The End of Evolution By Means of Natural Selection

I think the Zhang and Saier paper is an interesting basis for such a discussion. Although I see no need for it to support Darwinian evolution, surely it merely has to not contradict it? As has already been noted umpteen times Evolutionary Theory does not exclude everything other than random mutation and natural selection, that is a creationist/idist charicature.The particular 'mutation' in question is the insertion of a IS5 transposable element. These elements can insert but they can also excise Zhang et al., (2010) show that the IS5 element can precisely excise fully reconstituting the original insertion site. This means that this adaptive mutation is readily reversible compared to most mutations.It is also worth noting that what happens when the adaptive mechanism is activated is not in fact the targetted upregulation of insertion but rather a de-repression. The GlpR protein normally represses the insertion of IS5 elements upstream of the glycerol metabolising gene, in other words the insertion frequency is below the base rate for target sequences of IS5 insertion.Given the reversible nature of the change It is not implausible for such a system to evolve and be a target for selection, if it were irreversible I agree that it would seem problematic.As it stands the repressive activity of GlpR on inserion is only effective when it is binding a particular site, this site is a sequence duplicated 4 times upstream only one instance confers repression. It is not hard to see how a duplication of this sequence which led to the repression of a recurrent but unstable insertion which caused constitutive activation of the glycerol metabolising gene would be beneficial. In the absence of glycerol such constitutive activation would be wasteful.In terms of the glycerol dependent regulation of the system, this should have already been in place since GlpR also acts to directly repress the expression of the glycerol metabolising genes. In other words there is already a reponse upregulating glycerol metabolising genes when glycerol is in the environment. This system seems to allow the occasional occurrence of a transient turbo-charged glycerol metabolising strain when the IS5 element inserts in the correct position.I have to say I don't see how any such system could arise in larger multicellular organisms, but that doesn't mean that it couldn't.I also don't see why this should be any sort of problem for Evolutionary Theory. It certainly runs contrary to the canonical picture of random mutation, but then it is a different type of mechanism and one that seems fairly unstable. It seems more like the sort of heritable epigenetic effects that have been observed than a traditional mutation, but it is a direct change in the primary sequence of the DNA so it can hardly be characterised as epigenetic.TTFN,WK

This is more of what I would expect from an adaptive mutational response. Transposons are not your "classic" mutation, but they are a mutation nonetheless.However, these types of mechanisms are rare, at best. We can see bugs adapting to carbon sources, like nylon oligomers, that have never existed before. Also, the size of the bacterial genome (ca. 2-8 million bases) doesn't seem big enough to hold a specific mutational response to every possible carbon source or environmental challenge. A much more elegant system is random mutation which requires very few genes.

I agree that it runs contrary to random mutations as well. In order for this system to stay intact you would also need constant exposure to glycerol. Neutral drift could wipe out this system if the bugs were not exposed to glycerol over an extended period of time.But how could such a system come about? Well, I don't see why RM/NS could not produce this mechanism. Obviously, there is selection pressure on both the transposon insertion site and the sequence for the DNA binding protein. Transposon sites are not hard to come by, so the key to this whole system is the glycerol sensitive DNA binding protein. Once that evolved the system was in place.

My bad.
So, that paper effectively has beneficial mutations happening more often, simply because they're beneficial?If you're in a bad environment, then any mutation is more likely to be beneficial instead of um, not-beneficial, as compared to an okay or even good environment.Like: if every one of your alleles is perfectly suited to the environment, any change will be harmful ('living fossil' species for example, perfectly adpated to their nche, so they remain unchanged for millenia). If none of your alleles are suited to the environment, you're dead.But if you're only 70% suited, then there's a 70% chance a mutation will be bad (ignoring the whole "no effect" mutations that don't change the protein shape and stuff), which would mean a 30% chance of any mutation being beneficial.
If you're only 30% suited, then there's a 70% chance of a mutation being useful or beneficial. IOW something living in a bad environment/one it is less suited for is more likely to get a good mutation when compared to the same organism in a good environment.So, the closer you are to being suited to the environment, the less likely you are to receive a good mutation. The further you are from being suited, the more likely you are to receive a good mutation. I recall Percy's evo algorithmy thing. That indicated the same effect: as you approach the target, you become less and less able to get good mutations.Which means bacteria in the bad place will of course end up with more beneficial mutations. They hit rock-bottom already, so the only way through is up.If none of that made sense, then great, I'm not a biologist anyway if it did, I do get lucky sometimes.

