Is epigenetics an additional mechanism for natural selection?

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Mammals go through two rounds of epigenetic "reprogramming" -- once after fertilization and again during the formation of gametes (sex cells) -- in which most of the chemical tags are wiped clean.

The most complete disproof of the inheritance of somatic influence is demonstrated in almost every experiment in genetics. When an individual with a dominant character is mated to one with a recessive character, all the offspring show the dominant character, in some cases in full force, in others less completely. When the hybrid is bred back to the recessive stock, half of the offspring show the dominant character, half the recessive. This is the expected ratio if half the ripe germ cells of the hybrid carry the dominant, half the recessive element. This result could not happen if the bodily characteristics (dominant) of the hybrid produced a sympathetic effect on the germ cells. Furthermore, it is possible to breed continuously from hybrid forms only—a common procedure in certain Mendelian work—yet when after many generations the stock has been tested, the dominant character has never been found to have affected the recessive elements in the germ material. The facts here are positive and unquestioned and contradict thoroughly the claim that the germ cells are affected specifically by the bodily characteristics of the individual.

Lamarckism has been dismissed because there is simply no inheritance of somatic influence. But that does not mean that environment doesn’t have influence on offspring. Because somatic changes never influences the germ cells, and because sex cells are the only cells that are transmitted to the next generation, I don't quite understand the following examples:


The most comprehensive study to date of variations in parental investment and epigenetic inheritance in mammals is that of the maternally transmitted responses to stress in rats. Experiments shows that histone acetylation and DNA methylation of the glucocorticoid receptor gene promoter is a necessary link in the process leading to the long-term physiological and behavioral sequelae of poor maternal care. In adulthood, the offspring of mothers that exhibit increased levels of pup licking and grooming over the first week of life show increased expression of the glucocorticoid receptor in the hippocampus (a brain structure associated with stress responsivity as well as learning and memory). Moreover, rat pups that received low levels of maternal licking and grooming during the first week of life showed decreased histone acetylation and increased DNA methylation of a neuron-specific promoter of the glucocorticoid receptor gene.

Agouti mice normally have yellow fur. But if their diet is rich in methyl groups, their DNA methylation changes and their fur turns brown. That alone can cause their offspring to be born brown.

Part of the Netherlands experienced widespread famine during World War II (Dutch famine - Hongerwinter). As a result, it seems, the children of those Dutch mothers were shorter than usual, as were their grandchildren. Some environmental factor, not strictly genetic, seems to have been passed down. These mechanisms are possible, although we don’t yet know how or to what extent. A majority of epigenetic marks are lost when the zygote is formed: there is something like a reset, known as the Weismann barrier. But some can remain. “Certain methylation marks aren’t lost.

Tthe notion of punctuated equilibria, with its occasional periods of rapid change interspersed with long interludes of stasis, are by no means incompatible with the Darwinian tradition.

Lamarck and his ideas were ridiculed and discredited. In a strange twist of fate, Lamarck may have the last laugh. Epigenetics, an emerging field of genetics, has shown that Lamarck may have been at least partially correct all along. It seems that reversible and heritable changes can occur without a change in DNA sequence (genotype) and that such changes may be induced spontaneously or in response to environmental factors.


If you're still convinced that natural selection is the only process that can explain all genetic changes in living organisms, and between them in vertical reproduction, could you please explain to me me how all these epigenetic mechanisms, that seem to be at least partly incompatible with Darwinism, work?
 
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Lamarck and his ideas were ridiculed and discredited. In a strange twist of fate, Lamarck may have the last laugh.
Sorry, but no. Lamarck totally got it wrong, in every scientific sense. Just because later some minor roundabout perks bypassing genetic inheritance were found Lamarck won't turn to be a prophet. It's not working that way.
 
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some minor roundabout perks bypassing genetic inheritance were found
Epigenetics is not Lamarckianism. I'm only pointing out that natural selection isn't the only driver of genetic variation. But I don't understand how changes in somatic cells can have effect on the germ line. Do you?
 
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If you're still convinced that natural selection is the only process that can explain all genetic changes in living organisms, and between them in vertical reproduction, could you please explain to me me how all these epigenetic mechanisms, that seem to be at least partly incompatible with Darwinism, work?
You appear to have ereted a strawman. I'm unaware of any reputable biologist who asserts that "natural selection is the only process that can explain all genetic changes in living organisms". Feel free to correct me by providing an appropriate citation.

Genetic drift and sexual selection are acknowledged as significant contributors to evolution. Genetic drift, in particular, may well play a crucial role in speciation. The epigenetic effects are, as you noted, appear to be limited to a couple of generations. Fascinating and yet to be investigated further, but hardly a major deviation from the fundamentals of the Modern Synthesis.
 
