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Author Topic:   changes or mutations ... perhaps clarifying the terms in the process.
Wounded King
Member (Idle past 2170 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 16 of 22 (267729)
12-11-2005 7:49 AM
Reply to: Message 14 by RAZD
12-10-2005 8:08 PM


Types of mutation
There are a number of processes which cause heritable changes in traits and might be considered 'mutations'. Of these the discussion almost exclusively concerns genetic mutations, i.e. heritable changes in the DNA either in the exact makeup of the primary genetic sequence or in the large scale duplication of chromosomes or even whole genomes.

So the range of mutation extends from single point mutations, through gene duplications and right the way up to whole genome duplications. A distinction might be made between sub-chromosomal and whole chromosomal level mutations. In which case 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. 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.

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.

TTFN,

WK


This message is a reply to:
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Replies to this message:
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RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.4


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.


we are limited in our ability to understand
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RebelAAmerican.Zen[Deist
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RAZD
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Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
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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 :p) ... 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 responded

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RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.4


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 responded

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nwr
Member
Posts: 5585
From: Geneva, Illinois
Joined: 08-08-2005


Message 20 of 22 (267745)
12-11-2005 10:04 AM
Reply to: Message 19 by RAZD
12-11-2005 9:49 AM


Re: Why "mistakes in copying "?
RAZD writes:

Changes in DNA by differences in location, number and orientation of segments made during {reproductive\replication} processes


Looks good to me.

RAZD in message 17 writes:

You are also dealing with the layman's understanding of mutation - the B-grade horror movie radiation induced instant change at a macro level.


That sounds like a pretty good assessment of how most people view mutation.


What shall it profit a nation if it gain the whole world, yet lose its own soul.
(paraphrasing Mark 8:36)
This message is a reply to:
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RAZD
Member
Posts: 19756
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.4


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.


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Wounded King
Member (Idle past 2170 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 22 of 22 (278607)
01-13-2006 6:30 AM
Reply to: Message 18 by RAZD
12-11-2005 9:17 AM


Re: Types of mutation
I know this is rather belated but I was looking for another thread on mutation and came across this post which I never got round to addressing.

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.

Many people only consider genetic mutation to be mutation proper, i.e. changes in the amount and base composition of the DNA. There are other heritable states based upon chemical and structural changes in the DNA such as methylation of DNA or methylation and acetylation of histones, which are sometimes termed epigenetic mutations. These epigentic mutations are sometimes not as stable as genetic mutations and their roles are much better studied in cell populations, as in tumorigenesis, than in transgenerational studies of organisms. This is changing however and there are a number of heritable phenotypes associated with apparently stable epigenetic mutations.

These aren't mutations anyone is likely to come across much until studying at an undergraduate level, although epigenetics has a higher profile now than it used to due to the importance of epigenetic factors in nuclear reprogramming and its relevance to cloning and stem cell production.

Bad news for the 'half' that misses a critical one, but extra material to play with for the other.

It can easily be bad news for both. Extra chromosomes are often associated with genetic or developmental defects leading to infertility or sterility.

Do we know of any mechanism that control the rates of changes, and how do these impact the picture?

There are a number of different mechanisms. One is the development of a mutator phenotype, in some cases this is merely due to the loss of a proofreading enzyme which relaxes the error checking during DNA synthesis. There are a number of well studied bacterial mutator phenotypes and they are one of the explanations for apparently adaptive mutations, another possible mechanism is mutation leading to a decrease in activity of cell membrane transport proteins which act to export mutagenic metabolites.

Conversely there are mechanisms considered more truly adaptive, although they are still similar in mechanism, such as one described in a recent paper where stress caused a bacterium to actively switch from a high fidelity to an error prone mechanism of double strand break repair, the double strand break repair mechanism leads to a localisation of mutations to regions where breaks occur which limits the number of possible mutations but doesn't specifically target any specific gene per se (Ponder, et al., 2005).

TTFN,

WK


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 Message 18 by RAZD, posted 12-11-2005 9:17 AM RAZD has not yet responded

    
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