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The Neo-Darwinian Theory Of Evolution Is Incomplete Without Lamarck

Discussion in 'Scientific Studies' started by haidut, Nov 11, 2016.

  1. haidut

    haidut Member

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    After decades of denial that environmentally-driven traits can be inherited, more and more prominent geneticist are calling for a major revision to the Neo-Darwinian theory of evolution. There is nothing modern about the so-called Modern Evolutionary Synthesis, and it needs to be revised or replaced. I posted a few studies before that cast serious doubt on at least the primary role of genes as drivers of evolution.
    https://raypeatforum.com/community/threads/genes-do-not-matter-much.2972/
    The "selfish gene" may not be the driver of evolution after all

    This article touches upon many of the same ideas that Ray has written about over the years. The part that is especially concerning is that metabolic damage due to environmental factors continues for up to 10 generations in higher mammals, and likely in humans as well.
    The article also makes a point against the discrete nature of genetically driven inheritance of traits - i.e. genes acting like particles that match/connect/bond with other similar particles. I cannot help but bring up the continued accumulation of evidence that this idea, which was likely borrowed from physics, is wrong. Nature is fundamentally continuous like a wave, and accordingly the epigenetic mechanism of inheritance acts like a field with attenuating influence over the generations.

    On epigenetics: we need both Darwin’s and Lamarck’s theories | Aeon Essays

    "...The unifying theme for much of modern biology is based on Charles Darwin’s theory of evolution, the process of natural selection by which nature selects the fittest, best-adapted organisms to reproduce, multiply and survive. The process is also called adaptation, and traits most likely to help an individual survive are considered adaptive. As organisms change and new variants thrive, species emerge and evolve. In the 1850s, when Darwin described this engine of natural selection, the underlying molecular mechanisms were unknown. But over the past century, advances in genetics and molecular biology have outlined a modern, neo-Darwinian theory of how evolution works: DNA sequences randomly mutate, and organisms with the specific sequences best adapted to the environment multiply and prevail. Those are the species that dominate a niche, until the environment changes and the engine of evolution fires up again.
    But this explanation for evolution turns out to be incomplete, suggesting that other molecular mechanisms also play a role in how species evolve. One problem with Darwin’s theory is that, while species do evolve more adaptive traits (called phenotypes by biologists), the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed. Scientists, well-aware of the issue, have proposed a variety of genetic mechanisms to compensate: genetic drift, in which small groups of individuals undergo dramatic genetic change; or epistasis, in which one set of genes suppress another, to name just two.
    Yet even with such mechanisms in play, genetic mutation rates for complex organisms such as humans are dramatically lower than the frequency of change for a host of traits, from adjustments in metabolism to resistance to disease. The rapid emergence of trait variety is difficult to explain just through classic genetics and neo-Darwinian theory. To quote the prominent evolutionary biologist Jonathan B L Bard, who was paraphrasing T S Eliot: ‘Between the phenotype and genotype falls the shadow.’
    And the problems with Darwin’s theory extend out of evolutionary science into other areas of biology and biomedicine. For instance, if genetic inheritance determines our traits, then why do identical twins with the same genes generally have different types of diseases? And why do just a low percentage (often less than 1 per cent) of those with many specific diseases share a common genetic mutation? If the rate of mutation is random and steady, then why have many diseases increased more than 10-fold in frequency in only a couple decades? How is it that hundreds of environmental contaminants can alter disease onset, but not DNA sequences? In evolution and biomedicine, the rates of phenotypic trait divergence is far more rapid than the rate of genetic variation and mutation – but why?"

    "...The question is this: if natural selection isn’t acting on genetic mutations alone, then what molecular forces create the full suite of variation in traits required for natural selection to finish the job? One clue came almost a century after Darwin proposed his theory, in 1953, just as James Watson and Francis Crick were unravelling the mysteries of DNA and the double helix. In that year, the developmental biologist Conrad Waddington of the University of Edinburgh reported that fruit flies exposed to outside chemical stimulus or changes in temperature during embryonic development could be pushed to develop varying wing structures. The changes the scientists induced in that single generation would, thereafter, be inherited by progeny down the lineage. Waddington coined a modern term – ‘epigenetics’ – to describe this phenomenon of rapid change. Notably, before Watson and Crick had even revealed their DNA structure, Waddington recognised the potential impact his discovery could have on the theory of evolution: the single-generation change in the fruit-fly wings were supportive of the original ideas of the heretic Lamarck. It appeared that the environment could directly impact traits."

    "...All of these epigenetic mechanisms are critical and have unique roles in the molecular regulation of how DNA functions. The regulation of biology, it follows, will never involve a ‘genetic-only process’, nor an ‘epigenetic-only process’. Instead, the processes of epigenetics and genetics are completely integrated. One does not work without the other."

