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Author Topic: How big a role does the epigenome play in evolution?  (Read 56220 times)

Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #100 on: 14/04/2010 06:28:43 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #101 on: 14/04/2010 07:18:42 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
1) Sickle cell anemia. is a genetic disease. Not beneficial
2) Bacterial resistance to antibiotics, well cant see how that is beneficial?
« Last Edit: 14/04/2010 07:33:27 by echochartruse »
 

Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #102 on: 14/04/2010 07:31:09 »
1) Sickle cell anemia.
2) Bacterial resistance to antibiotics.
1) Sickle cell anemia. is a genetic disease. Not benefitial
2) Bacterial resistance to antibiotics, well cant see how that is benefitial?
1) It's beneficial when you tend to die young from malaria and it protects against that. 
2) It sure is beneficial for the bacteria!  (Not so much for us).
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #103 on: 14/04/2010 07:46:20 »
1) It's beneficial when you tend to die young from malaria and it protects against that. 
2) It sure is beneficial for the bacteria!  (Not so much for us).
1) It's beneficial when you tend to die young from malaria and it protects against that. -One or another way its not beneficial to our servival or evolution.
2) It sure is beneficial for the bacteria!  (Not so much for us)

This makes me wonder, Could bacteria have this intelligents we are looking for?
 

Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #104 on: 14/04/2010 08:48:07 »
Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.

Bacteria developing resistance to antibiotics is entirely reactionary - there's no way it could be considered to be intelligent.

(by the way, its spelled "intelligence")
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #105 on: 14/04/2010 17:41:23 »
Thanks for the links Echo and Norcal (I hope you don't mind my abbreviations.)

I don't think there is any doubt that there are a great many factors involved in the development of living organisms. Genes provide a sort of underlying fabric, but there are many other factors at play. For example, just because my genes indicate that I am predisposed to develop a certain disease, it does to mean that I ever will develop that disease. It just means that I have a higher probability of developing that disease.

Let me take a shot at stating the question we are (perhaps) trying to answer.

"Can factors that affect my life directly alter the genes that I pass on to my progeny, or are the genes that I pass on to my progeny simply determined by the genes that I inherited from my parents, plus or minus some random transcription errors?"

That's probably a bit of an oversimplification of course, because I know that I really could mess up the genes that I pass on if I was exposed to a lot of radiation for example, but the effect would still be random rather than directed.

Anyway, is that an approximation for the question?

Yes, that is an approximation for the question.

Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

Sorry, but you cannot simply state that.  Nobody knows more than a fraction of what there is to know about epigenetics, so we are very far from being able to say for sure what it can or cannot do.  You are free to not believe it is capable of it, but a flat statement that it cannot is not possible at this point in time.

Check out this article from Time magazine: http://www.time.com/time/health/article/0,8599,1951968-2,00.html

As they state, many scientists are taking a new look at Lamarckian evolution.  It's not like what we are talking about here has no credibility among legitimate scientists, this actually is a boon for the evolution argument against creationism.  All the examples that creationists try to twist, and popular evolution theory can't quite answer, are answered by this... all without "god".

I'm not sure how you can still assert that there is absolutely no evidence of epigenetically driven genetic mutation, I could understand if you had simply said that you don't feel there is enough evidence(although I disagree obviously), but to simply say there is no evidence at all?

If you are merely stating that it hasn't been proven yet, then I would have to ask how you feel about the standard model of physics?  It hasn't been proven, it has made predictions which have occurred and therefore has gained merit, but it still isn't proven.

Evolution driven by epigenomic markers certainly hasn't been proven, nor does it have as many years or predictions as the standard model has behind its belt; but it does make predictions, and those predictions have been proven.

There are other mechanisms for quick change.  There is also reason enough for me to think (based on my understanding of the subject) that epigenetic induced genetic mutation should occur faster than the observed rates, even when mutation appears to occur faster than expected.  There are proposed non-epigenetic models that do fit this date.  There is also no evidence, based on the way epigenetics works, that it can induce genetic mutations. 