Let's face it WK, you are pretty skeptical of the whole random mutation natural selection cock and bull story, aren't you? You have studied biology, and you realize that there is no way it can account for all the life on earth.And that is why you are trying to downplay its role in your theory, and you are always mentioning "other mechanisms". The problem is, those mechanisms you described, are not a mechanism at all, but in fact a process, a system. That is why you even used the word system.So without RM and natural selection, you realize your theory is in tatters, but you don't have any to replace it, so what can you do? You can say there are many other mechanisms involved in your theory, still try to call it Darwinian evolution, and each time a new discovery is made involving another process that organisms go through, just throw on another label of "other mechanisms." , when in fact you are talking about a system, not a mechanism.If an organisms sprouts a brand new head in a day, well you can just say that is another mechanism for evolution. The theory becomes so flexible and so accommodating as to become meaningless, and I honestly believe in the back of your mind, with what you have studied, you are starting to realize this.

Any theory of life, evolution or creationism being no exceptions, has to account for the full diversity of life on Earth. It has to be flexible enough to accommodate an explanation for every single living thing. You act like it's a fault that the theory has such wide-ranging explanatory power, that if the theory were true there would be living things it couldn't explain, but that makes no sense.And it's a double standard, as well; if we observed your hypothetical instant-second-head, and asked you to explain it from the perspective of the "theory" you advocate, what would you do?Throw up your hands in defeat? I doubt it. Wouldn't you suggest some variant of "God did it"? I mean, couldn't you say that for literally anything at all? "God made it that way." Can you explain why that doesn't make your "theory" "so flexible and so accommodating as to be meaningless"?By the curious standard you're setting up, the most meaningful theory would have to be the one so inflexible as to explain absolutely nothing at all. Why not?

This is interesting in that these particular bacteria hit the "panic button" when put into an environment that they have never been exposed to before. It is the same reaction that occurs in our immune system when exposed to a new virus or bacteria by using everything it has and in every combination to kill it, usually resulting in killing the host in the process.Both situations may not be the best response but apparently evolution needs more time to come up with a better strategy in dealing with the "unexpected and sudden" environmental stresses that rarely occurs in nature.

Or it's found someting that works long enough to allow the next generations to be produced, regardless of which environment it's in.I wouldn't have compared the "panic button" response that the bacteria use to anything in our immune system.
In the latter case, this is a system specifically set up (by whatever means, evolution or Godidit) to fight that stuff off. Naturally there is no point in withholding resources from the organism's defense - there's no point in saving stuff for later, when you're dead later. Hence the immune reaction is to fight until something is dead (if it happens to be you, well, that would have happened if you didn't fight).
However, the bacterial response is to make more mutations. It is not the individual organism that survives more, but the species/population as a whole, because as we all know, you can't create new mutations for yourself once your DNA/RNA is set. The good stuff gets passed on to the next set, just like in regular processes; difference in the "panicked" bacteria is the rate of mutations.Reading that myself, it might not make much sense. Does it for y'all?

I think that what Wounded King's account of what he thinks is superior to your account of what he thinks.This is because, if possible, your ability to read minds is inferior even to your knowledge of biology.

Are you reading WK's mind now?

