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Re: [evol-psych] Adaptive evolution: Mutations don't win out

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  • james kohl
    The topic of this discussion is: When timing is everything: Research says beneficial mutations need specific circumstances to win out The full text of the
    Message 1 of 97 , Mar 23, 2013
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      The topic of this discussion is: When timing is everything: Research says beneficial mutations need specific circumstances to win out The full text of the published work being discussed is here: Synchronous Waves of Failed Soft Sweeps in the Laboratory: Remarkably Rampant Clonal Interference of Alleles at a Single Locus "Regardless of starting genotype, for evolving populations to scale alternative fitness peaks, there must be reciprocal sign epistasis to guarantee that beneficial mutations that would bridge from one apparent optimum to another do not exist (Weinreich et al. 2005)."

      In my model, pheromones provide the reciprocal sign (of nutrient-dependent reproductive fitness) that enables the transition from pleiotropy to epistasis. The most recently published work on the "Synchronous Waves" appears to confirm what many people have known for many years.

      For example, Douglas Axe demonstrated the inability of Darwinian evolution to produce multi-mutation features in a 2010 peer-reviewed study. Axe calculated that when a "multi-mutation feature" requires more than six mutations before giving any benefit, it is unlikely to arise even in the whole history of the Earth.4 He provided empirical backing for this conclusion from experimental research he earlier published in the Journal of Molecular Biology, finding that only one in 1074 amino-acid sequences yields functional protein folds.5 That implies that protein folds in general are multi-mutation features, requiring many amino acids to be fixed before the assembly provides any functional advantage.
       
      Why can't anyone here address the facts, either via statistical analyses (above) or via what is currently known about the basic principles of biology and levels of biological organization required to link the sensory environment directly to adaptive evolution in species from microbes to man? There is no reason for anyone but Edgar and a few other fools to want this topic thread to degrade into discussion of personal attacks on me and my published works. Are all others willing to let the fools have their way?

      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: Sat, March 23, 2013 7:23:24 AM
      Subject: Re: [evol-psych] Adaptive evolution: Mutations don't win out

       

      From: Edgar Owen <edgarowen@...>
      Exactly right and an important point. Kohl NEVER, or almost never, gives direct answers to questions about this theory. The reason is obvious. Without cloaking his responses in extended string along scientific mumbo jumbo the truly adolescent level of his views would be obvious to everyone.


      He did slip up big time by finally clearly stating what has been obvious all along, that in his 'model' what an organism smells or tastes is what produces the genetic variation among species that drives evolution! One of the most absurd and non-scientific ideas ever produced, and one with zero evidence at all.

      Obviously if he just came out and said that in his 'peer reviewed' papers they'd never get published....

      JK: The concluding sentence from my most recently published peer-reviewed work is: "Olfaction and odor receptors provide a clear evolutionary trail that can be followed from unicellular organisms to insects to humans." The evolutionary trail is the one in which what an organism smells or tastes is what produces the genetic variation among species that drives evolution! See for example An Initial Evaluation of the Functions of Human Olfaction: "Of all areas of human olfactory function, the role of smell in reproductive behavior has consistently attracted the most popular attention (e.g., Hassett 1978; Kohl and Francoeur 1995)." Or, see any other article ever published in the journal "Chemical Senses."

      From: Edgar Owen <edgarowen@...>

      I do have to hand it to him though, he's quite a competent hoaxer who has built a minor position in the world of science out of smoke and mirrors without an iota of substance....

      JK: Edgar will now tell us about the substance that supports random mutations theory, won't he? For comparison see: Nutrient-dependent / Pheromone-controlled Adaptive Evolution and Nutrient-dependent / Pheromone-controlled thermodynamics and thermoregulation

      Perhaps by detailing ecological, social, neurogenic, and socio-cognitive niche construction I have built a minor position -- with awards for publication in social science and neuroscience. But I can guarantee that people like Edgar Owen, James Gray, and Clarence 'Sonny' Williams will never know the difference between a minor position and one that heralds a paradigm shift.


