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Author Topic:   what is a mutation?
lbhandli
Inactive Member


Message 1 of 5 (207)
03-12-2001 8:47 PM


In an effort to keep threads clear--I have moved this over from The Definition of the Modern Synthesis to address thmsberry's claims of random mutations. I will be taking quotes from both posts 2 and 5 in Definition of the Modern Synthesis

From Thmsberry:

quote:

Next, I already bought up this definition blur you guys want to make about the word mutation. If you semantically define mutation to just mean a change in an organisms genome. Yes, a horizontal mechanism would be a mutation. However, Big Big Big Big Big problem when you do that. The word then has no meaning at all in terms of how it is actually used in Biology and Genetics. You would be ignoring the fact that types of mutations are defined in Biology and Genetics and these types do not include horizontal mechanisms. You can't simply redefine the word out of context. And

quote:

Look at any Biology or Genetics textbook and see if the way and the types of mutations that they define allow for horizontal mechanisms and/or allow evolutionary mutations to be
non-random. If so, please present a quote. I am completely unaware of any respected
textbook that does. Also, at the very least, the infamous talkorigin link is wrong again. Look at
their primer on Evolutionary Biology. The way they define Mutation makes my Argument.

Random issue dealt with in another thread...
How so? I see it as exactly that ambiguity Percy points out in describing the use of the term mutation. Percy:

quote:

Third, your definition seems self-evidently reasonable. What's nreasonable is your insistence that the definition of mutation is the same everywhere in all contexts.

Let me quote some specific sources:

Lewin, Benjamin. Genes. 1997. Oxford University Press
"Mutations are heritable alterations that change genetic information." Pg. 65

Burns, W. George and Paul Bottino. The Science Of Genetics. 6th Ed. 1989. Macmillan
"A mutation then, is a sudden, heritable change in the structure of genetic material."

Griffiths, Anthony JF, Jeffrey H. Miller, David T. Suzuki, Richard C. Lewontin, and William M. Gelbart. An Introduction to Genetic Analysis. 5th Ed. WH Freeman (6th edition the same on the same issues--1996)

"Mutation: Process that produces a gene or chromosom set differing from the wild type. "

"Wild Type: The genotype or phenotype that is found in nature or instead of lab stock"

Hartl, Daniel L, David Freifelder, and Leon A Snyder. Basic Genetics. 1988.

Mutation: "a heritable alteration in a gene."

Strickberger, Monroe W. Evolution. 3rd Ed. 2000. Jones and Bartlett Publishing.

"A change in the nucleotide sequence of genetic material whether by substitution, duplication, insertion, deletion, or inversion."

Futuyma, Douglass. Evolutionary Biology. 3rd. Ed. 1998. Sinauer Associates, Inc.

"An alteration of genetic material, usually of a DNA sequence, that gives rise to a new allele (however distinguished) or haplotype."

Rieger, R., A. Michaels, M. M. Green. Glossary of Genetics: Classics and Molecular. 5th Ed. 1991. Springer-?

"Any heritable alteration whether a singe base change in DNA (or RNA) or a large-scale rearrangement, in the genetic material of a living cell or virus."

One of the best descriptions is probably found here that demonstrates that ambiguity:
Brown, T.A. Genetics: A Molecular Approach. 1990. Chapman and Hall.
"Strictly speaking a mutation is any alteration in the nucleotide sequence of DNA molecule, but the term is generally used to refer to a relatively small-scale change, often thought not always affecting just a single base pair. In contrast recombination involves the exchange of segments of polynucleotides between different DNA molecules and can give rise to quite substantial rearrangements. A third type of event, transposition, provides a link between the two, it occurs by recombination but often results in a mutation."

quote:

Let's examine some of the sites that you presented.

http://www.talkorigins.org/faqs/mutations.html#types

Great. Talkorigin has a section where it defines mutation the way your trying to. Fine. Where is the respected textbook where it is defined as Random or Nonrandom. It basically doesn?t address this issue. Also, the fact that it defines mutation differently in different section actually poses a problem for your blind reliance on this website, not a problem in my argument.


The above should create some question of your position at best. Mutation is used in different contexts. I think Brown's definition is quite good at pointing out the different uses.

quote:

http://www.msu.edu/course/mic/431/chapt03.htm

Pathetic. Website. It was a summary of study notes. It was not a respected textbook and in types of mutations did not mention all the horizontal mechanisms, if any. Brings up the Randomness issue. But presents Randomness in terms of Randomness vs. Directed. An argument that I have not even made.


