have nothing to do with the genome ...
        Message 3 of 7 , Jun 14, 2013
          B-b-b-but the epigenetic becomes the genetic landscape through blah blah blah*!

          *processes that have nothing to do with the genome

          --- In evolutionary-psychology@yahoogroups.com, Edgar Owen <edgarowen@...> wrote:
          >
          > Kohl,
          >
          > Much of that is just standard evolutionary biology about the influences on selection, much of which you seem unable to understand you've trashed in previous posts. The big lacuna in your theory is that there IS NO EXPLANATION AT ALL for how the genetic changes that are selected between originate.
          >
          > Of course nutrients and pheromones affect behaviors that are selected among. That's not the point you seem unable to comprehend. Your theory that genetic changes originate in what organisms eat and smell is totally crackpot..
          >
          > Edgar
          >
          <snip>
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