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The sad part is, something like this shouldn't even have to be defended. Especially from a doctor.

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In the paper in question it deals with three main mutations - V179D, L1001, and Y181C. These can occur sequentially in a population, and when either happens with the addition of L1001, they provide a 1000 fold increase in resistance to the antiviral medication. It is important to note that all the mutations confer slight resistance advantages alone; so only a single mutation is needed to these sites to increase resistance – and as long as that happens, the virus can stay around long enough for additional single mutations to occur, among which L1001 is the most potent, in combination with the others. In short, selection acts on a single mutation.

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Even sadder is that folks of your intelligence are completely unable and/or unwilling to separate biased interpretations, untestable hypotheses, and wild conjectures from factual, observable, meaningful knowledge. It is truly amazing how the religion of naturalism has warped the reasoning capacity of so-called "scientists" to such an extent!

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One of the times that we discussed this before, I asked you why there couldn’t be changes in organisms that were the result multiple coding mutations “adding up” after each of them had been selected for individually. In response, you said you’d explained this before and didn’t want to explain it again. The reason I brought up this paper is because it was an example of this; a change resulting from multiple coding mutations that have accumulated in a single organism. Are you saying now that you never doubted that this was possible?

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If that’s the case, can you tell me again what specific aspect of evolution you think is not possible? New species have already been observed forming in nature, and I’ve pointed you to examples of that. I’ve linked to this essay, which describes ways in which mutations can increase the information content of an organism’s genome, and the example I posted involving langur monkeys is an example of mutations being selected for that only provide an advantage as long as other mutations are present. And in this paper, we have an example of several selected-for coding mutations accumulating in a single organism. Even if I can’t find an example of all of these things occurring simultaneously in a single organism, all of them are apparently possible individually, so what is there that prevents evolution from happening as a result of these various changes adding up over a long period of time?

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In addition to ignoring the essay I posted a week ago, are you also going to ignore my question about why you haven’t had anything to say about it, despite my having specifically asked for people who disagree with its conclusion to explain why they do?

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Intelligent Design claims multiple unselected modifications to the genome working in concert to create a structure displaying combinatorial interdependencies is too improbable to occur by chance. If there were a structure or a system that could be shown to be the product of the same, then the primary critique of ID would be overcome; though obviously mine was as I said a much lower bar.

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Are you talking to me, or the person who you quoted?

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So it sounds like the aspect of evolution you think isn’t possible is just the evolution of structures that are deemed “irreducibly complex”. Is that right? For some reason I thought your argument here involved more than that.

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Behe presented this idea in Darwin’s Black Box. If this is basically the same thing he has to say in The Edge of Evolution, why does he need a second book about the same topic?

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I’d still like you to explain what problem you have with the line of reasoning presented in that essay.

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That's one aspect certainly.

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Well, at least you could pretend you have any idea what the book is about.

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You know I spent a few hours putting together a pretty cogent response to the paper you posted on antiviral drug resistance in the AIDs virus, apparently to no discernible effect. I have little motivation to tilting at another of your windmills.

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Can you please be specific about whether there are any other aspects of evolution that you don’t think are possible? I’m trying to get an understanding of your position here. I thought that one aspect was that you didn’t think it was possible for multiple selected-for coding mutations to accumulate in a single organism, but apparently I was wrong about your viewpoint on that.

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What I’m going by is the several pages’ worth of explanations you’ve posted about Behe’s arguments in that book during the time since I joined this forum, and the several times that amount I’ve seen looking through old threads. Is there more to his argument in this book that you just aren’t describing?

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Please don’t assume I’m finished with this topic entirely; the reason I’m trying to get a better understanding of your viewpoint is so I can address it properly. But in any case, I posted that essay around a week before you explained what you think of the HIV paper, so I think it’s still justified for me to be disappointed that you’ve declined to address this line of evidence for common descent.

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Well, my criteria were that five or more separate yet interdependent mutations (I didn't specify selected or unselected, though ID specifies unselected) couldn't produce novel "organs, limb types, body plans, functional capabilities" leading to increased viability and a separate evolutionary pathway.

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I don't think I ever mentioned irreducible complexity in conjunction with The Edge of Evolution. Why don't you just pick up the book and read it, so you can speak with a little bit of knowledge here?

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As you yourself pointed out, I did address common descent and ERVs.

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ORIGINAL: Agahnim
Five unselected mutations would just be another example of irreducible complexity, but can you please explain why you don’t think five selected mutations is possible?

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I’ve pointed out a new functional capability that was the result of one selected mutation; the ability to digest nylon in bacteria.

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You said you thought this was an ability the bacteria had always possessed, and in response I gave two reasons why that wasn’t possible.

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One is that bacteria with this ability are unable to survive without nylon, which was not invented until the 1930s,

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and the other is that the genome of this bacteria has been sequenced, showing that this was not a regulatory mutation.

