How big a role does the epigenome play in evolution?

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #50 on: 02/04/2010 06:17:29 »
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

Infectious disease has been shown to be a major cause of population declines in wild animals. However, there remains little empirical evidence on the genetic consequences of disease-mediated population declines, or how such perturbations might affect demographic processes such as dispersal. Devil facial tumour disease (DFTD) has resulted in the rapid decline of the Tasmanian devil, Sarcophilus harrisii, and threatens to cause extinction. Using 10 microsatellite DNA markers, we compared genetic diversity and structure before and after DFTD outbreaks in three Tasmanian devil populations to assess the genetic consequences of disease-induced population decline. We also used both genetic and demographic data to investigate dispersal patterns in Tasmanian devils along the east coast of Tasmania. We observed a significant increase in inbreeding (F(IS) pre/post-disease -0.030/0.012, P<0.05; relatedness pre/post-disease 0.011/0.038, P=0.06) in devil populations after just 2-3 generations of disease arrival, but no detectable change in genetic diversity. Furthermore, although there was no subdivision apparent among pre-disease populations (theta=0.005, 95% confidence interval (CI) -0.003 to 0.017), we found significant genetic differentiation among populations post-disease (theta=0.020, 0.010-0.027), apparently driven by a combination of selection and altered dispersal patterns of females in disease-affected populations. We also show that dispersal is male-biased in devils and that dispersal distances follow a typical leptokurtic distribution. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales. Ongoing management of Tasmanian devils must now attempt to maintain genetic variability in this species through actions designed to reverse the detrimental effects of inbreeding and subdivision in disease-affected populations.Heredity advance online publication, 10 March 2010; doi:10.1038/hdy.2010.17.

PMID: 20216571 [PubMed - as supplied by publisher]

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #51 on: 02/04/2010 06:26:02 »
If epigenomic markers actually allow life to direct mutation to any extent whatsoever, would that qualify as "intelligent design"?

If any process (epigentics)is involved rather than 'random change', you would think there is some 'intelligents'about it?

I think so.
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #52 on: 02/04/2010 16:45:53 »
echochartruse, I think the main point is still this:
Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
"You're going to have the same chip in there, the same genome, but different software. And the outcome is a different cell type."

Maybe I'm missing something obvious, but I can't find a point in any of those sources that says that epigenetics are causing genetic mutations.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #53 on: 02/04/2010 19:17:56 »
echochartruse, I think the main point is still this:
Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
"You're going to have the same chip in there, the same genome, but different software. And the outcome is a different cell type."


Maybe I'm missing something obvious, but I can't find a point in any of those sources that says that epigenetics are causing genetic mutations.

To be honest, I can't find anything in them about epigenetics causing genetic mutations.  I still haven't had a chance to put together a decent post with a lot of sources(hopefully later today), but I haven't seen anywhere that said epigenetics for sure caused genetic mutation.  My support comes from the evidence that some form of directed mutation exists, and I think logically epigenetics is the likely culprit.  Here is a quick example of the types of things I will post later today:

http://www.pnas.org/content/88/13/5882.full.pdf

Abstract: A previous study has demonstrated that
adaptive missense mutations occur in the tip operon of Escherichia
coli. In this study it is shown that, under conditions of
intense selection, a strain carrying missense mutations in both
trpA and trpB reverts to Trp+ 108 times more frequently than
would be expected if the two mutations were the result of
independent events. Comparison of the single mutation rates
with the double mutation rate and information obtained by
sequencing DNA from double revertants show that neither our
classical understanding of spontaneous mutation processes nor
extant models for adaptive mutations can account for all of the
observations. Despite a current lack of mechanistic understanding,
it is clear that adaptive mutations can permit advantageous
phenotypes that require multiple mutations to arise
and that they appear enormously more frequently than would
be expected.
« Last Edit: 02/04/2010 19:28:41 by norcalclimber »

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #54 on: 02/04/2010 23:08:03 »
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

............. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales.........

PMID: 20216571 [PubMed - as supplied by publisher]

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They must be wrong then
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #55 on: 02/04/2010 23:59:57 »
I'm not sure that this really supports directed mutation by epigenetic causation.  I can see how it is talking about evolution, but what it is saying doesn't really seem surprising, nor different from what has been previously thought.  If I am misunderstanding, please explain.
Quote from: http://www.ncbi.nlm.nih.gov/pubmed/20216571
Evidence that disease-induced population decline changes genetic structure and alters dispersal patterns in the Tasmanian devil.

Lachish S, Miller KJ, Storfer A, Goldizen AW, Jones ME.

School of Biological Sciences, University of Queensland, St Lucia, Brisbane, Queensland, Australia.

............. Our results show that disease can result in genetic and demographic changes in host populations over few generations and short time scales.........

PMID: 20216571 [PubMed - as supplied by publisher]

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They must be wrong then

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #56 on: 03/04/2010 05:27:30 »
In my words...... Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.

So if you go to the zoo where these animals are kept away from the toxins, you will find their genes are different from the ones in the wild.

The toxins are not leaving their water system any time in the near future, so if they continue to breed their genes will be passed down throughout many generations. While the captive Tassie Devils reproduce without the altered genes.

1.Cancer is an epigentic disease characterised by the break down of DNA.
2.Prior to the environmental change all the Tassie Devils genes were the same.
3. No change in Tassie Devil's genes in zoos or that have never come in contact with the toxic environment.
4. It took 2-3 generations for the environment to effect change in their genes.
5. If the captured, zoo's Tassie devils were released and returned to their native environment they would not survive. Their environment has directly effected their evolution.
6. As I believe, if the ones in the zoos continue to reproduce together without bringing in the new genes from their wild counterparts then 2 distinct species of Tassie Devils may occur over time. One group unable to live/reproduce/survive in it's natural habitat.
Survival of the fittest!

Anyway this example was for JP, to show that epigentics does change genes.
« Last Edit: 03/04/2010 05:38:07 by echochartruse »
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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #57 on: 03/04/2010 06:28:54 »
Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.