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Then how can you explain the examples I gave?
I don't have to. Just look up who discovered those things: none of them was Lamarck, but all of them was knee deep in 'orthodox' genetics.
Just look up what Lamarck did/discovered: none of that was those things you cited above.
Lamarck had a hunch that there might be something beside/instead of the 'orthodox' evolution, but he got nowhere with that. Yet, he had enough actual scientific contribution that we still regards him as scientist. That's all the story.

Ps.:
I'm only pointing out that natural selection isn't the only driver of genetic variation.
As it looks like, you are rather trying to give the credit for the actual epigenetics discoveries to Lamarck. That's just does not work.
By the way, (natural or any other type of) selection is actually about decreasing variation. Variation, especially genetic variation is driven by other means of the 'orthodox' evolution/genetics.
 
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I'm unaware of any reputable biologist who asserts that "natural selection is the only process that can explain all genetic changes in living organisms". Feel free to correct me by providing an appropriate citation.
I wasn't quoting a reputable biologist, but @BillTre, one of the Science Advisors on this forum, who in this topic said:

This just sounds like some kind of anti-Darwinist stuff.
You should review natural selection.
and
Your basic intellectual problem is not understanding natural selection.
This is actually easy to overcome. I understood natural selection by the fourth grade (about 9 years old).
Please go do that.
Here is a page of links on the subject.
This wasn't a discussion about the exact same subject, but this clearly sounds like every biological process of inheritance involves natural selection.

So in the last few weeks I was trying to find out how this could be the case. Instead, I found this, so that's why I came back to this forum, because I simply would like to understand how it works. If there is a biological inheritance mechanism that doesn't involve natural selection, but rather epigenetic alterations, then how could somatic changes ever affect the germ line (i.e. sex cells)? And if they don't affect the germ line, then how could you ever inherit parental traits? I simply don't understand this.
 
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I wasn't quoting a reputable biologist, but @BillTre, one of the Science Advisors on this forum, who in this topic said:
But @BillTre has not asserted that natural selection is the only mechanism at work in evolution. Also involved are variation within populations, fuelled by mutations. The genes that survive and prosper are determined via natural selection, sexual selection and genetic drift. Bill, rightly I think, felt that your misunderstanings could be addressed by a better grasp of natural selection. Perhaps you need to extend your study to the other factors.

Overlying this are short term ( a couple of generations) epigenetic changes that influence the character of offspring based on the environmental experiences of the parents, but do not continue beyond those couple of generations.
 
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The genes that survive and prosper are determined via natural selection, sexual selection and genetic drift.
But those processes still affect the germ line cells.

Take the maternally transmitted responses to stress in rats example I gave. Alterations are made to the glucocorticoid receptor gene in the hippocampus of the rat pup due to stress, but when this rat pup becomes an adult it can transmit those changes to the next generations. How?
 
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But those processes still affect the germ line cells.

Take the maternally transmitted responses to stress in rats example I gave. Alterations are made to the glucocorticoid receptor gene in the hippocampus of the rat pup due to stress, but when this rat pup becomes an adult it can transmit those changes to the next generations. How?
I am at a loss to know how best to answer this, in part because* the answer appears to be present in the link you provide in the post. Environmental factors, in this case maternal behaviour, lead to "increased DNA methylation of the promoter of the glucocorticoid receptor gene, decreased glucocorticoid receptor gene expression, and increased hormonal responses to stress".
The epigenetic changes impact on the way the gene is expressed. This leads to the heritability, all be it limited to a couple of generations, of the reaction to stress.
 
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But those processes still affect the germ line cells.

Take the maternally transmitted responses to stress in rats example I gave. Alterations are made to the glucocorticoid receptor gene in the hippocampus of the rat pup due to stress, but when this rat pup becomes an adult it can transmit those changes to the next generations. How?
You may have causation mixed up here. In many cases of transgenerational epigenetic inheritance, some environmental stimulus affects cells throughout the body causing changes in both somatic cells and germ cells. In this way, changes in the germ cells can be correlated with changes in the hippocampus, but it is not changes in the hippocampus that are driving changes in the germ cells.

However, it could be possible that changes to the hippocampus lead to some downstream signaling (e.g. release of hormones throughout the body) that more directly affect the germ cells. I'm not familiar enough with the example you cite to know what mechanisms are at play (if they are known at all, since this field is still very much under active investigation).
 
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I am at a loss to know how best to answer this, in part because* the answer appears to be present in the link you provide in the post. Environmental factors, in this case maternal behaviour, lead to "increased DNA methylation of the promoter of the glucocorticoid receptor gene, decreased glucocorticoid receptor gene expression, and increased hormonal responses to stress".
The epigenetic changes impact on the way the gene is expressed. This leads to the heritability, all be it limited to a couple of generations, of the reaction to stress.
Glucocorticoids travel throughout the bloodstream all around the body, but they affect only the gene expression in hippocampus, it says. Not that gene/receptor in all cells. But still, if I misinterpreted that part, and it affects the expression of that particular gene in all cells, even the germ line, the gene itself never changes: no mutation, no allelic variation, it becomes merely epigenetically methylated, and this shouldn’t affect the next generation because methyl groups are removed when an organism reproduces, preventing the heritability of epigenetic factors. Yet it does. So how can stress molecules affect the brain of the offspring, and its offspring?
 
