Understanding through Discussion


Welcome! You are not logged in. [ Login ]
EvC Forum active members: 64 (9073 total)
73 online now:
AZPaul3, kjsimons (2 members, 71 visitors)
Newest Member: MidwestPaul
Post Volume: Total: 893,320 Year: 4,432/6,534 Month: 646/900 Week: 170/182 Day: 3/47 Hour: 0/0

Announcements: Security Update Released


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Mutation and its role in evolution: A beginners guide
Wounded King
Member (Idle past 3334 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 1 of 60 (342714)
08-23-2006 10:23 AM


In the previous Natural Limitation to Evolutionary Processes (2/14/05) thread Faith expressed a desire to better understand the nature of mutation and to further discuss some specific examples of beneficial mutations which were raised in that thread.

To that end I think we should have a mutation thread in the science forums where it belongs, and perhaps Faith can start an accompanying thread in the Theology and ID forum if she wants to develop her own ideas about how what we are discussing could fit into her own ideas about the history of life on Earth.

Mutation is not a highly specific term in and of itself. As a fundamental basis for evolution all mutation needs to be is some sort of heritable change.

Obviously the major focus of research into such things focuses on genetic mutations since we have a large number of tools for investigating and manipulating genes and a reasonable understanding of how they operate. This does not mean that genetic mutation is the be all and end all of mutation in terms of evolution, but it is certainly the best starting point.

All genetic mutations are by no means equal either, not in their extent, nature or frequency. While we can make general observations about the relative frequency of particular types of mutation, and of regions in the genome or sequences of DNA which are more prone to mutations than others, we cannot accurately predict any specific mutation occuring at a specific locus in any given organism.

The best we can do is make estimates based on the various probabilities and study populations of organisms to see how well they reflect those estimates.

Naturally the best targets for such experiments are organisms which can be grown from a single organism such as selfing plants or many types of bacteria or yeast.

For animals it is harder to get a suitable experimental species. For years Drosophila was the standard model organism for developmental genetics, but now with the rise in transgenics mice and other species more closely related to our own are gaining prominence.

To get around the issue of not having clonal populations derived from one individual many of these populations are kept as genetically homogenous as possible by inbreeding.

Such conditions allow us to identify specific mutations when they present themselves. One of the perennial problems with the idea of reliably guaging rate of detrimental or beneficial mutations is the much more obvious nature of detrimental mutations.

We can argue to the double muscled cows come home over whether a mutated myostatin gene leading to muscular hypertrophy is really beneficial, but no one is going to quibble that a gene which leads to a total failure to develop as an embryo, or to an early death before reaching a reproductive age, is anything other than detrimental. Similarly medicine focuses specifically on syndromes and diseases we consider largely detrimental. It is only very recently that research has really taken off looking for genetic bases for things such as resistance traits to various diseases.

The only way to guage the beneficial nature of a newly arisen gene is to track its course through a population over a large number of generations. Unfortunately that has not really been tenable so far in human populations.

What can be done is to look at the prevalence of certain alleles in particular populations and make some conclusions about how selection has worked on those alleles. Naturally for biologists the origin of these alleles is ascribed to mutation, obviously that is something that Faith might wish to contend with on a thread other than this one.

This is rather a high level overview of certain isues that might be relevant to ones understanding of mutation. Ideally this thread should be a venue for others, particularly Faith, to ask specific questions about the nature of mutation and the science surrounding it.

TTFN,

WK


Replies to this message:
 Message 3 by Jazzns, posted 08-23-2006 3:01 PM Wounded King has replied
 Message 11 by Faith, posted 08-23-2006 9:52 PM Wounded King has taken no action
 Message 15 by Nighttrain, posted 08-24-2006 2:07 AM Wounded King has replied

  
AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 2 of 60 (342744)
08-23-2006 11:29 AM


Thread moved here from the Proposed New Topics forum.

  
Jazzns
Member (Idle past 3151 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 3 of 60 (342778)
08-23-2006 3:01 PM
Reply to: Message 1 by Wounded King
08-23-2006 10:23 AM


Obviously the major focus of research into such things focuses on genetic mutations since we have a large number of tools for investigating and manipulating genes and a reasonable understanding of how they operate. This does not mean that genetic mutation is the be all and end all of mutation in terms of evolution, but it is certainly the best starting point.

What is an example of a non-genetic mutation?


Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

This message is a reply to:
 Message 1 by Wounded King, posted 08-23-2006 10:23 AM Wounded King has replied

Replies to this message:
 Message 4 by Wounded King, posted 08-23-2006 3:32 PM Jazzns has replied

  
Wounded King
Member (Idle past 3334 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 4 of 60 (342789)
08-23-2006 3:32 PM
Reply to: Message 3 by Jazzns
08-23-2006 3:01 PM


Epigenetic mutations such as those that affect the methylation of DNA (Rakyan et al., 2003) or the acetylation or methylation of histones (Cheung and Lau, 2005) but which do not change the actual primary nucleotide sequence of the DNA.

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
 Message 3 by Jazzns, posted 08-23-2006 3:01 PM Jazzns has replied

Replies to this message:
 Message 5 by Jazzns, posted 08-23-2006 3:55 PM Wounded King has replied

  
Jazzns
Member (Idle past 3151 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 5 of 60 (342795)
08-23-2006 3:55 PM
Reply to: Message 4 by Wounded King
08-23-2006 3:32 PM


Although I could glean a bit from those abstracts, can you layman them up a bit for us. It sounds like there are aspects of heredity that are non-genetic? What then is a mutation in that context? I don't want to distract too much from the main topic, this just seemed interesting.


Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

This message is a reply to:
 Message 4 by Wounded King, posted 08-23-2006 3:32 PM Wounded King has replied

Replies to this message:
 Message 6 by Wounded King, posted 08-23-2006 5:02 PM Jazzns has replied
 Message 7 by Brad McFall, posted 08-23-2006 5:18 PM Jazzns has taken no action

  
Wounded King
Member (Idle past 3334 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 6 of 60 (342820)
08-23-2006 5:02 PM
Reply to: Message 5 by Jazzns
08-23-2006 3:55 PM


The first paper deals with an example where certain mice show a distinct kink in their tails. This phenotype is associated not with distinct allele but with distinct levels of DNA methylation at a specific locus.

DNA methylation is when the Cytosine of CpG doublets become methylated, either spontaneously or due to the action of a methyltransferase enzyme. In geeral the more highly methylated a sequence of DNA the less likely itis to be transcribed. Methylation also tends to lead to the recruitment of histone modifying enzymes which act to further suppress expression by compacting DNA to a heterochromatic state.

So the only difference between the mice with kinked tails and those without was the methylation status of the Axin locus.

the second paper deals mostly with the chromatin remodelling enzymes and does not cover transgenerational heritability but only the epigenetic equivalent of somatic mutations.

As I suggested before my own definition of a mutation would be any heritable change, and this could be subdivided into at least genetic and epigenetic mutation although there may well be other subdivisions with which we are not yet familiar.

TTFN,

WK


This message is a reply to:
 Message 5 by Jazzns, posted 08-23-2006 3:55 PM Jazzns has replied

Replies to this message:
 Message 8 by Jazzns, posted 08-23-2006 5:28 PM Wounded King has taken no action
 Message 13 by NosyNed, posted 08-24-2006 12:42 AM Wounded King has replied

  
Brad McFall
Member (Idle past 4272 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 7 of 60 (342825)
08-23-2006 5:18 PM
Reply to: Message 5 by Jazzns
08-23-2006 3:55 PM


in plants...
See contextually

Click to enlarge

quote:
SJ GOULD SETH

So while thinking about how the gap in a graft
pic of graft formation etc
is healed and graft hybrids may form
Callus Formation at Graft Interface in Ginkgo biloba L.
model
It is suggested that this discovery throws new light on the phenomenon of graft-hybridization. In spite of many reports to the contrary, graft-hybrids have so far been explained only on the basis of their being chimaeras.

independent of gene content in the ordinary sense

And so it might be that any phenotypic variation("occasional single variations" De Vries speaks for Darwin on(continued in the thumnail above)) that need not necessarily involve specific DNA genes (changing), could count as non-genetic "mutations", If you will.

Now what "single" means DOES mean not sexual but what else... well, Gould would have it not be more than rarely attached to "benefical" necessarily etc. Tricky thing language is indeed. There might be a small opening to dissent against the notion but it is small indeed.

Edited by Brad McFall, : ref

Edited by Brad McFall, : letter misig


This message is a reply to:
 Message 5 by Jazzns, posted 08-23-2006 3:55 PM Jazzns has taken no action

  
Jazzns
Member (Idle past 3151 days)
Posts: 2657
From: A Better America
Joined: 07-23-2004


Message 8 of 60 (342827)
08-23-2006 5:28 PM
Reply to: Message 6 by Wounded King
08-23-2006 5:02 PM


Somehow I replied with a message 8 but it is not showing up.