That is truly remarkable. If I understand what you are saying;

a) All Tasmanian Devils had identical genes.

b) The Tasmanian Devils that were subjected to toxins in their water showed significant changes in their genes in two to three generations.

Did I get that right?
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #58 on: 03/04/2010 07:19:25 »
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

In the section about exotic 5 carbon sugars we see a possible example of an overall mutation which may have started off with an epigenetic mutation, then had a genetic mutation, then had an epigenetic mutation (the author doesn't attribute epigenetics, merely states what effects occurred)
Quote

"Some five carbon sugars are very rare in nature, so very few organisms have the ability to use these exotic compounds in their metabolism. Robert Mortlock determined that the bacteria Klebsiella aerogenes was not immediately able to metabolize D-arabinose and xylitol by growing strains in media containing those compounds and noting the strains that were able to grow only after a lag time. This indicated that the original strain did not have the ability to process the compounds, but was able to evolve such a capability. Mortlock then went on to see how this capability was evolved.

In the case of D-arabinose, Mortlock showed that the arabinose could be utilized if it could be converted to D-ribulose by an enzyme (an isomerase). Unfortunately, K. aerogenes has no such isomerase for the conversion of D-arabinose. However, the isomerase for L-fucose has a low activity for D-arabinose.   But, the bad news is that the L-fucose isomerase is normally produced only when the cell is exposed to fucose. Nonetheless, in a few individuals, mutations occurred that allowed the fucose isomerase to be produced at all times - not just when L-fucose is present. This is normally a bad thing and would be selected against because it wastes the cells resources by constantly producing an unneeded enzyme. In this situation though, the mutation is a very good thing, and allows the cell to survive because it can now metabolize arabinose (albeit rather poorly). Although production of the fucose isomerase has been deregulated, the structure of the isomerase itself has not been changed. The next mutation was a change to the isomerase to make it more effective in the conversion of arabitol to ribulose. Finally (although I can't tell from Bell's description if this was actually done in the experiments), the culture could be selected to regain control of the expression of the isomerase - so that it is produced only when arabitol is present. "

It seems to me that perhaps the initial mutation which caused the isomerase for fucose to be produced without fucose present may have been epigenetic.  The next mutation seems to have been a genetic mutation which made the isomerase more efficient.  The final mutation seems to have been epigenetic again, to only produce the new isomerase when arabinose is present.

I am going off a limited understanding of the experiments involved, but it seems as if the bacteria was able to accomplish these mutations very quickly.

In another section of that page, we see this example of beneficial mutation(emphasis mine):

Quote
5.) Evidence of genetic divergence and beneficial mutations in bacteria after 10,000 generations
 

    Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R. E., Blot, M. (1999). Genomic evolution during a 10,000-generation
    experiment with bacteria. Proc. Natl. Acad. Sci. U. S. A. 96: 3807-3812

    Edited by John R. Roth, University of Utah, Salt Lake City, UT, and approved February 3, 1999 (received for review July 21, 1998)

    Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

The fact that each individual cell had its own genetic fingerprint, yet the pivotal mutations were shared by all descendants seems significant.

More from the same page:

Quote
4.) Adaptation to a Low Phosphate Chemostat Environment by a Clonal Line of Yeast
 

    P.E. Hansche and J.C. Francis set up chemosats to allow evolution of a single clonal line of beer yeast in a phosphate limited (due to high pH) environment. (A chemostat is a device that allows the propagation of microorganisms in an extremely constant environment.) The yeast clones grew slowly for about the first 180 generations when there was an abrupt increase in population density. This was later shown to be due to  better assimilation of the phosphate, presumably due to an improvement in the permease molecule. (Permease is an enzyme that controls what is allowed to come into the cell through the yeast's cell membrane.) After about 400 generations, a second improvement in cell growth rates occurred because of a mutation to the yeast's phosphatase (an enzyme that improves the cells ability to use phosphate). The phosphatase became more active overall, and its optimal pH (the pH where it is most active) was raised.  Finally, a third mutant appeared after 800 generations that caused the yeast cells to clump. This raised the population density in the chemostat because individual cells were no longer being washed out of chemostat (which is one of the methods that the chemostat uses to maintain very uniform conditions) as quickly as they had prior to the mutation. (This is just speculation on my part, but I wonder if it wasn't under some similar conditions that multi-cellularity became favored over unicellularity - perhaps on a sea bed or river bottom.)

    This experiment was repeated, and the same mutations occurred, but in different orders. Also, in one replication, the processing of phosphate was improved by a duplication of the gene that produces phosphatase. This is experimental evidence of an extremely important mechanism in evolutionary history! It is also a particularly elegant experiment because not only was all of this adaptation shown to occur in clonal lines (descended from a single individual), but the authors also determined the exact mutations that caused the improved adaptations by sequencing the genes and proteins involved.

    Francis, J.E., & Hansche, P.E. (1972) Directed evolution of metabolic pathways in microbial populations. I. Modification of the acid phosphatase pH optimum in Saccharaomyces cervisiae. Genetics, 70: 59-73.

    Francis, J.E., & Hansche, P.E. (1973) Directed evolution of metabolic pathways in microbial populations. II. A repeatable adaptation in Saccharaomyces cervisiae. Genetics, 74:259-265.

    Hansche, P.E. (1975) Gene duplication as a mechanism of genetic adaptation in Saccharaomyces cervisiae. Genetics, 79: 661-674.



These seem to be describing abrupt mutations which occur to a lot of the population at once, not gradual changes.  Also, the same mutations occurred when the experiment was repeated.  It seems so ordered, and quick, which to me implies some sort of direction.  I personally do not believe in a "higher power" so that is why I lean strongly towards something like epigenetics.


Here is an example where 2 separate mutations were required in order to metabolize salicin, and not only did they happen, but the initial mutation was not beneficial and only occurred in populations grown on mediums containing salicin:

Quote
http://www.ncbi.nlm.nih.gov/pubmed/2852143?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=1&log$=relatedarticles&logdbfrom=pubmed
Adaptive evolution that requires multiple spontaneous mutations. I. Mutations involving an insertion sequence.

