Evolution by Epigenesis: Farewell to Darwinism, Neo and Otherwise

@memester,

#1 Darwin hasn't written a paper in quite a while. Modern evolutionary biology is NOT Darwinism.

#2 Epigenetic regulation in and of itself is a phenotype with an underlying genotype. Evolution may favor changes in epigenetics, just as it may favor long fur versus short fur.

Evolutionary changes in epigenetics are demonstrable by polymorphisms in histones, histone deacetylases, promoter sequences, etc. In other words, even epigenetics all comes out of the genome too.

1 Reply

@Aedes,

Aedes;109258 wrote:

#1 Darwin hasn't written a paper in quite a while. Modern evolutionary biology is NOT Darwinism.

irrelevant

Quote:

#2 Epigenetic regulation in and of itself is a phenotype with an underlying genotype. Evolution may favor changes in epigenetics, just as it may favor long fur versus short fur.

Evolutionary changes in epigenetics are demonstrable by polymorphisms in histones, histone deacetylases, promoter sequences, etc. In other words, even epigenetics all comes out of the genome too.

all does NOT necessarily come out of the genome. or it would all be just genes, eh ?

1 Reply

@memester,

memester;109262 wrote:

irrelevant

YOU are the one who obsesses over the term Darwinism, as if anyone finds Darwin routinely mentioned in scientific publications. You may think you're rocking our world, but the fact that evolution has moved on since the age of Darwin has been widely understood for about a century now.

memester;109262 wrote:

all does NOT necessarily come out of the genome. or it would all be just genes, eh ?

Genes are part of a physiologic system -- they are FUNCTIONAL things. And all epigenetic regulation, ultimately, DOES come out of the genome. siRNA comes out of the genome. Histones come out of the genome. Promoters are IN the genome. Nuclear hormone receptors, such as that for thyroid hormone and for glucocorticoids, are all genetically encoded. Inorganic molecules, like zinc and magnesium, which affect gene transcription and polymerase function, are regulated by transporters encoded by the genome. You can't escape from it.

3 Replies

@Aedes,

Aedes;109293 wrote:

Genes are part of a physiologic system -- they are FUNCTIONAL things. And all epigenetic regulation, ultimately, DOES come out of the genome. siRNA comes out of the genome. Histones come out of the genome. Promoters are IN the genome. Nuclear hormone receptors, such as that for thyroid hormone and for glucocorticoids, are all genetically encoded. Inorganic molecules, like zinc and magnesium, which affect gene transcription and polymerase function, are regulated by transporters encoded by the genome. You can't escape from it.

Do you think all behaviors ultimately have a genetic basis? Twins?
Do you think that behaviors and structure of some cultures and societies confer survival advantage to some versus the others?

So survival of the fittest in some instances is independent of or at least loosely linked to the underlying genetics?

i.e. factors other than pure genetics determine changes in gene frequency in populations. In fact one could dispute the "selfish gene" hypothesis. The genes sometimes are undeserving beneficiaires of higher levels of behavior and social organization?

That is unless you think all behaviors have ultimately an underlying genetic basis but that seems like a difficult hypothesis to maintain and smacks a little too much of genetic determinism.?:perplexed:

1 Reply

@Aedes,

Aedes;109293 wrote:

YOU are the one who obsesses over the term Darwinism, as if anyone finds Darwin routinely mentioned in scientific publications. You may think you're rocking our world, but the fact that evolution has moved on since the age of Darwin has been widely understood for about a century now.

In the title..Neo Darwinism...you're not paying attention.

Quote:

Genes are part of a physiologic system -- they are FUNCTIONAL things. And all epigenetic regulation, ultimately, DOES come out of the genome. siRNA comes out of the genome. Histones come out of the genome. Promoters are IN the genome. Nuclear hormone receptors, such as that for thyroid hormone and for glucocorticoids, are all genetically encoded. Inorganic molecules, like zinc and magnesium, which affect gene transcription and polymerase function, are regulated by transporters encoded by the genome. You can't escape from it.

Everything comes from the Big Bang, too. But you confuse causes, with wild abandon.

0 Replies

@Aedes,

Aedes;109293 wrote:

YOU are the one who obsesses over the term Darwinism, as if anyone finds Darwin routinely mentioned in scientific publications. You may think you're rocking our world, but the fact that evolution has moved on since the age of Darwin has been widely understood for about a century now.