Percy is more charitable than I am on the issue. The site is to a college level class based on a text that is cited. You wanted texts--I provided several above that are exactly in agreement with the definition. Perhaps you can explain to me exactly what is pathetic about it again?

quote:

You posted: a link to a quote by Mike Syvanen

Before whining about this quote:
"It is difficult to imagine, mostly because that is not the way we are trained to think. If you
accept that mutation can fashion new structures, why is it so radical to include
the contributions of foreign genes as one of the mutational mechanisms?
Please look up Mike's citations in either academic journals or as far as books. One of the books
will make you look especially silly. ?

I must admit. This was great reading. I disagree with a major assumption made by the author
without evidence. But I could tell by some of his argument that he is aware of the issues in the
debate that we have yet to move on and discuss. But this is digression.


Percy castigated me for not saying what the book was, but I didn't because it would be so glaringly obvious if you had bothered to look it up. As usual you undertook no effort to look anything up. The book is entitled Horizontal Gene Transfer, eds Michael Syvanen and Clarence I. Kado. 1998. Chapman and Hall. What major assumption are you disagreeing with? I'll be happy to point you to his specific work that deals with that major assumption. What you disagree with above is unclear so I cannot respond.

However, I would say that given the quote from him, he does see horizontal transfer as a mutational mechanism. Additionally, Krassilov's article in the book, "Character Parallelism and Reticulation in the Origin of Angiosperms" describes horizontal transfer as a mechanism for macromutations to spread. I do agree the term is used in different contexts differently, but it seems to me that in the context of evolution, such a process is indeed a mutation. Other articles also refer to the insertions and deletions in context of a mutation in reference to HGT.

quote:

I mean come on. You must know this. When a human male and female have a kid. The child is the product of horizontal transfer of sorts, but the two organisms are clearly apart of the same
genome. But once again, where in these text books do they include a horizontal mechanisms exchanging DNA from a foreign Genome of an organism into the Genome of an entirely different organisms with a different Genome. Where does a textbook list the additional types of mutations that the talkorigin link attempts to lump together.

In generically discussing transposons including foreign transposons, Lewin (cited above) says:

[QUOTE]Transposons are interesting not just for the mechanisms involved in the manipulation of DNA, but also for the evolutionarly consequences of their mobility. They may provide the major source of mutations in the genome.[quote]
In Griffiths et al. they make no effort in discussing transposons that are entirely intra genomic and inter genomic when they refer to tranposon mutatants. Most texts simply don't cover the issue very well, btw. So claiming they are definitive one way or another is simply not very useful.

quote:

You see, Horizontal transfer is a horizontal mechanism, but so is sexual reproduction. But I am
talking about and have been talking about horizontal mechanisms that involve organism live and
not alive from different genomes. The problem that I think you might be having with debating
me is that I am extremely precise with my arguments.

I just wet my knickers. Thank you for a good laugh. We are discussing the same thing. You have now been provided very specific sources that demonstrate the definitions provided so far are quite typical in texts and other scientific sources. I'll admit there is differing use of the terms, but your claims to be the sole source of authority on such issues is not valid.

You asked me to define horizontal gene transfer, and frankly I am a bit confused. I use it as a horizontal transfer is between distantly related species that don't commonly share genetic material through reproduction like activities. The thing that confused me is you don't define it in your post, but fumble around with examples that don't appear to have any consistency with them.

quote:

In order to avoid these sort of semantic parachutes. It makes my post quite wordy, but effective. Oftentimes, you present some point later in your argument. But typically, I have already accounted for it. And it?s like I have to repeat the same argument over an over so that you can realize that it has already been addressed.

Several who have discussed issues with you have specifically cited your inability to address issues forthrightly. I suggest that while I may be unclear at times, it is a rare moment where you are clear.
Cheers,
Larry


Replies to this message:
 Message 2 by Thmsberry, posted 03-13-2001 1:51 AM lbhandli has responded

Thmsberry
Inactive Member


Message 2 of 5 (211)
03-13-2001 1:51 AM
Reply to: Message 1 by lbhandli
03-12-2001 8:47 PM


Larry,

Do you see that you have not proven your argument?

You need to show a text that defines mutation broadly and then goes into detail on exactly what it means by defining the types of mutation.