I think the broader context was lost because of the focus on technical details. The Zhang and Saier (2009) paper focuses on a process that is entirely natural. While it takes place there is no evidence of any outside intervention by an intelligence. It's just another very complex biochemical process like much life chemistry.The process itself must also have had a natural origin driven by random mutation and natural selection. In a rapidly changing environment, any mutations that increased the rate at which possible solutions could be explored would be strongly selected for. Wherever adaptation is involved natural selection must by necessity be the most influential factor, and mutations provide the grist for the mill of natural selection. Natural selection must have the variation provided by mutation in order to function. But none of this was the topic of the paper, so naturally WK didn't mention it.I think your erroneous conclusion that WK sees that "his theory is in tatters" might have its beginnings in this passage from WK in Message 781: This does indeed have this feel that behind the scenes WK actually does see problems for evolutionary theory in the Zhang/Saier paper but is stubbornly refusing to admit it publicly. But what I think he meant was that the paper is narrowly focused on the biochemistry of a specific mutational mechanism and was not in any way ever intended to focus more broadly on the whole process of evolution, but that it is fully consistent with modern evolutionary theory.--Percy

Well, its really up to Wk to respond, and I certainly don't believe he is going to reject the Darwinian theory; but I also think he is at least one of the more honest and contemplative posters here, and so even though I know he is a committed evolutionist, I do believe that deep down he would agree that there is still a lot of room for speculation about what is really going on.As someone who studies biology, he has seen that there are plenty of things in nature and science that can't be so easily explained by simple random mutation and natural selection, as you believe. So he has emphasized that there are many more mechanisms than those, but of course he can't really define those mechanisms-because there is simply too much unknown about what is really going on.But your suggestion that ultimately random mutation and natural selection can account for the existence of all of these characteristics is your conclusion not his. I realize you are fighting to contain the idea to a natural one (because that is your desired conclusion), even if we don't know what it is, but the fact is that unless you can fully explain how these mechanisms came to be, their cause could be natural, un-natural or something in between, and we just don't know. As such, your speculation that natural selection produced it is not really scientific, it is just your imagination of what you think is happening-which may or may not be true.

No.Creationists ... you really do have to explain everything to them, don't you?

This belief is leading you far astray in many discussions here. The label of "natural" is a key part of your misunderstanding. The focus is actually on evidence. We don't care what label you put on the observed evidence, we don't care how the observations were carried out, we don't care if it was seen, heard, tasted, smelled or touched, we don't care if complex instrumentation was involved, but there must be evidence. We postulate no mechanisms for which there is no evidence.Whether the IDer is labeled natural or not is beside the point. If he's manipulating genes then he's observable and there should be evidence of him. In the absence of evidence he cannot be included as a possible mechanism.No one here is casting accusations at you that you actually realize your beliefs are in tatters but can't bring yourself to admit it. It would have nothing to do with the topic. If you've got evidence for anything you're advocating please focus on that, just please realize that things we don't know aren't evidence of anything. There have always been things we don't know and there always will be, but the history of science is one of unknown things becoming known, and not one unknown thing has ever become known by pointing to things unknown.Behind all your thinking lies this mistaken belief that if we can't explain it then God (or the IDer in this case) was responsible, but though he was purportedly responsible for the creation of every species throughout all time, he is nowhere in evidence. Put him in evidence, then claim him as a mechanism. Until you have evidence there cannot be anything that we're ignoring, except your claims that your religious beliefs somehow constitute evidence.By the way, there's nothing special about your religious beliefs that causes science to ignore them. Science ignores the unevidenced religious beliefs of all other religions, too.--Percy

I was having a scientific conversation with Wk, that you opted to get into. You are making all kinds of statements that I never said-such as saying that i claimed if it can't be seen, God must have done it. What I actually was saying was that if the mechanisms begin appearing to be much more than random mutations and natural selection, then the whole theory becomes a whole new ball game.You have speculated that even adaptive mutations could arise through random mutations and natural selection. Fine-site any evidence if you have it, or don't preach about not caring if the evidence can be "seen, heard, tasted, smelled or touched,..". In this instance what you have is none of those. You only have your speculation. What is that worth?About my religious beliefs, since you don't know what they are, and I didn't bring them up here, why bring them into anything. I am talking abut what the science is showing about adaptive mutations.