Genes are part of a physiologic system -- they are FUNCTIONAL things.

The gene cannot be synonymized with its function.

0 Replies

@prothero,

prothero;109304 wrote:

Do you think all behaviors ultimately have a genetic basis? Twins?

No, but the discussion is about EVOLUTION and not BEHAVIOR.

There is a certain amount of biological determinism that comes from genetics, but a lot of our biology is acquired as well. Genetic short stature can make you short, but so can malnutrition. Genetic factors can make you demented, but so can acquired factors.

prothero;109304 wrote:

Do you think that behaviors and structure of some cultures and societies confer survival advantage to some versus the others?

So survival of the fittest in some instances is independent of or at least loosely linked to the underlying genetics?

That's well known. No argument. But again, as I'm saying for about the billionth time on this forum, natural selection is not the only mechanism behind evolution. We've known this for decades. So fine, there are social selections that can asymmetrically bias population genetics. But so does the mere fact that our populations are not infinite.

Look, even when there is strong natural selection on a single gene, do you think that our 100,000 other genes somehow stop evolving? No, they continue to evolve by different mechanisms. If they're close to the selected gene, they also become coincidentally selected (because of "linkage" -- this is a formal term). If they're distant, then founder effects, genetic drift, whatever can affect their heritability.

prothero;109304 wrote:

That is unless you think all behaviors have ultimately an underlying genetic basis but that seems like a difficult hypothesis to maintain and smacks a little too much of genetic determinism.?:perplexed:

Well, that has nothing to do with what I was talking about, though.

---------- Post added 12-08-2009 at 10:44 PM ----------

memester;109451 wrote:

The gene cannot be synonymized with its function.

Nor did I say so. In fact I said the opposite. The gene is part of a system, that includes its own regulation all the way through processing of its own gene product.

---------- Post added 12-08-2009 at 10:49 PM ----------

memester;109308 wrote:

In the title..Neo Darwinism...you're not paying attention.

I object to the label either way. It's absurd. We're talking about a natural science and not a philosophy when we discuss the genetic mechanics behind evolution. Neo-Darwinism, whatever that is in your mind, is not what I'm reading about when I read an article in PLoS Genetics or in Nature.

memester;109308 wrote:

Everything comes from the Big Bang, too. But you confuse causes, with wild abandon.

There's a point at which the "cause" becomes so removed from the topic that we can take it for granted. Whatever forces in the universe potentiated the existence of genes, it really doesn't matter for this conversation.

But what I do know is that if I take a human zygote's nucleus and stick it into a chimp ova, then put that into a female chimp, the embryo (and perhaps baby) will be human and not chimp. So genetics at a very fundamental level define an organism. Genetics are not simply the sequence, but also a function, including epigenetics. But so what?

1 Reply

@Aedes,

Aedes;109454 wrote:

No, but the discussion is about EVOLUTION and not BEHAVIOR.

Untrue. That's like claiming that the discussion is about Evolution, not SELECTION. :sarcastic:

Quote:

Look, even when there is strong natural selection on a single gene, do you think that our 100,000 other genes somehow stop evolving? No, they continue to evolve by different mechanisms. If they're close to the selected gene, they also become coincidentally selected (because of "linkage" -- this is a formal term). If they're distant, then founder effects, genetic drift, whatever can affect their heritability.

what has this to do with the price of tea in China ?

Quote:

Nor did I say so. In fact I said the opposite. The gene is part of a system, that includes its own regulation all the way through processing of its own gene product

call it system "X". Then we have the statement:
"The gene is part of system "X", that includes it's own regulation all the way through to it's own gene product."

It's incoherent.

Quote:

I object to the label either way. It's absurd. We're talking about a natural science and not a philosophy when we discuss the genetic mechanics behind evolution. Neo-Darwinism, whatever that is in your mind, is not what I'm reading about when I read an article in PLoS Genetics or in Nature.

And your mind is the entirety of investigation on this topic for the entire world ?
I'm quite sure that others accept that term.

Quote:

There's a point at which the "cause" becomes so removed from the topic that we can take it for granted. Whatever forces in the universe potentiated the existence of genes, it really doesn't matter for this conversation.

What does matter is that you are sucessfully contradicted when you attempt to assert a cause improperly.

e.g. Medically, the cause of my itchy butt is pinworm, not the big bang, not genetics, not neurons. :perplexed:

1 Reply

@memester,

What with all these evolution threads?

also, lol at the term "Darwinism"...

