mrmike5133,
You stated
"Yes, dogs give birth to dogs. But if you could follow the geneology of any dog back thousands of years eventually you would get to wolves..."
And would wolves belong to any other "kind" of animal? Like the horse kind? Cat? No...wolves are still part of the dog kind of animal.

Plunge is correct in all he is saying, Ryan. You are using the same smoke and mirror logic that all proponents of ID use in an attempt to discredit natural selection and evolution, and none of them hold up to rational thought. A great example is the article referenced by *ChristJesustheonlyway*. The article tries to debunk evolution by saying that dogs only give birth to dogs. The basic concept you and other proponents of ID fail to understand is that evolution occurs through many small changes over a long period of time. Yes, dogs give birth to dogs. But if you could follow the geneology of any dog back thousands of years eventually you would get to wolves...because those are the animals from which the modern dog arose through the process of human selection. Humans took those first wolves who approached their camps looking for food and selected traits they found desirable, then bred pairs which showed those traits. Eventually, the offspring that were produced were more like the dogs the humans wanted and less like wolves. This is not a change which can be observed over 1 generation.

Listen to Plunge...there's a reason he keeps stressing the environment. Environmental pressures are the motor that powers evolution. But organisms do not evolve overnight, it takes hundreds, even thousands of generations.

Take it from someone who already has his degree in Biology - your arguments show a complete lack of understanding of natural selection, evolution, and biological processes in general.

plunge, in this statement:
" "To further address your question over the point of “ID”, it is testable and provable, that new species have and can arise through natural selection. Some of my own research has indicated this very premise. Evolution is great at tinkering with the currently available resources."
your reply:
This claim stands in direct contradiction to your entire previous line of discussion! "

I believe he's talking about micro-evolution (outlined in Michael Dentons book: Evolution:theory in crisis). Variation within a species is observable and testable; you can watch the changes that occur: breeding. The problem comes when you say that breeding or micro-evolution creates an altogether new kind of animal.
Read this ariticle:
http://www.answersingenesis.org/creation/v18/i2/dogs.asp

" My attempt to quote you was not an attempt at dishonesty"

In leaving out a crucial element of what I said, you virtually reversed my meaning.

"As I said however, dispite some studies that demonstrate the amelioration of cost, no one asserts that mutations do not come at "some cost" (as vague as that may be.)"

Really? Can you find even one mainstream biologist who believes that a mutation is inherently "costly" in all cases by some deep principle? The very idea makes no sense. Mutations are random alterations. They can affect fitness in virtually any way: by improving some feature without affecting anything else, harming it with affecting anything, harming some feature while improving another, and so on. The very idea that mutations are somehow drawing upon some limited account of benefit that must be paid back in harm is bizarre and mystical, not scientific.

"All scientists realize that mutations come with inherant costs. And your logic is right. It is a two way street, we have just never observed traffic going in the opposite direction."

That's sheer nonsense. We've seen bacteria, in real time, evolve entirely new pathways to process lactose after we've deleted entirely their original systems. And an endless number of other examples. There is no logical reason why mutation wouldn't go in both directions: mutations are random and have no preference TOWARDS incurring extra costs any more than they have in avoiding them.

"It has been proven to be very instramental primordial germ cell differentiation."

Hunh? Again, the problem isn't that _I_ don't understand what you're saying, but that I don't understand what your point is. You aren't addressing the issue of relevance: whether gradual changes can accumulate is not the same thing as whether a very specific set of changes in a single instance is plausible or not. Spouting a bunch of jargon and then declaring the issue demonstrated is just not going to fly., especially when it turns out to be just a substitution for an actual argument.

"And lastly to your rash comment about morphological mutations. I hate to tell you this but you are absolutely wrong. No one, dispite years of labratory experiments, have been able to derive a benifical morphological mutation; just hypothetical models of how one had to have happened at some point in the past."

First of all, they aren't simply hypothetical models: they are near mutation for mutation accounts of changes based on the comparison of often thousands of related individual genomes. But second of all, even a quick scan through a Futuyma textbook would tell you that you are wrong and that the literature is chock full of such changes.

"Our argument in this case is hopefully one of semantics. But surely you cannot claim that this has ever been demonstrated in a published scientific work. Search the literature and feel free to send me examples of anything you find."

Good grief. Beneficial changes in morphology include even things like slight alterations in skin color (all of which require underlying mutation). Are you really claiming that the literature is not chock full with examples of such things? That's just sheer denial at work.

