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Re: [evol-psych] News: How predictable is evolution?

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  • james kohl
    My comment: Novel receptor-mediated functions emerge in a three-step process that must be refined to exploit nutrient availability. 1)potentiation makes a
    Message 1 of 3 , Feb 19, 2013
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      My comment: Novel receptor-mediated functions emerge in a three-step process that must be refined to exploit nutrient availability. 1)potentiation makes a trait possible, 2) actualization makes the trait manifest, 3) refinement makes it effective. -- see Blount et al (2012) for the current perspective on non-random 3-step adaptive evolution for citrate use in E. coli. The nutrient-dependent adaptive evolution is pheromone-controlled. Pheromones are step 3; the refinement that makes that adaptation effective.

      If individual organisms cannot signal their ability to metabolize a new nutrient that helps to control their nutrient-dependent reproduction, their species is not going to survive. The species will out-reproduce its food supply. The same molecular mechanisms ensure non-random adaptive evolution in species from microbes to man. I may already have mentioned that only a change in a single amino acid can result in exquisitely fine-tuned epigenetic effects on phenotypic expression and selection via asexual and sexual reproduction.

      Random mutations theory always was a ridiculous waste of critical thinking skills -- a form of "evolution for dummies." Hang in there, dummies, now it's an RNA World that you cannot comprehend because you missed the start of the paradigm shift and everything has changed so quickly you can never catch up. No worries, however, people may continue to use the term mutations, as in the article below, so you can still talk with other dummies about that ridiculous theory for a few more years.

      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: Robert Karl Stonjek <stonjek@...>
      To: Evolutionary-Psychology <evolutionary-psychology@yahoogroups.com>; Evolutionary Psychology News <evol_psch_news@yahoogroups.com>
      Sent: Tue, February 19, 2013 10:20:20 PM
      Subject: [evol-psych] News: How predictable is evolution?

       


      How predictable is evolution?

      February 19th, 2013 in Biology / Evolution

      Understanding how and why diversification occurs is important for understanding why there are so many species on Earth. In a new study published on 19 February in the open access journal PLOS Biology, researchers show that similar—or even identical—mutations can occur during diversification in completely separate populations of E. coli evolving in different environments over more than 1000 generations. Evolution, therefore, can be surprisingly predictable.

      The experiment, conducted by Matthew Herron, research assistant professor at the University of Montana, and Professor Michael Doebeli of the University of British Columbia, involved 3 different populations of bacteria. At the start of the experiment, each population consisted of generalists competing for two different sources of dietary carbon (glucose and acetate), but after 1200 generations they had evolved into two coexisting types each with a specialized physiology adapted to one of the carbon sources. Herron and Doebeli were able to sequence the genomes of populations of bacteria frozen at 16 different points during their evolution, and discovered a surprising amount of similarity in their evolution.

      "In all three populations it seems to be more or less the same core set of genes that are causing the two phenotypes that we see," Herron said. "In a few cases, it's even the exact same genetic change."

      Recent advances in sequencing technology allowed Herron and Doebeli to sequence large numbers of whole bacterial genomes and provide evidence that there is predictability in evolutionary diversity. Any evolutionary process is some combination of predictable and unpredictable processes with random mutations, but seeing the same genetic changes in different populations showed that selection can be deterministic.

      "There are about 4.5 million nucleotides in the E. coli genome," he said. "Finding in four cases that the exact same change had happened independently in different populations was intriguing."

      Herron and Doebeli argue that a particular form of selection—negative frequency dependence—plays an important role in driving diversification. When bacteria are either glucose specialists or acetate specialists, a higher density of one type will mean fewer resources for that type, so bacteria specializing on the alternative resource will be at an advantage.

      "We think it's likely that some kind of negative frequency dependence—some kind of rare type advantage—is important in many cases of diversification, especially when there's no geographic isolation," Herron said.

      As technology advances, Herron believes that similar experiments in larger organisms will soon be possible. Some examples of diversification without geographic isolation are known in plants and animals, but it remains to be seen whether or not the underlying evolutionary processes are similar to those in bacteria.

      More information: PLOS Biol 11(2): e1001490. doi:10.1371/journal.pbio.1001490

      Provided by Public Library of Science

      "How predictable is evolution?." February 19th, 2013. http://phys.org/news/2013-02-evolution.html

      Posted by
      Robert Karl Stonjek
    • james kohl
      Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli Summary: The causes and mechanisms of evolutionary diversification are central
      Message 2 of 3 , Feb 20, 2013
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        Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli
        Summary:
        The causes and mechanisms of evolutionary diversification are central issues in biology. There is well-established theory that predicts that adaptive diversification can arise because of ecological interactions between individuals, such as competition or predation, but there are no empirical examples in which this process has been observed at the genetic level. We documented the genetic basis of adaptive diversification resulting from competition for resources in populations of the bacterium Escherichia coli. The populations diversified into two coexisting ecotypes representing different physiological adaptations. We found that similar but independently evolved phenotypes often shared mutations in the same gene and, in four cases, shared identical mutations at the same nucleotide position. Timelines of allele frequencies extracted from the frozen “fossil record” of three evolving populations showed parallel evolutionary dynamics, suggesting that mutations causing one type of physiology changed the ecological environment and allowed invasion of mutations causing an alternate physiology. The results provide empirical evidence of adaptive diversification as a predictable evolutionary process.
        ------------------------
        My comment: It would be great if any proponent of random mutations theory  -- or of any other mutations theory -- would address the facts presented in this open access article.