3 Replies

@Kielicious,

Well, what can you say. It's apparent that it's Darwinism or Neo Darwinism to many
Dawkins

Quote:

WIKI Neo-Darwinism - Wikipedia, the free encyclopedia

[quote]Neo-Darwinism is a term used today to describe the modern evolutionary synthesis of Darwinian evolution by natural selection with Mendelian genetics, the latter of which Darwin himself had been unaware, but which entails that the mechanism of inheritance in evolution involves the digital, particulate entities known as genes, rather than the 'blending process' of pre-Mendelian evolutionary science.[/quote]

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@memester,

I am not quite sure what the dispute between the two of you is. I just got curious about the relationship between behavior, genetics and evolution when reading the posts.

[QUOTE=Aedes;109454] No, but the discussion is about EVOLUTION and not BEHAVIOR. [/QUOTE] But isn't part of the dispute the role of behavior in evolution? Can you just exclude behavior like that? Behavior at least on the human level is not so clearly reflected at the genetic level.

[QUOTE=Aedes;109454] That's well known. No argument. But again, as I'm saying for about the billionth time on this forum, natural selection is not the only mechanism behind evolution. [/QUOTE] No but it is one of the mechanisms. Perhaps not the most important one but the one that was first suggested and which is best known?

[QUOTE=Aedes;109454] Look, even when there is strong natural selection on a single gene, do you think that our 100,000 other genes somehow stop evolving? ? [/QUOTE] My understanding is there is a lot of conservation of genes. That corn and humans share a lot of genes. In fact genetic conservation and cross gene similarities are one of the powerful pieces of evidence for evolution. The few % gene differences between humans and apes are hard pressed to explain the differences in behavior.

What are you trying to say versus what he is trying to say?
How does this relate to Dawkin's concept of memes if at all?

2 Replies

@prothero,

Quote:

Look, even when there is strong natural selection on a single gene, do you think that our 100,000 other genes somehow stop evolving?

Noted that there are some differences of opinion

Human Genome Project Science

Quote:

Each chromosome contains many genes, the basic physical and functional units of heredity. Genes are specific sequences of bases that encode instructions on how to make proteins. Genes comprise only about 2% of the human genome; the remainder consists of noncoding regions, whose functions may include providing chromosomal structural integrity and regulating where, when, and in what quantity proteins are made. The human genome is estimated to contain 20,000-25,000 genes.

Wiki

Quote:

The haploid human genome contains ca. 23,000 protein-coding genes, far fewer than had been expected before its sequencing.

Science Daily

Quote:

ScienceDaily (Jan. 15, 2008) - Estimates of the number of genes in the human genome have ranged wildly over the past two decades, from 20,000 all the way up to 150,000. By the time the working draft of the human genome was published in 2001, the best approximation stood at 35,000, yet even that number has fallen. A new analysis, one that harnesses the power of comparing genome sequences of various organisms, now reveals that the true number of human genes is about 20,500, thousands fewer than what is currently listed in human gene catalogs.

Was it the last century that I heard maybe 100,000..or this century ?

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@Kielicious,

Kielicious;109482 wrote:

What with all these evolution threads?

also, lol at the term "Darwinism"...

Interesting isn't it! From a Cultural Studies viewpoint (as distinct from one or another side of the debate) it has to do with the idea of the narrative into which we fit - our 'creation story'. The Biblical narrative, like it or not, believe it or not, was at least 'a narrative'. I think society is taking poorly to the attempt by persons in white coats to dismantle it and replace it with a statistical theory. Even if it is true, it doesn't resonate, and I think this is one reason why the issue will continue to boil.

Humans are meaning-seeking-beings. They need a story to relate to. 20th Century science, rightly or wrongly, settled on a worldview in which there is no meta-story or narrative in any meaningful sense (or maybe the story is, there is no story). What you have is the interaction of selfish genes through statistical change processes (etc). The nature-is-blind-we-are-creatures-of-accident view.

Leaving aside whether the scientific account is true, my feeling is that the majority of ordinary people (as distinct from the educated intelligentsia) will continue to reject this understanding of life. And this is actually happening. The Muslim world at large is experiencing an upsurge of creationism. It is already the case that the majority of US citizens also reject the scientific account of human origins. Meanwhile, much to theconsternation of the Chinese government, Chinese Christians now outnumber members of the Chinese Communist party. You would have thought that after half a century of determined Communist propoganda and suppression, the Christian meme would be extinguished in China once for all. In fact it appears to be growing more vigorously than ever.