Hey Plunge,
My attempt to quote you was not an attempt at dishonesty. You are right that what works in one environment may not work in another. As I said however, dispite some studies that demonstrate the amelioration of cost, no one asserts that mutations do not come at "some cost" (as vague as that may be.) All scientists realize that mutations come with inherant costs. And your logic is right. It is a two way street, we have just never observed traffic going in the opposite direction. Maybe one day we will and my argument will be null and void.
Using plain English - The Transcription Factor (TF) I am speaking of is Sonic the Hedgehog (Shh) which operates on Gli (pronounced just as it is spelled). It has been proven to be very instramental primordial germ cell differentiation. Look it up and then let's talk.
My comments over speciation do not serve as contradiction to my argument in anyway. If you were truely a scientist you would know that there are dozens of species concepts, and that the idea of speciation is in no way a testament to evolution or mutation. Homologous recombination is more than sufficent for speciation to occur. (Darwin's finches are great examples of this)
And lastly to your rash comment about morphological mutations. I hate to tell you this but you are absolutely wrong. No one, dispite years of labratory experiments, have been able to derive a benifical morphological mutation; just hypothetical models of how one had to have happened at some point in the past. Our argument in this case is hopefully one of semantics. But surely you cannot claim that this has ever been demonstrated in a published scientific work. Search the literature and feel free to send me examples of anything you find.

"Plunge realizes that the mutant strains come with certain defects."

That's not what I said at all: that's a gross distortion of what I said bordering on dishonest. What I said is that there is no universal definition of a defect or a benefit and that leaving this out of the picture is highly misleading (to simply ignore this point seriously makes me question your motives). You cannot speak of mutations incurring costs as if there were some universal measure of fitness that mutations can increase on only buy causing defects elsewhere. The parent strain in your example only thrives over the mutant strain because you switched back to the original environment in which the mutant strain no longer has any special advantage. Furthermore, the example is not generalizable: not all mutant strains are outcompeted by parent strains even if the environment remains unchanged throughout.

Your basic argument, that mutation is inherently costly, is simply wrong on its face in principle. Consider: anything that a mutation can undo, it can do (mutations are, after all, random changes to the genetic code, and we'll consider point mutations in this case as an example). Because this street is two way, then if you can claim that mutation can universally reduce fitness, you must also admit that a mutation can universally increase fitness. There's no way out of that conclusion, even if there WAS some universal definition of fitness.

"In direct response to “plunge” this does become a make or break necessity for evolving novel systems."

That's simply bizarre. You are claiming that a single example of a specific possible change that you don't think can work proves that no complex interlocking system could ever have evolved? Again: how do you explain the ample demonstration of how blood clotting, a Rube goldbergian system if there ever was one, evolved?

The fact that you used technical jargon instead of explaining the example in a way that laypeople could understand (which would be easy enough) is a red flag that you simply through that out there to make your argument obscure and confusing. Dembski does this all the time: takes an unconvincing argument in English, translates it into math, and then presents it to laypeople without the ability to decipher what he's arguing. The move is far more akin to an octopus squirting ink than it is any real attempt to make an argument.

"To further address your question over the point of “ID”, it is testable and provable, that new species have and can arise through natural selection. Some of my own research has indicated this very premise. Evolution is great at tinkering with the currently available resources."

This claim stands in direct contradiction to your entire previous line of discussion! If evolution can be responsible for successful speciation, ultimately mutation must have played a role in creating the continuing range of variations necessary. Point me to an example where evolution caused speciation... but at a terrible price in deleterious effects that your claims about mutation would suggest are inevitable.

"This argument does not stand up under a clear scrutiny of the nature of mutations."

A nature that you and you alone apparently know better than the entire biologists who would find your claims bizarre. You could write an _introductory_ textbook on mutation that would still have to run hundreds of pages and would STILL only scratch the surface of the subject, and yet you claim to have figured out a "nature of mutations" that can be summed up in just a few sentances.

"This argument does not stand up under a clear scrutiny of the nature of mutations. Have we ever, despite all human attempts, seen any mutation that gives a morphological selective advantage to any species?"

There are hundreds of articles a year which not only describe such things but aren't even considered an important or interesting aspect of the article. I have to ask whether you even know what morphological means: how can you at one point claim that natural selection can cause speciation and then that it can't ever lead to morphological advantage. Can you please cite some speciations which DON'T involve any morphological changes or mutations whatsoever?