Jeff's First Response:
Why not?

Intelligent Design, I would define this way: all the organisms that we observe today were designed by someone (or something, or some group of things) that was (and maybe still is) intelligent. All organisms were created in essentially their current form, but not necessarily all at the same time. Their genes were designed with a certain amount of extra information that creates variations between individuals, so that populations can adapt, to a limited extent, to changes in their environment.

Now, with those definitions, let's make some predictions. I'm going to list predictions of both theories in several areas, to emphasize the point that Intelligent Design is at least as valid a scientific theory as Evolution. If you would like to add more predictions that Evolution makes, I'll add corresponding predictions for Intelligent Design.

1. Fossils

A. Evolution predicts that the fossil record will be full of innumerable transitional forms of organisms that show the slow progression from simple forms to increasingly complex forms. From fish to amphibian, from amphibian to reptile, from land mammal to aquatic mammal, etc.

B. Intelligent Design predicts that organisms will appear in the fossil record fully formed, and will remain relatively unchanged until they go extinct or until the present time.
(Note that neither theory really predicts how many or how few fossils will be found. That's a question for geology more than for life-origin theories.)

The most notable aspect of the fossil record, for ID'ers, is the Cambrian explosion. Before that, there was only single-celled life. [Long theorized, and predicted by evolution, soft-bodied Precambrian worms have been recently discovered. This completely matches the claims by scientists that fossils from this time are very hard to come by. Scientists have also found the primitive Precambrian ancestor to the mollusk. It has a foot, but no shell, early sponges, and arthropod embryos. They have also found fossilized tunnels from worm like creatures. This is all between 10 and 60 million years before the Cambrian period. This is how long ago the large dinosaurs went extinct so there is plenty of time to evolve into the explosion. New species appear throughout the fossil record and are sometimes linked to their soft bodied ancestors. These ancestors are very rare since it is unlikely they will fossilize. Further, in the three most famous Cambrian sites, Greenland, China, and Canada, there is a growing diversification of life matching the age difference of the three sites, roughly 5 million years between each. This is completely consistent with evolution. How does ID explain the length of time it took to create the Cambrian explosion? 15 million years is eternity to an intelligence capable of creating a human.]
Alright, it's true that soft-bodied organisms are unlikely to ever fossilize, though some obviously have been, so let's restrict our discussion to hard-bodied, more easily fossilized organisms. According to the International Subcommission on Precambrian Stratigraphy (ISPS),
the evolution from the first hard-part animals to the presence of most of the present-day phyla was restricted to an interval of probably less than 10 m.y. Multicellular life evolved at an incredible supersonic speed, and for this reason this part of organismal evolution is termed the "Cambrian Explosion", or "Evolution's Big Bang."
This rate of evolution is clearly not what Darwin predicted, or what anyone predicted until the Cambrian Explosion was discovered, or they would not describe it as 'incredible.' Still, 10 million years does seem like a long time, so let's talk about dates a little. How are these three Cambrian sites dated? All of them are sedimentary rock, of course, which cannot be radiometrically dated. Quoting from the same ISPS site,
Accordingly, the International Subcommission on Cambrian Stratigraphy (through its Working Group on the Precambrian-Cambrian Boundary) made the official decision in 1991 to draw the base on the Cambrian at the first appearance date (FAD) of Trichophycus pedum in the reference section at Fortune Head, southeastern Newfoundland.
This is the most common method of dating sedimentary rock - by the index fossils it contains. I did some research about Fortune Head, and found information about two layers in it that have been radioactively dated. They are both older than the Cambrian Explosion, the younger is dated at 608 Ma. I found no mention of any layer that has been radioactively dated after the Cambrian Explosion. From the picture linked to the ISPS site, it looks like that's because the formation is sedimentary all the way to the top. So the Trichophycus pedum fossils there could be any age younger than 608 Ma. I can find no indication that any of the Cambrian sites you mentioned were radioactively dated, they were all dated by the fossils in them. So, if the assumed ages of the fossils are incorrect, then the ages of the formations are incorrect as well.
In some of the age discussions, I have seen mentions of fossil A being X meters above fossil B. Is the number of meters between the fossils an accurate measure of age? Only if we can determine that the sediment was deposited at a relatively constant rate. But since all these formations have such exquisitely preserved fossils, everyone agrees they must have been buried by floods which stirred up lots of sediment and then deposited it all rapidly with the organisms inside it. So we actually know that the sediment was deposited in fits and spurts, and there could have been any amount of time between the individual floods. We really can't nail down the ages of these three Cambrian formations with pinpoint accuracy, so they might have all been formed at the same time, or even in the 'wrong' order with the most complex organisms being the oldest.