The way the debate has unfolded, many in the scientific camp insist, with passionate intensity, that the universe must be meaningless. To think otherwise is seen to be giving ground to the hated 'creationists'. Or so it seems. But human beings need to feel they are part of a meaningful universe. It is just a basic fact of existence.

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@prothero,

prothero;109539 wrote:

isn't part of the dispute the role of behavior in evolution? Can you just exclude behavior like that? Behavior at least on the human level is not so clearly reflected at the genetic level.

No argument here. Again, (and again and again), a simple relationship between phenotypic fitness and an advantageous genotype is not all there is to evolution. Yes, behavior asymmetrically affects inheritance, and therefore population genetics. I'll say it again: behavior asymmetrically affects inheritance, and therefore population genetics.[/COLOR]

[QUOTE=prothero;109539]isn't My understanding is there is a lot of conservation of genes. That corn and humans share a lot of genes. In fact genetic conservation and cross gene similarities are one of the powerful pieces of evidence for evolution. The few % gene differences between humans and apes are hard pressed to explain the differences in behavior.[/quote]Even the most conserved genes have some intrinsic sequence differences between otherwise highly divergent organisms. But gene regulation (including the AMOUNT of expression of gene X, the interaction of gene X's product with other things, the timing of gene X expression, and the cells in which it's expressed) are markedly different, so even if the sequence is similar the gene's actual expression may differ.

Please refer to the two papers I linked in the Darwin thread about the genetic analysis of domestic dogs. All of the enormous morphological differences among different dog breeds are directly tied to repeat sequences in just a few genes.

[QUOTE=prothero;109539]isn't What are you trying to say versus what he is trying to say?[/quote]He's saying anything at all -- I'm just calling him out on it.

prothero;109539 wrote:

How does this relate to Dawkin's concept of memes if at all?

I've never read Dawkins. He annoys me.

---------- Post added 12-09-2009 at 08:41 AM ----------

memester;109551 wrote:

Noted that there are some differences of opinion

Was it the last century that I heard maybe 100,000..or this century ?

It doesn't matter, that wasn't my point -- but thanks for the trivia.

1 Reply

@Aedes,

Aedes;109581 wrote:

It doesn't matter, that wasn't my point -- but thanks for the trivia.

I just happen to notice falseness. You are welcome. There's lots more of that in your posts, perhaps not so obviously wrong . You might re-read some of what you've written ( particularly some of what you claim some level of expertise in ) . I mean, the Monarch thing, the parasite thing..this, the rest....indicates that some of the information is decades old and much of it wrong to start with, or based on a less than optimal understanding of the Science involved . this is a constructive criticism. You can see that I mention, correct, and offer support on the things which are in question.

I'd be happy to try my best to answer any questions you might have, on some areas where, or if, I could help.

Quote:

He's saying anything at all -- I'm just calling him out on it.

It's something, that 20 is stated as 100. It can make a big difference to the outlook on the nature of what is going on with genes and other influences. I bet that you'd have a different outlook than "trivial" if someone gave you change for $20 when you handed them $100.

Heck, if it were accepted the other way round, one could retire on that income alone; Making Change for a $20 instead of $100.

this is more serious error, as it has deeper implications than the difference of $80 does.

You would feel how important it was, when the store also started TAKING back some of that "already-not-enough" change.

what I am saying, is that approach to questions is CHANGED upon receipt of the information on whacking big overestimation on number of genes, and ongoing lowering of that number.

People have realized that they had to adjust their thinking when they learned this.

---------- Post added 12-09-2009 at 10:00 AM ----------

http://old.dnalc.org/bioinformatics/Resources/count_human_genes_4.pdf

interesting reading

Quote:

Yes, behavior asymmetrically affects inheritance, and therefore population genetics. I'll say it again: behavior asymmetrically affects inheritance, and therefore population genetics.

and what is the relationship between behaviour and gene, and the relationship between behaviour and Evolution ?

Is all behaviour to be said to be caused by gene ?

Example for one aspect of this:
The ability to sing - or better said - to vocalize, is a genetic trait for humans. That means it's something every normal human has, to some degree, apparently without specifically learning to vocalize.

but the lyrics sung...is gene THE cause for those words ? the melody...caused by gene ?

