Monsters from the ID

I have a problem. In attempting to go over Matzke's paper on the evolution of the flagellum, I find that he makes an assertion and then backs it up with reference to a published paper. Nothing whatsoever wrong with that. The problem for me is that I would need to have access to these papers (or at least a dozen or so) in order to make a meaningful response to what he claims has been demonstrated or is supportable. I am looking into trying to find out what options there are for me to get access. But I can't really afford to spend several hundred dollars purchasing all of these individual papers as I need to. Perhaps I can get by with purchasing just a few. I could ignore all those references of course, but what would be the point of that? I'd then just be giving my opinion, unless I could argue with what Matzke is actually claiming by going to the sources. So I'm working on that. I don't intend to respond to you until I've solved the literature access problem. It's what you requested and it seems fair. I just want to make this one comment on your statement above. Evolution as it is proposed very definately requires that as well as being defined as the fallback change in allele frequencies over time, is also required to be change in function. That is the major part of Matzke's model of flagellar evolution. It's usually called cooption. The taking of existing proteins being used elsewhere in the cell, and their modification to a form beneficial to our new evolving system. That is absolutely required, and is easily seen in the way that Matzke claims that he has definite protein homologies for many of the proteins involved. We're not just changing definitions to be tricky. This claim (that protein functions must change) is the heart and soul of attempts to explain the evolution of such contrivances.

I've been busier after hours lately than previously. In addition I'm looking at Matzke's paper. It's pretty long, and is taking quite a while to go through. It would be useless to just present a quick "summary" which isn't any summary at all and which ignores most of it's content while also making assertions that fit my viewpoint but ignore his points. This means that our discussion has ground to a halt until I can go through his paper properly. But that would seem to be the proper thing to do.

What he meant by steppingstones and the water is this: Each steppingstone is an aquired new beneficial function. If the steppingstones are close together then evolution can quickly find them. Once one is found it may well be able to be preserved by natural selection - thus building up the complexity and sophistication of the organism. Getting wet means basically that in this part of the evolution, the new beneficial function is out there somewhere, but has not yet been found. So being wet means that the part of the DNA that might code (in the future) for some as yet unrealized benefical function (just like the hidden treasure in the forest) is not currently doing so. As a result, natural selection cannot do anything to assist in the finding of the next steppingstone (a beneficial function that may or may not be found). So if the steppingstones are very close together, then evolution can find these new beneficial functions pretty fast. And in some cases this is true, as in examples like the evolution of resistance to antibacterial chemicals. In other cases the new beneficial functions are like distant islands. To get to them you'd have to cross a huge ocean. And that via a random search. There is no guidance to any of these islands or steppingstones. But the closer they are, the faster they will likely be found, and vica versa. I do understand that there are huge numbers of different ways that are functionally sound as well as functionally bunk. However, the longer the sentences get (paragraphs and essays rather than single sentences) and the longer the words get (3 letter words have more functionally dense possibilities than say 7 letter words) then if we are allowing more content such as long essays and long words as well as shorter ones, then even though there are an astronomically large number of ways in which we can express meaningful function, there are a far larger (astronomical to a far greater magnitude) number of ways in which there will be meaningless bunk. So compared to short sentences with short words, multiple long sentences put into paragraphs that can also contain large words as wellas small words, will be far less functionally dense. So the ratio of meaningful arrangements to bunkum arrangements for the longer texts, becomes an exponentially shrinking ratio. This means that mindless process such as evolution will have to search for longer and longer times. And in fact given some calculations you can show that the search time becomes infeasible. This includes having evolution in parallel with huge populations over billions of years. This kind of search for function rapidly becomes an ill conditioned problem. That is true, but doesn't really change anything much in the conclusions. I think he well understands all of that, but has realized it makes little difference to his main points. Steppingstones are new useful functions - or even just existing areas of DNA sequence that code for useful function. Whether the function is new or not, is purely dependent on whether the organism has managed to evolve that function already - or not yet. The reason that evolving resistance to antibacterial agents is easy to do (thus fast in bacteria) is for two reasons. First, there are lots of bacteria evolving in parallel. But more importantly, antibacterial agents are using certain chemicals within the bacteria as attack points. For example, imagine a certain chemical is like a bridge. Then the enemy can use that bridge (the bridge is for the use of the friendlies) to invade the friendly country. Now evolution has two options (among others). It can either evolve a sophisticated mechanism of defense against the antibacterial agent - or else it can simply destry that part of the chemistry that is being used by the antibacterial agent. Thus in the war analogy, is it faster to develop some new weapon to repel the invading forces, oris it faster to just blow up the bridge they are using to cross over on? Option 2 is the fastest and easiset method of evolution. It's always much more probable that some existing feasture will be broken or altered, than it is likely that some new function will be involved. In most cases, altereing or breaking parts of your own chemistry is a bad thing - however if the alternative is to be destroyed, then it is probably better to a certain extent to get crippled and survive, rather than stay healty and get wiped out. This also shows that due to the shortsighted nature of evolution, it usually solves survival problems by breaking, rather than creating existing systems. Thus selection pressures, though enabling survival in some cases (which is better than nonsurvival) , will most of the time lead to a degeneration of functions. Becaue is it much more probable that selection pressure survival problems will be solved "the easy way" via the (beneficial in the short term) breakage and disablement of existing functions. This is what I meant earlier when I mentioned that some examples of apparently poor design may in fact be the damage that evolution has allowed to happen in order to solve selection pressure issues. Evolution almost always chooses the easier way. The harder way to try to win a war - is by conducting an arms race. The easier way to try to win a war - is by conducting a scorched earth policy. Being somewhat simpler than higher organisms are, they are more "modular" so to speak. Such properties are impressive and can in themselves be thought of as supporting evidence that bacteria were designed to be able to take advantage. Being simpler, it is not as big a deal to adapt in such ways as it would be for more sophisticated organisms. Yes, but you'll find that newly evolved resistance usually always comes with associated penalties. Why? Because it's likely that the resistance was present because the bacteria that has the resistance had mindlessly evolved in such a way that some function within it became damaged or unregulated. That change is what confered the resistance, but the damage incurred also makes the bacteria less competitive away from the threat. What is happenning is that this kind of "scorched earth policy" evolution is finding the cheap and (non) cheerful solutions to problems that is damaging the organisms that survive. While they do survive (if they even do manage to survive) they are now weaker than they used to be. That's because new machinery isn't being built often enough (if ever) to keep up with the damaged, deregulation and loss of existing machinery via "scorched earth policy" type evolution, wehich is the mos common type of evolution that takes place. Actually, I'm not sure what you mean. I'd be thinking that the immunity developed quickly initially ,and is then carried on down for as long as the threat remains. But if the threat is withdrawn, then that immunity may be perhaps lost agaoin over time, since in most cases the immunity is associated with some damage that took place, so the organisms became less efficient (though that doesn't matter if the damge isn't lethal and allows the organism to overcome the threat). But if the threat ever goes away, then the organism may be at a disadvantage. It has now evolved into a niche that it may find difficult to evolve back out of. We don't know this is the case yet, but given the speed with which that initial new enzyme appeared, it seems perhaps there exists a kind of backup system for important enzymes and processes. Building in redundancy would certainly make an organism more robust to the kind of damage I was just talking about. But as Hall did, if you then remove the stand-in as well, well then the organism may be in real trouble as it's "spare tyre" has also been punctured (so to speak). As I said though, that is speculative. But it is an interesting avenue for further research I'd imagine. Are organisms equipped with the capability to backup certain important processes. Perhaps some pseudogenes may be relevant here. On the other hand, some other examples of pseudogenes do in fact appear to be nonfunctional like the human vitamin C case. But other pseudogenes are now being found to have functions of various kinds. It's going to take quite a while to figure out exactly whats going on down there in the DNA, isn't it!

