
Epigenetics: The Evolution Revolution - techrede
http://www.nybooks.com/articles/2018/06/07/epigenetics-the-evolution-revolution/
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daemonk
There should be a better distinction made between EPIgenetics and epiGENETICS.
The former is more about regulatory mechanisms (methylation, histone
modifications, polycomb-like mechanisms, etc) on top of our DNA. The latter is
more about non-DNA inheritance of information across generation, which is not
completely clear yet.

I think people tend to conflate these two ideas.

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asdff
I think most people don't even know that much, this isn't something that is
deeply covered in most intro to bio courses in college; you have to learn a
bit about how DNA is packaged and transcribed which you'd get in upper
division courses. At least in the field, there is no confusion. Non-DNA
inheritance is inheritance of these epigenetic regulatory states in which
you've described, but the term used specifically for this is transgenerational
inheritance.

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mannykannot
"It is as though nature employs epigenesis to make long-lasting adjustments to
an individual’s genetic program to suit his or her personal circumstances,
much as in Lamarck’s notion of 'striving for perfection.'"

It would be something of a category error to see a rehabilitation of
Lamarckism in these discoveries. They show that our previous understanding of
information flow across generations was incomplete, but it does not challenge
the understanding that evolution occurs through variation and selection.

One fundamental problem for Lamarckism is 'how does the body know what is good
for it?' Lamarck used as an example the idea that blacksmiths' sons had
stronger arms on account of their fathers' work (I do not know whether he
considered their daughters...) Putting aside the question of whether that is
actually true, suppose that blacksmiths were also prone to musculoskeletal
occupational injury. How is the body to 'know' that the stronger arms are
desirable but the injury is not, especially if the former is promoted by the
micro-injury of constant hammering?

The rest of the article contains within itself a long list of deleterious
consequences of epigenetic inheritance. While the epigenetic mechanisms
probably constrain (or perhaps expand the possibilities for) variation, it
does not present a fundamental challenge to Darwinian evolution.

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mxwsn
The impact of epigenetics can be powerful.

A neat example is sex, one of the most obvious and striking axes of biological
variation. Unlike humans where the presence or absence of an entire chromosome
(X or Y) determines sex, there are turtles and reptiles that determine their
sex based on ambient temperature alone.

The logical consequence is that a pair of female and male turtle twins can
share exactly the same genome yet be different sexes — their sex is determined
solely by how their genome is read (epigenetics).

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azeotropic
Epigenetics is not "how the genome is read" \-- you're describing the normal
action of transcription factors.

Epigenetics is heritable information that is not encoded in DNA base sequence.
Common mechanisms include DNA methylation patterns, histone binding patterns,
and histone modifications, all of which can be stably inherited from one cell
division to the next, but not necessarily transgenerationally, from parent to
offspring, through the germ line.

You are also confused about turtle sex determination. The master regulator of
sex determination (which must respond directly to temperature) is unknown. The
epigenetic regulator KDM6B is required to mediate the temperature signal for
male development, but there is no evidence that it is the master regulator.
Maybe you read a press release instead of the actual paper in Science.

Environmental sex determination is not that unusual, and need not depend on
epigenetics or even transcription factors.

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mxwsn
"Epigenetics is heritable information that is not encoded in DNA base
sequence." I agree with this. Combined with the observation that temperature-
dependent sex determination occurs within a specific window of time, after
which sex cannot be changed for the remainder of the organism's lifetime, I
believe it follows logically that somatic cells (certainly those within the
sexual organs) must be receiving heritable information not encoded in DNA base
sequence from their adult stem cells. Thus environmental sex determination
must occur through epigenetics as you have defined.

To the best of my knowledge, DNA methylation patterns, histone binding
patterns, and histone modifications all have causal biological impacts solely
by their causal influence on "how the genome is read". Epigenetics _is_ "how
the genome is read", as well as more beyond that. But how the genome is read
is substantial portion of epigenetics and, for better or worse, the aspect of
epigenetics that receives the most attention when discussed with general
audiences. I think it's inaccurate to deny the role of "various readings" of
the genome in a definition of epigenetics.

