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Author Topic:   changes or mutations ... perhaps clarifying the terms in the process.
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 1 of 22 (267497)
12-10-2005 10:38 AM


just what are mutations?
This is an offshoot of the {the phylogeographic challenge to creationism (mick)} thread.
The question was about what changes in DNA are strickly speaking mutations in the DNA and what are due to other mechanims.
The first bump this runs into is the definition of all changes in the DNA as mutations. Personally I find this definition to be useless. Presumably a hand of a designer (human or other) actively reaching into the DNA strand and rearranging things is still a mutation. Such a wide definition has no predictive or differentiative ability.
So let's start the discussion by focusing on different mechanisms for changes to the DNA {structure\order\sequence}, and seeing how many different mechanisms can be {defined\described\categorized}.
Off the top I would submit these possible categories of changes to the DNA makeup of a cell (whether single cell or part of a multicellular organism):
  1. change to DNA by interaction with {particle radiation\energy\chemical\atom\etc}
  2. Changes in DNA caused by differences in location, number and orientation of segments made during {reproductive\replication} processes change to DNA by mistakes in copying during reproductive processes (2){cbe3}
  3. changes to DNA by sections being cropped out, inserted or cropped out and reinserted (indels, transposons, etc)
  4. change to DNA by {virus infection\insertion, plasmid insertion, horizontal transfer}
  5. the addition of alternative DNA sequences to the cell (plasmids, viruses, mitochondria ...}
  6. intentional physical interference and alteration of the DNA for a specific purpose (genetic engineering)
  7. Change to the DNA proportions due to differential {separation\segregation} of DNA elements during cell division.(1){abe1}
I would say that #6 is not technically a mutation, although such things could cause other mutations ...
Are there other mechanisms that result in changes to an organisms DNA makeup?
Enjoy.


(1) -
Wounded King, msg 16 writes:
one of which , the chromosomal and above, would be almost exclusively based on errors in the process of chromosome segregation durin cell division.
{/abe2}
{abe3}
(2) - from NWR, see Message 5, Message 19, Message 20{/abe3}

{abe1}edited to highlight the primary {question\topic\purpose} of the thread to be dealt with first, the rest is just the preamble and context once this is done
specifically this is not about the definition of "mutation" at this time.
{/abe1}.
This message has been edited by RAZD, 12*10*2005 05:55 PM
This message has been edited by RAZD, 12*11*2005 09:39 AM
This message has been edited by RAZD, 12*11*2005 10:35 AM
Edited by RAZD, : colors arrangement for readability
Edited by RAZD, : No reason given.

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Replies to this message:
 Message 4 by pink sasquatch, posted 12-10-2005 10:56 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 3 of 22 (267504)
12-10-2005 10:49 AM
Reply to: Message 2 by AdminNWR
12-10-2005 10:43 AM


answers to another post on the topic.
dang that was fast. I was trying to add reply below and got a {{topic closed}} error. ... regrouping and running on:
answer to Wounded King: http://EvC Forum: the phylogeographic challenge to creationism
When mutagenic factors alter DNA they frequently only affect 1 strand and the alteration they produce is frequently not a chemical conversion of a nucleotide to a totally different valid nucleotide but to a particularly chemically altered form of the original nucleotide or an aberant form of a different nucleotide (Alberts, et al, 2002). It is only when the DNA is copied and a new strand syntesised using the altered nucleotide as a template that a proper complementary nucleotide is introduced into the base pair, and only after a subsequent round of reproduction that a double strand will be produced with 2 properly complementary normal nucleotides.
I'm not disagreeing with that. That is how I understand mutation to be passed on from {A} to {B}.
Arguably retroviral insertions don't require DNA synthesis, at least on the part of the host cell,
I'm assuming here that you {mean\imply} that the retroviral insertions cause the replication of the virus (by the affected section of DNA) to cause the {replication\repetition\reproduction} of the insertion in other DNA (new and old alike). Isn't this really an infection of the DNA to hijack the mechanism to produce copies of the infector?
Because these aren't 2 different cases. Virtually every single instance of a mutation of any kind, point, inversion, duplication, deletion is the result of the process of DNA replication.
So you're saying that copy error is the ne plus ultra cause of all mutations? (leaving out the issues of viral {infection\insertion} and horizontal transfer)?
{abe} For this thread let's address whether there are one or two mechanims involved here. {/abe}

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 6 of 22 (267517)
12-10-2005 11:39 AM
Reply to: Message 4 by pink sasquatch
12-10-2005 10:56 AM


Re: a non-issue or issue not dealt with.
what I want to talk about is the different kinds of changes the different mechanism.
glossing it over as all the same process is not helping that end.
If you are using mutation and change as totally interchangeable terms and other people don't, then using "change" is providing more clarity to the discussion of how many kinds of changes there are, and NOT derailing it into a discussion of the definition of mutation.
so how many mechanisms are there?

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This message is a reply to:
 Message 4 by pink sasquatch, posted 12-10-2005 10:56 AM pink sasquatch has replied

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 Message 7 by pink sasquatch, posted 12-10-2005 12:35 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 8 of 22 (267539)
12-10-2005 12:56 PM
Reply to: Message 7 by pink sasquatch
12-10-2005 12:35 PM


Re: Q: a non-issue or issue not dealt with? A:: still not dealt with.
so
how many different mechanisms are there?
to repeat the topic question a third time...