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Glucocorticoids travel throughout the bloodstream all around the body, but they affect only the gene expression in hippocampus, it says. Not that gene/receptor in all cells. But still, if I misinterpreted that part, and it affects the expression of that particular gene in all cells, even the germ line, the gene itself never changes: no mutation, no allelic variation, it becomes merely epigenetically methylated, and this shouldn’t affect the next generation because methyl groups are removed when an organism reproduces, preventing the heritability of epigenetic factors. Yet it does. So how can stress molecules affect the brain of the offspring, and its offspring?
Could it be that changes in the hippocampus change how these mothers treat their pups? If that were the case, it would not be transgenerational germ line transmission of epigenetic marks.

The review linked by @TeethWhitener in post #8 looks interesting. It does use the term Lamarckian (!): "In conclusion, in plants and in some animals such as nematodes, transgenerational epigenetic inheritance is well-documented and relatively common. Epialleles may even form the basis of some complex traits in plants, where epigenetic inheritance is usually, if not always associated with transposable elements, viruses or transgenes and may be a by-product of aggressive germ line defense strategies. In mammals epialleles can also be found, but are extremely rare, presumably due to robust germ-line reprogramming. How epialleles arise in nature is still an open question but environmentally induced epigenetic changes are rarely transgenerationally inherited, let alone adaptive, even in plants. Thus, although much attention has been drawn to the potential implications of transgenerational inheritance for human health, so far there is little support. On the other hand, the human transmission of culture and improved habits is clearly Lamarckian. To quote SJ Gould (The Panda's thumb, 1980) “Human cultural evolution, in strong opposition to our biological history, is Lamarckian in character. What we learn in one generation, we transmit directly by teaching and writing.” In this and other respects, perhaps it is premature to compare humans to plants (as Burbank did) in terms of their capacity to recall past environments, in this generation and the next."
 
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Glucocorticoids travel throughout the bloodstream all around the body, but they affect only the gene expression in hippocampus, it says. Not that gene/receptor in all cells. But still, if I misinterpreted that part, and it affects the expression of that particular gene in all cells, even the germ line, the gene itself never changes: no mutation, no allelic variation, it becomes merely epigenetically methylated, and this shouldn’t affect the next generation because methyl groups are removed when an organism reproduces, preventing the heritability of epigenetic factors. Yet it does. So how can stress molecules affect the brain of the offspring, and its offspring?
After reading the link you provided earlier, I don't think the source is claiming that the stress can affect the germline of the stressed mice. The article says only that lack of maternal nurturing leads to changes in gene expression in the brain of pups that can persist to adulthood. Perhaps if these changes in gene expression lead the stressed female pups to exhibit lower levels of maternal care to their own offspring, these changes could be transgenerationally inherited without transmission through any genetic means (including changes to DNA methylation or histone modification in gametes).

Here's the relevant section from the article:
The most comprehensive study to date of variations in parental investment and epigenetic inheritance in mammals is that of the maternally transmitted responses to stress in rats. In rat pups, maternal nurturing (licking and grooming) during the first week of life is associated with long-term programming of individual differences in stress responsiveness, emotionality, cognitive performance, and reproductive behavior (Caldji et al., 1998; Francis, Diorio, Liu, & Meaney, 1999; Liu et al., 1997; Myers, Brunelli, Shair, Squire, & Hofer, 1989; Stern, 1997). In adulthood, the offspring of mothers that exhibit increased levels of pup licking and grooming over the first week of life show increased expression of the glucocorticoid receptor in the hippocampus (a brain structure associated with stress responsivity as well as learning and memory) and a lower hormonal response to stress compared with adult animals reared by low licking and grooming mothers (Francis et al., 1999; Liu et al., 1997). Moreover, rat pups that received low levels of maternal licking and grooming during the first week of life showed decreased histone acetylation and increased DNA methylation of a neuron-specific promoter of the glucocorticoid receptor gene (Weaver et al., 2004). The expression of this gene is then reduced, the number of glucocorticoid receptors in the brain is decreased, and the animals show a higher hormonal response to stress throughout their life.
Perhaps the confusion here is coming from the various competing definitions people use for the term epigenetic. Some use the term epigenetic to describe phenotypic changes that can be inherited in the absence of genetic changes (e.g. if lack of maternal nurturing leads to changes in the brains of pups that cause the pups to exhibit less maternal nurturing later in life). Others use the term epigenetic to describe modifications to DNA and histones that help to regulate gene expression. Often, conflating these two definitions leads to confusion (see this thread from more discussion).
 
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