Hall BG.

Molecular and Cell Biology, University of Connecticut, Storrs 06268.

Escherichia coli K12 strain chi 342LD requires two mutations in the bgl (beta-glucosidase) operon, bglR0----bglR+ and excision of IS103 from within bglF, in order to utilize salicin. In growing cells the two mutations occur at rates of 4 x 10(-8) per cell division and less than 2 x 10(-12) per cell division, respectively. In 2-3-week-old colonies on MacConkey salicin plates the double mutants occur at frequencies of 10(-8) per cell, yet the rate of an unselected mutation, resistance to valine, is unaffected. The two mutations occur sequentially. Colonies that are 8-12 days old contain from 1% to about 10% IS103 excision mutants, from which the Sal+ secondary bglR0----bglR+ mutants arise. It is shown that the excision mutants are not advantageous within colonies; thus, they must result from a burst of independent excisions late in the life of the colony. Excision of IS103 occurs only on medium containing salicin, despite the fact that the excision itself confers no detectable selective advantage and serves only to create the potential for a secondary selectively advantageous mutation.


Really I could go on and on, the evidence supporting some form of directed mutation is everywhere.  Yes, each individual event can have a possible different explanation, but it seems to happen over and over.  If we as scientists are constantly searching for a new way to explain why something observed isn't impossible, maybe we need to go back to the fundamentals and look at why we thought something was impossible to begin with.

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Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #59 on: 03/04/2010 10:24:03 »
In my words...... Tassie Devil's genetics, prior to the toxins in their water, were all the same throughout their species. After the toxins from the mono culture effected their water, their genetics changed over 2-3 generations to cope with the toxins and to survive and reproduce.
In that case, I think you've got entirely the wrong end of the stick with that paper.

Quote
So if you go to the zoo where these animals are kept away from the toxins, you will find their genes are different from the ones in the wild.

The toxins are not leaving their water system any time in the near future, so if they continue to breed their genes will be passed down throughout many generations. While the captive Tassie Devils reproduce without the altered genes.

That's not what the paper says.

Quote
1.Cancer is an epigentic disease characterised by the break down of DNA.

No it's not.  And in particular, DTFD is a contagious cancer - tumour cells from one individual can cause tumours in another.

Cancer is a disease that can be caused by DNA damage - not the other way around.

Quote
2.Prior to the environmental change all the Tassie Devils genes were the same.
No they weren't - that would make them clones.

Quote
3. No change in Tassie Devil's genes in zoos or that have never come in contact with the toxic environment.
Well, it's not a toxin in the environment - if DTFD isn't introduced, why would you expect any change?
Quote
4. It took 2-3 generations for the environment to effect change in their genes.
The abstract says:
"We observed a significant increase in inbreeding in devil populations after just 2-3 generations of disease arrival, but no detectable change in genetic diversity."

Quote
5. If the captured, zoo's Tassie devils were released and returned to their native environment they would not survive. Their environment has directly effected their evolution.
The paper doesn't say anything about this.  It may be true that captive animals don't do well in the wild, but that may be nothing to do with their genes.
Quote
6. As I believe, if the ones in the zoos continue to reproduce together without bringing in the new genes from their wild counterparts then 2 distinct species of Tassie Devils may occur over time. One group unable to live/reproduce/survive in it's natural habitat.
Survival of the fittest!
Spot on.  This is why captive breeding programmes often swap males (or sperm) to try to keep variation high.


My analysis of the paper (based only on the abstract) is that DFTD leads to population and distribution changes, that can lead to genetic changes over a few generations.  This doesn't necessarily mean mutations, it means variability - different proportions of different alleles etc.

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Offline BenV

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Re: How big a role does the epigenome play in evolution?
« Reply #60 on: 03/04/2010 10:29:57 »
If epigenomic markers actually allow life to direct mutation to any extent whatsoever, would that qualify as "intelligent design"?

If any process (epigentics)is involved rather than 'random change', you would think there is some 'intelligents'about it?

I think so.

I don't think so.

Intelligence requires consciousness and forethought.  Epigenetic changes do not.

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #61 on: 03/04/2010 10:33:19 »
Here is a few more examples which I feel indicate epigenetics causing mutation. . .

Cool.  Thanks for the links.  I'll take a look over them when I have a chance.

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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #62 on: 06/04/2010 06:15:01 »
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

Quote
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions.  I'm also guessing that the reason they are theorizing the mutators might exist is because we consistently see in experiment after experiment that beneficial mutations tend to happen very rapidly when they are really needed, but almost not at all when the organism is not under stress.  Even if the mutations afterward were indeed random, doesn't this still represent the ability of an organism to control mutation, and evolution to some extent?

If I have misunderstood anything I apologize, it is surely not my wish to put forth a misinterpretation of science.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #63 on: 06/04/2010 23:52:00 »

1.Cancer is an epigentic disease characterised by the break down of DNA.

No it's not.  And in particular, DTFD is a contagious cancer - tumour cells from one individual can cause tumours in another.

Cancer is a disease that can be caused by DNA damage - not the other way around.


Quote
http://webcache.googleusercontent.com/search?q=cache:-deFKSjLe1sJ:assets0.pubget.com/pdf/17458893.pdf+Cancer+is+an+epigentic+disease+characterised+by+the+break+down+of+DNA.&cd=49&hl=en&ct=clnk&gl=au

Epigenetic alterations, such as modifications in DNA methylation patterns and post-translational modifications of histone tails, behave extremely
different from genetic modifications,

see also
www.epidna.com/showabstract.php?pmid=15881895

www.epidna.com/showabstract.php?pmid=16210093

www.ncbi.nlm.nih.gov/pubmed/19069364

www.docstoc.com/docs/20476934/02-Cancer-Epigenetics-Group/

http://atlasgeneticsoncology.org/.../GenetInstabilityCancerID20056.html

informahealthcare.com/doi/full/10.1517/17530059.1.1.17?select23...

www.pebc.cat/grupodetalle.php?idg=7

http://ajp.amjpathol.org/cgi/content/full/164/6/1883

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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #64 on: 07/04/2010 06:13:41 »
I must admit to being totally confused (Yea, yeah. Save the cheap shots till later.)