I'm unsure how your citing of KDM6B is related to or addresses any confusion
in my statement on temperature-dependent sex determination. From what I can
understand, you point out that KDM6B histone demethylase acts epigenetically
and that it regulates temperature-dependent sex-determination, both of which
are consistent with what I said earlier...

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toasterlovin
> Epigenetics is "how the genome is read"

I'm not a molecular biologist, so take this all with a grain of salt. There
are two things which get confused when discussing epigenetics. First, you have
gene expression which is mediated by the environment. That is what you are
talking about with your turtle example. This is pretty common. After all,
being able to respond to environmental stimuli is useful.

But there is another phenomena that gets labelled as epigenetics: stuff in the
environment which modifies the DNA of the germ line cells (eggs and sperm) of
an organism. The part about it being germ line cells is important, because
that means that the changes to DNA will be passed on to the offspring, whereas
epigenetic changes in any of the other cells of the body will not. People are
in love with this aspect of epigenetics because, frankly, there's a certain
type of person who is enamored with the idea that this might "disprove"
Darwinian evolution (OMG Lamarck was right!).

It's extremely frustrating because this second phenomena is, as far as we
know, extremely uncommon. I mean, it almost has to be. Large organisms are
like a house of cards; if you make too many changes, everything comes crashing
down. So, if there were epigenetic changes to germ line DNA happening all the
time, there would be unfeasible levels of mutation happening from one
generation to the next. But the fact that it is extremely uncommon does not
stop people from hearing about how this second meaning of epigenetics is a
weird end-run around Darwinian evolution, then hearing about how common the
first meaning of epigenetics is, and coming to the conclusion that Darwinian
evolution is invalid.

Incidentally, these two meanings are the root cause of you and the person who
responded to you misunderstanding each other.

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ancorevard
Looks like the theory of evolution needs modifications due to epigenetics.

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teilo
Not sure why this is being downvoted, but it's definitely the case that as we
learn more about epigenetics, we will need to modify our understanding of
evolution substantially, particularly the relationship between epigenetic
expression and mutation, in which the latter can "lock in" the changes from
the former and lead to more rapid speciation. Exciting stuff.

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asdff
I think the existing understanding of evolution is still fine. Darwin wrote,

1.More individuals are produced each generation that can survive.

2\. Phenotypic variation exists among individuals and the variation is
heritable.

3\. Those individuals with heritable traits better suited to the environment
will survive.

4\. When reproductive isolation occurs new species will form.

When Darwin proposed this, he didn't have any idea of molecular genetics, let
alone epigenetics. Mendel too wrote about alleles but he didn't know about
base pairs of DNA. Evolution really only concerns phenotypic variation, not
the underlying basis for it, so it doesn't matter if the variation is due to a
genetic or epigenetic change.

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dandare
In this article there is annoyingly little information about actually
permanently passing epigenetic changes to offspring. If that indeed doesn't
happen then epigenetics has little to add to evolution.

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Nomentatus
"What findings have made it possible?"

Recent evidence is cited, but it's interesting to note that evidence of
epigenetic effects (that were ignored as known anomalies) is ancient (of
course the mechanism wasn't known.) Such as, the Hinny.

"Horses and donkeys are both equids, but their evolution diverged millions of
years ago. Still, they are closely enough related that they can interbreed.
But the hybrids they produce look different from each other depending on
whether the mother is a horse or a donkey. If she is a horse, her baby is a
mule and has very long ears. If she is a donkey, her baby is a hinny. Hinnies
are rare, but they are generally smaller than mules, with shorter ears.

People have known for thousands of years that horse—donkey hybrids differ
depending on which species is the mother and which the father. The process
thought to be responsible for these differences—genomic imprinting—has been
known for only a few decades. Genomic imprinting is an epigenetic mechanism,
one of the forms of biological inheritance that operate outside the
traditional Mendelian mode. Imprinting is a particularly useful model for
investigating epigenetic gene regulation and is a major source of epigenetic
regulation in the brain.

With genomic imprinting, DNA methylation silences some genes or gene
clusters—in egg, sperm, or zygote—depending on which parent they came from.
For an imprinted gene, the allele from one parent or the other is shut down
and makes no product. The other allele is expressed and produces
characteristic outcomes in the offspring. Thus, mom's and dad's chromosomes
are not functionally the same.