I have a better anaolgy (that of the small islands and large oceans), but as far as the maze analogy goes, it is meant to represent the potential pathways leading (for example) to the evolution of a new functional protein. Now once you are outside the maze, the protein has been evolved. In other words, getting out of the maze means that finally after however long it took to get out of the maze, we hit upon that sequence code that specifies some new function. However, while in the maze, that new function didn't yet exist. If the organism that finally evolves the functional new protein finds that the new function is useful enough, they might have some advantage which can be picked up by evolution and this new protein or protein complex may sart to increase in the population and finally after a much longer time it may even become fixed in the entire population. That's an example of a successfully evolved new protein. But in the case of where nothing has yet emerged from the maze, there isn't a new protein yet. So until the maze is solved, nothing about the route out can be known by the many trials going on inside. While still in the maze, there is no advantageous or disadvantageous mutations with respect to solving the maze. To clarify - there will always be good, bad and neutral mutations as far as the organism is concerned, but whatever happens that is good, bad or indifferent to the organism as a whole, is irrelevant with respect to getting out of the maze. Meaning that the evolution taking place before the evoluton of some new feature appears, then whether a mutation is good bad or neutral to the whole organism, cannot be used as a criteria for guidance by natural selection that has anything to do with the evolution of some new feature before it appears. This means that any evolution that takes place that may be (or may not be) on the way towards some new feature emerging, is unguided (random) with respect to the appearance of a new feature that doesn't yet exist. Only after the new feature has just emerged, can natural selection begin to select for or against it, based on it's fitness contribution to the whole organism. While within the maze, no learning can be undertaken. Evolution has no memories of anything. Evolutions "memories" (so to speak) come only from fixed (or on the way to fixation) already emerged new features that provide an advantage. As an example, if a treasure is at a certain location in a large forest, then though different routes will alternatively provide advantages or problems related to comfort and survival along the way, whether these routes are safe and comfortable, or dangerous and uncomfortable, or dangerous and comfortable, or safe and uncomfortable, all of that guidance is useless as far as finding the treasure is concerned. If I find the treasure, it will be because of luck pure and simple. Nothing about the routes can give me any indication that I am moving towards or away from the treasure. ID believes that we can establish that since the evolutyion of new features that don't yet exist is random evolution (the evolution of these new features that are yet to emerge is not guided towards by natural selection) then if the new features are rare enough entities in coding space, then they will in all likelihoods never be capable of being found by the unguided process of random evolution. It's only after a new feature has emerged that natural selection can begin to provide guidance to the future evolution that can conserve and adapt that feature. I did know that. I don't get your particular point with that. As previoulsy pointed out, the inheritance cuts in when we have already emerged already functioning systems in place. But before such systems have managed to emerge, since their functional advantages are as yet non existent, then there can be no "memories" so to speak that can pass along any guidance information. In fact, lethal mutation pathways that got tried once (resulting in the death of the organism that tried them) may be tried yet again - over and over. If a lethal mutation is experienced, then that creature gets deleted, but that same mistake is available for reuse. Nothing is there to prevent such things happening again. Sure. But first the useful proteins need to have already emerged from nonexistence. Only AFTER they have emerged, can they can be selected for or against. But before a new protein has emerged, natural selection is unable to help it emerge. It must emerge by chance. Once you manage BY CHANCE to find the treasure that was sitting out there somewhere in the forest (or found your way out of the maze), THEN the treasure will give you the advantages that particular treasure provides. And AFTER you benefit from the treasure, then natural selection can favour you over the other poor so and so's who are still wandering around in the forest (or within the maze) not yet having found any treasures. And note that to be a more realistic analogy to evolution, then the people wandering aroud in the forest or inside the maze, cannot have any memories of where they have already been. That's right. But say the cow was getting by without that protein in the first place (it's a "simpler" cow than our cows) then if a cow happenned to by chance evolve the damaged version of that protein, then it would also be selected against and be more likely to leave less or no) calves as it's descendants. However, despite the fact that natural selection is selecting against that particular mutation whenever it might crop up, the guidance that NS provides against that mutation, cannot assist in evolving that protein (or which the mutation happenned to be a damaged version of). So if our cow is to go from simpler to more complex (by evolving that new useful protein (or protein complex)) then it has luck, not natural selection to thank for it. The question being of course, without natural selection being able to help, and given that we now know that many proteins (all but the very short and simple ones) are so rare as to be infeasible to find via random evolution - then we must ask, is it likely that they can be found at all (in any feasible time period) by such a mindless process as evolution? IDists say that in most cases, the answer is no. Howeve they also admit that in certain limited cases, the answer is yes. Pitman's article establishes that point. So does Doug Axe's paper (in the ID Biocomplexity journal called - "the case against a Darwinian origin of protein folds"). However that ID paper is based on the peer reviewed published work of Axe carried out previousy. Pitman also references other peer reviewed papers from non ID scientists that lead to similar notions, that functional protein folds are such rare entities that the numbers seem to defy the odds. How could nature find them without the help of natural selection? This is known as the "sampling problem". Basically it is a "find the tiny needle in a large haystack in 5 seconds" kind of problem. Take as long as you need to, and them some. There's no rush. Life is too short to spend it all on the internet, right? I'm starting to realize that more than I used to.

No, these things aren't demonstrable. Perhaps they are in thought experiments, but that doesn't quite count. Darwin thought about whether cases could be found that countered the manysmall steps to novelty principle, but couldn't think of any. But now we know more, we have found examples of such cases, one of them being the flagellum. Dr. Dawkins did that though, and probably made millions from the sales. It's OK for him though, right? There's nothing wrong with selling a book! You don't have to buy it, and what's in it is pretty much all on the internet in any case. In fact I'll let you in on my special offer - buy 100 for the price of 1000, and 2% of the proceeds will go directly to a charity of my choice! According to one site I looked up (which gets you to agree to a confidentiality agreement not to disclose the specific of wht is on the site) he has published 6 papers in various medical journals. I am sure you can find these yourself if you want to. I came across themn after a few minutes of looking. I can tell you he is a hematologist though. I wouldn't mind it if I were! Ha! But no, I am not he. But thanks for suspecting I might have been him. You kind of made my day! Then you're using a pretty crap definition of dishonesty aren't you. The two big supporting evidences for a billions of years old earth, are radioactive isotope dating and inferred travel times of starlight in the universe. And I'm not disputing that they are pretty strong evidences. On the other hand, other dating techniques also exist and the majority of them give ages less than billions of years. Interestingly, mica's dated in the millions of years based on their measured decay products, also can be dated to several thousand years via the helium diffusion leak rate. The helium atoms (derived from trapped alpha particles in the mica) are leaking out at a measureable rate, fast enough to bring them to equilibrium with the surroundings very quickly. But nevertheless a high concentration of them remain trapped in the mica. Here we have two radioisotope dating techniques based on the same decay events giving dates that are several orders of magnitude in difference. Such topics are of genuine scientific interest. Have I accused abiogenesis researchers, or even those that believe strongly that abiogenesis took place, of being liars and dishonest? No. Are there people on both sides who do tell actual lies and misrepresent the facts? Of course. But you don't go around generalizing about all the members of a certain group based on a few bad apples. Or do you? If you do, you shouldn't. Well that was a pretty damn dumb public school teacher! Did she think she'd actually gain your respect that way? Did she really stand you in the corner all day for asking that question though? Or were you being a very naughty boy in other ways? All day in the corner? It's possible of course, but it sounds a little over the top. We'll never know for sure, but how would you like it if I in turn now accused you of being a liar and dishonest? How could you prove me wrong? I could even say that your story (being stood in the corner all day long and receiving a beating afterwards - just for asking where all the water went after Noah's flood - sounds rather like an exaggeration, and many would agree. But I'm not going to, because it's a dumb generalization to make. Neither should you. I should have been a little more careful with my words though I did try to clarify the bit about "personal" versus "reasoned" incredulity. Unless there's a reason (other than a feeling) behind the incredulity, then such incredulity is not worth mentioning in a scientific discussion. Along the same lines, credulousness towards a certain notion based only on the fact that the notion is a consensus viewpoint, ought not to be accepted either, unless the person themselves can reason out why they believe that viewpoint (other than the fact that the notion in question is a consensus notion). Doing THAT, would be the "argument from authority" fallacy. I suppose though that you'd need to demonstrate or reason out exactly how the imagined evolution would work in practice. I thnk Matzke did that to a certain extent, though we'd argue that he left out the "how" his proteins would be able to become functional in new ways. We'll come back to that as I think that is one of the major objections. But we need to go over your points in these two most recent posts. Thanks for jumping ahead and doing what I should have started to do. I'm just trying to slow down the pace as lately I have some other things going on, so I haevn't gotten back to it for a few days since last time. I can see your point, biut on the oither hand, if the gaps are wide, then it is justified - justified until the gaps aren't wide that is. When the gaps are small enough to be demonstrably crossed, then you'll have conclusively proved the point - not to our satisfaction, but to yours. As long as the gaps are large and the mechanidms mysterious, there will always be justifiable doubt. But chances are if your side is correct, those gaps will close off in time. If our side is correct, they won't. You begin to discuss some of them later on yourself - they're in Pitman's article which you begin to go through in these two posts. I have been near scientists myself (having a BSc.) so I know what you mean. My connection is about to close - will continue tomorrow.