Are we, or are are we not, debating about the existence of an intelligent designer? (which is usually what is strongly implied by the term "intelligent design".)

or;

are we debating the complexity of the process of evolution and how factors other than random mutation can play an important role in the process?

If it's the former, fine, then we are debating about the existence of an intelligent designer.
If it's the latter, does anyone mind if we change the title of this topic, because it is very confusing?
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #65 on: 07/04/2010 18:31:32 »
My intent when I started the topic was to debate the evidence and logic in support of organisms choosing mutation, rather than merely random chance mutations resulting in the diversity of life we have.  I posted it the way I did, because if life has a way to influence and choose mutation then life would in a sense be "intelligently designed" but not by some god figure, rather by the organisms themselves.

A lot of people seem to be stuck on me using "intelligent design" in the title, I suppose I can see how with as many replies as there are it could be awfully confusing as to whether I am talking about a higher power or not.  I am most definitely not talking about "god", so if the title is just too confusing for people it should probably be changed.  Actually, it could even probably be merged with "Is evolution really down to random mutation?", since that is a very similar topic I posted before I had learned a little more on the subject.

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Offline Geezer

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Re: How big a role does the epigenome play in evolution?
« Reply #66 on: 07/04/2010 19:17:26 »
Thanks for the clarification. That should do the trick. It's probably best not to change the topic title, as that might lead to even more confusion.  [:D]
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #67 on: 07/04/2010 23:29:12 »
Just a few interesting links for those who are not bias.

Quote from: http://www.abc.net.au/catalyst/stories/s1486827.htm
Intelligent Design or ID, is being put forward as a serious scientific theory. It's even found it's way into some high schools.


Quote from: http://internationalstem.com/
Intenational Institute of Stem Cell Research and Regenerative Medician
Introduction:  California is currently becoming the main international hub of stem cell research.   Our staff is fully committed to creating this international center for stem Cell Research and clinical applications.  Dr. Schafer has been a twenty year pioneer in adipose tissue harvesting and fat transfer.  He is currently involved in the harvesting and preservation of “Intelligent” Stem cells which are naturally occurring in our bodies and not from fetuses or evoke religious taboos.   These Adult stem cells are extremely valuable and have great potential for future therapies.  It is important to note that these cells do not induce any type of immune reaction in the body.  Our Institute is at the forefront of this emerging technology.  Many of the pharmacological protocols as well as cosmetic proceedures  of  the twentieth century are being replaced by the utilization of stem cells for a cosmetic procedure.  This Institute provides world leading innovations in fat grafting with stem cells and regenerative medicine.  Dr. Schafer provides the vision and scientific guidance to advance the Institute to it’s potential of scientific excellence.

Quote from: http://en.wikipedia.org/wiki/Microbial_intelligence
Microbial intelligence (popularly known as bacterial intelligence) is the intelligence  shown by microorganisms. The concept encompasses complex adaptive behaviour shown by single cells, and altruistic and/or cooperative behavior in populations of like or unlike cells mediated by chemical signalling that induces physiological or behavioral changes in cells and influences colony structures.

Quote from: http://www.world-science.net/exclusives/exclusives-nfrm/050418_bact.htm
Yet the humble microbes may have a rudimentary form of intelligence, some researchers have found.

Quote from: http://www.astrobio.net/interview/2111/bacterial-intelligence
If you look up consciousness in the dictionary, it says, "awareness of the world around you," and that's because you lose it somehow when you become unconscious, right? Well, you can show that microorganisms, or bacteria, are certainly conscious. They will orient themselves, they will work together to make structures. They'll do a lot of things. This ability to respond specifically to the environment and to act creatively, in the sense that that precise action has never been taken before, is a property of life. Of course, it has to be moving life, or you can't tell. You can't tell if a plant is thinking, but in organisms that move, you can tell their intelligence.

So yes I think life itself is intelligent and there is a degree of design about it which we have not yet been able to understand
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Re: How big a role does the epigenome play in evolution?
« Reply #68 on: 07/04/2010 23:52:06 »
Intelligent Design, otherwise known as ID, has nothing to do with science. It is creationism wrapped up in pseudoscience and mumbo-jumbo. The fact that George W. Bush fell for it should tell you something, both about ID and GWB.

ID was invented in an attempt to require schools in the USA to teach creationism by pretending that it is some sort of science.

Perhaps we will have to change the title of this topic after all.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #69 on: 08/04/2010 03:07:00 »
It is unfortunate for all that "intelligent design" can not be looked at scientifically. That we are all in a bias pot of random selection fighting for survival.
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Re: How big a role does the epigenome play in evolution?
« Reply #70 on: 08/04/2010 04:26:45 »
It is unfortunate for all that "intelligent design" can not be looked at scientifically. That we are all in a bias pot of random selection fighting for survival.

ID would be looked at scientifically if its proponents presented some scientific evidence. However, proponents of ID are not interested in conducting real science. They are only interested in pursuing their political agenda by deceiving gullible individuals into believing that ID is science.

Personally, I have no problem with religions, but I have a very big problem with religions that masquerade as science in an attempt to trick people.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #71 on: 08/04/2010 05:19:23 »
It is unfortunate that Science can't prove that ID is totally and specifically scientific.
I am not a religous person, yet feel that our earth's evolution and everything in it  has not been entirely random.

Quote from: http://www.livescience.com/strangenews/050923_ID_science.html
Darwin himself admitted that if an example of irreducible complexity were ever found, his theory of natural selection would crumble.
 
"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down," Darwin wrote.

"complex specified information," or CSI for short.

An example of CSI from nature is DNA, the molecule found in all cells that contains the genetic instructions for life. DNA is made up of four repeating chemical bases arranged into complimentary pairs. The bases can be thought of as "letters" in a four-letter alphabet and can be strung together to form genes, which can be thought of as the "words" that tell the cell what proteins to make.

