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Author Topic:   Mutation and its role in evolution: A beginners guide
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 36 of 60 (436243)
11-24-2007 7:31 PM
Reply to: Message 33 by Wounded King
08-25-2006 4:46 AM


Re: An example of inherited epigenetics
WK writes:
...the inheritance operated transgenerationally rather than simply being inherited in the differing somatic lineages of the organism.
OK, so epigenetic material is heritable "...in the differening somatic lineages of the organism." Is all that verbosity necessary? It's a genetic deal and it's heritable. Nuff said. Lot's of alleles operate transgenerationally. So what? I assume epigenetic material physically survives crossing-over and other genetic dispersions of meiosis and makes it all the way to fertilization and a zygote. Then, in the new organism, this epigenetic stuff has certain controls over the expressions of certain alleles. But why is this any different from other genetic inheretances? So the epigenes are switches. But so are certain other genes, inherited in the same way. So what's the big deal? Why isn't the propagation of this epigenetic stuff understood simply as genetic heritability? Should it come as a surprise to anyone that histones and methyl groups ride along those meiotic pathways?
I notice two things: 1) Epigenes don't change a allele's expression beyond what it is already capable of. The epigene works only on what has been genetical disposed. 2) Epigenes don't come in from the side or over the top of a meiotic or fertilization event to affect "differeing somatic lineages of the organism." They have to use the same molecular routes traveled by genes. When all is said and done it's still purly genetic business, isn't it?
”HM

This message is a reply to:
 Message 33 by Wounded King, posted 08-25-2006 4:46 AM Wounded King has replied

Replies to this message:
 Message 37 by Wounded King, posted 11-25-2007 1:30 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 38 of 60 (436383)
11-25-2007 1:58 PM
Reply to: Message 37 by Wounded King
11-25-2007 1:30 PM


Allelic centricity
WK, I don't mean to be impertinent, but I have an allele-centric POV. If epigenetics explains certain modifications of allelic expression, then what has been explained other than more things about how the alleles express themselves on not? Histones and methyl groups are just part the genetic ensemble, with the critical aspect always coming down to allelic expression. Please, I'm sincere, is there more to it than the show ultimately put on by alleles? Can those mythyl groups and histones do anything on their own?
”HM

This message is a reply to:
 Message 37 by Wounded King, posted 11-25-2007 1:30 PM Wounded King has replied

Replies to this message:
 Message 39 by Wounded King, posted 11-25-2007 2:37 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 40 of 60 (436409)
11-25-2007 3:44 PM
Reply to: Message 39 by Wounded King
11-25-2007 2:37 PM


Re: Allelic centricity
An allele is a variant of a gene. Allelic centricity (my term) would assert that all heritable phenotypic traits, and changes in those traits, ultimately can be accounted for by alleles. Epigenetics is to alleles what paint is to a barn. You can change its tint, its hue, and even its color, but afterwards it's still a barn.
”HM

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 41 of 60 (436439)
11-25-2007 7:36 PM
Reply to: Message 39 by Wounded King
11-25-2007 2:37 PM


Re: Allelic centricity
WK, let me use this definition of epigenetics from Wikipedia to focus my question:
quote:
Epigenetics is a term in biology used today to refer to features such as chromatin and DNA modifications that are stable over rounds of cell division but do not involve changes in the underlying DNA sequence of the organism. These epigenetic changes play a role in the process of cellular differentiation, allowing cells to stably maintain different characteristics despite containing the same genomic material. Epigenetic features are inherited when cells divide despite a lack of change in the DNA sequence itself and, although most of these features are considered dynamic over the course of development in multicellular organisms, some epigenetic features show transgenerational inheritance and are inherited from one generation to the next.
  —wikipedia
Simply put: Do those epigenetic features participate in biological evolution on their own, or does biological evolution require those epigenetic features to first affect changes in the alleles?
”HM
Edited by Hoot Mon, : No reason given.

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Replies to this message:
 Message 42 by molbiogirl, posted 11-25-2007 8:20 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 45 of 60 (436539)
11-26-2007 11:29 AM
Reply to: Message 42 by molbiogirl
11-25-2007 8:20 PM


Epialleles and the germ-soma division
molbiogirl, thanks for the article. It hits the spot pretty well. But now I'm left with more questions:
1. What is an epiallele? Is it an intron?
2. When, if ever, does "soft inheritance" turn "hard"?
3. Exactly how could "soft inheritance" turn "hard"?
4. How does mitiosis affect meiosis? How vast is the so-called "germ-soma division"?
5. How come Wounded King doesn't know about epialleles? He said in Message 37:
Hoot I can't tell from this if you even have the faintest idea what you are talking about. There is no such thing as an epigene nor epigenetic material.
6. And once again: Can evolution occur only on an epigenetic level and without the fixation of new alleles?
I realize were traipsing around in fronteer territory here. From E. J. Richards:
quote:
There are many questions to address about the mechanistic aspects of epigenetic inheritance and the significance of inherited epialleles.
How much of this epigenetic stuff is speculative and how much has been confirmed empirically?
Oh, and one more question:
7. Why don't you post your synthesis of this material rather than quoting someone elses?
”HM

This message is a reply to:
 Message 42 by molbiogirl, posted 11-25-2007 8:20 PM molbiogirl has replied

Replies to this message:
 Message 46 by molbiogirl, posted 11-26-2007 11:55 AM Fosdick has replied
 Message 49 by Wounded King, posted 11-26-2007 12:08 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 47 of 60 (436542)
11-26-2007 11:58 AM
Reply to: Message 43 by RAZD
11-25-2007 9:14 PM