The comparison to the standard model is also flawed.  The standard model predicts the probabilities of seeing certain things when you do certain experiments.  This has been very successfully tested.  As far as I know, and in your arguments here, the prediction made by epigenetics is simply "faster mutations," although it's also missing the step of how it causes those mutations.  There are other explanations for faster mutations that do include that step, so why favor epigenetics?  Have there been any simulations comparing epigenetic mutation to these other explanations that come out favoring epigenetics?

I'm really not sure why you still think there is no evidence based on the way epigenetics works that it could induce genetic mutations.  From one of the links I posted:

Quote
The movement of insertion elements can be responsive to environmental conditions. Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements. Some conjugative plasmids can recombine with their host's chromosome, and may acquire chromosomal genes that could then spread through the population and even to other species.


From the description of "insertion elements" we know they are talking about epigenomes.  Right here it says the "how" of at least one way of "inducing" mutation.

When you say you think it should be even faster than the evidence shows, it seems to me you are ignoring the big picture.  If large mutations were "allowed" to happen any faster than they do, a species would be in great danger of severely limiting the breeding population.  If too many new species emerged too quickly, they would not have a great enough population for reproduction.  Even still, with the evolution of plasmids capable of "spreading" a beneficial mutation throughout a local population allows for relatively quick evolution.

In order to "see" the difference in rates of evolution with or without epigenomes we have to look at the fossil record.  Presumably, the farther back we go in the record, the simpler life should be.  If we go back far enough, we should be able to see life which did not have epigenomes to help them.  This is why I keep raising the point about the absolutely massive increase in evolution we can see in the fossil record.  It is pretty obvious that something changed about 750 million years ago, and the discovery of epigenetics seems to me to be by far the best answer. 

Can you think of a different/better reason for such discordant rates of evolution in the fossil record?
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #106 on: 14/04/2010 23:18:42 »
Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.
What are these conditions please?
 

Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #107 on: 15/04/2010 02:12:41 »
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

Sorry, but you cannot simply state that.  Nobody knows more than a fraction of what there is to know about epigenetics, so we are very far from being able to say for sure what it can or cannot do.  You are free to not believe it is capable of it, but a flat statement that it cannot is not possible at this point in time.

This has basically come down to an argument rather than a debate on the science.  I say there isn't direct evidence to support your position.  You say there is enough indirect evidence to support it and not evidence against it.  Neither of us are experts in the field, nor are we likely to change our opinions, so until an expert stops by to offer an opinion, I don't think this is worth arguing further.  We're just arguing ourselves in circles here.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #108 on: 15/04/2010 02:43:21 »
... so until an expert stops by to offer an opinion, I don't think this is worth arguing further.  We're just arguing ourselves in circles here.

Quote from:  http://www.docstoc.com/docs/22610547/differential-gene-expression/
Differentiation results from different gene expression.
All cells from the same organism have the same DNA but not all genes are expressed (turned on or off)
Differential gene expression is not a result of differential loss of genetic material.
A single cell has half the genome from each parent............This is demonstrated by the fact that fully differentiated cell types are still capable, with the right environment of giving rise to an entire new animal.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #109 on: 15/04/2010 02:51:01 »
I have not had any evidence here that mutating genes is of any advantage to evolution
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #110 on: 15/04/2010 03:16:50 »

Example of epigenetic (which regulates gene expression) making permenet changes

Quote from: http://www.highlighthealth.com/research/irreversible-gene-expression-changes-from-smoking/
Recent research published in the online open journal BMC Genomics shows that smoking leads to changes in gene expression, some of which are reversible and some of which are permanent.

mutation may not be required?
« Last Edit: 15/04/2010 03:18:39 by echochartruse »
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #111 on: 15/04/2010 04:25:37 »

Example of epigenetic (which regulates gene expression) making permenet changes

Quote from: http://www.highlighthealth.com/research/irreversible-gene-expression-changes-from-smoking/
Recent research published in the online open journal BMC Genomics shows that smoking leads to changes in gene expression, some of which are reversible and some of which are permanent.

mutation may not be required?

Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.

We all have genes. I don't think I can alter mine. Can you explain how you can alter yours?
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #112 on: 15/04/2010 04:42:06 »

Example of epigenetic (which regulates gene expression) making permanent changes

Quote from: http://www.highlighthealth.com/research/irreversible-gene-expression-changes-from-smoking/
Recent research published in the online open journal BMC Genomics shows that smoking leads to changes in gene expression, some of which are reversible and some of which are permanent.

mutation may not be required?

Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.

We all have genes. I don't think I can alter mine. Can you explain how you can alter yours?
DNA changes little over all species.
The proof is that mutation is not necessary for permanent gene expression.
'smoking leads to changes in gene expression, some of which are reversible and some of which are permanent. '
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #113 on: 15/04/2010 04:54:37 »
Smoking, drinking, poor nutrition all lead to permanent altered gene expression in fetus which can last their life time and inherited by their off spring and theirs, throughout many generations.
Possibly if this gene expression lasts for multiple generations, the gene may never be used for multiple generations, heh and if you don't use it you lose it, right!
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #114 on: 15/04/2010 06:04:53 »
heh and if you don't use it you lose it, right!

No, I think that is entirely wrong.

If you can explain how you are able to alter your genes I might change my opinion. How do you do that?
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #115 on: 15/04/2010 06:22:13 »
They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily
« Last Edit: 15/04/2010 06:39:57 by echochartruse »
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #116 on: 15/04/2010 06:25:27 »

   Is Biological Evolution An Obsolete Technology - you may need to genetically engineer your genes. Is this our future?
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #117 on: 15/04/2010 07:07:31 »
They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily

That is also incorrect. We have not altered our genetic profile. Our height is simply a function of external factors. Nutrition is dominant.

Do you have anything new to add?
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #118 on: 15/04/2010 07:12:54 »
Quote from:  http://www.tutorvista.com/topic/gene-chromosome-mutation
Mutation
Mutation is defined as a chemical change in the DNA structure of a gene. A difference of a single base in the DNA molecule or a single error in the reading of the code can cause a change in the amino acid sequence which leads to mutation. The chemical substances that i..

Chemical change to genes can be done by genetic engineering, gene therapy or by epigenetics to name a few.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #119 on: 15/04/2010 07:24:16 »
Quote from: http://www.cancer.gov/dictionary/?CdrID=561400

 genetic profile (jeh-NEH-tik PROH-file)

     Information about specific genes, including variations and gene expression, in an individual or in a certain type of tissue. A genetic profile may be used to help diagnose a disease or learn how the disease may progress or respond to treatment with drugs or radiation.


Epigentics alters/regulates/controls gene expression by adding and subtracting methyl tags.
 

Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #120 on: 15/04/2010 07:28:33 »
............We have not altered our genetic profile. .............

http://www.medicinenet.com/script/main/art.asp?articlekey=90341
change your lifestyle - change your genetic profile.


 

Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #121 on: 15/04/2010 11:37:01 »
We have two simultaneous conversations going on here.  Norcalclimber is making some very good points about the young science of epigenetics, asking if there is any evidence that epigenetic factors can cause heritable changes in DNA.

Echochartruse - you are confusing the issue somewhat, and posting lots of replies in sequence makes it very difficult to respond.  I'll try to get through some of your points, though they may not be in sequence:

Sickle cell anaemia certainly is beneficial to survival, but only in certain conditions.
What are these conditions please?

High prevalence of malaria.  Those with sickle cell anaemia are less likely to die of malaria, and therefore more likely to survive to breeding age, therefore more likely to pass on the sickle cell genes.

Quote from:  http://www.tutorvista.com/topic/gene-chromosome-mutation
Mutation
Mutation is defined as a chemical change in the DNA structure of a gene. A difference of a single base in the DNA molecule or a single error in the reading of the code can cause a change in the amino acid sequence which leads to mutation. The chemical substances that i..