The human genome is made up of some 3 billion DNA base pairs and contains about 25,000 genes. DNA is obviously complex. The fact that humans always give birth to humans and not chimpanzees or naked mole rats shows that DNA is also specific.

When science takes the god out of 'intelligent design' that will be the day science can go forward. Until then we will continue going in circles trying to prove the theory of evolution by natural selection.
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Re: How big a role does the epigenome play in evolution?
« Reply #72 on: 08/04/2010 05:51:42 »
It is unfortunate that Science can't prove that ID is totally and specifically scientific.

You don't seem to understand. It's not up to "Science" (whatever that is) to prove that ID is scientific. It's up to ID to prove that it has some legitimate scientific foundation.

Thus far, ID  has done nothing but try to appeal to non-science and religious fundamentalism. (Apparently, in that regard, it has been quite successful.)

We may "wish upon a star" all we want, but, unfortunately, that does not make science.
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Re: How big a role does the epigenome play in evolution?
« Reply #73 on: 10/04/2010 16:59:27 »
It is unfortunate that Science can't prove that ID is totally and specifically scientific.

You don't seem to understand. It's not up to "Science" (whatever that is) to prove that ID is scientific. It's up to ID to prove that it has some legitimate scientific foundation.

Thus far, ID  has done nothing but try to appeal to non-science and religious fundamentalism. (Apparently, in that regard, it has been quite successful.)

We may "wish upon a star" all we want, but, unfortunately, that does not make science.

Ok, but like I said, this topic has nothing to do with creationist intelligent design.

What do you think about the evidence that I posted regarding directed mutation via epigenetics?

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Re: How big a role does the epigenome play in evolution?
« Reply #74 on: 12/04/2010 05:10:45 »
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

. . .

Sorry it took me so long, but after reading through all of those sources and watching the last 5 minutes of the Naked Science video, I still have to disagree that there's evidence for epigenetic changes causing genetic mutation.  Those experiments all show that you can "rapidly" develop a lot of genetic diversity, but they don't attribute that to epigenetics.  I still haven't seen any direct evidence of epigenetic change causing genetic mutation. There's also the difference in time scales of "rapidly."  The sources you cite seem to be talking about time scales that are long compared to the life cycle of an individual, 10,000 generations in one study and mutation probability of ~10-8 per cell division in the other.  Epigenetics seems to be a much faster process, allowing single organisms to change (so changes on the scale of 1 generation).  If epigenetics induced mutation, then I would expect it to happen orders of magnitude faster than any of those studies show. 

Again, it's not that I think epigenetics isn't interesting and promising.  It's just that there doesn't seem to be enough evidence to link it to actual genetic mutations.  If that link is made, then it certainly would change things.

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Re: How big a role does the epigenome play in evolution?
« Reply #75 on: 13/04/2010 04:38:30 »
Epigenetic regulation may be an important mechanism of both preserving and modifying genomic structure.

Quote from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691666/

Both genetic and epigenetic changes contribute to development of human cancer.
... While there has been considerable progress in understanding the impact of genetic and epigenetic mechanisms in tumourigenesis, there has been little consideration of the importance of the interplay between these two processes.

A transposon-induced epigenetic change leads to sex determination in melon
Quote from: http://www.nature.com/nature/journal/v461/n7267/full/nature08498.html
Sex determination in plants leads to the development of unisexual flowers from an originally bisexual floral meristem1, 2. This mechanism results in the enhancement of outcrossing and promotes genetic variability, the consequences of which are advantageous to the evolution of a species3.

The behavior of a person's genes doesn't just depend on the genes' DNA sequence--it's also affected by so-called epigenetic factors.

http://www.nature.com/scitable/topicpage/Epigenetic-Influences-and-Disease-895
http://www.nature.com/scitable/topicpage/Gene-Expression-Regulates-Cell-Differentiation-931

Quote
........In addition, gene expression changes can lead to changes in an entire organism.

......DNA and its associated histone  proteins (together known as chromatin) can be chemically modified by a cell's own machinery.

....Together, these lines of evidence have led to an emerging hypothesis that cell-cell signaling and epigenetic changes converge to guide cell differentiation  decisions both during development  and beyond.

I would say that epigentics doesn't need to modify DNA to cause these changes and definitely has an influence in evolution.


« Last Edit: 13/04/2010 04:50:37 by echochartruse »
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Re: How big a role does the epigenome play in evolution?
« Reply #76 on: 13/04/2010 04:48:08 »
Quote from: http://www.abc.net.au/science/articles/2009/11/26/2754494.htm?topic=
Scientists create Chinese 'gene map'
A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.........
"Different dialect groups are definitely not identical ... language is a reflection of our evolution, that's why you see the differences," says Liu.

This is an example of genetic and epigentics working together to create subtle genetic differences
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Re: How big a role does the epigenome play in evolution?
« Reply #77 on: 13/04/2010 07:14:31 »

I would say that epigentics doesn't need to modify DNA to cause these changes and definitely has an influence in evolution.


You don't say! (Well, I suppose you did.)

Er, but how exactly do parents pass on their inherited characteristics by means other than the transmission of their DNA?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #78 on: 13/04/2010 19:05:38 »
"Selective Pressure"

Quote from:  http://blogs.monografias.com/sistema-limbico-neurociencias/2010/03/02/culture-and-evolution-genetic-epigenetics-exaptations-spandrels-and-jumping-genes%E2%80%A6/
The best evidence available to Dr. Boyd and Dr. Richerson for culture being a selective force was the lactose tolerance found in many northern Europeans. Most people switch off the gene that digests the lactose in milk shortly after they are weaned, but in northern Europeans — the descendants of an ancient cattle-rearing culture that emerged in the region some 6,000 years ago — the gene is kept switched on in adulthood.

Lactose tolerance is now well recognized as a case in which a cultural practice — drinking raw milk — has caused an evolutionary change in the human genome. Presumably the extra nutrition was of such great advantage that adults able to digest milk left more surviving offspring, and the genetic change swept through the population.