RADZ writes:
If I try to put this into more general (layman?) terminology, is it fair to say that:
  • Environment during development plus genotype produces a phenotype,
  • The same genotype in a different environment could produce a different phenotype (depending on what is affecting the development of the organisms),
  • Natural selection operates on the phenotype,
  • Thus the effect of the environment on the phenotype can be selected and inherited as long as the population stays in that environment?
Can these phenotype changes not due to genotype become fixed in a population?
Would you still class this as hereditary traits (as in "evolution is the change in hereditary traits in populations from generation to generation") or do we need some new terminology?
Good questions. But I don't think there are conclusive answers to any of them. I would like to know, for example, how "...phenotype changes not due to genotype become fixed in a population." "Fixed"? Fixed where? In what? And when molbiogirl answers simply "Yes" to all of your questions I get the queezy feeling nobody around here really understands how biological evolution works.
”HM

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 48 of 60 (436543)
11-26-2007 12:03 PM
Reply to: Message 46 by molbiogirl
11-26-2007 11:55 AM


Re: Epialleles and the germ-soma division
molbiogirl writes:
Because I got bitchslapped by Jadaeris for not posting enough CnP from the literature.
mbg, you're too cute to be bitchslapped by a stinkin' admin. Don't let them intimidate you into becoming a googleized lit parrot.
”HM

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 Message 46 by molbiogirl, posted 11-26-2007 11:55 AM molbiogirl has not replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 50 of 60 (436549)
11-26-2007 12:17 PM
Reply to: Message 49 by Wounded King
11-26-2007 12:08 PM


Re: Epialleles and the germ-soma division
WK writes:
He does, but an epiallele is neither an epigene nor epigenetic material. It is in fact the reason why I asked you to explain what you understood by the term allele and which you somehow managed to come to the completely wrong conclusion about despite your 'allele centric' view.
By changing the way a gene is expressed epigenetic modification essentially creates a further allelic variation of that gene, although the primary genetic sequence is not directly changed, unless you count DNA methylation.
So it's all about allelic variation. Thank you. That is what I thought all along. It's whatever affects the allele in the final analysis. So biological evolution is allele-centric in that regard.
”HM

This message is a reply to:
 Message 49 by Wounded King, posted 11-26-2007 12:08 PM Wounded King has replied

Replies to this message:
 Message 51 by Wounded King, posted 11-26-2007 12:25 PM Fosdick has replied
 Message 52 by molbiogirl, posted 11-26-2007 1:24 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 53 of 60 (436560)
11-26-2007 1:30 PM
Reply to: Message 52 by molbiogirl
11-26-2007 1:24 PM


Re: Epialleles and the germ-soma division
Because I'm stupid?

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 54 of 60 (436564)
11-26-2007 1:50 PM
Reply to: Message 51 by Wounded King
11-26-2007 12:25 PM


Re: Epialleles and the germ-soma division
WK writes:
But what constitutes an allele is open for discussion
You mean an allele is not a variant of a gene?
You saying 'That is what I thought all along.' worries me when you have so clearly had no idea what you are talking about 'all along'.
I'm just trying to squeeze out some of the ambiguity, Wounded. Is there something wrong with that. You know, there were other scientists in history who asked weird questions, such as What is the difference between heat and temperature? or Why couldn't time be a variable and the speed of light a constant? I don't compare myself to those guys, of course, but you seem awfully opposed to my kinds of questions. When I ask you if an epiallele is an intron I picture some poor allele that was shuffled off to the junk yard and forgotten by the genome, but nevertheless trying to send epigenetic signals to its exonic relatives back home.
And I'm pretty sure molbiogirl won't like my conjecture any better than you.
”HM

This message is a reply to:
 Message 51 by Wounded King, posted 11-26-2007 12:25 PM Wounded King has replied

Replies to this message:
 Message 55 by Wounded King, posted 11-26-2007 2:04 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 56 of 60 (436573)
11-26-2007 2:31 PM
Reply to: Message 55 by Wounded King
11-26-2007 2:04 PM


Re: Epialleles and the germ-soma division
WK writes:
In this case, given the usual understanding of what consitutes a gene, no. The gene, as represented by a sequence of nucleotides, is not changed. That is why the term epiallele is used, to distinguish it from the normal conception of an allele. An epiallele is formed by a set of extragenomic factors which act upon the gene causing a change in its expression sufficient to impact the phenotype.
That's nicely stated. But must it be only extragenomic factors that create epialleles? If a gene is coded to add leucine, for example, to build a protein the requisite codon could have any of four nucleotide configurations: CUU, CUC, CUA, and CUG. Why couldn't those differences amount to some sort to epigenetic effect? Obviously there is ambiguity even in the codon itself. Why couldn't junk DNA also have epigenetic roles to play as switches or something? Those would be intragenomic causes of epialleles. Or not?
”HM

This message is a reply to:
 Message 55 by Wounded King, posted 11-26-2007 2:04 PM Wounded King has replied

Replies to this message:
 Message 57 by Wounded King, posted 11-26-2007 2:47 PM Fosdick has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 58 of 60 (436596)
11-26-2007 6:30 PM
Reply to: Message 57 by Wounded King
11-26-2007 2:47 PM


Re: Epialleles and the germ-soma division
WK, thanks for your help. I'll admit to you and mbg that I had Disney-level appreciation of the epiallele. What was and still is hard for me to swallow is this notion that epigenetic factors play a role in neo-Darwinian evolution. If epialleles are merely chemically tweaked regular alleles then I am struggling to understand how their epiallelic features get communicated to the offspring. I suppose I just have to go along with those who say that meiosis and fertilization will bring forward what ever is epiallelic about them. I suppose I have to agree that chromatin carries more evolvable information that just genetic code. Am I right?
”HM

This message is a reply to:
 Message 57 by Wounded King, posted 11-26-2007 2:47 PM Wounded King has not replied

  
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