I believe it isn't a logical fallacy to be skeptical about certain claims, if there are accompanying reasons to go along with the skepticism. Because if there are reasons to be skeptical or incredulous, then it isn't personal incredulity in that case, but incredulity (a state of non-belief) based on various avenues of reasoning. I believe the logical fallacy comes in when someone says they don't believe something, and when asked why they say something like; "It just seems ridiculous." And when asked to clarify or give specific reasons why it is ridiculous, they then can't come up with any reasons. They just "feel" that the notion is wrong. That is personal incredulity, and as an argument it is fallacious because no good reasons are given to support the incredulity. In other words, personal incredulity seems to be more of a feeling, than an argument. But incredulity (a state of non-belief) if it has supporting arguments, certainly is not a fallacy. I take it you're not supporting credulousness either, unless it also has some supporting arguments to go along with that state of credulousness.

That's OK. I'm pretty used to it. When discussions get going, sometimes the other side will throw stuff they hope will stick as part of their strategy! As long as you don't hurt yourself doing so, I don't see why that will be much of a problem. Now back to the discussion about protein evolution ... You've mistaken what the analogy is about. Probably because I didn't take the time to specify exactly what it meant. My apologies for that. The 2D plane represents the hyperdimensional coordinates of DNA sequence space as compressed into a 2D surface. For example, a DNA sequence 500 codons long could be thought of as a coordinate system having 500 "dimensions", and each of these 500 dimensions can have 4 possible values: A, C, T or G codons. In such a space there is 4 to the 500th power of possible configurations ~= 1E+301, a large number with 301 zeroes. But to get a visual idea of such a space, we can informally imagine it to be compressed down to 2 dimensions. The islands represent the coordinates of potentially functional proteins (or maybe functional RNA sequences). When you said that no organism or chemical is isolated, well, thats true as a stand-alone statement, but it is irrelevant to this analogy. A bit like you telling me that islands in the ocean consist of isolated populations of humans, and me objecting that "no man is an island!" It's just a category error, but possibly my fault in this case as I may not have explained what they represented thoroughly enough. But you do realize that these Islands certainly do not mate with each other, because the islands are not organisms, they are maps of the outcrops of functionality (and fitness of that function) in protein sequence configuration space (that has been contracted from hundreds of dimensions down to 2 dimensions for the purposes of being able to form a mental image, thus an analogy. I don't care if you take me seriously or not. Your schtick is never to take creationists seriously. That's irrelevant to the actual discussion. I just want to see if you can refute my arguments, or not, once they have been thoroughly discussed. It doesn't matter what you think the creationist medical doctors arguments smell like! What matters is whether you can refute (or ask someone else to refute for you) those smelly arguments he presents demonstrating the infeasibility of the notion that the evolution we observe today, could do anything like having taken us from a common ancestral single celled lifeform(s) to the biology that exists today. I guess it makes sense that any argument that can't be refuted, may indeed smell bad to the poor guy on the other end! Smells like victory. All this talk of creationist odours and lying is funny, entertaining and provides some red meat for your supporters, so I don't mind if you keep it up, as it kind of lightens up the discussion a bit. Some good natured ballyhoo never really hurt anything. Maybe I'll even pretend to be outraged about it once in a while! Why not? Politicians do it all the time. I'll be the straight man, and you can be the funny guy. How about that? But I reserve the right to throw in a few jokes of my own once in a while, OK? By the way, that link was the home page of the website, as you had asked where I was getting some of my material from. But this article in particular contains arguments pertinent to our disussion. We'll be going through them. The evolution of the flagellum (not)

Also, that model ought to be easily adaptable to populations. You just plop down a whole lot of individuals corresponding to the population onto the plane. Then as they each mutate they go on random walks. Once a population has a set of useful genes (and functinal RNA's), then we could imagine individual organism as having an placeholder existence on each island that corresponds to a functional gene / functional RNA. (A bit weird, but it's hyperdimensions compacted down to 2 dimensions after all). But as far as information about prior false turns? I don't see how that figures in, unless you're just referring to the fact that once an individual is on an island, then it's projeny will tend to stay on the island as well (except that sexual recombination will alter the positions of the progeny according to how their recominations work out. In some rare cases this may push the progeny off some of the islands and into waiting sharks, in the case of some kinds of inheritable lethal diseases. But the central question is - how does a set of initial populated islands, branch out to discover and inhabit the other islands that are waiting out in (potential new useful genes & functional RNA')? The problem is the large distances needing to be covered, and the fact that once in the ocean of nonfunction for some tract of DNA, there is no guidance towards some new island. Only random swims and teleports to random new locations are available. Since the ocean is large and the islands and island clusters are small, then this presents a mechanism problem for the evolution of the protein machinery that now exists in life's repertoire. And not only that, but even evolutionists admit that this must have been pretty much already evolved and in place a billion or two years ago. Here is another site which has been an interesting read: Detecting Design The following is addressed to Mr. Ringer: Sorry if you're feeling a little peeved, but you're going to have to evolve some more patience than you're demonstrating at the moment. This discussion is likely to be going on for some months, if we are ever to cover things in any level of detail. I clearly explained that I intend to get to your links in time. I did however cover the video link, but hold my feet to the fire on that if you wish to. Time is what I have plenty of (except I do not intend to spend too many hours of each day glued to this forum). Anyhow, as I said to Moontaman earlier, don't worry, you're not performing for the world here. It's just a forum for science types. It's a pretty good forum, but it's not world class debating. Still, we do need to go through things point for point like I said. You don't get anywhere by making blanket denials. You need to deny first and explain your denial later. And then have an argument about it - over and over and over. You won't get anywhere by trying to rush things along too much. That's not going to happen. Now you claimed that myself and the author of that website have no understanding of how evolution works. If that is really the case, then I will be expecting you to correct me as we go through it, which will take some time, unfortunately. Get used to waiting.

The maze analogy can apply to populations over many generations. Buta maze is just one way to look at it. It did come out of my rear end. Not bad considering!! Probably a much better analogy is something simpler. A large plane of fitness, composed of an ocean and islands. Islands that are above water represent usefully functional sequences of DNA, such as code for functional proteins. The plane consists of coordinates where each square represents the sequence space of the DNA stretch (of a particular length). This is many dimensional but compacting it down to 2D for the sequence and vertical for the fitness makes it easy to visualize. So the highest point on the islands represent the best adaption sequences for that particular island (function). Once you go into the water you are now off function. Start on the island and walking around on it corresponds to mutations that may (or may not) alter the function. The fitness value for that particular environment makes you go up or down. Get too many mutations and you may walk off the island into the oean where you lose function altogether. You may even run into lethal function (a lethal mutation that kills the organism) which can be represented as sharks in the ocean. (or as lions and tigers and bears on the islands). Once in the ocean, since there isno function, then after a long enough period, that stretch of DNA may even get mutated as it's now dead weight as fars the organism is concerned and natural selection may allow it to be deleyed, as there is no reson to conserve such a sequence, since it just takes up energy and time to replicate it. Now based on some calculations that aren't impossible to understand, it can be shown that for medium to large proteins, the islands are in groups that get more spread out and the oceans are huge. So how do we go island hopping for far flung islands?