This instance of gene-culture interaction turns out to be far from unique. In the last few years, biologists have been able to scan the whole human genome for the signatures of genes undergoing selection. Such a signature is formed when one version of a gene becomes more common than other versions because its owners are leaving more surviving offspring. From the evidence of the scans, up to 10 percent of the genome — some 2,000 genes — shows signs of being under selective pressure.

DNA carries information. Epigenetics is the conductor/regulator/, the switch that turns genes on and off.
The information in all living things is very much the same throughout species as I have been told by TNS and is what evolution is based on as far as I can understand.

This information carried by a species can be unchanged but regulated, switched on or off.
If this information regulator had a permanent effect there would not be evolution only permanent change.
(if the sea creature left the ocean to walk on land, the information required to be able to return to water and survive would have been lost)

DNA in identical twins have exact same DNA but may have very different immunity issues.


« Last Edit: 13/04/2010 19:10:54 by echochartruse »
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #79 on: 13/04/2010 19:09:36 »
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

Quote
A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions.  I'm also guessing that the reason they are theorizing the mutators might exist is because we consistently see in experiment after experiment that beneficial mutations tend to happen very rapidly when they are really needed, but almost not at all when the organism is not under stress.  Even if the mutations afterward were indeed random, doesn't this still represent the ability of an organism to control mutation, and evolution to some extent?

If I have misunderstood anything I apologize, it is surely not my wish to put forth a misinterpretation of science.

I know the other links I posted don't specifically attribute results to epigenetics, but doesn't this one specifically state that it is epigenomic markers which "allow" large genomic changes to happen?

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Re: How big a role does the epigenome play in evolution?
« Reply #80 on: 13/04/2010 19:21:46 »
L=E3

Life=epigenetics, ecology, and evolution (L=E3)
quote from Greengard, who won the 2000 Nobel Prize in Physiology or Medicine for research into how neurons communicate.
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Re: How big a role does the epigenome play in evolution?
« Reply #81 on: 13/04/2010 19:35:30 »
Er, but how exactly do parents pass on their inherited characteristics by means other than the transmission of their DNA?

Please read this you may have a better understanding.
Quote from: http://pn.psychiatryonline.org/content/45/5/12.1.full
In other words, epigenetics is the place where nature and nurture converge. The genes we are born with can determine some but not all of who we are and who we become.
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Offline norcalclimber

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Re: How big a role does the epigenome play in evolution?
« Reply #82 on: 13/04/2010 20:47:06 »
Here is a few more examples which I feel indicate epigenetics causing mutation:

http://www.gate.net/~rwms/EvoMutations.html

. . .

Sorry it took me so long, but after reading through all of those sources and watching the last 5 minutes of the Naked Science video, I still have to disagree that there's evidence for epigenetic changes causing genetic mutation.  Those experiments all show that you can "rapidly" develop a lot of genetic diversity, but they don't attribute that to epigenetics.  I still haven't seen any direct evidence of epigenetic change causing genetic mutation. There's also the difference in time scales of "rapidly."  The sources you cite seem to be talking about time scales that are long compared to the life cycle of an individual, 10,000 generations in one study and mutation probability of ~10-8 per cell division in the other.  Epigenetics seems to be a much faster process, allowing single organisms to change (so changes on the scale of 1 generation).  If epigenetics induced mutation, then I would expect it to happen orders of magnitude faster than any of those studies show. 

Again, it's not that I think epigenetics isn't interesting and promising.  It's just that there doesn't seem to be enough evidence to link it to actual genetic mutations.  If that link is made, then it certainly would change things.

The last 5 minutes of the Naked Science video "Was Darwin Wrong?" specifically states that it appears evolution can happen for faster than previously thought using epigenetic means.  The narrator actually states that new evidence shows life may be able to(and I quote) "make" evolution happen.  It also states that the answer to how whales "lost their legs" may have been initiated due to epigenetics and the expression of the PITX1 gene(I think that was the one at least).  So I'm not really sure how you could say their was no evidence for epigenetic induced mutation in the evidence I provided.

The link I posted regarding mutation of the Trp genes in e. coli bacteria states that beneficial mutations were observed at a rate which was orders of magnitude higher than what could be expected via random mutation alone.  This is exactly what is predicted if genetic evolution via epigenetically induced methods is a reality.

I didn't see how the Tasmanian devil bit applied in what echo posted, but since that post echo has posted several links which seem to me to provide legitimate evidence of epigenetically driven evolution.

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.

Evolution by purely random mutation predicts a steady rate of evolution over a large time scale.  When we look at the fossil record we see this to be false, as very little evolution at all seems to have happened over the first few billion years; then a massive explosion of life seems to have occurred and continued since.  We also see repeatedly in experiments that very few beneficial mutations seem to happen when the environment isn't stressed; yet when an environment is stressed and there is even the slightest chance at all for an organism to survive, all of a sudden the necessary mutation occurs in relatively short periods of time.

The fact that our fossil record, and the last 100 years of experiments continue to have results which are predicted by epigenetic induced genetic mutation and not predicted by purely random mutation gives a great deal of weight to the theory, whether it has been "proven" yet or not. 

When you talk about the different time scales in the experiments, it is important to consider how advanced the organism in question is.  It stands to reason that if epigenetically controlled genetic mutation first evolved ~750 million years ago, then even that control should have been evolving since.  Wouldn't this result in more advanced forms of life having more advanced forms of epigenetic control?  So when we look at experiments using "simple" bacteria, their control should be "simple" as well?  Shouldn't we expect epigenetic mutations and epigenetically controlled mutations to actually take fewer generations in more complicated/advanced forms of life?


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Re: How big a role does the epigenome play in evolution?
« Reply #83 on: 13/04/2010 22:14:05 »
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?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #84 on: 14/04/2010 00:00:24 »
"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?"

"Transcription errors?"

Is this what is described as Random Mutation?

My personal view is that there is some type of Intelligents behind the mutations which are not errors at any length.