I'll repeat my reply.

Ok. Lets see if I can distill this into something I can understand.

It is the action of these enzymes is what causes the change in phenotype?
The enzymes or creation of them is somehow heritable yet not genetic?
Is a "mutation" in this sense have to do with the differential presence of the enzymes or what they do the phenotype?

Do those questions even make sense?

Edited by Jazzns, : No reason given.


Of course, biblical creationists are committed to belief in God's written Word, the Bible, which forbids bearing false witness; --AIG (lest they forget)

This message is a reply to:
 Message 6 by Wounded King, posted 08-23-2006 5:02 PM Wounded King has taken no action

Replies to this message:
 Message 9 by Aegist, posted 08-23-2006 9:33 PM Jazzns has replied

  
Aegist
Member (Idle past 2939 days)
Posts: 23
From: Sydney NSW Australia
Joined: 08-21-2006


Message 9 of 60 (342857)
08-23-2006 9:33 PM
Reply to: Message 8 by Jazzns
08-23-2006 5:28 PM


The questions almost make sense, but I think I detect an underlying confusion about the whole process.

The 'Enzymes' which i think you are referring to are the Methyltransferases. They are enzymes present in all cells with their own tasks and they are not mutations in themselves in anysense. They are the mediators of the form of mutation called Epigenetic mutation.

What these enzymes do is attach a molecule (a methyl group) to a DNA base pair thereby slightly altering the chemical nature of that base pair and interupting how it normally functions. This is not permanent (unlike genetic mutations) and can be undone quite easily by another enzyme (If my memory serves me correctly, perhaps I should get some references for this before I state it :o).

So, these enzymes change the way DNA works (at that particualr base pair) thereby stopping the expression of any gene present at that site. So methylating a gene is basically turning it 'OFF' which is similar to mutating it away...making it no longer exist. An organism with a gene turned off is functionally the same as an organism without that gene. The obvious difference being in the fact that the organism with the gene turned off can turn that gene back on by a simple reaction while the organism without the gene can't get the gene back!

The heritability of the enzyme is not the question. the enzymes (methyltransferases) are made from the DNA (which is heritable). The heritability of the "Mutation" is that once these methyltransferases has methylated a genetic site, that methylation is heritable. In other words, once a site has been inactivated, it will be inactivated in the offspring and their offspring and so on until something happens which causes the gene to be turned back on. This is the heritability of the mutation.

Hopefully the answer to your third question is already clear, but just in case: The enzyme itself is virtually irrelevent (it isn't even necessary for the enzyme to exist for DNA to be methylated!). The mutation is the Methyl-group addition to the DNA base pair which changes the chemical structure of that nucleotide. This change in chemical structure affects the way that DNA sequence acts, and therefore affects how it is expressed, and therefore affects the phenotype.

I hope these answers make sense! :) Please correct me where appropriate others who are more versed in this topic than I!

Shane

Edited by Aegist, : clarity


----------------------------------
http://shanegreenup.blogspot.com
www.sportsarbitrageguide.com

This message is a reply to:
 Message 8 by Jazzns, posted 08-23-2006 5:28 PM Jazzns has replied

Replies to this message:
 Message 10 by Brad McFall, posted 08-23-2006 9:45 PM Aegist has taken no action
 Message 18 by Jazzns, posted 08-24-2006 3:46 PM Aegist has taken no action

  
Brad McFall
Member (Idle past 4272 days)
Posts: 3428
From: Ithaca,NY, USA
Joined: 12-20-2001


Message 10 of 60 (342858)
08-23-2006 9:45 PM
Reply to: Message 9 by Aegist
08-23-2006 9:33 PM


taking a constitutional
I do not want to modify anyone's desire for a better constitution but it might re-p(l)ay to think about the thread with Huxley's words on the topic in hand.


Click to enlarge


Click to enlarge

quote:
Evolution The Modern Synthesis by Julian Huxley 1964

This message is a reply to:
 Message 9 by Aegist, posted 08-23-2006 9:33 PM Aegist has taken no action

  
Faith 
Suspended Member (Idle past 684 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 11 of 60 (342859)
08-23-2006 9:52 PM
Reply to: Message 1 by Wounded King
08-23-2006 10:23 AM


Sorry I somehow overlooked this thread
Hi WK, Sorry, although I thought I looked, I didn't see this thread you put up as we'd discussed you might do, and I just ended up putting together a PNT of my own, which I also thought should go in a science forum after all.