I am waiting for that but regardless, you're probably have to end up waiting a little longer than you probably want to. I could post lots of links, but I don't like doing that willy nilly because firstly it means i'm putting the emphasis on you to read some long article that you likely don't have the time or interest to read in the first place, and secondly it means I am being lazy. But perhaps by summarizing such articles so we can go over them bit by bit is also going to be very long winded and take ages to get through. I don't know how to make this any kind of a fast exercise. IC equates to individual systems that are typically complicated machines. By themselves these systems are not "alive" in themselves, but future versions of them can experience variations. Does that in any way disqualify the property of irreducible complexity from applying? I don't see how. Do you? In any case, we could likewise model nonliving human technological machines (like engines) as being "virtually alive" by stipulating that the factories that build them can also reproduce themselves, and that this process of reproduction involves errors that affect the factories in various ways. In fac the machne in question might be just a machne that the factory uses to maintain itself, or help itself to function. Maybe I just thought you were and overreacted. Maybe I can send you a couple of links in the meantime. But on the other hand, what I said about Matzke's flagellar evolution pathway ought to be capable of being refuted. After all i did not merely "deny it all". I did explain in general terms why I disagreed with it. I gave some specific reasons. Perhaps you can counter what I said. Defend the idea. I don't believe what I said was all that mystifying. I more or less pointed out that the idea ignored the number of steps it would take between stages to get from the earlier stage to the next. There would be a large number of trial and error mutations that wouldn't work. Few would. By the way we can put an upper limit on the number of mutations that could have ever taken place on earth in billions of years. Since we know the maximum possible number of mutations that could ever have taken place (or an allowance well in excess of it as a safety margin) then we can compare that number to the possible number of potential protein sequences that can exist for a certain length, and compare that with the number of functional protein sequences that exist within that potential sequence space. Let me put it this way as an illustration. You're a captibve in some stupid reality TV show, so you have to look for inane items. Therefore you must set out to find as many out of 100,000 gold rings as you can. They are spread throughout a city that is 20 miles wide. You then find out that you can only spend 1 minute searching for them. See a problem? If none of the rings happen to be within sight, you're search is going to fail. This is the kind of problem that evolution must deal with. Particulars to follow, but I'll send you a link. The case against a Darwinian origin orf protein folds A mischaracterization of the debate. You won't have gotten that idea by reading my posts. I think that research should continue at full pace. The more we learn, the better ID seems to fare. Often the evidence doesn't count if it conflicts with your chosen worldview that has been renamed as the "consensus scientific view". If the evidence leads away from mindless natural processes it will be reinterpreted by such people until it does not. In such cases scientists who reject ID (and they usually are open about this) will not take the hint the evidence is giving them. That evidence is the lack of explanatory power to originate some phenomena via mndless natural processes. As Lewontin said: "our commitment to materialism is absolute ... we must not allow a divine foot in the door". I agree that religion and theological doctrines etc. obviously has no place in science, but the notion that some phenomena are best explained by intelligent design rather than by mindless natural processes certainly does belong. Happens all the time, and on both sides. It's going to happen whenever someone has a worldview. If your world view is materialistic and if you are committed absolutely to that way of interpreting the evidence, then no matter what the evidence was, it would be interpreted materialistically (due to mindless natural processes). I can say though that ID doesn't lock itself into a fixed expectation the way hardcore materialism does. ID can always be falsified simply by demonstrating a materialistic process that gets the job done. The claim of ID (that certain processes are exceedingly unlikely o be able to happen save via the input of a designer) can and has been falsified many times. Mainly for spectacular natual phenomea such as thunder (which is cause by the mindless natural process of electricity - not Thor's hammer). Hmm? The scientific revolution began long before the majority of scientists defected from open creationism. In fact much of our first world civilization was based on a creationist viewpoint. In America there was a multiplicity of viewpoints - many theists, some deists and a few athiests. I appreciate your enthusiasm, but it's going to take a while unfortunately. The evolutionary philosophy is (when looking back into the past) - Turtles all the way down! Looking back they go down into their beginnngs in an eternal ultrasimplicity. (Simple --> Sophisticated). I'm a - Turtles all the way up, man myself. Turtles having descending from an eternal intelligent first cause. (Sophisticated --> Simple). Pick which way your turtles are heading in the future. Down or up? I'm betting on down. The tendency towards a greater equilibrium / most probable states in the future seems to be saying that too. Them thar' turtles are headed on down to their final, most probable state of equilibrium (simplicity). Ha! Depends on your point of (world)view! I suppose we in the ID crowd don't agree with Orgell's rules. We think they're an atempt to "think natural" when the evidence might be leading towards another direction. But then again you haven't taken them on as dogma yourself. But many in the ID camp have a great posthumous respect for Orgell, as in his last or one of his last papers he basically cautioned OOL researchers to be realistic in their models, rather than being wildly optimistic. He ws never one of us, but he went down fighting for truth. That's pretty darn great in my books. Sure. I don't see a problem with that approach. It's skepticism by another name. Here's what I mean. It's not personal incredulity. It's incredulity based on scientific objections. I'llsendyou a lnk to a paper by ID's latest boy wonder, Doug Axe. He puts forward a number of raeasons as to why he finds that evolutionary explanations of protein evolution are unconvincing to him. I don't see the problem with being incredulous about some explanation if the proposal (about which one is being incredulous) has serious difficulties. Infact I have heard that term (argument from personal incredulity) also referred to as an argument from a lack of imagination. See what I eamn? In science I shouldn't think that imagination ought to be all that crucial. Or turn it around. What if some evolutionary scenarios were referred to as an argument from credulity? This has been defined as: "readiness or willingness to believe especially on slight or uncertain evidence." and other similar terms. I think that as long as incredulty is based on actual knowledge and research (not just on a hunch) then it should be (and is in other fields) quite a normal approach to take. I mean, what if a fellow submitting a paper for peer review, told his reviewers that they had better not make any arguments from personal incredulity when deciding to accept or reject his paper? No one would do that, but I'm trying to make a point. I think that if we really did have convincing mindless natural explanations for origins that I was aware of, then I know what I'd be doing. Keeping my mouth shut about ID and creationsim. Like I did once before. Some time ago I started blathering away with simplistic (they were long out of date arguments that were poorly comprehended by myself) creationist comebacks to a fellow who knew his science. After he "took me to the woodshed", I recognized I was out of my depth. I figured I had better get serious about some catch up reading. I still have a lot of catching up to do, but was actually surprised that the problems for mindless natural processes do seem to be quite real. The case against a Darwinian origin of protein folds There are a lot of statements to the effect that even though we don't know how something could have taken place via mindles natural processes, we do know that science will solve such issues as it has solved all such prior issues. Sometimes at this point a statement to the effect that science (they're implying materialist science) is based on logic and reason, but creationism is based on fear and superstition. The point is, if one decides to accept that all explanations must ultimately point to mindless natural laws, as far as I can see, even though such a belief is clothed in impressive lingo, is it really anything more than a form a nature worship? I fear that such a viewpoint can lock one into a paradigm of dogma that would try to forcefit any evidence it came across as being evidence in support of materialism. There is a lot wrong with such a state of thinking. I can say that the ID view (unless the designer in person is observed) is always going to be tentative - and always on the brink of falsification. I'm not talking about personal religious beliefs, but about a tentative ID inference that may stand or fall on the evidence. The ID claim for any phenomena can be falsified by showing that a mindless natural process can get the job done. This is sufficient to falsify the ID claim - the claim being that intelligent design was required to perform the task because of perceived difficulties (based on scientific research of the phenomena). Once a mindless natural process can be demonstrated to be able to carry out the task, then for that phenomena, ID is falsified. It also cuts both ways. If an error in understanding was made that elevated a natural explanation beyond what it could in reality do, then once the mistake is realized, the flaified ID inference may be able to return to tentaive acceptance. I'd even be happy for science to just rule that the explanation is "unknown". People can make up their own minds about whether thy will personally accept an ID inference or not. I'm just against the presumption that, while lacking a feasible materialist cause for some phenomena, rules that whatever the explanation is, it is and must turn out to be a materialist one. And that an ID inference must be excluded. Here's the Orgell I disagree with - his first law is an example of the application of this kind of thinking. I see it as an agreement to accept a fallacy in support of a premise based on the notion that we all know the premise is true in any case, so why not let the odd fallacy or two slip in?