Imprinting is required for normal development, although if the functioning
imprinted gene is defective, as sometimes happens, the outcome can also be
fatal, or at least debilitating. Some 30 serious disorders are attributed to
disrupted imprinting. Some are rare, but more common afflictions, such as
cancers and autism, have also been linked to genomic imprinting."

[https://www.academic.oup.com/bioscience/article/61/8/588/336...](https://www.academic.oup.com/bioscience/article/61/8/588/336969)

Had we cared to investigate this sort of anomaly more closely, I can't help
but think that we would have discovered epigenetics decades earlier. I well
remember when any such discussion was entirely inadmissable amongst
biologists, and proof of one's idiocy if you raised the idea of the genetic
mechanism allowing any moderation of DNA as a result of environment or
experience (a possibility I did in fact raise in a letter to Jacques Monod in
the seventies - only silence came back, such craziness was not worthy of a
response.)

There's an interesting list of early experiments, some of which may actually
have been valid, but were dismissed, here:
[https://en.wikipedia.org/wiki/Lamarckism#Weismann's_experime...](https://en.wikipedia.org/wiki/Lamarckism#Weismann's_experiment)

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whataretensors
Slippery slope here. Most people don't understand or accept evolution, even
engineers. For example, anyone who accepts equitable distribution of
attributes across genetic variances(a commonly accepted social narrative).

Evolution is messy. Epigenetics makes it even messier. We have to be careful
not to conflate the value of someone by anything genetic. Especially not
epigenetics, which seems from this article to be related to childhood trauma.

I'm interested in how we can use AI to modify genetic code to improve and fix
our past epigenetic and genetic shortcomings.

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Terr_
> people don't understand or accept evolution [...] For example, anyone who
> accepts equitable distribution of attributes across genetic variances

Even if the straw-man "everybody is totally equal" can't stand up, I think
there's a good argument for:

"We have to assume everybody is equal by default,(A) because we are absolutely
too ignorant and limited to determine the long-term value or trade-offs within
a gene or gene-combination, (B) because some diversity is itself a collective
benefit to the species, and (C) because history shows most people who claimed
they had the answers were often wrong and racist."

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danieltillett
The only thing I don't like about people who deny the strong influence of
genes on the individual are they tend to shout racist at anyone trying to
study this question. This shouting has made whole areas of human research
impossible to study in practice.

Does anyone know of anyone who became a racist because they looked at the
scientific literature? My experience is people become racist for a variety of
reasons and then (occasionally) draw upon a paraody of science to try and
justify their beliefs.

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remarkEon
>This shouting has made whole areas of human research impossible to study in
practice.

Maybe here in the West, but something tells me China isn't going to get caught
up in either the ethical or political implications of such research. They'll
just do it and quickly operationalize (or weaponize) whatever they discover as
fast as possible.

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zizek23
This is just jingoistic scaremongering. These things are not done in the open.
Not just China anyone could be doing anything.

Everyone familiar with history knows the consequences of surveillance, most
people don't like surveillance but is that stopping anyone?

China is not the one bombing random countries and killing hundreds of
thousands of people and setting entire societies back decades. These are
crimes against humanity with no accountability and consequences for those
involved so where is the ethics and morality? China is not the one who used
just discovered nuclear weapons recklessly on a civilian population, not once
but twice.

Blanket statement of ethics and morality are meaningless when not consistent
with actions on the ground. They merely serve to fabricate a non existent
moral high ground whose existence requires a denial and diminishment of one
own actions while pointing fingers and demonizing others. Posturing may be fun
but ignoring the ethical deterioration in your own society has consequences.

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remarkEon
I'm amazed you think US foreign policy history is relevant here, and your
characterization of it is frankly childish, but the Chinese record on human
rights is _demonstrably_ bad. It isn't a stretch, at all, to think that the
Chinese are not going to too much care about where this research might lead.

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Nomentatus
Now that we know all this, do people (capable of having children) have a right
to smoke? Do you have a right to significantly harm the health of not just
your children, but even your great-grandchildren?

Also, cuddle your kids: [http://www.sciencealert.com/cuddling-babies-alters-
their-gen...](http://www.sciencealert.com/cuddling-babies-alters-their-
genetics-dna-for-years)