One of these textbooks or when you put them all together needs to show that te types of mutations need to include all of the known horizontal mechanism for exchanging DNA from distinct genomes.

You have yet to show this.

The reason I had you define Horizontal Gene Transfer because it is quite clear that you are trying to define a term that is used within the realm of Bacteria and claim that it is used more broadly and encompassing.

Your are going to have to prove that Biologist and Geneticist use the term Horizontal Gene transfer for organisms considered to be distinct genomes. Your going to have to show that it is used for multi-celled organisms.

Your transposon point I covered months ago. There is a difference between foreign transposon and transposons within an organisms' genome. Many claim that foreign transposons or retroviruses consisting of transposons are the evolutionary precursor of transposons within an organisms genomes. But the transposon defined as a mutation under types of mutation in respectable resources clearly only defines itself as within in the genome. It usually even goes as far as saying they are part of the organisms junk DNA. If you disagree, Evidence please.

And finally, Can we stop with the straw man that I am arguing that the word mutation can't be defined broadly? That has never been this argument. The argument is whether or not, including horizontal mechanism involving organisms from other genomes, would be consistent with the types of mutations defined by respectable sources, such as textbooks, of Biology and Genetics.

This is such a minor point but I would be more than happy to find out that I was wrong on it. But I do need some respectable textbook to confirm that you are indeed correct.


This message is a reply to:
 Message 1 by lbhandli, posted 03-12-2001 8:47 PM lbhandli has responded

Replies to this message:
 Message 3 by Thmsberry, posted 03-13-2001 3:01 AM Thmsberry has not yet responded
 Message 4 by lbhandli, posted 03-13-2001 1:22 PM Thmsberry has responded

Thmsberry
Inactive Member


Message 3 of 5 (213)
03-13-2001 3:01 AM
Reply to: Message 2 by Thmsberry
03-13-2001 1:51 AM


Percy,

Look at this other tangent on the meaning of the word mutation. Why is this argument a diversion as well? Because using Modern Synthesis the way that it was actual defined in the previous argument, one realizes that when the framers of MS used the term mutation, they did not even consider the credibility of the notion of horizontal mechanisms outside the genome and were unaware of most of the one’s that we know of today.

But you wrote:
“I own three textbooks on genetics (two by accident, but that's another story), and none mention horizontal mechanisms in their definitions of mutation. In fact, they don't mention horizontal mechanisms at all. They all deal solely with changes to the existing genome, never anywhere with additions to the genome from the outside. I don't know if this is typical for genetics textbooks, but all were published after 1998, so they're fairly recent.
But when I read in other places, such as books or articles on evolution, or in the aforementioned genetics textbook by Snyder and Champness, I see mutation defined more expansively in a way that includes horizontal mechanisms. “

The evidence that you personally own supports my argument about the definition of mutation and the context (types of mutation). Then you bring up something about Snyder and Champness. You present it as if it is evidence against me. Where is this evidence? The link that Larry gave did not list a horizontal mechanism from outside of the genome as a possible type of mutation.

You see, I think you are missing my argument here as well. The word mutation can be ambiguously defined. That is what makes semantic arguments possible. But the actual biological/genetic usage of the term stems from the types of mutations that the textbook actually lists. My whole argument has been that if you take the meaning out of the context, you can include horizontal mechanisms. But if you place the meaning within the context that Biology and Genetics actually use the term, horizontal mechanisms are not possible. So once again, where is your sides evidence to the contrary? If Snyder and Champness or any other respected test book actually list horizontal mechanisms outside the genome in their types mutations, I love to see it. Where is the evidence?

You mention “when I read in other places, such as books or articles on evolution… I see mutation defined more expansively in a way that includes horizontal mechanisms.” Are you saying that the term is defined in a way that allows for horizontal mechanism or are you saying that horizontal mechanism are in fact defined as types of mutation? The first use is to be expected and does not contradict my argument. The second way this sentence can be interpreted would be direct evidence against my argument and I would love to see it. Where is this evidence?


This message is a reply to:
 Message 2 by Thmsberry, posted 03-13-2001 1:51 AM Thmsberry has not yet responded

lbhandli
Inactive Member


Message 4 of 5 (215)
03-13-2001 1:22 PM
Reply to: Message 2 by Thmsberry
03-13-2001 1:51 AM


quote:
Originally posted by Thmsberry:

You need to show a text that defines mutation broadly and then goes into detail on exactly what it means by defining the types of mutation.