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So we have an example of a new functional capability that’s the result of one selected mutation, and in this thread we have an example of how multiple selected mutations can accumulate in a single organism.

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If a single selected mutation can add a new functional capability, and multiple selected mutations can accumulate in a single organism, why isn’t it possible for there to be a new functional capability resulting from multiple selected mutations?

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I should have been more specific. What I meant is that you’ve said you have a problem with the idea of common descent, which means you presumably disagree with the conclusion drawn by that essay, but you haven’t attempted to explain where you think the flaw in its reasoning lies. That’s what I was disappointed by.

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Jhud, please don’t make the mistake of assuming that any of what Betta posted is an answer to what I’m asking you.

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Five unselected mutations would just be another example of irreducible complexity, but can you please explain why you don’t think five selected mutations is possible?

I’ve pointed out a new functional capability that was the result of one selected mutation; the ability to digest nylon in bacteria. You said you thought this was an ability the bacteria had always possessed, and in response I gave two reasons why that wasn’t possible. One is that bacteria with this ability are unable to survive without nylon, which was not invented until the 1930s, and the other is that the genome of this bacteria has been sequenced, showing that this was not a regulatory mutation. It was a frame shift mutation which modified an existing coding gene. You haven’t attempted to argue with my explanation of why this must be a novel ability of the bacteria, so I assume you don’t disagree with this being the case.

So we have an example of a new functional capability that’s the result of one selected mutation, and in this thread we have an example of how multiple selected mutations can accumulate in a single organism. I’m not sure if I’ll be able to find an example of this involving exactly what you’re asking for, but in this case I think what is and isn’t possible can be demonstrated independently of what I can personally come up with. If a single selected mutation can add a new functional capability, and multiple selected mutations can accumulate in a single organism, why isn’t it possible for there to be a new functional capability resulting from multiple selected mutations?

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What you said was this: And I set the bar pretty low; Behe’s definition of an irreducibly complex evolutionary pathway is one that contains one or more unselected steps, which would seem to be required for an irreducibly complex structure. I assumed you were referring to what Behe says in The Edge of Evolution, since that’s the main thing we were discussing here. Is that explanation of something in Darwin’s Black Box instead?

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I should have been more specific. What I meant is that you’ve said you have a problem with the idea of common descent, which means you presumably disagree with the conclusion drawn by that essay, but you haven’t attempted to explain where you think the flaw in its reasoning lies. That’s what I was disappointed by.

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ORIGINAL: Jhud
Well you are generally ignoring the “separate yet interdependent” aspect of my requirement.

I explained this pretty well in the thread ‘Designing a bat’ , if one looks at the genetic basis for the morphology of the bat and compares it to other mammalian genomes, one finds that bat morphology (longer forelimbs, greatly extended phalanges, a thin skin membrane, etc) is the product of a number of very specific modifications (generally through gene regulation) of a number of different genes that work together in concert to produce the overall morphology of the bat.

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Well, my main problem with common descent is that in reality, a number of major phylogenies have not been able to be resolved within the expected trees that Darwin predicted. But that would be a separate issue.

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The key point here is that the mutation occurred in an enhancer---one of those regulators that govern gene expression. But because it occurred here, a multitude of separate yet independent mutations were not required (one for extra bone, one for realigning blood vessels, one for more nerve tissue, etc.)

I am not clear on why a similar genetic basis could not underlie the appearance of a bat's wing. It can't be that extending the phalanges meant they poked through the skin, for example, or that the extra length of the digit was not served by appropriate nerve, muscle and blood vessel formation. Due to the way genes and their regulators program embryonic development, a mutation that lengthened the phalanges would be naturally accompanied by several necessary accompanying changes without separate mutations.

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Good Lord, why should that be a problem? Scientists don't always make correct predictions after all. We should not expect Darwin to be completely prescient.

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Surely the actual issue is whether the phylogenies as they presently stand pose a problem for common descent. And if they do, what are the specifics of the problem?

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ORIGINAL: Jhud
So your argument is that a mutation to the regulatory processes that cause “congenital abnormalities” is sufficient to explain the specificity and interdependence of the morphological structure of a bat? I find this more than unconvincing. In fact, is there a single case of polydactyly that produces a novel function in an organism?

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Gosh, I always thought that robust predictive power was the hallmark of good science; but we aren’t all that concerned about good science here are we?

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I think that the inability to place a number of different organisms into expected phylogenies is problematic for common descent.

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Trying to dismiss the argument by overstating it?

The novel function is flight. Yet the morphological change doesn't seem to be all that great. As you said: longer forearms, extended phalanges, a thin skin membrane, etc. And you further noted that most of the genetic differences are modifications of gene regulation---exactly the same type of modification that produces polydactyly. The latter was a consequence of one single simple mutation in one regulator. I cannot for the life of me see why a few changes in a few regulators might not account for multiple changes in the development of a forelimb.