 Then, all of a sudden (in geologic terms), hundreds of diverse and complex life forms appeared. These included trilobites, with fully-formed eyes very similar to modern ones. There is no fossil evidence of any intermediate steps leading up to trilobite eyes or any of the other biodiversity. [Even today there are creatures with very simplified eyes that are consistent with eyes having evolved. The fossil record also shows eyes of greater and lesser complexity. If eyes are made, why make inferior ones?]
Humans make computers which vary vastly in complexity, from IBM's gigantic Blue Gene supercomputer, to lowly cell phones, and even simpler embedded systems in cars. Cell phones are much simpler and less powerful than supercomputers. If computers are made, why make inferior ones? The existence of simple and complex eyes is no better evidence for eyes having evolved than the existence of cell phones and supercomputers is evidence that computers evolved. The existence of simplified eyes today makes the case for evolution even worse. Why are there still simple eyes, if more complex ones are superior? Why did trilobites, some of the earliest organisms, have such astonishingly complex eyes, some with over 15,000 lenses? And why did they, so early in the fossil record, have such a wide variety of types of eyes? The fossil record does not show a nice progression from a few simple eyes to wider and wider variety and more and more complexity. It shows a wide variety of eyes, from very complex to relatively simple, existing from the beginning of hard-bodied life to the present day. It is far more consistent with the hypothesis that all the eyes were designed by a common designer than the hypothesis that all the eyes evolved independently or came from common ancestors.
So, this seems much more consistent with the theory that all these forms of life were designed and created at about the same time, than with the theory that they slowly evolved over millions of years. This pattern is repeated with the sudden appearance and disappearance of the dinosaurs. [Slow evolution is largely dead. I don’t think any scientist today believes that evolution can only happen slowly. There are too many examples of rapid evolution in the fossil record,
Alright, so here you agree that there are so few transitional forms in the fossil record, not only during the Cambrian Explosion, but also at many other points, that scientists have been forced to abandon the slow evolution proposed by Darwin and propose a modified version known as Punctuated Equilibrium. Now, as I mentioned before, Punctuated Equilibrium hypothesizes that evolution happens so fast that it leaves no trace in the fossil record. So, how can we verify or falsify this theory? The only way I can think of is to observe it happening. The theory states that with an isolated population and strong selectionary pressure, species evolve quite rapidly. I haven't heard many exact numbers of how many generations it should take, but the Wikipedia mentions increasing limb length by 50 centimeters over 10,000 generations. (If you know of a more reliable statement of how many generations we should consider, let me know. It seems that if we go much higher than 10,000, then, in long-lived organisms like elephants and turtles, the change should take long enough to be observable in the fossil record) So, we should be able to take a short-lived organism, like bacteria or fruit flies, isolate a small population, apply selectionary pressures, and observe the evolution of a flagellum or stingers or something within a few years.
in laboratory experiments, and witnessed in the real world.
I found a report about the experiment that I just described. They took a single E. coli bacteria, subjected it to selectionary pressure by putting it in a glucose-limited medium, and observed what happened after 10,000 generations. They observed increasing diversity over time, and also a few beneficial mutations that were selected for. ID'ers would expect this result just as much as evolutionists. From the paper, it is unclear to me what the beneficial mutations were, so correct me if I'm wrong, but it appears that they did not involve the evolution of new genetic information, like some new protein or new molecular pathway that allowed more efficient utilization of glucose. The mutations were apparently things like sickle-cell anemia, which provides a particular benefit against malaria, but makes the individual overall less fit. ID'ers believe that such beneficial mutations can and do happen, the critical thing that they believe cannot happen is new information, like new proteins, or new structures like a flagellum.
I know of no such experiment that has demonstrated the evolution of new genetic information. The bacteria experiment did not create any new species, or any new function. Experiments have produced white-eyed and red-eyed fruit flies, fruit flies with deformed wings, and fruit flies that have legs where their antennae should be. None of these demonstrates the evolution of new genetic information that evolution requires. Have any been done? If not, then Punctuated Equilibrium is an unsupported hypothesis.