I offered several sources that define mutation broadly. When they define mutations in more detail they leave it unclear as to how such a change would be regarded. My original question regarded wouldn't such a change be a mutation if it is a change in the genotype. I provided the editor of a book on Horizontal Gene Transfer referring to HGT as a mutational mechanism and another author in that book also referring to it in that way. A third author describes the effects in terms of mutations.

This is still unclear because Syvanen was referring to a specific case. So I asked him and got this response on talk.origins:

quote:

"OK. If a transfer event results in a change of phenotype in the recipient then, by definition , the recipient would be considered a mutant. Thus the event that caused the mutant would be called a mutation. Once the mechanism is uncovered as being due to gene transfer, there is often a reluctance to use the term "mutation", unless, as Ron O mentioned, the foreign DNA is fused into the host genome."

Ron's comments were:

quote:

"It depends, sometimes it is an insertion mutation, but the insert is foreign DNA. There has been horizontal gene transfer of whole mitochondrial genomes between mouse species that has been documented, and I would not consider this type of transfer to be a mutation. It is just a swapping of genetic
material. I wouldn't consider any horizontal transfer due to hybridization between species to be a mutation unless there was chromosomal fusions or translocations involved."

When deja/google picks up the thread, I'll post the urls.

Additionally Mike added this:

quote:

"In the past, when this topic has been discussed, I have received requests
for reprints. These are now available as pdf files at my website:

http://www.vme.net/hgt/


I'm going to be adding that to the Links and Information section because it has 5 reprints of articles by Syvanen on HGTs.

quote:

The reason I had you define Horizontal Gene Transfer because it is quite clear that you are trying to define a term that is used within the realm of Bacteria and claim that it is used more broadly and encompassing.

The interesting things is that the texts don't draw clear lines between the two. While I agree one might be better labeled gene flow, the texts I read were not that clear. And it appears that Okimoto and Syvanen disagree in part at least. The confusion is largely over the complexity of process. And in reference to the original discussion, this seems to me to be why such events might be included in the Modern Synthesis as Futuyma explains the tenets. The understanding of genetics was so minimal that any sort of event like these would probably fit.

The counter to this is that such events may be almost saltational in nature which certainly would be counter to the Modern Synthesis. The first of the papers by Syvanen seems to suggest that is a possibility.

From what I can gather at this point, HGTs may be mutations in the traditional sense, but other times they may not be depending on the exact processes and material exchanged.

quote:

Your transposon point I covered months ago. There is a difference between foreign transposon and transposons within an organisms' genome. Many claim that foreign transposons or retroviruses consisting of transposons are the evolutionary precursor of transposons within an organisms genomes. But the transposon defined as a mutation under types of mutation in respectable resources clearly only defines itself as within in the genome.

What evidence do you have for this. I found it to be much less clear. Please provide sources that are very clear. I found one expert who finds it much less clear than you assert it is and I find the texts get very vague on this very point.

quote:

It usually even goes as far as saying they are part of the organisms junk DNA. If you disagree, Evidence please.

I've provided an extensive list that are quite ambiguous on the issue and asked an author in the field I would suggest that it is your turn to do a little work.

quote:

And finally, Can we stop with the straw man that I am arguing that the word mutation can't be defined broadly? That has never been this argument. The argument is whether or not, including horizontal mechanism involving organisms from other genomes, would be consistent with the types of mutations defined by respectable sources, such as textbooks, of Biology and Genetics.

I am arguing that the texts aren't real clear. Of course the problem is that most of them don't really address HGT in any detail so I'm not sure how one could make such a strong conclusion as you claim. What sources are you using?

Cheers,
Larry Handlin

[This message has been edited by lbhandli (edited 03-13-2001).]


This message is a reply to:
 Message 2 by Thmsberry, posted 03-13-2001 1:51 AM Thmsberry has responded

Replies to this message:
 Message 5 by Thmsberry, posted 03-14-2001 2:11 PM lbhandli has not yet responded

Thmsberry
Inactive Member


Message 5 of 5 (230)
03-14-2001 2:11 PM
Reply to: Message 4 by lbhandli
03-13-2001 1:22 PM


Outside the context of a definition of Modern Synthesis debate, this thread is irrelevant.

This message is a reply to:
 Message 4 by lbhandli, posted 03-13-2001 1:22 PM lbhandli has not yet responded

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