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ORIGINAL: Jhud

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A mutation is a permanent nucleotide change in the genome. What are these "radically different things" you speak of?

Well, again, that is one word to describe mutiple disparate processes, and as such, fairly useless.

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ORIGINAL: Jhud
Well, that is one of my problems with the vague notion of ‘mutation’ – it can mean a number of radically different things.

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An ERV doesn’t ‘re-write’ a genome, it introduces a bit of code in the genome to be replicated.

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I think we are seeing a bit of confusion between the purpose of the infecting retrovirus and the purpose of the resulting ERV. Delivering new genetic code is indeed the purpose of the retrovirus. But creating an ERV is not. Had the program of the infecting retrovirus been carried through, the result would have been the replication of viruses and the destruction of the infected cell. So, from the perspective of the cell, the purpose of the delivery of new genetic code is indeed malicious for the purpose is to divert the cell machinery from its ordinary work to the replication of viruses.

Well, first off this is of course the ordinary assumption.

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Though it is really quite odd that an organism would evolve to kill or sicken it’s host when it could instead accomplish the same goal (replicate it’s genome) but simply inserting it into it’s hosts genome and let the host do all the work. In fact, it is generally detrimental to kill off one’s hosts, and certainly less effective.

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An ERV only occurs when the retrovirus is NOT successful in carrying out its purpose of stimulating the replication of viruses. So the creation of an ERV is by its very nature, never designed. It is a testimony to thwarted design---whatever the nature of its subsequent impact on the species in which it occurs.

Well, again that is the assumption.

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– indeed, I believe there is some theorizing that viruses are a decayed form of bacteria.

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Of course, at least from a theological perspective, it may be that viruses are intentionally harmful, and were designed to be that way.

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ORIGINAL: Jhud
Incorporating means exactly what it says - utilizing extant genetic material as a basis for producing the human genome.

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though to be clear, unlike other creatures, I think a human is much more than the product of a genome alone.

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ORIGINAL: Jhud

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A mutation is a permanent nucleotide change in the genome. What are these "radically different things" you speak of?

Well, again, that is one word to describe mutiple disparate processes, and as such, fairly useless.

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ORIGINAL: Jhud
Incorporating means exactly what it says - utilizing extant genetic material as a basis for producing the human genome.

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I don't think that this could happen apart from intelligence, though to be clear, unlike other creatures, I think a human is much more than the product of a genome alone.

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I still don't get where you are coming from on this. A mutation is a permanent nucleotide change in the genome. One can of course catalogue various changes into categories: point mutations, indels, transpositions, etc. Is this what you are getting at?

I don't find that any more vague than using the word "tree" to refer to pines, elms, palms, cypress, cherry trees, etc.

Nor do I find it at all useless.

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ORIGINAL: Jhud
But I think mutation is even less specific than that, because it is an attempt to describe a process, and is equivalent to 'change'. How did that gene state producing that protein? It 'changed'!

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The reality is some mutations constitute the removal of information, some the duplication of information, some the rearranging of information, and some the insertion of significant portions of novel information. Equating them all under the rubric of 'mutation' is like equating writing a book with ripping out the pages of a book.

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"Mutation" describes a result. A heritable change. It was this way within Lamarckism. Darwin showed that these mutations were not acquired but were variations from birth. Luria, Delbruck, and the Lederbergs went even farther and showed that the process that produces mutations does not reference the environment. That is, mutations are random with respect to fitness. With all of this work already in the bag DNA was finally discovered and the chemical basis of mutations was understood.

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Using your book analogy, mutation is equivalent to changing the text of the book with each new edition.

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ORIGINAL: Jhud
I fully understand where the term was derived - that doesn't change it's short comings as a description.

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Except if you changed a book by incidentally inserting, duplicating, and rearranging the words and letters, you would have nonsense.

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Then give us a better word that fits the observations that I listed before.

Science, like any other profession, is loaded with jargon. When scientists speak of mutations we know what each other are talking about but it may not be obvious to the layperson.

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But that is not so with DNA. All analogies have their limits.

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ORIGINAL: Jhud

Again, I fully understand the 'jargon' - but the terminology is still vague, and part of the reason why many evolutionary explanations are lacking.

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So DNA doesn't change by way of incidental insertions, duplications, and rearrangments?

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Then what would be a better word?

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Incidental is too vague, so your explanation is lacking.

I can do it too.

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ORIGINAL: Jhud

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Then what would be a better word?

We could start by calling a deletion a deletion, an erv an erv, a duplication a duplication, etc.

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ORIGINAL: Jhud
We could start by calling a deletion a deletion, an erv an erv, a duplication a duplication, etc.

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Incidental means without forethought - what is vague about that?

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And we can call a change a change. There is a reason languages develop generic terms.

When specification as to what kind of change is necessary, then of course we ought to use specific terms.

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What would we call them as a group of DNA changes? That's quite a mouthful in order to say "how DNA changes".

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Forethought is way too vague.

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ORIGINAL: Jhud
Why would we consider them a group?

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Not if one knows the language.

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ORIGINAL: Jhud

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And we can call a change a change. There is a reason languages develop generic terms.

When specification as to what kind of change is necessary, then of course we ought to use specific terms.

Exactly!

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Because you do. You consider them as fuel for selection.

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And if someone knows english they know what mutation means.

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ORIGINAL: Jhud

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Because you do. You consider them as fuel for selection.

Well I consider tree limbs, uranium, and wind to be fuel as well, but I don't think they are al that similar.

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And if someone knows english they know what mutation means.

Certainly - they will know that it means 'change' - and change isn't a mechanism.

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But do you consider them fuel for selection?

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Is "deletion" a mechanism?

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ORIGINAL: Jhud

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But do you consider them fuel for selection?

I think they are potentially fuel for selection.

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Is "deletion" a mechanism?

Sure, it's a great way to eliminate information.

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What are?

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Really? A removal of DNA can not produce novel morphology or novel function?

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ORIGINAL: Jhud
Insertions, deletions, duplications, and ervs.

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Oh, it can certainly change morphology, but I don't think that it will produce a novel function without straining the meaing of that word.

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What are insertions, deletions, duplications, and erv's?

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Could it produce an enzyme with a function not seen in the full length enzyme?