      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.






      On Mar 22, 2013, at 9:08 PM, James Gray wrote:

      > I would not say that is correct. At this time I have no idea what parts of
      > Kohl's model (that he says is not a theory) is correct. He will not give
      > direct answers to direct questions on the human ethology list so it is
      > impossible to assess his model. As far as I can tell he is about equally
      > evasive on this list. I have found it is a mistake to try to answer his
      > posts.
      >
      > James Gray
      >
      > On Fri, Mar 22, 2013 at 11:38 AM, hibbsa <hibbsa@...> wrote:
      >
      >> **
      >>
      >>
      >>
      >> According to what you are saying Kohl's theory could be correct except
      >> his misunderstanding about the word "mutation". Is that correct?
      >>
      >> In evolutionary-psychology@yahoogroups.com, James Gray <James@...>
      >> wrote:
      >>>
      >>> Edgar,
      >>> Iing almost never post on this list. I want to complement you for
      >> taking the
      >>> time to examine and critique the claims of Kohl. I think that his
      >> model is
      >>> so vague and inadequately explained that it does not deserve the label
      >>> "theory". It appears that he is unwilling to say what he means. The
      >>> puzzling thing is that his claim that what an organism eats and smells
      >>> changes the genome rather than mutations changing the genome does not
      >> make
      >>> logical sense. "Random" mutation is not an assertion about what
      >> changes
      >>> the genome. It is just that it changes. If what the organism eats and
      >>> smells is the cause of changes in the genome, then his theory seems to
      >> be
      >>> that chemicals in food and smells causes mutations. Yet, Kohl seems to
      >>> reject any mutation at the same time that he says nutrients and
      >> pheromones
      >>> cause the changes that in any body else's words would be mutations.
      >> Where
      >>> is the logic in this? Go figure!
      >>>
      >>> James Gray
      >>>
      >>> On Fri, Mar 22, 2013 at 6:15 AM, Edgar Owen edgarowen@... wrote:
      >>>
      >>>> **
      >>>>
      >>>>
      >>>> Once again the article Kohl cites in support of his wacko theory
      >> that what
      >>>> organisms eat or smell is what changes their genome (rather than
      >> mutations
      >>>> doing it) simply DOES NOT support it...
      >>>>
      >>>> It's a FALSE citation which I'm sure the authors of the article
      >> would
      >>>> reject....
      >>>>
      >>>> Edgar
      >>>>
      >>>>
      >>>>
      >>>> On Mar 21, 2013, at 8:39 PM, james kohl wrote:
      >>>>
      >>>>
      >>>>
      >>>> As I noted, the chemical senses: tasting and smelling, generate new
      >> DNA
      >>>> sequences in organism from microbes to man. The crux of my model is
      >>>> addressed here Interchromosomal Interactions and Olfactory Receptor
      >>>> Choice
      >>>>
      >> <http://www.sciencedirect.com/science/article/pii/S0092867406008555>in a
      >>>> paper with senior author and 2004 Nobel Laureate, Richard Axel. The
      >> crux of
      >>>> my model is also addressed here How keeping active pays off in the
      >>>> olfactory system <http://elife.elifesciences.org/content/1/e00326>
      >> in the
      >>>> context of the recently identified protein that orchestrates the
      >>>> frequencies at which different olfactory receptors are expressed,
      >> which is
      >>>> how it facilitates pleiotropic plasticity and adaptively evolved
      >> epistasis
      >>>> via the direct link from the odor environment to the olfactory
      >> system.
      >>>> Thus, the epigenetic environment becomes the physical environment of
      >> DNA