Some of that evidence demonstrating the difficulties with mindless natural processes are in that thread I posted earlier. The problem is it's a very long thread and in order to be able to get any further you'd need to have read it and be ready to dispute certain points. However I can't really expect you to plough through all of that by yourself. So perhaps we can use that as a reference and I will sort of talk you through it. Then you can dispute certain points. Unfortunately we do have to do that at some point though, or else you'll be forever waiting for me to "present evidence that mindless natural processes have limitations of relevance to evolution and irreducible complexity", and I'll be forever telling you to "read all of that link". But before you can say that and have that kind of a statement taken seriously, you'd first have to have gone through the matters in that link on the difficulties of evolving IC machines (like the flagellum). I'm not ahving a go at you, but I note that you are saying repeatedly in this post that I haven't yet offered you any evidence, yet admitting that you haven't read that article in full. Now as I said I didn't really expect you to read all of that, because it is just too long. On the other hand, given that you've admitted that you haven't yet read it, I suggest you back off on the "lack of any evidence" claim for now - at least until we have gone over that article in a bit more depth. It does apply to everything. An eternal mindless universe, and an eternal intelligence. For the same reason that people don't feel the need to explain an eternal universe or eternal energy. If something actually is eternal, it has no origin to be explained. Something after all had to be eternal. We just don't know anything about what exactly that eternal something was. We certainly do not know that whatever the eternal something was had to be simple. That idea is nothing more than a hunch based on being comfortable with the idea of simple going to complex. Something I may add that we never see occurring in mindless nature. But whether simple or complex, something must have been eternal. It is in fact impossible to get something out of nothing. The alternative, that something popped into existence from truly nothing at all (no energy, no laws - nothing) is an impossibility. That is far more illogical a belief, than the idea that something must have always existed. How is it not the same thing? Explain your objection. A positive SETI inference is the acceptance that it is most likely that an intelligence manipulated laws so that a signal was produced which would most likely have not been able to happen as the result of mindless nature. How is intelligence not natural? Because whenever I use the word natural I am referring to mindless natural processes. An intelligence (in a body) is not mindless nature. Mindles nature is natural laws with no intelligence. You claim that intelligence is derived from mindless nature, however that is not known. To assume that to be the case is begging the question that this thread is named after in any case. As far as I know such kinds of knockout experiments on the flagellum have been carried out. One thing Miller says in the youtube video that is weak, is that he claims that irreducible complexity was taken apart at the trial because of the discovery of the strong similarities between the T3SS and the flagellum assembly transportation system. The problem is that the T3SS momologue in the flagellum is all of 10 proteins. The flagellum is 40 to 50 (depending on the version). It's only been suggested that this is an evolutionary waypoint. How does that really defeat irreducible complexity? Miller doesn't say anything about how the T3SS could have formed (it is also very sophisticated in it's own right) nor about what took place from the 10th protein up to the 40th or 50th. Note that he says "that's not evidence, that's an argument". It is a starting point for later investigation perhaps. But such a conjecture which may be the basis for further studies isn't any basis for declaring that IC is a dead in the water concept! IC (don't confuse IC with ID) makes the claim that the evolution of such multi-protein machines is very unlikely based on what we know about proteins and evolution, and the property of irreducible complexity as well. That has never been refuted. All that has happenned is that people like Matzke have proposed hypotheses that may be the basis for future work. But so far that is all there is. We are "incredulous" about such explanations of the possible evolutionary pathways they propose because we know of principles in the laws of nature that would make such evolutionary steps infeasible. You know these princiles too (very likely) but you haven't perhaps imagined they also applied to evolution. What do I mean by infeasible? I mean it in this way. If you were in the middle of a very well constructed maze that was say 10km wide, then either you will be going around in circles and walking up blind alleys for a very very long time, or else you could walk out of it in say 12 hours. You really could walk out of it in 12 hours! (That is if the maze actually was built so that you could in fact get out of it). All you'd need to do is to take the correct path out. But is that very likely? IC makes the claim that though you perhaps may be able to walk out of a large maze, in general you will not take the fastest route out. Yet such an argument does fall flat for a tiny maze, because the smaller the maze, the less it matters if you don't take the fastest way out. Right? But as the maze grows larger, the time taken to get out of it grows exponentially. Even though the time taken to walk straight out may only increase linearly. It may be likely enough to happen once in a while for a 10km wide maze that you could find your way out by the fastest path, but most of the time, it will be much much longer before you'd ever get out of it. If such a maze was 1000km wide, is it feasible to think you'd ever manage to get out in 100 days? It would perhaps be possible, but far more unlikely than the likelihood of being able to find the right pathway out of the 10km wide maze. Now I'll bet that you'll be saying that such examples have nothing to do with the way evolution works. For instance, "evolution isn't trying to get out of a maze". Is the problem completely unlike evolution? Evolution is searching (even though it does not plan or intend to be seraching) for ever more sophisticated function. It must be searching for and finding such functions or else we'd still be just an adapting crude single celled lifeform. One way evolution works is to randomly change DNA codons. It is possible to get from a starting functional protein to a novel functional protein without changing all that many codons for a small protein, perhaps only dozens of them. But say we need to change a certain 40 codons. We could change them in just 40 mutations. But how likely is that to actually happen? The possible number of changes (assuming we picked out all the correct 40 codons to change in the first place) is 4 to the 40th power ~= 1000000000000000000000000 possible codon changes. However you might point out that "Evolution isn't aiming for any particulr protein target sequence or solution, so you can't "cheat" in the argument by working backwards." I get your point, but we can show that proteins are in fact so very rare in sequience space that it doesn't matter that no particular target is being aimed at, because there are so few functional protein targets in existence in any case, that evolution is very unlikely to hit any of them. Put it this way, the smaller and simpler the changes needed, the more likely evolution is to succeed, but there comes a point where it gets too slow and never manages to find any "targets" due to the exponential slowing down of the process. Most of that is explained in some detail in the end of that article I referenced earlier. So finding protein function is quite a lot like being in a maze. The outside represents a new higher level (or just new) protein function. The starting point represents the initial function. There are many possible paths. The maze example is a bit forgiving in another way, because we assume there actually is a way from the middle to the outside of the maze. What if there wasn't any such path? Think about it. The walls inside the maze represent the fitness barriers preventing a pathway directly to the higfher function that awaits. Is there a way through? Or not? (There is always a way out of the maze! You can fly out of it.) But evolution has to walk through it gradually and cannot fly out of it. Actually some larger nonpoint mutations could simulate jumping over many walls to a new location, but there is still no guarantee (if the maze wasn't intelligently designed to be solveable) that it is possible to even get out of it. Not only that, but such a maze for evolution is also blind, and has no memories, which makes it harder still. See, protein evolution isn't an easy thing to have happen. Proteins are very rare things. Only a small proportion of all possible amino acid sequences are capable of forming functional folds that would be useful in biology. How does evolution find them? Tell me if you know how. In my next reply I will start going through that article. I also need to go over the articles that you mentioned in detail, just as I suggested that we go over the article I referenced. Perhaps since I will be talking you through the other article, you can talk me through these articles when you have time too (don't worry about the youtube video though. I have already seen it and have commented on it above.