We know a sudden change in climate and environment killed the dinosaurs. We are almost certain it was a meteor that hit the Caribbean. New England is known for all of its deciduous trees that change colors in the fall. New England used to be covered in White Pine. Settlers cut down all the pines and the deciduous trees rushed in to fill the void. We know there were mammals living with the dinosaurs, but were mostly niche animals. When many of the dinosaurs died they swept in. Mammals and small dinosaurs survived.]
All of these are examples of one species taking over from another. They are not examples of new genetic information evolving.
 Evolution theorizes that amphibians evolved from fish. This means that at some point there must have been some creature that would be classified as a fish which gave birth to a creature that would be classified as an amphibian. [Only by assuming that nature really lives in our convenient categories.]
That is exactly my point. Why does nature, in almost all cases, live in nice, convenient categories? Quoting from Origin of Species, "Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?" Darwin recognized that his theory would suggest that nature should be a continually changing spectrum, but it is not. It is easy and convenient to group animals into Fish, Amphibians, Birds, Reptiles, and Mammals. Each of these classes shares not just one, but several traits that make them easily definable. The few exceptions that there are, such as the duck-billed platypus mentioned below, make the case even better for ID and even worse for evolution. The duck-billed platypus does not appear to be halfway through the process of changing from a mammal to a bird, it has fully-formed traits of both classes: a bill and webbed feet similar to a duck's, fur similar to a beaver's, a leg structure similar to a lizard's, and poisonous 'fangs' (on its legs) similar to a viper's. So which of the four is it most closely related to? Whichever we choose, we must then assume that it independently evolved to be similar to the other three, even though its closest relative didn't. I have read on several evolutionist websites that evolution could be falsified by "true chimeras, that is, organisms that combined parts from several different and diverse lineages (such as mermaids and centaurs)". The duck-billed platypus is a true chimera.
Obviously, the parent and offspring would have been very, very similar, somewhere in between a fish and an amphibian, and the offspring of the offspring would have continued to change over many more generations until they looked like modern amphibians. The ID'ers point is that there should be lots of fossils that are hard to classify because they are somewhere in between fish and amphibians. [Well, there are. I assume by lots of fossils we are talking in relative terms. Fossils are extremely rare themselves.
Extremely rare? Below, you say, "Now, compare that rarity to the fossil record and even Darwin did not predict we would find so much." You are using the richness of the fossil record as evidence for evolution, and, at the same time, its sparsity to explain the lack of transistional fossils. Here are some examples of what Darwin said. I'm piecing together several sentences from different parts of Origin of Species that refer to the fossil record, which I think do not twist his meaning, but show accurately what he said about fossils:
If my theory be true, numberless intermediate varieties, linking most closely all of the species of the same group together must assuredly have existed... Consequently evidence of their former existence could be found only amongst fossil remains...But, as by this theory innumerable transitional forms must have existed, why do we not find them embedded in countless numbers in the crust of the earth?...
Some fossils are claimed to be transitional forms, but we certainly do not have 'countless numbers'. Even relative to the number of known fossils, the percentage that are claimed as transitional forms is very small. We have many pre-humans, proto-humans, proto-chimps, where does Australopithecus fit? The reason there is no missing link is because there are many. Even today, where does the Platypus fit? The walking catfish? The mudskipper?
Do we really have that many missing links? In making the case for Punctuated Equilibrium, the prominent evolutionist Stephen Jay Gould admitted that we do not:
"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils"
As for all the pre-humans, proto-humans, and proto-chimps, please look at the diagrams on this site, most notably the one that compares two of Ian Tattersall's diagrams of human evolution. Notice that the new tree is even more full of question marks and dead ends than the earlier one. It looks very much like adding 'epicycles' all over the place to try to make the data fit the theory. The six cladograms from Science are also interesting. Rather than seeing a nice progression from ancestor to descendent, we see confusion and disagreement. This shows that the evidence from which the trees are being constructed is either extremely fragmentary or outright contradictory.
 Genetics are causing biologists to reclassify species into new families because even today it is hard to properly classify anything.]
 This basically admits my overall point in "2. Genetics" below, that genetic analyses do not match up with each other or with morphological analyses. It is not any harder today to classify animals as fish or amphibians or birds than it ever was. What is hard is deciding which families are most closely related.