Quote from: http://www.abc.net.au/science/articles/2007/12/11/2115575.htm
Many of the recent genetic changes reflect differences in the human diet brought on by agriculture, as well as resistance to epidemic diseases that became mass killers following the growth of human civilisations, the researchers say.

For example, Africans have new genes providing resistance to malaria. In Europeans, there is a gene that makes them better able to digest milk as adults. In Asians, there is a gene that makes ear wax more dry.

prior to the TDFT “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” Geneticist and devil researcher Dr Kathy Belov http://www.tassiedevil.com.au/research.html#different

although there was no subdivision apparent among pre-disease populations (theta=0.005, 95% confidence interval (CI) -0.003 to 0.017), we found significant genetic differentiation among populations post-disease (theta=0.020, 0.010-0.027),

Prior to the cancer appearing, the Devil’s genetic diversity was so low, it was thought that in 10 years we could lose the species.

Quote from: http://www.time.com/time/health/article/0,8599,1951968,00.html
Yes we can influence our children’s genes and our children’s children and theirs so they become alcoholics, diabetic, have cancer, schizophrenia, autism, Alzheimer's and many others. All depending on how we live our lives today.

Why Your DNA Isn't Your Destiny
By John Cloud
http://www.time.com/time/health/article/0,8599,1951968-2,00.html#ixzz0jukwTf7h

I know this is exactly what I submitted in this forum previously, hope this is easier to understand.
« Last Edit: 14/04/2010 00:01:59 by echochartruse »
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Re: How big a role does the epigenome play in evolution?
« Reply #85 on: 14/04/2010 00:42:57 »
"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?"

"Transcription errors?"

Is this what is described as Random Mutation?

I believe that is correct. The genetic duplication process is not perfect, so in the process of copying DNA, some errors creep in. There are also external factors like, for example, radiation.

Anyway, perhaps you could answer my question. I don't think it was terribly complicated.
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Re: How big a role does the epigenome play in evolution?
« Reply #86 on: 14/04/2010 01:13:25 »

My personal view is that there is some type of Intelligents behind the mutations which are not errors at any length.


Of course you are entitled to hold a personal view, but if you can't prove that mutations are driven by some intelligence, then it's just your personal view. On the other hand, there is plenty of evidence that mutations are simply caused by transcription errors.

Perhaps you should start by proving that the DNA transcription process is infallible and base your argument on that.
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Re: How big a role does the epigenome play in evolution?
« Reply #87 on: 14/04/2010 01:14:02 »
I believe that is correct. The genetic duplication process is not perfect, so in the process of copying DNA, some errors creep in. There are also external factors like, for example, radiation.

Anyway, perhaps you could answer my question. I don't think it was terribly complicated.

Firstly isn't radiation an environmental/epigentic issue?

If evolution only required a copy of hereditary DNA, wouldn't we be clones?

Quote from:  Geezer on 13/04/2010 22:14:05
"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?"

Sorry I thought you might read the links and decide for yourself.

here is another example:
Alcohol during pregnancy chemically alters fetal DNA
www.newscientist.com/.../dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html -

We are aware today that what we allow our children to do, will effect future generations for example...smoking at early increases the size of their children at birth, sitting in front of the computer for extended long periods, malnutrition, over eating, gambling, where we live, religion, etc, etc does have an ever lasting effect on generations to come, even though it has been established that these inherited traits may jump generations.

Some genetic diseases are carried through the male generation, some female and others both.

I was once told I am more like my gradparent than my direct parent, yet I could be visually mistaken for my cousin.

Maybe, the errors you speak of are just the genes being switch off or on by epigentics regulators?
« Last Edit: 14/04/2010 01:17:16 by echochartruse »
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Re: How big a role does the epigenome play in evolution?
« Reply #88 on: 14/04/2010 02:22:06 »
Firstly isn't radiation an environmental/epigentic issue?
You're consistently misunderstanding what epigenetic changes are throughout this thread.  There is some debate as to the subtle points of epigenetics, but it's basically defined as changes to DNA expression that occur without changes to the underlying DNA itself.

Therefore radiation is environmental, and not epigenetic.


Quote
here is another example:
Alcohol during pregnancy chemically alters fetal DNA
www.newscientist.com/.../dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html -
Alcohol is environmental.

All the links you've been posting have been missing the point, since you're confusing epigenetics with non-epigenetic methods that induce changes in DNA.

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Re: How big a role does the epigenome play in evolution?
« Reply #89 on: 14/04/2010 02:40:47 »
I just came across this, and I'm not sure if I am understanding or interpreting it correctly:

http://www.ncbi.nlm.nih.gov/pubmed/10690404?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_SingleItemSupl.Pubmed_Discovery_RA&linkpos=3&log$=relatedreviews&logdbfrom=pubmed

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A decade of research on adaptive mutation has revealed a plethora of mutagenic mechanisms that may be important in evolution. The DNA synthesis associated with recombination could be an important source of spontaneous mutation in cells that are not proliferating. 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. Finally, a subpopulation of transient hypermutators could be a source of multiple variant alleles, providing a mechanism for rapid evolution under adverse conditions.

The first part of the underlined section seems to be referring to epigenomic markers.  "Insertion elements not only activate and inactivate genes, they also provide sequence homology that allows large-scale genomic rearrangements." seems to be saying epigenomic markers are responsible for the mechanism which allows an organism to make a large mutation?

"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."  This seems to be saying that certain plasmids may be able to "carry" beneficial mutations throughout a population?  If this occurs, mustn't it have evolved at some point?  The only reason I can think of as to why a mutation like that would be beneficial is because it allows beneficial mutations to be transmitted without direct mating.  If that is true, it seems to be just another element which is starting to show us just how advanced life is, and how much it seems to recognize(consciously or not) the need to evolve into a fitter organism is paramount to survival of future generations.

To be honest, I'm not precisely sure what transient hypermutators are specifically, but I'm guessing from the name that they are theoretical cellular "machines" capable of increasing the rate of mutation under adverse conditions. 
They aren't.  Transient hypermutators are cells that mutate quickly when put under selective pressure.  The big question about them is why they happen and why they seem to favor beneficial mutations.  The cited paper on it is here: http://www.genetics.org/cgi/reprint/126/1/5?ijkey=052e053149bad47e2eaa9e5103b0b085358501d3 and gives some explanations (none of them epigenetic).