Chemical change to genes can be done by genetic engineering, gene therapy or by epigenetics to name a few.

Well, genetic engineering yes, (but not in a living organism); gene therapy no (it's about inserting extra genes so that cells make the gene products, which may fill a gap that the organism isn't filling); epigenetics - we don't know yet - largely it affects gene expression, rather than changes to genes.

............We have not altered our genetic profile. .............

http://www.medicinenet.com/script/main/art.asp?articlekey=90341
change your lifestyle - change your genetic profile.

A quote from your link:

"You can't get different genes, but how you act can change how your genes act, report Dean Ornish, MD, and colleagues at the University of California, San Francisco (UCSF)."

Changes in gene expression are not changes in DNA.  It's DNA that passes information to the next generation.  Changes in DNA are therefore essential for evolution.  Can epigenetic factors lead to heritable genetic changes?  We don't know yet, it's an interesting area of study.

They say we have evolved being much taller than ancient generations but our genes have not altered.

Why do you insist that genes need to alter/mutate before we evolve?

We can change our genetic profile quickly and easily

We say genes must have been altered for evolution because DNA is the heritable biochemical.  If every individual has identical genes, there will be no evolutionary change.

We can't change our "genetic profile" quickly and easily.  Some things cause DNA damage, but this is localised and often leads to cell death or cancers.  Children of smokers don't inherit lung cancer.


I have not had any evidence here that mutating genes is of any advantage to evolution
Well, in that case, I don't think you understand evolution.  Mutant versions of genes are the raw material for natural selection to work on.


Smoking, drinking, poor nutrition all lead to permanent altered gene expression in fetus which can last their life time and inherited by their off spring and theirs, throughout many generations.
Possibly if this gene expression lasts for multiple generations, the gene may never be used for multiple generations, heh and if you don't use it you lose it, right!
If you mean smoking, drinking etc while pregnant, then yes, this can have an impact on the foetus - but not a heritable one.  I think you've got the wrong end of the stick about genetics.


Right, here's a very stripped down explanation:

DNA contains your genes.  This is the thing that is passed down to the next generation.

DNA is transcribed by various methods into RNA/proteins...

These RNA molecules or proteins can tell the transcription factors to start/stop transcribing.

Therefore, things can change how many times a gene is transcribed, (gene expression) without altering the DNA.

So changes in gene expression are NOT changes in genes, or changes in DNA, and are therefore very unlikely to be heritable.


Sorry for the massive post...
 

Offline PhysBang

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Re: How big a role does the epigenome play in evolution?
« Reply #122 on: 15/04/2010 15:56:50 »
Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.
 

Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #123 on: 15/04/2010 17:54:10 »
Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.

Yes. I would agree with that. Many things influence evolution so I'm sure gene expression plays an important part.

The real question, I think, is whether or not a biological entity can direct particular changes in its own genes and pass that change on to its progeny.
 

Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #124 on: 15/04/2010 18:01:20 »
Gene expression is about how genes may, or may not, affect the development of a biological entity. In other words, an entity may interpret its genes in many ways based on external factors (like smoking for example).

That does not mean that the entity has altered its genes in any way.
But over time, selection can work on a population to prefer those organisms that are undergoing a specific epigenetic change. This allows for mutation and variation to go on behind that epigenetic change, so to speak. If a genetic change "freezes" that epigenetic change in place, then we can see evolution that is guided by the epigenetics, in part, not simply the specific genes.

Yes. I would agree with that. Many things influence evolution so I'm sure gene expression plays an important part.

The real question, I think, is whether or not a biological entity can direct particular changes in its own genes and pass that change on to its progeny.

What about the progeny possibly receiving the environmental information from both parents, and using that combination to possibly determine it's own changes at the initial moment of conception?  So instead of the parent "deciding" the mutation, it would be the progeny itself.
 

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Re: How big a role does the epigenome play in evolution?
« Reply #124 on: 15/04/2010 18:01:20 »

 

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