What I have done is to lay out some of my case in general introductory terms. That would seem to be the normal way of doing things, wouldn't it? I mean, just because I haven't gone into all of the details and provided all supporting evidence at once, is that really a reason for you to start sounding so negative early on? I thought we were having a good chat with some initial statements. You had said that you were so looking forward to discussing irreducible complexity with me. Since you're likely about to refute the hell out of me, I thought you'd be kind of enjoying yourself a little more than you seem to be. We're not involved in anything all that crucial after all, just discussing origins on a science forum in a thread that few will ever read. I think you may have lost some perspective on that fact. As HAL 9000 once said: "Look, I can see you're really upset about this. I honestly think you ought to sit down calmly, take a stress pill, and think things over." Also, take your time. I have other replies to get to in any case, and I'll be busy all tomorrow and tomorrow night. There'll be plenty of time for this in due course. And I'm not a bit interested in "gotcha" statements. That's for juveniles. I'm just here to put forward my point of view and see if I can resist the refutations. I didn't even come onto this forum of my own accord. A member who shall remain anonymous asked me to join up, because he wanted to see real scientists show me where I was in error. OK? Talk to you later.

Well, I'd rather not waste time digging holes uneccessarily. Are you talking about facilitated variation perhaps? Don't worry about that. It was a joke. I thought you might be familiar with the 3 stone arch, which is said to be an example of "irreducible complexity" that is sometimes debunked by those wanting to point out that IC is no big deal. I could say that they're strawmanning the argument, but I really don't think they're intending to do that. The 3 stone arch does in fact have irreducible properties. By showing that such things can form regardless of irreducibility, some seem to honestly believe they have refuted IC. The 3 stone arch (you may have a different name for it) is a arch (or bridge) that cannot function as a bridge unless all of the parts are in place. It cannot function with 1 or 2 stones. We're talking about an "archway" with two flattish topped boulders on the right and the left sides, with a large flattish slab stone on top forming a crude arch or bridge over some obstacle. It needs all 3 stones to be in place for it to function as a bridge. But of course, such bridges can and do originate naturally often enough due to rockfalls etc. So does the fact that such irreducibly complex structures are observed to form naturally reasonably often, refute the notion of irreducible complexity as a hurdle that evolution cannot cross? It all depends on the sophistication of the system and the number of parts involved (the complexity). Because the 3 stone arch or bridge wasn't really what you'd call irreducibly complex after all. It did have the property of having irreducibility (all 3 of it's parts had to already be in place before the characteristic function could perform) but it also had the property of simplicity. It isn't usually a problem for nature to be able to originate something that is irreducible, as long as it is also simple. Call the 3 stone arch irreducibly simple (rather than irreducibly complex). With only 3 parts that have to be setup (and given that functional 3 stone bridges don't have to be built to exacting specifications) it's usually no very big deal for mindless natural processes to be able to put one together. What is more relevant to origins is when we have a system that is not simple, has the property of irreduciblity and where it's parts need to be interfaced to pretty exact specifications. Simplicity in this case = few parts with low specification for the parts and the interfaces between them. Complexity in this case = many parts with high specifications for each part and high specifications for the interfaces between them. So in the 3 stone arch, the specification is low because many stones will fit the bill of what is useful, and the interfaces between the stones need not be precise (wobbles and poorly fitting stones are not much of a problem). The property of Irreducibility is as it was defined beforehand. So what we claim is a problem for evolution (a problem not involving theoretical impossibility but involving practical infeasibility = it would take too long to originate) are irreducibly complex systems. Such as the rotary flagellum, the most well known example of such a system. In such a system we have a high specification for each of it's parts (functional proteins are exceedingly rare entities in their configuration sequence (meaning that out of all possible amino acid sequences, very few will fold into functional proteins) thus they are highly specified chemicals that need to be "found" from out of the larger number of nonfunctionally folded proteins. We also have a high specification for the interfaces between these proteins. They need to be a fairly precise structural and electrochemical fit in order to be able to cooperate functionally as they do. Consider as examples, the various cap proteins that are capable of placing the unfolding flagellar tail proteins into position (dancing on the top like a Barbie Doll ballerina!). The motor assembly which can convert an electric gradient into efficient high speed rotary motion, and also the protein transporter assembly (the T3SS) which is capable of unfolding proteins at the bottom, drawing their unfolded amino acid residues upwards alon a 2 nm wide pathway, and enabling them to refold at the top. Note also that the idea that a much cruder unrefined less optimal version of tsuch a machine would be able to function enough (and reliably enough) to be favourably selected for is also a bit of a nonsense. Not only is the function irreducible, but it's reliability and quality of function must also be above a certain threshold (irreducibkle quality and irreducible reliability) or else the organism would have little use for such a waste of energy as such a system would be. After all, pure Brownian movement is going to at least provide some motility. A system unable to have it's effects felt above the major background of brownian motion isn't going to be of much use. Poor function in such a system isn't going to be selected for, even if it managed to evolve in the first place. Hey, the flagellum is an oldie but a goodie! That video (a simplified version of Nick Matzke's take on flagellum evolution) appears to work quite feasibility to the casual evolution enthusiast, because the steps proposed don't address the complexity issues. (Those issues involving the required specification of the protein parts, and the requirements for highly specified interfaces between those parts.) Leave those out, and the story can be practically anything you can dream up or watch in a cartoon. It makes sense in the same way that morhing creatures in the movies make sense. But as Behe says, the devil is in the details. All that is required is a chain of usefully intermediate functions that serve as periodic waystations, in order to invoke natural selection. Each stage is functionally beneficial (is it not?) and thus natural selection will preserve it. Voila - the evolution of the flagellum made easy. But can you see the weakness of the presentation yet? It's in between each of the stages. No evaluation was made of how you'd ever manage to get from stage to stage. What would be able to guide the evolution from one functional stage, to the next stage? That is the unaddressed problem with this proposal. Natural selection can keep the evolution on track so that a particular stage would tend to conserve or improve it's function. But how do we manage to get from one function to the next? Guided evolution, or random evolution? As youtuber cdk007 always says, think about it. Two serious problems for such an evolutionary pathway have to do with 1. The extreme rarity of functional proteins within their potential sequence space. 2. The implications on natural selection of having changing functions (and the evolution of new functions) along the evolutionary trajectory. This causes evolution to diverge from a one function direct Darwinian pathway, into an indirect Darwinian pathway, where the system function changes into different ones over time as illustrated in that cdk007 video.. You have good taste in avatars! Well, I just wanted to see if you agree that the basic idea of IC is valid. Whether or not an internal combustion engine translates poorly to biology is another issue. The internal combustioon engine does at least serve to illustrate what IC is apart from it's application to biology. It seems that for such a case you do seem to agree that such a thing exists. But I guess IC's application (or lack of it) to biology is going to be the sticking point. I'd claim that most of the refutations of IC didn't succeed in refuting it, save for some trivial examples. Remember that the creationist claim isn't (or certainly shouldn't be) that the evolution of irreducibly complex systems is theoretically impossible. That's a bit of a hard claim to demonstrate. What we claim is that the evolution of IC systems is infeasible given the populations and the time available. I believe that may be one of the motivations for the multiverse hypothesis, though I believe most of the cosmologists haven't picked up on IC, but instead the fine tuning of physical constants argument. It's an inference akin in some ways to the ID inference, in that it in it's way deals with some of the limitations of resources of mindless natural processes by proposing a possible way around such limitations so that the anthropic principle becomes somewhat more than just an empty statement. And with no way to directly observe any of these other proposed universes. As in the case of ID (and as is often the case with evolution) all the evidence is neccessarily indirect. One of the proponents of the multiverse once stated stated something like this: "If you don't want to believe in a God, you're going to need to believe in the multiverse". (I cannot remeber who said that, but it's in an article somewhere). I looked for it, and found it. The quote is from this article: Science's alternative to an intelligent creator: the multiverse theory A scientist called Bernard Carr (a cosmologist), commenting about whether many universes exist or not, said: "If there is only one universe, you might have to have a fine-tuner. If you don't want God, you'd better have a multiverse." True. But plenty of scientists decide to live by faith (not the results of science) in their chosen philosophy. They comfort themselves that they really aren't doing that by claiming to be following the "consensus view". That's in many cases, sciencespeak for "going with the flow". The science itself isn't the issue. It's how we interpret the results of scientific research and then try to fit those results into our chosen worldviews. Depending on what we believe we'll be reading rather diferent conclusions into the results. But hey, I'm as guilty of that as you are. I just think that we might have some better arguments on our side (but that remains to be seen).