    "...For epigenetics to have a significant impact on evolution, its alterations must be inherited by subsequent generations, just like DNA sequences and gene mutations. But epigenetic inheritance does not follow many of the Mendelian rules that apply to classic genetics and the neo-Darwinian theory of evolution. These rules hold that DNA sequences and genes function discretely, like particles; upon reproduction, the ‘particles’ from each parent unite at random with a matching pair from the other parent, leading to a new DNA sequence and new expression of inherited traits. Epigenetic transgenerational inheritance, by contrast, occurs when the germline (sperm or egg) transmits epigenetic information between generations, even in the absence of continued direct environmental exposures. Environmental stress and exposure is especially impactful during germline development – for instance, when foetal sex organs develop into testis for men or ovaries for women to produce sperm or eggs later in life. Indeed, environmental exposure during this critical time can trigger permanent epigenetic changes via DNA methylation, histone modifications and alteration of non-coding RNA."

    "...Evidence for this non-genetic form of inheritance, which my team at Washington State University identified in 2000, is persuasive. Findings published by my group in Science in 2005 showed the ability of environmental chemicals to promote inheritance of disease in rats through three generations, to great-grand offspring and beyond, in the absence of any continued exposures. The phenomenon has been further documented by many labs in a number of different species over the past decade. An example is when Graham Burdge and his team at the University of Southampton in the United Kingdom reported that excessive nutrition in rats created epigenetically induced metabolic abnormalities three generations out."

    "...In other work, Sibum Sung and his colleagues at the University of Texas Austin found that drought and changes in temperature induced epigenetic evolution in plants, leading to alterations in growth and flowering traits, generations out. More recently, a number of studies have indicated that environmental stress can promote epigenetic alterations that are transmitted to and induce pathologies in subsequent generations. A recent study by Gerlinde Metz and her colleagues at the University of Lethbridge in Canada demonstrated that restraining pregnant rats or, alternatively, forcing them to swim, produced epigenetic damage that put newborns at risk. This ancestral stress also promoted the epigenetic transgenerational inheritance of abnormalities in the great-grand offspring of the exposed gestating female. Several studies now support the role of environmental stress in promoting the epigenetic transgenerational inheritance of disease."

    "...Environmentally induced epigenetic transgenerational inheritance has now been observedin plants, insects, fish, birds, rodents, pigs and humans. It is, therefore, a highly conserved phenomenon. The epigenetic transgenerational inheritance of phenotypic trait variation and disease has been shown to occur across a span of at least 10 generations in most organisms, with the most extensive studies done in plants for hundreds of generations. One example in plants, a heat-induced flowering trait first observed by Carl Linnaeus in the 18th century, was later found to be due to a DNA methylation modification that occurred in the initial plant, and has been maintained for 100 generations. In worms, traits altered by changes in nutrition have been shown to propagate over 50 generations. In mammals with longer generation times, we have found toxicant-induced abnormal traits propagated for nearly 10 generations. In most of these studies, the transgenerational traits do not degenerate but continue. Even Waddington’s experiment with flies was taken out to 16 generations, and the altered traits have been propagated and continue to exist today."

    "...Much as Lamarck suggested, changes in the environment literally alter our biology. And even in the absence of continued exposure, the altered biology, expressed as traits or in the form of disease, is transmitted from one generation to the next."

    "...One example that we studied in our lab involved the impact of environmental chemical exposure on trait variation and disease. In our study, we set out to investigate the ability of an environmental toxicant – vinclozolin, the most commonly used fungicide in agriculture today – to alter traits through epigenetic change. First, we briefly exposed a gestating female rat to the fungicide; then we bred her progeny for three generations, to great-grand-offspring, in the absence of any continued exposures. For nearly all males down through the lineage, we observed a decrease in the number and viability of sperm and an associated incidence of infertility with age. And we observed a variety of other disease conditions in both males and females three generations removed from the direct exposure, including abnormalities in the testis, ovaries, kidneys, prostate, mammary glands and brain. Corresponding epigenetic alterations in the sperm involve changes in DNA methylation and non-coding RNA expression."

    "...Our research showed that ancestral exposure to the toxicant vinclozolin also affected sexual selection in animals three generations down the lineage. Considered a major force in evolution since Darwin first posed his theory, sexual selection – also known as mate preference – was assessed by allowing females from other litters to choose between either descendants of exposed or unexposed males. Females overwhelmingly selected those who lacked the transgenerational epigenetic alterations and whose ancestors had not been exposed. In conclusion, exposure to the fungicide permanently altered the descendant’s sperm epigenetics; that, in turn, led to inheritance of sexual selection characteristics known to reduce the frequency with which their genes might propagate in the broader population and directly influence evolution on a micro-evolutionary scale."

