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Author Topic:   changes or mutations ... perhaps clarifying the terms in the process.
RAZD
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From: the other end of the sidewalk
Joined: 03-14-2004
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Message 1 of 22 (267497)
12-10-2005 10:38 AM


just what are mutations?
This is an offshoot of the www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=641&m=1>{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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we are limited in our ability to understand
by our ability to understand

RebelAAmericanOZen[Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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

  
AdminNWR
Inactive Member


Message 2 of 22 (267501)
12-10-2005 10:43 AM


Thread moved here from the Proposed New Topics forum.
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RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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. :D ... regrouping and running on:

answer to Wounded King: http://http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=5&t=641&m=272#271

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}


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.


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pink sasquatch
Member (Idle past 4102 days)
Posts: 1567
Joined: 06-10-2004


Message 4 of 22 (267508)
12-10-2005 10:56 AM
Reply to: Message 1 by RAZD
12-10-2005 10:38 AM


a non-issue
RAZD, I find this incessant questioning of the terminology quite silly, honestly.

RAZD writes:

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.

Why is the definition useless? Don't you think we should have a word that means "all changes in the DNA"? I think a word defining that is damn useful.

Is "dog" a useless word because it doesn't specify the breed of dog?

You give your list of "types of changes". All these are qualified mutations.

This is what the scientific world does. They use qualifiers to further define the mutation, as in "point mutation", or "duplication mutation", or "translocation mutation." (Noun. Adjective. Get it? Non-issue.) In many contexts, terms are shortenened - "duplications" or "indels" for example.

In other words, all of the descriptive terminology needed is already in place and use, and your personal decision to start referring to "mutations" as "changes" has only made a more confusing situation - because you have used an even more generic term than the one you were complaining was too generic to begin with...

A non-issue.


This message is a reply to:
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nwr
Member
Posts: 5585
From: Geneva, Illinois
Joined: 08-08-2005


Message 5 of 22 (267511)
12-10-2005 11:02 AM


Why "mistakes in copying "?
Evolutionary biologists are usually careful to avoid language that suggests teleological committments. That is, except when talking about mutations. There they use terms such as "mistakes in copying" or "copy error", which suggests that the purpose was to make an identical copy but some sort of error crept in.

The literature seems to strongly suggest that evolution would not occur if there were none of these "copy errors". So we have an apparently strange system that only works because it doesn't work.

Why not a different terminology, such as using "different" or "discrepancy" instead of "error".

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.


What shall it profit a nation if it gain the whole world, yet lose its own soul.
(paraphrasing Mark 8:36)
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RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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?


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 4 by pink sasquatch, posted 12-10-2005 10:56 AM pink sasquatch has responded

Replies to this message:
 Message 7 by pink sasquatch, posted 12-10-2005 12:35 PM RAZD has responded

  
pink sasquatch
Member (Idle past 4102 days)
Posts: 1567
Joined: 06-10-2004


Message 7 of 22 (267537)
12-10-2005 12:35 PM
Reply to: Message 6 by RAZD
12-10-2005 11:39 AM


Q: a non-issue or issue not dealt with? A: a non-issue
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.

I feel like you are the only one having issue with this.

No one is glossing over it, though it has been pointed out that you seem to make some unnecessary distinctions; sometimes seemingly incorrect distinctions.

There is existing language to specify the type and mechanism of any particular mutation.

Why add the redundant, generic term "change"? Weren't you just arguing that mutation was so generic is was "useless"? Isn't "change" even more generic, and thus more "useless"?

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.

Your statement is anything but "clear". It seems self-contradictory nonsensical doublespeak.

Moo-moo dogface to the banana patch?


This message is a reply to:
 Message 6 by RAZD, posted 12-10-2005 11:39 AM RAZD has responded

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 Message 8 by RAZD, posted 12-10-2005 12:56 PM pink sasquatch has responded

  
RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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...


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 7 by pink sasquatch, posted 12-10-2005 12:35 PM pink sasquatch has responded

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

  
TimChase
Inactive Member


Message 9 of 22 (267589)
12-10-2005 5:29 PM
Reply to: Message 5 by nwr
12-10-2005 11:02 AM


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

Evolutionary biologists are usually careful to avoid language that suggests teleological committments. That is, except when talking about mutations. There they use terms such as "mistakes in copying" or "copy error", which suggests that the purpose was to make an identical copy but some sort of error crept in.
The literature seems to strongly suggest that evolution would not occur if there were none of these "copy errors". So we have an apparently strange system that only works because it doesn't work.

Why not a different terminology, such as using "different" or "discrepancy" instead of "error".

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.