1 Reply

@memester,

memester;109588 wrote:

I just happen to notice falseness. You are welcome. There's lots more of that in your posts, perhaps not so obviously wrong . You might re-read some of what you've written ( particularly some of what you claim some level of expertise in ) . I mean, the Monarch thing, the parasite thing..

I'm a published researcher on the "parasite thing" -- the two organisms I've studied and published on are Plasmodium falciparum and Babesia microti, which are very close relatives of Toxoplasma gondii (and Toxo is used as a model organism for studying Plasmodium and Babesia, and I have an entire drawer of Toxo papers in my office). The monarch thing and the gene number thing I've pulled from recollection rather than expertise, and I'm fine with standing corrected about that. The monarch thing I was completely wrong about; the gene number I was wrong as well but the point I was making is true irrespective of our gene number. I stand by everything I said about neurocysticercosis and toxoplasmosis. I've not been a close student of the human genome project; my major exposure to evolutionary biology research has been in my two years in a lab that was doing global haplotype mapping of parasites.

At any rate, it would be nice to cool this off because we're clearly both interested in this topic and it's getting unnecessarily snarky on both of our parts -- I apologize from my end.

The debate at hand here is about two things: 1) the biology of evolution, and 2) the conflation of biology with a philosophical viewpoint.

The first point is very complicated, but it's easy to debate because it's easily referenced. The second point is I believe a matter of bias that comes from different kinds of interfaces with evolutionary biology.

1 Reply

@Aedes,

Hi Paul.
Thanks, and I apologize .
As to our subject, to me both 1 and 2 revolve endlessly about causes and identifying cause properly.

What I mean, is that in any field, we have parameters constraining what our questions are to be, and so also how the answers will be.

If we are talking about Medicine, Law, and many parts of Biology, then we are pretty well using a model of Deterministic nature with cheating allowed; there IS cause/effect, and yet there IS Will.

e.g. A coroner examining in a case of suspicious death, which let's say was a murder.

He is asked to name cause of death and time of death, that kind of thing.

He cannot name guilty party, and he cannot name the Big Bang as cause.

Big Bang or intitial event may be ultimate cause of every event since then, but it's not pertinent to this enquiry of how the person came to be dead.

So it is with allowing the gene to be named as cause of everything observed in biology. We might as well say being born was cause of my eating breakfast.
It answers nothing as to our question of what causes me to need nutrition, or what causes me to eat. Mor directly, the question could be "What causes THE CHANGE from 'not hungry' to 'hungry' ?" that elimates the possibility of naming "cause of eating", as hand, mouth, fork, plate, oven, mom, gene or God.

Some Evolution fans will cite the gene every time, and some Determinists will cite Initial Event every time, and that is 2) the philosophical problem involved, which I do not think of as a conflation.

It's a real problem in itself; limiting the choices to the pertinent.

1 Reply

@memester,

memester;109794 wrote:

If we are talking about Medicine, Law, and many parts of Biology, then we are pretty well using a model of Deterministic nature with cheating allowed; there IS cause/effect, and yet there IS Will.

I suppose I agree with this -- I certainly agree with the analogy. I won't take it as far as there being "will" other than the individual wills of sentient organisms playing a role in their survival and reproduction.

Evolution at its most pared down, simplest definition, is about allele frequencies in a population and how they change over time.

But how you get there is a different matter. This involves evolution from just mere statistics and probability (finite populations, founders effects, and drift), evolution from natural selection, evolution from self-aware human behaviors, and probably many other things.

memester;109794 wrote:

Some Evolution fans will cite the gene every time, and some Determinists will cite Initial Event every time, and that is 2) the philosophical problem involved, which I do not think of as a conflation.

It's a real problem in itself; limiting the choices to the pertinent.

I think that when there are impasses in conversations here, at least among reasonable people, it often comes down to getting terms straight with one another and making sure we're talking about the same thing. One CAN have a discussion that's only about molecular biology. One CAN have a discussion on the philosophical ramifications. But we need to make sure it's clear which conversation we're having.

1 Reply

@Aedes,

How much did Darwin know about genetics?

When I saw Jurassic Park, I thought about the project where scientists tried to make a sustainable biosphere in a sealed-off building. It failed because of the lack of some organism nobody expected was so essential.

I'm wondering if an attempt to recreate a dinosaur would fail for the same reason.

1 Reply

Evolution by Epigenesis: Farewell to Darwinism, Neo and Otherwise

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