      >>>> via nutrient-dependent chromatin remodeling and pheromone-controlled
      >> de
      >>>> novo gene creation.
      >>>>
      >>>> What Edgar now infers is that the movers and shakers of molecular
      >> biology
      >>>> are WHACKOs, and that a Nobel Laureate is one of the WHACKOs. Note,
      >>>> however, that Edgar has never addressed any aspect of the biological
      >> facts
      >>>> I have offered with cited published works (above and below) as
      >> support,
      >>>> including my own published works. If there be WHACKOs here, we all
      >> know who
      >>>> they are, since Williams has also already added more of his nonsense
      >> to
      >>>> this topic thread.
      >>>>
      >>>> If there are WHACKOs among the world's top molecular biologists, it
      >> would
      >>>> not be Edgar or Sonny telling us who they are.
      >>>>
      >>>> 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.<http://dx.doi.org/10.3402/snp.v2i0.17338>Socioaffective
      >> Neuroscience & Psychology, 2: 17338.
      >>>>
      >>>>
      >>>> ------------------------------
      >>>> *From:* Edgar Owen edgarowen@...
      >>>> *To:* evolutionary-psychology@yahoogroups.com
      >>>> *Sent:* Thu, March 21, 2013 6:22:28 PM
      >>>> *Subject:* Re: [evol-psych] Adaptive evolution: Mutations don't win
      >> out
      >>>>
      >>>>
      >>>>
      >>>> Jim,
      >>>>
      >>>> This is so WHAKO it's ludicrous. Kohl actually believes that all the
      >> new
      >>>> DNA sequences in all the diverse organisms on earth arose from
      >> epigenetic
      >>>> changes caused by what those organisms tasted or smelled!
      >>>>
      >>>> He finally actually says so below in plain English for a change and
      >> I
      >>>> quote...
      >>>>
      >>>> *From:* Edgar Owen edgarowen@... Tasting and smelling simply DO NOT
      >>>> generate new DNA sequences in an organism....
      >>>>
      >>>> *JK:* Of course they do, Edgar. That's what I've detailed. See also
      >> Born
      >>>> (2013) <http://www.ncbi.nlm.nih.gov/pubmed/23283334> for the role of
      >>>> taste receptors, and Clowney
      >> (2012)<http://linkinghub.elsevier.com/retrieve/pii/S009286741201286X>
      >> for
      >>>> the role of olfactory receptors.
      >>>>
      >>>>
      >>>> Everyone on the group should take note and remember this is the crux
      >> of
      >>>> Kohl's childish model. We know he never attended college but he
      >> should have
      >>>> at least learned better in high school...
      >>>>
      >>>> Edgar
      >>>>
      >>>>
      >>>>
      >>>> On Mar 21, 2013, at 10:09 AM, james kohl wrote:
      >>>>
      >>>>
      >>>>
      >>>> *From:* Edgar Owen edgarowen@...
      >>>> Give me one actual study that provides any evidence at all of any of
      >> the
      >>>> nonsensical mechanism you posit generating any new DNA sequences in
      >> the
      >>>> genome...
      >>>>
      >>>> *JK*: The individual studies included in my model provide evidence
      >> for
      >>>> the conserved molecular mechanisms I have detailed, Edgar. The most
      >>>> recently developed theories also do this. For example, see: A
      >> quantum
      >>>> theory for the irreplaceable role of docosahexaenoic acid in neural
      >> cell
      >>>> signalling throughout
      >> evolution<http://www.plefa.com/article/S0952-3278%2812%2900147-0/fulltex\
      >> t <http://www.plefa.com/article/S0952-3278%2812%2900147-0/fulltext>>.
      >>>> Compare the role of DHA uptake
      >> here<http://www.the-scientist.com/?articles.view/articleNo/33047/title/P\
      >> UFAs-At-Work/<http://www.the-scientist.com/?articles.view/articleNo/33047/title/PUFAs-At-Work/>>to
      >> the evolution
      >>>> of citrate use <http://dx.doi.org/10.1038/nature11514> in an
      >> experimental