I also do not comprehend why it should make a difference that one change in form did not produce a novel function and the other did. What changed primarily in the bat forelimb was morphology. And that is what is inherited. That the change in morphology enabled a new function does not necessarily require that the morphological change be difficult to accomplish.

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As you mentioned in your “designing a bat” thread, a single mutation (or even two mutations) appears to not be enough to create all the different functions of a bat’s wing. All they managed to accomplish in this test was make the mouse’s arms longer, and change their morphology somewhat, which still falls far short of what’s necessary for a bat’s ability to fly. However, by saying these mutations would have not been useful to the animals that had them, you’re making the mistake of only judging their value based only on how useful they would have been for flight. I’m not as familiar with bat evolution as I am with bird evolution, but why are you so sure that a mutation causing a mouse-like animal to have longer fingers would not have been useful? My first inclination would be to think that in a tree-dwelling animal, longer fingers would be useful to improve its climbing ability. And then if a second mutation causes it to have a skin membrane, still without the traits necessary for powered flight, that would have provided an advantage for the same reason that the skin membrane on a flying squirrel provides an advantage.

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Well, we are systematically deciphering the actual changes required; notions such as survivability can be tested.

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ORIGINAL: Jhud
A few changes?

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Its been demonstrated that just to lengthen the phalanges and forearms involve at least two changes.

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Shorten the rear legs, modify the skull with respect to the it’s alignment on the vertebrae, modify nervous and cognitive functions to deal with flight behaviors, modify the nature of the skin membrane so it is thin, strong, and light enough to act as a wing, and modify food finding behaviors. All these changes of course are specific, not simply the random appearance one sees polydactyly. And the changes are interdependent; there is no indication that they are beneficial alone; indeed, they are conceivably detrimental.

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Indeed, this is another of my problems with evolutionary arguments; they regularly oversimplify what is required for organisms to function as they do.

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But as I pointed out elsewhere we can now test these modifications for viability, so it’s no longer a matter of your ‘comprehension’.

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A few changes in regulatory genes that have multiple effects. Not just a few changes.

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And note that each of these would have to have multiple effects. The lengthening of the bone would not be the sole effect. You also need the correlated changes in soft tissue.

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Some would not be beneficial alone. But most would be beneficial enhancements of a gliding function consequent upon an early re-shaping of the forelimb. The earlier existence of a thicker skin fold would not be detrimental in and of itself, but once gliding behavior has been established, a thinner skin membrane would provide a clear benefit, whether or not rear legs were shortened previous or subsequent to this change. But a thinner skin membrane occurring before gliding behavior has been established would likely be detrimental.

So the order in which changes occur is important. What is conceivably detrimental in one case is conceivably beneficial in another.

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That was Cuvier's objection to evolution too. What you are both overlooking is that organisms do not need to function as they do to function successfully. The question is whether there is a plausible pathway for them to function successfully in some manner at each stage of a transition from an earlier functioning pattern to the current functioning pattern.

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Good. I look forward to learning more about it. Now if we could improve your comprehension of evolution, we would really be making progress.

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Deciphering the changes required is certainly valuable, but how can one test whether or not they would have provided an advantage? We’re talking about an evolutionary change that would have occurred in an animal that lived around 50 million years ago, where the only thing we know about its lifestyle is what can be inferred from fossils. We might not even know what kinds of predators it had to evade, if the remains of the animals that would have preyed on it haven’t been discovered.

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Suppose that in 50 million years, some new structure has evolved from an anteater’s tongue, and colonial insects such as ants are extinct by that point. How would scientists be able to determine whether the mutations responsible for an anteater’s tongue provided an advantage, without knowing anything about the food source of the animal that had them? This is the question you seem to expect us to be able to answer for certain about the ancestors of bats, when we probably know just as little about their lifestyle as in my anteater example.

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As a side note, if your point here is that none of these mutations would have provided an advantage, we seem to be talking about unselected mutations again. I asked you why a new structure can’t evolve from five selected mutations, and you don’t appear to have answered that yet.

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Jhud, you’re completely missing my point. The reason I mentioned my anteater example is because just because something does or doesn’t provide an advantage to mice living in a laboratory, that doesn’t mean it would have been the same way for the ancestors of bats.

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Whether a trait provides and advantage or disadvantage often depends entirely amount on the animal’s lifestyle and the environment in which it lives. The tongues of anteaters are one example of this, and I could probably list dozens of others if you need me to, where a trait that provides an advantage in one environment is useless or harmful in another. I would even say this probably is the case more than half of the time.

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So, let me rephrase my question: how can observations of mice, living in a laboratory, provide a definite answer to the question of what would or would not have been beneficial to the 50-million-year old animals from which bats are descended?