Well, this could, I suppose, spawn yet another thread. However, I personally have very little problem with teleology in the description of biological systems. What is the purpose (or if you prefer, "function") of an eye? To see. And of course we could come up with a vast number of other examples, whether they involve a variety of enzymes, intracellular structures, endogenous retroviruses which become active when needed to create a barrier to the mother's immune system in the placenta, or what have you. The important thing is that there is no externally-imposed teleology to the evolutionary process itself. But the biological world is rife with teleological (goal-directed) action and organs for performing such action. The important thing (in terms of naturalism) is the fact that such causation is an emergent phenomena -- and it is internal to the system which exhibits it.

If one attempts to avoid such language (where we understand the form of causation of biological systems by analogy with the goal-directed causation of our own existence), trying instead to state things in purely mechanical, reductive, value-free language, one loses sight of the biological systems themselves as systems. For example, how would one explain in thoroughly mechanical terms the function of an eye in relation to an organism's surivival or interaction with its environment (e.g., a cheetah hunting its prey) without any explicit or implicit reference to its function or purpose? How much much more would one have to write in order to avoid the role of vision while describing the role of vision in life -- and what precisely would be the point? So in this respect, I see no problem with the terms "mistakes, copying, errors, purpose" or for that matter, "reproduction, construction" or "creative" (although the last of these would be more at the level of a metaphor -- unless one considers the possibility that the capacity to evolve may itself be something which has evolved -- but that probably belongs to yet another thread). It may be possible to avoid teleological language in biology, but I cannot see how it would be desirable, and in all likelihood, the attempt to do so would simply result in a great deal of violence being done to one's logic and prose.

This message has been edited by TimChase, 12-10-2005 07:19 PM


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TimChase
Inactive Member


Message 10 of 22 (267598)
12-10-2005 6:07 PM
Reply to: Message 8 by RAZD
12-10-2005 12:56 PM


Re: Q: a non-issue or issue not dealt with? A:: still not dealt with.
RAZD writes:

so
how many different mechanisms are there?

to repeat the topic question a third time...

I think part of the problem lies in the question itself. 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.

For example, a "transposition" is a "deletion" and an "insertion." "Transposition" and "retrotransposition" involve "insertions," where what was inserted may have originated from another part of the same genome, from an endogenous symbiont (e.g., a mitochondrion or chloroplast), or an infectious exogenous agent (e.g., possibly a bacteria, but far more likely some kind of virus). Any of these changes to the code could at least hypothetically take place during the copying of the genome in either meiosis or mitosis (although single nucleic polymorphisms -- also known as SNPs or point mutations -- would probably be more likely, yet I am aware of a random stuttering which sometimes lengthens the repititive sections known as teleomeres during the copying process), or they could take place at an earlier or later point. Similarly, a retroviral insertion (category 4) is a change to DNA as the result of chemistry (category 1), and a result of a viral infection (category 5), and may be due to some scientist intentionally or unintentionally exposing the host organism to a virus (category 6).

These categories which you have listed belong to different schemas which are used in different albeit often closely-related contexts. And sometimes those processes which you have pidgeon-holed into the same category actually belong to different schemas and contexts themselves.

This message has been edited by TimChase, 12-10-2005 06:19 PM


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RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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? :D

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.


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:
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RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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?


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.


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 Message 10 by TimChase, posted 12-10-2005 6:07 PM TimChase has not yet responded

  
pink sasquatch
Member (Idle past 4102 days)
Posts: 1567
Joined: 06-10-2004


Message 13 of 22 (267611)
12-10-2005 6:43 PM
Reply to: Message 8 by RAZD
12-10-2005 12:56 PM


silly
so
how many different mechanisms are there?

to repeat the topic question a third time...

Perhaps if the thread intent is to list mechanisms of mutation, and NOT about defining mutations and changes, you should have thought of a better freakin' title than "changes vs mutations... perhaps clarifying the terms in the process".

I also think it's silly to write a post, and then tell others what they can and can not respond to, especially telling them they're not supposed to respond the part of the OP that corresponds to the title of the thread.

I'm sick of this crap. It seems like you are only interested in discussion if you are being told you are right. Otherwise you just post short, evasive, ambiguous comments.


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RAZD
Member
Posts: 19759
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 5.8


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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Nighttrain
Member (Idle past 2073 days)
Posts: 1512
From: brisbane,australia
Joined: 06-08-2004


Message 15 of 22 (267696)
12-10-2005 11:17 PM


A Layman`s View
Pardon the intrusion of a layman, but I thought the length of the phylogeograpic thread was extended by the continued explanation of evolution as mutation and selection as if mutation came from a single cause. So that responders kept hammering about single-source 'damage' leading to reduction in diversity. 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. Explanations of bacterial remnants in cells might have helped, too. OTOH,this may have been covered and it slipped by me.
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