      >>>> E. coli population. You can then see how the multi-step origin of a
      >> key
      >>>> innovation was conserved across species from microbes to man (via
      >>>> receptor-mediated cause and effect).
      >>>>
      >>>> *From:* Edgar Owen edgarowen@... Tasting and smelling simply DO NOT
      >>>> generate new DNA sequences in an organism....
      >>>>
      >>>> *JK:* Of course they do, Edgar. That's what I've detailed. See also
      >> Born
      >>>> (2013) <http://www.ncbi.nlm.nih.gov/pubmed/23283334> for the role of
      >>>> taste receptors, and Clowney
      >> (2012)<http://linkinghub.elsevier.com/retrieve/pii/S009286741201286X>for
      >> the role of olfactory receptors.
      >>>>
      >>>> *From:* Edgar Owen edgarowen@... .... and even if they did they
      >>>> would not be passed on to the next generation.
      >>>>
      >>>> *JK: *What kind of idiot claims that transgenerational epigenetic
      >>>> inheritance (e.g., for the receptor-mediated events I have detailed)
      >> does
      >>>> not occur? That was a rhetorical question. Have you been discussing
      >> this
      >>>> with Clarence 'Sonny' Williams?
      >>>>
      >>>> *From:* Edgar Owen edgarowen@... You simply don't seem to
      >>>> understand basic biology. New DNA sequences MUST be produced for
      >> evolution
      >>>> to proceed by selecting among them. There is NO mechanism in your
      >> 'model'
      >>>> for the generation of new DNA sequences that can be passed on....
      >>>>
      >>>> *JK: *In my model, the mechanism is clear. How is the generation of
      >> new
      >>>> DNA sequences that can be passed on accomplished via random
      >> mutations? That
      >>>> question addresses the understanding of the basic principles of
      >> biology and
      >>>> levels of biological organization I detailed in my model, and it is
      >>>> discussed in the paper that is the topic of this
      >> thread<http://medicalxpress.com/news/2013-03-beneficial-mutations-specif\
      >> ic-circumstances.html<http://medicalxpress.com/news/2013-03-beneficial-mutations-specific-circumstances.html>
      >>> .
      >>>>
      >>>>
      >>>> The answer to that question is: Mutations don't "win out." Adaptive
      >>>> evolution is nutrient-dependent and pheromone-controlled. It occurs
      >> via
      >>>> ecological, social, neurogenic, and socio-cognitive niche
      >> construction.
      >>>> "Olfaction and odor receptors provide a clear evolutionary trail
      >> that can
      >>>> be followed from unicellular organisms to insects to humans." --
      >> Kohl (2012)
      >>>>
      >>>> You should probably quit trying to tell people there is no means of
      >>>> producing new DNA sequences in my model, since it details how the
      >> new DNA
      >>>> sequences are produced via epigenetic effects on intracellular
      >> signaling
      >>>> that result in organism-level thermoregulation in species from
      >> microbes to
      >>>> man. In reality, however, you should probably also quit trying to
      >> tell
      >>>> people anything. Nothing you can say is likely to change their
      >> opinion
      >>>> about your ability to participate in intelligent discussion of
      >> biological
      >>>> facts.
      >>>>
      >>>>
      >>>> 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.<http://dx.doi.org/10.3402/snp.v2i0.17338>Socioaffective
      >> Neuroscience & Psychology, 2: 17338.
      >>>>
      >>>>
      >>>> On Mar 20, 2013, at 8:30 PM, james kohl wrote:
      >>>>
      >>>>
      >>>>
      >>>> *From:* Edgar Owen edgarowen@...
      >>>> *To:* evolutionary-psychology@yahoogroups.com
      >>>> *Sent:* Wed, March 20, 2013 7:24:28 PM
      >>>> *Subject:* Re: [evol-psych] Adaptive evolution: Mutations don't win
      >> out
      >>>>
      >>>>