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #90 on: 14/04/2010 03:04:14 »
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?

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #91 on: 14/04/2010 03:16:07 »

Therefore radiation is environmental, and not epigenetic.


Alcohol is environmental.

All the links you've been posting have been missing the point, since you're confusing epigenetics with non-epigenetic methods that induce changes in DNA.

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author = http://www.newscientist.com/article/dn18390-alcohol-during-pregnancy-chemically-alters-fetal-dna.html

Alcohol during pregnancy chemically alters fetal DNA
This suggests that if women drink too much in pregnancy, epigenetic changes may cause some of the permanent symptoms seen in fetal alcohol syndrome in their children.

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1993 Academic Press -  Delayed Heritable Damage and Epigenetics in Radiation-Induced Neoplastic Transformation of Human Hybrid Cells, by Marc S. Mendonca, Ronald J. Antoniono and J. Leslie Redpath © 1993 Radiation Research Society.
We have reported previously that under identical experimental conditions both the establishment of plateau phase and the onset of the expression of lethal mutations also occur after Day 9. We therefore propose that radiation-induced neoplastic transformation of HeLa × skin fibroblast hybrid cells is a consequence of the delayed expression of heritable damage under epigenetic control with a resultant loss of tumor-suppressor function.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #92 on: 14/04/2010 03:27:38 »
There is also no evidence, based on the way epigenetics works, that it can induce genetic mutations. 

In regard to the links and posts I contributed for this forum about the Tassie Devil....
The genetically modified mono culture planted in the devil's region has caused the tumors.
prior to the TDFT “The majority of devils in Tasmania were immunological clones and therefore susceptible to DFTD,” Geneticist and devil researcher Dr Kathy Belov http://www.tassiedevil.com.au/research.html#different
In 3-5 generations Devil's have genetic diversity changed.

All I can say is that epigenetics controls change and mutations in genes, would you except that?
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #93 on: 14/04/2010 03:52:59 »
WHAT IS EPIGENETICS?
The development and maintenance of an organism is orchestrated by a set of chemical reactions that switch parts of the genome off and on at strategic times and locations. Epigenetics is the study of these reactions and the factors that influence them.

EPIGENETICS & THE ENVIRONMENT
The genome dynamically responds to the environment. Stress, diet, behavior, toxins and other factors activate chemical switches that regulate gene expression.
http://learn.genetics.utah.edu/content/epigenetics/

I believe I'm on the right track, Could JP explain my mistake please. Confussed.
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #94 on: 14/04/2010 04:17:51 »
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #95 on: 14/04/2010 05:27:41 »
Epigenetics does not lead to gene mutations.  You're citing many examples of gene mutations which can be explained by other mechanisms.

So we have established that epigenetics changes the cell's gene expression.
We know they do this by adding and removing mythal tags.(turning on and off genes)and this epigeneome acts as a cellular memory.(tags and records onto DNA)This continues through life and is inherited.

It doesn't have to lead to mutation to make vast alterations or variations in our DNA. But could over time.[quote A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.]

Epigenetics may well be the initiating stage for gene mutation since it controls whether or not the gene is active. over generations of the gene being turned on/off

Remembering that not a single gene mutation has ever benefited life, in my opinion mutation is neither beneficial or necessary for the survival of the fittest.
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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #96 on: 14/04/2010 05:40:52 »
is skin cancer which is a mutation of the melonomas epigenetic or not and why please so I can understand.
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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #97 on: 14/04/2010 05:43:00 »
It doesn't have to lead to mutation to make vast alterations or variations in our DNA. But could over time.[quote A large genetic analysis of ethnic Chinese has revealed subtle genetic differences within the world's most populous nation.]
Yes, it does.  Altering DNA itself is a mutation.  Altering the expression of DNA is epigenetics.  Those are the points you're confusing.

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Epigenetics may well be the initiating stage for gene mutation since it controls whether or not the gene is active. over generations of the gene being turned on/off
It certainly may well be, but that makes it a hypothesis to be tested and so far there hasn't been evidence of that.  

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Remembering that not a single gene mutation has ever benefited life, in my opinion mutation is neither beneficial or necessary for the survival of the fittest.
If I'm reading this correctly, your opinion is counter to mainstream science and evidence.  See Geezer's comment above: http://www.thenakedscientists.com/forum/index.php?topic=30685.msg306631#msg306631

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Offline JP

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Re: How big a role does the epigenome play in evolution?
« Reply #98 on: 14/04/2010 05:48:07 »
is skin cancer which is a mutation of the melonomas epigenetic or not and why please so I can understand.

It could come from a variety of sources, none of which are epigenetic.  Off the top of my head (and from a limited understanding of the cellular processes involved), it is often caused by UV radiation damaging the DNA.  This damaged DNA can then cause the cell to go haywire, causing a cancer.  It could also be caused by transcription errors which occur when a cell copies its DNA.  These errors change the DNA which could then cause a cell to go haywire.

Epigenetic changes occur when a cell wants to turn off the action of a part of the DNA.  It doesn't destroy its DNA, but just says that it should stop following instructions from that part of the DNA.  The DNA itself is still intact and will be copied properly.  Future cells will have the same DNA as their parent (unless one of the other processes for DNA damage occurs).  The cells shouldn't go haywire since there's no error in the DNA that would make them do so.

At the very least, what I'm saying throughout is that there is no evidence that epigenetic processes can damage or change DNA in the same way as radiation or transcription errors.

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Offline echochartruse

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Re: How big a role does the epigenome play in evolution?
« Reply #99 on: 14/04/2010 05:56:30 »
If I'm reading this correctly, your opinion is counter to mainstream science and evidence.  See Geezer's comment above: http://www.thenakedscientists.com/forum/index.php?topic=30685.msg306631#msg306631

Please explain one mutation that is benefitual to life. I can't find one.
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