    "...Support for an epigenetic role in evolution continues to mount. One interesting study compares Neanderthal and human DNA, where genetic differences are significantly less pronounced than the epigenetic ones, which involve alterations in DNA methylation in the genomes. In short, integration of neo-Lamarckian and neo-Darwinian concepts into a unified theory provides a far more efficient molecular basis for how evolution works. Neo-Darwinian and neo-Lamarckian mechanisms both drive evolution, and they appear to be intertwined. Indeed, because environmental epigenetics can increase trait variation within a population, it empowers natural selection, which works by promoting adaptive traits over others. Classic neo-Darwinian evolution involves genetic mutation and genetic variation as the main molecular mechanisms generating variation. Add to these mechanisms the phenomenon of environmental epigenetics, which directly increases trait variation, and you enhance the ability of the environment to mediate natural selection and evolution."


    "...A critical additional consideration for our lab involves the ability of epigenetics to alter genome stability and, thus, to directly induce the kind of genetic mutations observed in cancer biology. The gene mutations we’ve found here include copy number variation (the number of times a short DNA sequence is repeated) and point mutations (alteration of a single nucleotide within the DNA sequence) in later generations. Nearly all types of genetic mutations are known to have a precursor epigenetic change that increases the susceptibility to develop that mutation. We observed that direct environmental exposure in the first generation had epigenetic changes and no genetic mutations but, transgenerationally, an increase in genetic mutations was identified. Since environmental epigenetics can promote both trait variation and mutations, it accelerates the engine of evolution in a way that Darwinian mechanisms alone cannot."


    "...The unified theory of evolution has many skeptics, especially in light of the genetic determinism paradigm that has influenced the biological sciences for more than 100 years. Genetic determinism sees DNA as the basic building block of biology, and the DNA sequence as the ultimate molecular control. Perhaps the key pentacle of genetic determinism was the sequencing of the human genome, which was to provide the ultimate proof of the primacy of the gene. Genome-wide association studies were predicted to provide biological marks for normal and abnormal phenomena of life and reveal the underpinnings of disease. But in the wake of that sequencing, the major prediction of genetic determinism – that the majority of human biology and disease could be understood through the lens of genetics – has not borne out."
     
  2. tca300

    tca300 Member

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    @haidut Thanks for the post! Do you know of any good books on Lamarckian evolution that are pretty accurate? Thanks!
     
  3. OP
    haidut

    haidut Member

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    The first link from my post above - the one about genes not mattering much - has an attached file for a book called "Developmental Plasticity". It is pretty good and quite "Lamarckian".
     
  4. chispas

    chispas Member

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  5. Dante

    Dante Member

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    The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome
    quoting from the study-
    "Many xenobiotics, ubiquitously present in the environment, have estrogenic and/or other hormonal properties and function as endocrine disruptors. Their potential to modify the epigenome remains largely unexplored. Recently, the Avy model was utilized to evaluate the effects of maternal exposure to the endocrine active chemical bisphenol A (BPA) on the fetal epigenome. Moreover, the BPA-induced hypomethylation of the fetal epigenome was abolished by maternal dietary nutritional supplementation with either methyl donors (folic acid, betaine, vitamin B12, and choline). These findings demonstrate that simple dietary changes can protect against the deleterious effects of environmental toxicants on the fetal epigenome"
     
  6. OP
    haidut

    haidut Member

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    It was August Weismann, not Lamarck who did the tail cutting experiment. I doubt Lamarck was that cruel :):
    Also, Lamarck said that tails would be lost through disuse and not through chopping them off. So, if the environment still favors a tail the animal will have progeny with tails. But if say the ground somehow heated up and was hurting the tail and also raising the body temp of the animal too much, I would not be surprised if the tails are lost within a few generations.
     
  7. OP
    haidut

    haidut Member

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    That's a good find, thanks. I wonder why they focused on opposing the hypomethylation effects of BPA instead of the estrogenic, nutagenic, anti-metabolic, etc. Clearly, it's the latter ones that are a bigger problem.
     
  8. Dante

    Dante Member

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    I think those estrogenic,nutagenic effects manifest itself as hypomethylation in the preinatal period( for those EDC properties , they must interfere with the fetal epigenome), i just quoted the selected lines. there are some more lines/texts between the sentences i posted. Read the whole paper. There is a growing consensus in mainstream that inherited genetics are not the destiny. I even read this is newspapers.
     
  9. chispas

    chispas Member

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    How do environments favor one thing over another - they can't hold opinions.

    What is so hostile about the environment of the Manx cat on the Isle of Man that makes the tail drop off, if the environment is the hypothetical influence leading to the eventual physical adaptation?