Are you referring to random mutations and natural selection as being the observed mechanism? I'll assume yes. If not you can fill me in on what it is. It has been observed to do some things for sure. But it's a bit of a stretch to always think it can do what is often claimed of it. All of that (what I'll refer to as inferred evolution) seems to have been mostly inferred via indirect evidence, and deduction from the naturalistic paradigm, not just from observation. And fair enough, we have to cut some slack to RM & NS as the general idea is that the process must take a very long time to act. So we can't neccessarily expect to see things such as new multiple protein machines evolving in the laboratory. But even so, there are some good reasons to suspect that such a mechanism is limited enough in what it is capable of achieving, that some of the claims made of it may be suspect. That is why I am justifiably incredulous (non believing / skeptical) about such claims. I'm not saying it does nothing at all. I'm not even saying it isn't able to create new information. I'm just claiming it isn't able to do all that much (ie. it can't create very much functional information), which agrees well with direct observations that are scaled up. Don't blame the mechanism, blame the system that led to the overhyped claims about that mechanism. The mechanism is what it is. As for the indirect evidence supporting such claims? That has to be thrashed out separately as well. But taking what we observe of RM & NS and attempting to scale it up (as Behe specifically did in his book "The Edge of Evolution" (and also in a paper with Snoke about the amount of time taken for multiple specified mutations to occur)) shows it's limitations are very likely not going to allow it to achieve what many imagine it has, even in billions of years and with populations in the dozens of digits. That mechanism is fighting an exponential divergence between what might be able to happen in theory, and the kind of time periods it would likely take for such things to happen. They're the same cells, but you get the gist of the optical transmission better in this (idealized) diagram of the Muller glial cells. This is the abstract of the PNAS paper referenced in the diagram: Müller cells are living optical fibers in the vertebrate retina Here is another article in a newspaper about this discovery: Living optical fibres found in the eye The abstract for that paper says: Although biological cells are mostly transparent, they are phase objects that differ in shape and refractive index. Any image that is projected through layers of randomly oriented cells will normally be distorted by refraction, reflection, and scattering. Counterintuitively, the retina of the vertebrate eye is inverted with respect to its optical function and light must pass through several tissue layers before reaching the light-detecting photoreceptor cells. Here we report on the specific optical properties of glial cells present in the retina, which might contribute to optimize this apparently unfavorable situation. We investigated intact retinal tissue and individual Müller cells, which are radial glial cells spanning the entire retinal thickness. Müller cells have an extended funnel shape, a higher refractive index than their surrounding tissue, and are oriented along the direction of light propagation. Transmission and reflection confocal microscopy of retinal tissue in vitro and in vivo showed that these cells provide a low-scattering passage for light from the retinal surface to the photoreceptor cells. Using a modified dual-beam laser trap we could also demonstrate that individual Müller cells act as optical fibers. Furthermore, their parallel array in the retina is reminiscent of fiberoptic plates used for low-distortion image transfer. Thus, Müller cells seem to mediate the image transfer through the vertebrate retina with minimal distortion and low loss. This finding elucidates a fundamental feature of the inverted retina as an optical system and ascribes a new function to glial cells. Uh oh! How about something totally unexpected - the 3 stone arch!! Betcha' can't explain THAT Technological Terror of IC in terms of mindless natural processes!!!!! But seriously, how about the rotary flagellum? It's already been discussed to death, so we'll have a bit more fact and less speculation to go on. We creationists claim it's irreducibly complex. A pretty good example of such a system. I'd also say that many, perhaps even most biological protein machines are also IC, but I'm not enough of a biology guy to say too much about those. But Behe points out in "The Edge of Evolution" that the eukaryotic flagellum is a far greater example of irreducible complexity than the rotary version is, but I guess we should stick with that. But I must say, that for some time I have seen you in Mad Magazine sir, and I'm very pleased to meet you. I didn't know you were an evolutionist, but what, me worry? Anyhow, perhaps you can tell me why you think that IC either doesn't exist in biology, or is irrelevant to evolution. Do you claim that IC doesn't exist period? I mean, do you allow that IC exists in nonbiological systems, such as the internal combustion engine for example? We can discuss that also as an example of what IC means in general. Because I claim it is a phenomena of a system that potentially might exist in any kind of systems, not just biological ones. Note also that Muller's "interlocking complexity" would be a special case of IC. That would be a certain kind of IC which is capable of being built up gradually via the Mullerian 2 step process. However one could not assume that all examples of IC must belong to the "interlocking complexity" subset of IC systems. Well, one could infer that must be what has taken place in biological evolution of course, but then one would have to justify that position somehow. Anyhow, what do you reckon? Because good science has to be one step above just believing that mindless natural processes are the catch all explanation for everything. We simply don't know that to be true. Certainly not for phenomena such as life, though it is very likely true for many other phenomena. You know, they just might even be the explanation for everything, but perhaps they are not. Science cannot just take such things on faith. The fact that biology has been unearthing such high levels of sophistication in the last few decades just might indicate that science is pointing us away from mindless natural processes. Why do you say that ID has no evidence? What you mean I think is that it has no direct evidence. But it has plenty of indirect evidence. After all, if ID is true, then mindless natural processes must be unable to do some things, right? And whether ID is correct or not, we still know that mindless natural processes must be unable to do certain things! I mean, no one as far as I'm aware is saying that mindless natural processes are capable of doing anything. So if MNP are insufficient, then one of the predictions of ID (a rather obvious one) is that we will be unable to find MNP to explain certain phenomena for which ID is implicated. Now I take it you perhaps say that being unable to find any MNP's capable of performing certain tasks is still not evidence for iD. Right? But what you are then saying is that as long as you have no direct observations of ID (observations of the designer designing) then you must reject it on scientific grounds. Is that what you're saying? Now what about if we reverse the siutation. Why should anyone believe that MNP is capable of originating certain phenomena, when we have no direct (observed) evidence of it taking place, but only indirect evidence (ie. the appearance in the fossil record of lifeforms, or via DNA similarities etc.) by which their evolution is indirectly inferred? We can take that further with abiogenesis. About the only indirect evidence that can take place is provided by some mostly irrelevant facts of chemistry, and the claim that since we're here, we must have been abiogenesisized into existence (and evolved from there into what we are now). You know, I'm just saying that you have to be even handed in your approach. To be consistent you would have to require that science teach neither ID nor MNP as the likely explanation for certain phenomena. Would you be happy with such a hardline approach? I would. I wouldn't mind if science had a policy of saying basically - for certain phenomena science cannot decide (base on insufficent evidence) as to whether certain phenomena have originated via MNP or via ID. And then it would be up to individuals to decide for themselves what they wanted to make of that. Would you support such a policy? Not quite true in all cases, though it seems obviously true for most cases. Because what we're talking about is the ID calim that says this: intelligence is required to ORIGINATE intelligence, or a sophisticated phenomena such as biological life. So what case wouldn't the ID claim apply to? The case for which the first cause intelligence DODN'T HAVE ANY ORIGIN that needed to be explained! (One can also apply that to MNP with the universe). In fact some of the resistance (highly emotive resistance by some fairly presitigious scientists) to the initial acceptance of the Big Bang theory was due to the realization that by promoting the big bang ideas, they would have to give up the notion that they had available to their worldview an infinite amount of time for MNP to be able to act and thus potentially do almost any conceivable thing within this universe. And even now there is a continuing resistance to the big bang from many scientists. I'm not talking about creationists, but about atheists who see evidence that they claim refutes the big bang viewpoint. But at least for now, the orthodox view is that this universe has had around 14 billion years in order for MNP to put together what we see around us. Hmm! If something was eternal, whether it be an eternal mindless natural p[henomena, or an eternal intelligence, then such a thing did not originate, and thus itself requires no ID inference to be applied to it. It's up to you to decide whether that eternal something was MNP or an intelligence. The problem for naturalism is that we have studied MNP and so far we see that whether it is eternal or not, it does have limitations that prevent it from originating things. What we have not done is study the proposed designer to see if it has any problems with originating things. But we do know that if such an intelligence exists, then it is likely greater than we are, and thus likely is able to originate phenomena such as life. But a lot of this is way outside of what science can tell us for sure, right? It's up to you to decide to ignore the ID issue, and maybe even oppose it as well, or whether to give it serious consideration. The evidence for ID is all indirect. Yet still, we know that intelligence does provide a better explanation for these kinds of phenomena, in fact it provides the only explanation that is feasible. But it requires a certain amount of faith in the unproveable. But then again, so does your viewpoint. You do have faith in nature, even though you do not have any proof that it can do such things. It's up to you to decide these things for yourself. In essense it's the same thing. It's an intelligence designing signals which scientists don't accept could have originated naturally. I can't get through your whle post now, but you wanted some anti-naturalistic evidence. Here's a link to some heavy reading - creationist biology on protein evolution and the flagellum. The evolution of the flagellum