        Adaptive evolution has become adaptive diversification that is non-random and nutrient-dependent. It is described in terms of mutations that change the ecological environment to enable other mutations. An unknown feedback mechanism somehow establishes epistasis, which is flexibly demonstrable, and dependent on the supply of nutrients.

         "... it seems unlikely that the consistent pattern of alternating invasions observed in our three lines is due to chance alone..."

        Is anyone familiar with a means by which a consistent pattern of alternating invasions could occur that did not involve social niche construction via the metabolism of nutrients to species-specific pheromones? If not, adaptive evolution (no matter what it's called) is predictable based on the availability of nutrients and their metabolism to pheromones that control reproduction.  Isn't it? If so, theorists can now proceed to address the neurogenic niche construction and socio-cognitive niche construction I have detailed.

        Or they can run and hide.
         
        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: james kohl <jvkohl@...>
        To: evolutionary-psychology@yahoogroups.com
        Sent: Wed, February 20, 2013 12:55:11 AM
        Subject: Re: [evol-psych] News: How predictable is evolution?

         

        My comment: Novel receptor-mediated functions emerge in a three-step process that must be refined to exploit nutrient availability. 1)potentiation makes a trait possible, 2) actualization makes the trait manifest, 3) refinement makes it effective. -- see Blount et al (2012) for the current perspective on non-random 3-step adaptive evolution for citrate use in E. coli. The nutrient-dependent adaptive evolution is pheromone-controlled. Pheromones are step 3; the refinement that makes that adaptation effective.

        If individual organisms cannot signal their ability to metabolize a new nutrient that helps to control their nutrient-dependent reproduction, their species is not going to survive. The species will out-reproduce its food supply. The same molecular mechanisms ensure non-random adaptive evolution in species from microbes to man. I may already have mentioned that only a change in a single amino acid can result in exquisitely fine-tuned epigenetic effects on phenotypic expression and selection via asexual and sexual reproduction.

        Random mutations theory always was a ridiculous waste of critical thinking skills -- a form of "evolution for dummies." Hang in there, dummies, now it's an RNA World that you cannot comprehend because you missed the start of the paradigm shift and everything has changed so quickly you can never catch up. No worries, however, people may continue to use the term mutations, as in the article below, so you can still talk with other dummies about that ridiculous theory for a few more years.

        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: Robert Karl Stonjek <stonjek@...>
        To: Evolutionary-Psychology <evolutionary-psychology@yahoogroups.com>; Evolutionary Psychology News <evol_psch_news@yahoogroups.com>
        Sent: Tue, February 19, 2013 10:20:20 PM
        Subject: [evol-psych] News: How predictable is evolution?

         


        How predictable is evolution?

        February 19th, 2013 in Biology / Evolution

        Understanding how and why diversification occurs is important for understanding why there are so many species on Earth. In a new study published on 19 February in the open access journal PLOS Biology, researchers show that similar—or even identical—mutations can occur during diversification in completely separate populations of E. coli evolving in different environments over more than 1000 generations. Evolution, therefore, can be surprisingly predictable.

        The experiment, conducted by Matthew Herron, research assistant professor at the University of Montana, and Professor Michael Doebeli of the University of British Columbia, involved 3 different populations of bacteria. At the start of the experiment, each population consisted of generalists competing for two different sources of dietary carbon (glucose and acetate), but after 1200 generations they had evolved into two coexisting types each with a specialized physiology adapted to one of the carbon sources. Herron and Doebeli were able to sequence the genomes of populations of bacteria frozen at 16 different points during their evolution, and discovered a surprising amount of similarity in their evolution.

        "In all three populations it seems to be more or less the same core set of genes that are causing the two phenotypes that we see," Herron said. "In a few cases, it's even the exact same genetic change."

        Recent advances in sequencing technology allowed Herron and Doebeli to sequence large numbers of whole bacterial genomes and provide evidence that there is predictability in evolutionary diversity. Any evolutionary process is some combination of predictable and unpredictable processes with random mutations, but seeing the same genetic changes in different populations showed that selection can be deterministic.

        "There are about 4.5 million nucleotides in the E. coli genome," he said. "Finding in four cases that the exact same change had happened independently in different populations was intriguing."

        Herron and Doebeli argue that a particular form of selection—negative frequency dependence—plays an important role in driving diversification. When bacteria are either glucose specialists or acetate specialists, a higher density of one type will mean fewer resources for that type, so bacteria specializing on the alternative resource will be at an advantage.

        "We think it's likely that some kind of negative frequency dependence—some kind of rare type advantage—is important in many cases of diversification, especially when there's no geographic isolation," Herron said.

        As technology advances, Herron believes that similar experiments in larger organisms will soon be possible. Some examples of diversification without geographic isolation are known in plants and animals, but it remains to be seen whether or not the underlying evolutionary processes are similar to those in bacteria.

        More information: PLOS Biol 11(2): e1001490. doi:10.1371/journal.pbio.1001490

        Provided by Public Library of Science

        "How predictable is evolution?." February 19th, 2013. http://phys.org/news/2013-02-evolution.html

        Posted by
        Robert Karl Stonjek
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