      >>>>
      >>>> Jim,
      >>>>
      >>>> Evolution requires new genetics, new DNA sequences, to be generated
      >> so
      >>>> that evolution may select between them.
      >>>>
      >>>> In your theory there is NO MEANS of producing new DNA sequences. You
      >> claim
      >>>> "Adaptive evolution is nutrient-dependent and pheromone-controlled".
      >>>> Certainly neither nutrients nor pheromones (what an organism eats or
      >>>> smells) actually produce new DNA sequences. That's totally
      >> laughable!
      >>>>
      >>>> Thus your theory is totally ridiculous and totally unscientific. I'm
      >>>> amazed that it's not just laughed off the group. It would be if this
      >> group
      >>>> had the smarts it's supposed to have or any self respect or
      >> scientific
      >>>> credibility.....
      >>>>
      >>>> Jim, where do the new DNA sequences that evolution chooses among
      >> come from
      >>>> in your theory? You claim not from mutations. Then WHERE?
      >>>>
      >>>> *JK: *Please pay attention, Edgar, and stop playing the fool. I have
      >> a
      >>>> model, not a theory. Nutrient-dependent intermolecular changes
      >> enable de
      >>>> novo gene expression (new DNA sequences) via amino acid
      >> substitutions in
      >>>> species from microbes to
      >> man<http://dx.doi.org/10.6084/m9.figshare.643393>.
      >>>>
      >>>>
      >>>> This model of systems
      >> biology<http://dx.doi.org/10.6084/m9.figshare.155672>represents the
      >> conservation of bottom-up organization and top-down
      >>>> activation via:
      >>>> Nutrient stress-induced and social stress-induced intracellular
      >> changes in
      >>>> the microRNA (miRNA) / messenger RNA (mRNA) balance;
      >>>> Intermolecular changes in DNA (genes) and alternative splicing;
      >>>> Non-random *experience-dependent stochastic variations in de novo
      >> gene
      >>>> expression* and biosynthesis of odor receptors;
      >>>> The required gene-cell-tissue-organ-organ system pathway that links
      >>>> sensory input directly to gene activation in neurosecretory cells
      >> and to
      >>>> miRNA-facilitated learning and memory in the amygdala of the
      >> adaptively
      >>>> evolved mammalian brain;
      >>>> The required reciprocity that links gene expression to behavior that
      >>>> alters gene expression (i.e., reciprocity from genes to behavior and
      >> back)
      >>>> in model organisms like the honeybee.
      >>>>
      >>>> 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.<http://dx.doi.org/10.3402/snp.v2i0.17338>Socioaffective
      >> Neuroscience & Psychology, 2: 17338.
      >>>>
      >>>> On Mar 20, 2013, at 12:22 PM, james kohl wrote:
      >>>>
      >>>>
      >>>>
      >>>> When timing is everything: Research says beneficial mutations need
      >>>> specific circumstances to win out
      >>>>
      >>>>
      >> http://medicalxpress.com/news/2013-03-beneficial-mutations-specific-circ\
      >> umstances.html<http://medicalxpress.com/news/2013-03-beneficial-mutations-specific-circumstances.html>
      >>>>
      >>>> Mutations don't "win out." Adaptive evolution is nutrient-dependent
      >> and
      >>>> pheromone-controlled. It occurs via ecological, social, neurogenic,
      >> and
      >>>> socio-cognitive niche construction. "Olfaction and odor receptors
      >> provide a
      >>>> clear evolutionary trail that can be followed from unicellular
      >> organisms to
      >>>> insects to humans." -- Kohl (2012)
      >>>>
      >>>> 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.<http://dx.doi.org/10.3402/snp.v2i0.17338>Socioaffective
      >> Neuroscience & Psychology, 2: 17338.
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>>
      >>>
      >>
      >>
      >>