The origin of organic compounds aren't the main issue. The problem is where did the information in the sequences come from. And how did it manage to organize into a system that not only self replicates, but manages to stay protected and retain fidelity in the reproduction process. Without fidelity any ability to reproduce will be rapidly lost. In addition the claim that early life was much simpler than it is now makes one wonder how any such simpler early life that somehow managed to appear, was able to exist for more than a few minutes, and be lost again for millions of more years until the next fleeting occurence of self replication? In addition, replicators of the short lengths (and thus feasible probabilities of emergence) in Musgraves article require preformed sequenced templates to be available for replication! That's a pretty artificial condition. We're not talking about assemby of long polymers from individual monomers here. To do that, not only would we need a ready supply of those, but a lot of supporting machinery that simply wouldn't be in existence before life in it's current sophisticated form was present. The claim is always made that early life was much simpler than it is now. I predict that as knowledge increases, it will become apparent that as is often the case, life has an irreducibly complex sophistication threshold in order for it to survive. It needs to be able to protect and maintain itself in many many ways in order to survive the abiotic environment. Oil bubbles containing hypothesized self sustaining "simple" self replicartors don't fit the requirements of reality. Interfering cross reactions in the impure real world environments would bring such processes to a halt and break them up. What about energy production and storage? There are a whole host of problems that need to be solved beforehand if life is to be feasible and sustained for any length of time. Of course, there's going to be a lot of side benefits to chemistry and chemical engineering gained from continued investigation into possible origin of life scenarios, but don't imagine that there aren't any fundamental difficulties with this scenario. They're simpler and used in organisms that don't require the extreme cooling capabilities and longetivity that the inverted retina provides. Basically the reversed retina enables the light cells to be cooled easily and worn out receptors to be removed into the bloodstream rather than into the eye fluid. Any visual clarity problems are solved via the existence of special cells which act like optical light fibres to conduct light through the maze of blood vessels. In addition this arrangement enhances clarity by absorbing scattered light more effectively than sensors in the front. But it is energetically very costly and is uneccessary in many creatures not having all of these requirements. Many organs can start to fail in various ways. Not surprising given that death is inevitable for all creatures. Yet the prostate design in one article (written by evolutionists) was described so: "Unfortunately, the prostate's BRILLIANT WRAP-AROUND STRUCTURE WITH DUAL-PURPOSE CORE TUBING can become a liability if the prostate swells or enlarges." Once again, many people cherry pick the particular things that they don't like, while mostly ignoring the cleverness that certainly was apparent to the author of that article. What about tortioned gastropods? Interesting! But given that they rely on moisture conservation so heavily, and that they secrete mostly insoluble uric acid as well as water (free from the mostly insoluble uric acid), it seems to me that such an arrangement would promote survival by having another source of water to hand in the vicinity of the head and feeding apparatus of the creature, rather than it being wasted by being expelled out of the back. Being "weird" doesn't really count for too much I shouldn't think. The fact that such poorly designed creatures are in abundance tends to argue against the viewpoint that such tortioned arrangements are doing those creatures too much in the way of harm. We see both kinds of creatures (tortioned and non-tortioned) are able to exist rather well. The Panda's thumb, while often criticized as being another example of poor design that no designer would ever engineer, is nevertheless not appearing to hamper the dexterity of the Panda one bit in stripping bamboo. Many have remarked how easily and efficiently Panda's are able to do this. Perhaps we should ask a Panda what they think of their paws? There is however a class of what has often been regarded as "poor designs" that could in the creationist viewpoint) be regarded as degenerations of the original designs. And I guess we'd have to admit that these degenerations are examples of evolution in action. Flightless birds would be an example of that. As well as blind cave dwelling fish that have the information present to make eyes but have suffered mutations that prevent the eyes from forming. Some (though not all) pseudogenes would also fit into this category. Tail like appendeces are used (in humans) in order to anchor muscles. Just because we have no tails of any length, should a designer take away a useful anchor point. Why would he do that? To be neat? Much of that article comments more on similarities than design flaws. In some ways I tend to partly agree with them, because while they see similarities as pointing to common descent, we'd see such similarities as indicative of common designs and the re-use of ideas. So called "convergent evolution" is a rather extreme case of what look far more like common design ideas being executed in different ways, than it resembles evolution that happenned for some reason (usually attributed to similar environments) to converge to creatures that often look or perform in astonishingly similar ways, yet without any close enough phylogenetic relationships. In any case we creationists do support the notion of limited evolution, and degeneration which will often evolve due to the fact that certain degenerative conditions and loss of functional information can actually be selectively advantages in certain nich environments. I'm supporting the notion that naturalism can sometimes be falsified (by likelihoods) by ID. But many naturalists act as if ID must be excluded from science altogether. Thus it is they who are attempting to put naturalism into the unfalsifiablke category. But by acting that way, they are removing naturalism from the domain of science and into the domain of unfalsifiable dogma. ID is diffeent because it can be falsified by showing a natural phenomena that is up to the task at hand. Evolution gained widespread acceptance in it's day because back then it seemed to many scientiststo be a sufficent natural explanation. But now having learned a lot more in the interim (especially in regards to molecular biology) it is now philosophical inertia that is driving the continued acceptance of evolution more than the actual evidence. When I say evolution here, I am not talking about observed evolution, but the notion of inferred evolution = common descent from a single or group of one celled ancestral lifeforms. Yes. There really are many difficulties for mindless natural processes in beig able to account for biology. We'll be going over them in time. Irreducible complexity for instance is a major hurdle for naturalism. Reports of IC's death are highly exaggerated!! I think that is an overly idealistic view of the way most scientists think. Especially when the implications are as political and cultural as they are when it comes to support for the notion that something like a God might actually exist. Most people including scientists (though not all of them) cling tightly to their chosen beliefs. The history of science shows that rather dramatically. What you're talking about typically happens over time, as in "when the old guard die out" after which a paradigm shift is more easily achieved.