This is the same thing we observe with human-designed machines. It is easy to classify vehicles as planes, trains, or automobiles. But what if alien archaeologists tried to decide which of them evolved from which? Automobiles and trains both travel on the ground, so they might conclude that automobiles evolved from trains. But then if they discovered that the rubber tires of automobiles are more similar to the rubber tires of airplanes than to the metal wheels of trains, they might decide that automobiles actually descended from airplanes. That would explain why some cars have vestigial tail fins that don't serve much purpose. The aliens would have difficulty deciding how the evolution happened because it really didn't happen. We observe a similar difficulty in classifying human ancestors (and many other ancestor-descendent relationships), so we could reasonably view that as evidence that the evolution didn't happen.
But we have found many fossilized fish and amphibians, but no such intermediate forms between the two. So the fossil evidence suggests that there was no evolution, and that both fish and amphibians were designed and created. [On this entire planet Darwin had to go to one extremely remote spot to see evolution. To be fair, he went to several but one spot is so famous. Now, compare that rarity to the fossil record and even Darwin did not predict we would find so much. We have found fossils that are not one, nor the other. Have we found any that are exactly half way? I don’t know, and I don’t think it really matters. If I see a train go into a tunnel, and then come out the other end, I don’t assume a new train was created in between. And many of these tunnels are very short.
I don't think the metaphor about a train going into a tunnel and coming out is a very good representation of evolution. Let me propose a metaphor: If I see a train go into a tunnel, and an airplane come out the other end, I wouldn't assume that the train turned into an airplane.
 Not only does evolution predict we will find these transitional species, but tells us how deep to dig and in what strata to look. It is remarkably accurate. Scientists decide they want to find the predecessor to birds, figure out about how long ago to look, what areas would be good to look, and when one of these creatures are found that IDers dismiss as not being a missing link, it is right where it was predicted to be unless geology decided to play games and toss the site around.]
 I haven't heard of any remarkably accurate predictions made by evolution. On the contrary, I read things like this:
Intermediates are not necessarily the same as the exact predicted ancestors; in fact, it is rather unlikely that they would be the same. Simply due to probability considerations, the intermediates that we find will most likely not be the true ancestors of any modern species, but will be closely related to a predicted common ancestor. Therefore, the intermediates we do find will likely have additional derived characters besides the characters that identified them as intermediates. Because of these considerations, when a new and important intermediate fossil species is discovered, careful paleontologists will often note that the transitional species under study is probably not an ancestor, but rather is "representative of a common ancestor" or is an evolutionary "side-branch".
This suggests that actual findings are usually so different from expected findings, that newly discovered species are usually not even claimed to be actual common ancestors.
As for finding fossils in the predicted strata, strata are usually dated by the fossils in them, as I discussed above. Thus, if paleontologists expect that a certain common ancestor lived about 200 million years ago, and then they find a fossil similar to the expected ancestor, they conclude that the layer it is in must be about 200 million years old. It's easy to be remarkably accurate when you conclude the same thing that you assumed in the first place. I'm not saying that all the proposed dates are wrong, but radiometric dating methods can only give rough estimates, when they can even be used at all.
As for the very existence of fossils that are similar to proposed intermediates, regardless of age, let's go back to our hypothetical alien archaeologists. Let's say they found a 1940's era telephone, and a modern tablet PC, and that they decide that the PC evolved from the telephone. Now they would expect to find a machine that has an earpiece and a mouthpiece, like a telephone, and a microprocessor and an LCD monitor, like a PC. They do some more digging, and they uncover a cell phone. They are very pleased, because not only is the microprocessor much simpler and the LCD screen much smaller than the computer's, showing how they were in the process of becoming bigger and more powerful, but the earpiece and mouthpiece are much smaller than the telephone's, because they are becoming vestigial, as the machine changes its function from communication to information processing. But did any of these machines actually evolve into any of the others? We know that they didn't. This hypothetical situation is very similar to the real situation involving reptile jaws and mammal ears. Once again, we can conclude that the proposed intermediates might be examples of common design rather than common descent.