    • charles beck
      Hello James and Leif Re ASD and pheromones I believe there is good evidence that the increase in ASD and other neonatal neural deficits is in part due to
      Message 97 of 97 , Apr 1, 2013
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        Hello James and Leif

        Re ASD and pheromones

        I believe there is good evidence that the increase in ASD and other neonatal neural deficits is in part due to delayed child birth (ageing uterus, eggs and sperm- see recent post fr RKS). Have there have been changes in breeding pop pheromones that made/make couples delay having children? These pheromone changes were likely to have been due to dietary changes, e.g. GM foods. For example the author of the book Wheatbelly gives examples of the many untoward effects of GM wheat altered to yield high levels of gluten.

        Best regards

        Charles

         

         

        From: evolutionary-psychology@yahoogroups.com [mailto:evolutionary-psychology@yahoogroups.com] On Behalf Of Leif Ekblad
        Sent: Monday, April 01, 2013 4:28 AM
        To: evolutionary-psychology@yahoogroups.com
        Subject: Re: [evol-psych] Adaptive evolution: Mutations don't win out

         

        




        James,

         

        In my paper that is in peer-review, I prove that there is no increase in neurodiversity since the 1800s with multiple methods. It even seems like there is a decrease starting around 1980 because of extensive discrimination.

         

        In addition to that, there is absolutely no proof that forgetting scent is correlated to ASDs. To the contrary, most senses are more accute in ASD, except for pain.

         

        There are some evidence that heavy metals are accumulated in the brains/bodies of autistics, but that seems to be some missing mechanism for getting rid of heavy metals, and is not related to olfaction or pheromones. It could partly be because of dental fillings and grinding teeth, which is more common in ASD.

         

        You also have not yet outlined which part of ASD your model fits with, and how. I'm still waiting for an answer on that one.

         

        Leif Ekblad

         

         

        ----- Original Message -----

        From: james kohl

        Sent: Sunday, March 31, 2013 11:49 PM

        Subject: Re: [evol-psych] Adaptive evolution: Mutations don't win out

         

        Re: Pesticide makes bees forget the scent for food, new study finds : neonicotinoids

        Pesticide makes bees forget the scent for food, new study finds.
        Widely-used pesticides have been found in new research to block a part of the brain that bees use for learning, rendering some of them unable to perform the essential task of associating scents with food.


        From a correspondent:

        - very relevant to the increase in autism rates and to why so many establishmentarians trumpet the industry-protecting notion merely better diagnosis. 

        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: Leif Ekblad <leif@...>


        JK: I've detailed the evidence for the validity of the extrapolation in species from microbes to man and how it involves the molecular mechanisms common to all species, Leif. Is there a species you can think of with molecular mechanisms of protein biosynthesis that are not thermodynamically regulated, which results in organism-level thermoregulation?

        Leif Ekblad: I fail to see what thermoregulation has to do with this. We have honeybees that have some distinct, highly conserved, phenotypes that are only present in honeybees, and you think this can be extrapolated to every species typical difference. The facts are that no mammal have more than two phenotypes (male and female), and that being male and female does not correlate to which species a specimen is part of, and nor is species-typical differences in mating behavior in any way related to pheromones or olfactory. At the very least, there exists no published research that can detail how exactly the species differences in mating behavior are coded by pheromones or nutrition, but you are welcome to publish this and outline the exact mode this operates in. You certainly have no managed to describe how this works here.

         

        In addition to that, I described to you how the ASD spectrum worked, and indicated a genetic spectrum of traits from a common phenotype that in no way resembles the honeybee phenotypes that are highly consistent and conserved, and you didn't bother to describe how this fit into your model, but just claimed that it did fit in. I also described the environmental component of ASD, which might be related to epigenetics and vulnerabilities, and which you and Nils often use as evidence for your "models". However, you couldn't even detail if you meant your model described the genetic spectrum of traits (neurodiversity) or environmental components of ASD, but instead appear to claim you can explain both with your model. Too me, this indicates that you either cannot explain any of them, that you don't understand ASD, or that you are trying to sell a model like any other product, regardless if it fits or not. 

         

        Leif Ekblad

         




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