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This message is a reply to:
 Message 7 by pink sasquatch, posted 12-10-2005 12:35 PM pink sasquatch has replied

Replies to this message:
 Message 10 by TimChase, posted 12-10-2005 6:07 PM RAZD has replied
 Message 13 by pink sasquatch, posted 12-10-2005 6:43 PM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 11 of 22 (267604)
12-10-2005 6:23 PM
Reply to: Message 5 by nwr
12-10-2005 11:02 AM


Re: Why "mistakes in copying "?
Yes, but "alterations during copying" implies intentional change... "change during copying" gets cumbersome in the context of the phrasing above, and (besides) the process is commonly known as copy errors yes?
It seems to me that we could consider reproduction to be a creative process of constructing the next generation, with "variation on a theme of ..." as part of the creative process.
... and that's not a purpose envisaged in the process?
Variation on a theme is what we end up with due to all the different mechanisms for inducing change in the theme. I like the concept personally, philosophically, more than a "stuff happens" approach.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 12 of 22 (267608)
12-10-2005 6:36 PM
Reply to: Message 10 by TimChase
12-10-2005 6:07 PM


types of changes
There isn't one schema consisting of mutually-exclusive, jointly-exhaustive categories. There exist numerous schemas with categories which overlap with other categories in a variety of ways.
They overlap in the ways in which they affect the DNA and they overlap in the way specific causal agents can trigger the different processes, agreed.
What I was looking at was specific ways the DNA was altered and what the different mechanisms were that caused those changes to occur. This does lead to listing some causes in several categories (virus for example)
Perhaps what we need is a grid approach rather than a list?

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
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Message 14 of 22 (267637)
12-10-2005 8:08 PM
Reply to: Message 13 by pink sasquatch
12-10-2005 6:43 PM


then stop.
yaknow? I really got to wonder what you are so upset about that you just can't open to the question of how many different kinds of mechanisms exist for change.
If you don't want to participate in that discussion nobody will hold you to it.

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Replies to this message:
 Message 16 by Wounded King, posted 12-11-2005 7:49 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 17 of 22 (267736)
12-11-2005 8:41 AM
Reply to: Message 15 by Nighttrain
12-10-2005 11:17 PM


Re: A Layman`s View
no intrusion, but an interesting insight.
With knowledge of the multiple ways to alter the basic DNA, they might have grasped the significance of mutation and given it a little slack.
You are also dealing with the layman's understanding of mutation - the B-grade horror movie radiation induced instant change at a macro level.
Maybe that is overstating it a little, but ask the average person on the street what mutation is and I bet they all mention radiation as the cause.
Thanks.

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 18 of 22 (267741)
12-11-2005 9:17 AM
Reply to: Message 16 by Wounded King
12-11-2005 7:49 AM


Re: Types of mutation
Thanks.
There are a number of processes which cause heritable changes in traits and might be considered 'mutations'.
Are there any that can't be considered 'mutations' and if so what do you call them what are they and how do they operate? I'm curious because of the "all change is mutation" crowd here.
So the range of mutation extends from single point mutations, through gene duplications and right the way up to whole genome duplications.
Got that: including polyploidy.
you would have two categories of mutation one of which , the chromosomal and above, would be almost exclusively based on errors in the process of chromosome segregation durin cell division.
Add that to the original list. Similar to differential separation of plasmids and mitochondria\chloroplasts and such. Bad news for the 'half' that misses a critical one, but extra material to play with for the other.
All of the sub-chromosomal mutations not attributable to an ouside factor such as a retrovirus, would then be the result of changes brought about by a combination of chemical alterations to nucleotides and subsequent mis-repair or mis-copying, or the result of mis repair after more severe damage such as double stranded breaks, or the result of factors such as non-homologous recombination.
And also including your standard radiation induced molecular change, relatively minor within the overall picture.
You could therefore seperate some of these out to stages in which the mutation occurs, i.e. S-phase when the DNA is synthesised or M- phase when the cells divides and chromosomes segregate.
Sounds useful to me. This also tends towards a matrix approach rather than a list approach.
What about mechanism that change the rates of change? There have been several studies that show an increased rate of mutations in bacteria when put in stress condition: it seems that there is some (one or more) mechanisms that control how many "variations on a theme" are thrown out to the wolves in the casino of life.
It seems that the rate of change in species is "fine tuned" to the need for change, and yet it (the rate of change) is not constant.
Part of it can be due to different levels of selection pressure, thus in the aftermath of an extinction event there is very little competition to all the different vartiations thrown out (plus maximizing fecundity because of plentiful resources plus founder subpopulations - not really segregated from the main populations but just out eating the north 40 - while changes occur, plus ... getting off topic ) ... but these don't explain an increase in mutations when things are bad and selection pressure is high.
Do we know of any mechanism that control the rates of changes, and how do these impact the picture? The random radioation type would not be impacted, but certainly the cell process (replication etc) changes are open to adjusting the level of corrections used.
thanks again.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 16 by Wounded King, posted 12-11-2005 7:49 AM Wounded King has replied

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RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 19 of 22 (267742)
12-11-2005 9:49 AM
Reply to: Message 5 by nwr
12-10-2005 11:02 AM


Re: Why "mistakes in copying "?
looking at this again.
2. change to DNA by mistakes in copying during reproductive processes
what about
2. changes in DNA by differences in location, number and orientation of segments made during {reproductive\replication} processes
That gets away from the "mistakes" issue and also provides more information on what is involved.

we are limited in our ability to understand
by our ability to understand
RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 5 by nwr, posted 12-10-2005 11:02 AM nwr has replied

Replies to this message:
 Message 20 by nwr, posted 12-11-2005 10:04 AM RAZD has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 21 of 22 (268428)
12-12-2005 9:05 PM
Reply to: Message 20 by nwr
12-11-2005 10:04 AM


good reasons.
That sounds like a pretty good assessment of how most people view mutation.
And a good reason to talk about the different kinds of changes that occur, why\how they occur and when they occur.
I edited the OP to make that change.

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we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.

This message is a reply to:
 Message 20 by nwr, posted 12-11-2005 10:04 AM nwr has not replied

  
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