    Not having a tail is only one problem that the Manx cat faces - it appears this is just one symptom of many systemic issues. In fact, not having a tail seems to interfere with the cat's internal organs throughout its life - is this a case of the environment "favouring" cruelty and suffering?

    Could one not accurately say that the lack of genetic diversity in the environment of the Isle of Man is the main stressor?
     
  10. chispas

    chispas Member

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    If anything, it looks like the cold rainy weather might cause a cat's tail to drop off on the Isle of Man.
     
  11. OP
    haidut

    haidut Member

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    I'd be thrilled if this growing consensus you mention makes its way to the dietary guidelines FDA puts out and in medical treatments. The main barrier for trying aspirin and other pro-metabolic drugs on cancer, diabetes, AD, etc is that the mainstream believes these diseases are due to genetic mutations and as such the only cure is some sort of "cut, poison, burn" approach or managing symptoms. I have not seen any sing of that changing. In fact, the new "War on Cancer" that President Obama promised (he called it the Cancer Moonshot) is once again based on genetics mapping and not environmental/metabolic approaches.
     
  12. OP
    haidut

    haidut Member

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    I can't predict what environment will result in disfavoring of what organs or body parts. Maybe like you said, it is the cold environment on that island that made the cat be that way. Bottom line is that it is still probably the environment that caused in a directed way and not some random unguided mutation, which then is simply tested by the environment for fitness.
     
  13. Dante

    Dante Member

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    Well, You have a new president now
     
  14. chispas

    chispas Member

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    It's funny how the language of genetics seems to view bad changes in the organism as being due to mutations, but when a change is positive, suddenly the change supposedly reflects "adaptation" and "evolution".

    Obviously the environment on the Isle of Man isn't one conducive to any cat doing too well. Perhaps if the breed was relocated to a sunny climate, its anatomy would change for the better.

    Here in Australia, I can't say there are any deformed organisms that I can think of, except Pauline Hanson of course.

    60,000 years ago during the time of the mega fauna, Australia's animals were significantly larger than today. I suppose there is too much sun for the animals to do too badly metabolically. I mean really the platypus looks like a "mutation", but it is just going along, living its happy life, no problems. The Aboriginal Dream Time stories refer to the platypus as a mixture of a few different animals, and these narratives date back 45,000 years.
     
  15. OP
    haidut

    haidut Member

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    I heard the aborigines sing their ancestral stories. Is this true? I also heard they believe a man can change into an animal within a lifetime if he really knows how to work with mother nature. Their stories are so fascinating and I would not be surprised if a good portion of them turn out to be true. "Primitive" cultures have been shown to harbor almost no habit for lying and use it only when absolutely necessary. So, they have no reason to come up with an elaborate story of the world unless they saw most of it play out in the real world.
     
  16. chispas

    chispas Member

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    How do you mean, "sign"? Like signature?

    They are stories carried down verbally, and often illustrated on rock walls. Aboriginal people traditionally have over 8000 different dialects, and have myriad different tribal areas, so they aren't all "one people" despite the popular ignorance that clumps them all together.

    Very interestingly, before I had even heard of Ray Peat, I had spoken with Indigenous people who told me stories of how sick they had become from leaving their traditional land and one would assume, community. Even a small move from NSW to QLD was enough to illicit psychological upset, metabolic problems, rapid and severe health decline. Then they would return home, meet back up with their family, and the issues with resolve.

    I've heard anecdotes like this so many times now, that I interpret it as the strong, ancient connection that Indigenous people have with the land. European settlers here have no connection at all.
     
  17. chispas

    chispas Member

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    It's not important if stories are true or not, but rather if they are convincing.

    All convincing stories seem true, but the more true they seem, the more contrived and often complex they are.

    Aboriginal Dream Time stories are convincing, and easy to understand, a bit like Aesop's fables, but they are very deep texts. They speak to something essential in the relationship between humans and the land.

    Anthony Mundine, the great Australian boxer and footballer was interviewed recently by the ABC. He is Muslim and claims that there are a lot of similarities between Islam and the Indigenous view of nature. I need to read more about Islam to compare.
     
  18. OP
    haidut

    haidut Member

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    Sorry, I meant sing as in singing as a way of speaking.
     
  19. chispas

    chispas Member

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    Sort of. What the Aborigines use is "song lines" and "dream tracks", which are songs passed down through the generations that work much like maps, but without the need for a physical map. It's a song that helps navigate the land.

    I think Bruce Chatwin famously wrote about this in his book Songlines. There's a lot of info about it, it's really amazing stuff.
     
  20. moss

    moss Member

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    :rofl
    I remember a talk I attended awhile ago and the fellow talked about the connectiveness of sites, time, songlines and lines of the country is weaved in language, dreams, art, stars, song etc. like an organized matrix of networks of algebraic complexity, a sort of multi-layered system which resembles the neurological patterning of the brain.
     
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