But maybe I can adjust mine to the Theological Creationism thread somehow. It does, after all, raise the usual YEC concerns.

In setting up my PNT I collected a couple of definitions of mutations, one that defines it as the "driving force of evolution." Your definition is more tentative on that score. But it makes sense to me that it is the engine that drives evolution if evolution is true. There's no other process that generates new genetic material. All the other processes merely select or rearrange existing genetic material.

But I do have to say this thread of yours is most likely going to be way over my head. I will try to follow it but I wonder if I'll even be able to come up with a useful question.

Edited by Faith, : No reason given.

Edited by Faith, : No reason given.


This message is a reply to:
 Message 1 by Wounded King, posted 08-23-2006 10:23 AM Wounded King has taken no action

Replies to this message:
 Message 12 by crashfrog, posted 08-23-2006 9:55 PM Faith has taken no action

  
crashfrog
Member (Idle past 706 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 12 of 60 (342860)
08-23-2006 9:55 PM
Reply to: Message 11 by Faith
08-23-2006 9:52 PM


Re: Sorry I somehow overlooked this thread
I think your questions in your other topic are very useful. If it doesn't get promoted, I hope you post an abridged version of your OP over here.

This message is a reply to:
 Message 11 by Faith, posted 08-23-2006 9:52 PM Faith has taken no action

  
NosyNed
Member
Posts: 8968
From: Canada
Joined: 04-04-2003


Message 13 of 60 (342888)
08-24-2006 12:42 AM
Reply to: Message 6 by Wounded King
08-23-2006 5:02 PM


Over heads K.I.S.S.
I notice WK that Faith has joined in here. Her comment about "over my head" is a valid one.

This is supposed to be a "beginner's guide". This post and a preceding one are not particularly useful to a beginner. Can we try to keep the material at a much clearer level.

It would be nice if this thread did not assume any previous knowledge.

You may write:

DNA methylation is when the Cytosine of CpG doublets become methylated, either spontaneously or due to the action of a methyltransferase enzyme.

But one reads:
"DNA something strange sounding is when something else really strange sounding happpens, either spontaneously or due to the action of abracadabra chemical term."


This message is a reply to:
 Message 6 by Wounded King, posted 08-23-2006 5:02 PM Wounded King has replied

Replies to this message:
 Message 14 by kuresu, posted 08-24-2006 1:01 AM NosyNed has taken no action
 Message 16 by Wounded King, posted 08-24-2006 5:17 AM NosyNed has taken no action

  
kuresu
Member (Idle past 1752 days)
Posts: 2544
From: boulder, colorado
Joined: 03-24-2006


Message 14 of 60 (342892)
08-24-2006 1:01 AM
Reply to: Message 13 by NosyNed
08-24-2006 12:42 AM


Re: Over heads K.I.S.S.
DNA something strange sounding is when something else really strange sounding happpens, either spontaneously or due to the action of abracadabra chemical term

yep. Exactly what I understood. only thing is, the only way to know what a methyl group is to see a picture of it and the elements in it. my guess--it's got carbon and hydrogen, hence the meth. the -yl suggests like maybe an OH attached, but who knows (someone does).

I run across the KISS problem whenever I try to explain something that I know--like civ4, or history, or something else. I just can't leave out the complexity. urgh.


All a man's knowledge comes from his experiences

This message is a reply to:
 Message 13 by NosyNed, posted 08-24-2006 12:42 AM NosyNed has taken no action

  
Nighttrain
Member (Idle past 3233 days)
Posts: 1512
From: brisbane,australia
Joined: 06-08-2004


Message 15 of 60 (342895)
08-24-2006 2:07 AM
Reply to: Message 1 by Wounded King
08-23-2006 10:23 AM


The basic controls
Thanks for the primer, WK. I`m sure it will sort out a few problems in my mind as well in other members of EVC. Before we tackle the concept of what mutations mean to TOE, could we backstep and show a list of all known causes of change to genomes, e.g. solar radiation, mineral radiation, radon, toxic chemicals, etc. Which (if known) causes the most change? Are common environmental factors a force, or does it take abnormal states to effect change?

This message is a reply to:
 Message 1 by Wounded King, posted 08-23-2006 10:23 AM Wounded King has replied

Replies to this message:
 Message 17 by Wounded King, posted 08-24-2006 6:10 AM Nighttrain has replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2018 by EvC Forum, All Rights Reserved

™ Version 4.1
Innovative software from Qwixotic © 2022