2. Genetics

A. Evolution predicts that DNA similarity between organisms should reflect their common ancestry. Reptiles should be more genetically similar to all other reptiles than to any birds or mammals, because all reptiles evolved from one reptile ancestor. Apes and humans should be more genetically similar to each other than to anything else, because they share a more recent common ancestor with each other than with any other species. DNA analyses of various areas of the genetic code should generally point to one common evolutionary tree. So Evolution predicts that the more DNA analyses we do, the more they will reinforce the same evolutionary tree.

B. Intelligent Design predicts that DNA similarity between organisms should reflect their common design. Many organisms should share many genes, especially if they are designed to live in similar environments, or if they function in similar ways. But the relationships will probably not fit into one common tree. DNA analyses of various areas of the genetic code will show that organism A is most similar to organism B in some areas but most similar to organism C in other areas. Some genes, such as the genes for eyes, which almost all organisms need, will be shared among vastly different organisms, like humans and squid. So Intelligent Design predicts that the more DNA analyses we do, the more different relationships we should find, including some that link organisms which appear to be vastly different.

We mentioned briefly before that human insulin is most similar to that of pigs, while our immune system is most similar to a rat's, while structurally, we are obviously most similar to apes. If humans and apes shared a common ancestor more recent than their common ancestor with any other animal, then all of our genes should be more similar to those of apes than those of pigs or rats or anything else. [If all our genes were the same as apes, we would be apes. Our genes differ by a fairly small amount. All living things are something like %30 the same. The number of variations in genetics is finite. It is not remarkable that given a finite number of variations there will be matches with very distant relations. Somewhere on this planet is a car with the same numbers and letters in its license plate as on mine. This is not astonishing and does not mean we are related.]
 I'm not sure how the license plate analogy applies. You're right, no one would conclude that a car with the same license plate as yours was closely related to it.
The point I'm trying to make here is not how similar or different our genome should be from chimp's. My point goes back to the hypothetical alien archaeologists having difficulty establishing the relationships between planes, trains, and automobiles. We have similar difficulties establishing genetic relationships, so it could easily be because of the same reason. Planes, trains, and automobiles didn't evolve from a common ancestor, so maybe humans, chimps, pigs, and dogs didn't either.
 Whales are another example cited by ID'ers. Evolutionists once believed that whales evolved from Ambulocetus and several other extinct fox-like creatures. But then DNA analysis showed that whales were much more genetically similar to hippos than to the family that Ambulocetus belongs to (whose name I forget). Since various DNA analyses have produced very different evolutionary trees than morphological analyses and other DNA analyses, genetics supports common design much better than it supports common ancestry. [Dr Tavison of Sweden,( I only know his name because it is a name I have used for years believing I made it up), about 4 years ago discovered a fossil that linked Hippos to Whales.
 I can't find anything about Dr. Tavison on the web. Can you refer me to any more information about him?
 How would IDers explain why a whale has knees? It’s a foolish waste of time to add something that has no use at all.]
 I can't find anything that says that whales have knees. I found some sites that said that some whales have a couple of bones in the pelvic area that the male reproductive organs are anchored to, but nothing about knees.

3. Environmental effects

A. Evolution predicts that changes in the environment will create selective pressures, which will in turn cause organisms to evolve so that they are suited to the new environment.

B. Intelligent design predicts that when the environment changes, organisms will adapt as far as their genes allow, but the adaptation will be limited. If that limit is exceeded, they will simply become extinct.

To quote one of your earlier emails: "Why is there so much diversity of life when we know extinction is real?" We certainly have observed many species become extinct, usually due to changes in the environment. We have not observed any new species evolve. [That is not true. The first artificial species were created in the 1920s, and scientists have observed the formation of new species in the wild. Mice on the island of Madeira have evolved into 6 new species over the course of only 500 years completely naturally. Apparently along I-80 there is a new species that was artificially created. Fruit flies have been evolved into new species by climate change, artificial culling, and changing the process of natural selection.]
 Ok, my original statement was not quite what I meant. What I should have said is, "We have not observed any new genetic information arise." Speciation events depend on the definition of species, which is disputed, even by evolutionists. One example of speciation that I've heard about was an experiment that kept two populations of fruit flies separated for several generations, one in a cold environment, and one in a hot environment. After a while, when the two populations were reunited, they would not mate with each other. Thus, by one definition of species, that meant that they were now different species. However, I bet that if we put a population of Chihuahua males with a population of Great Dane females, they will not produce any offspring. To avoid getting sidetracked on a discussion of the definition of species, I suggest that we focus on new genetic information. That is the key thing that we have not observed. If information is being lost due to extinction, and not being gained by any process, then my overall point of decreasing biodiversity is valid.
By the way, can you point me to some info about the new species along I-80? I'm very curious about that, but I couldn't find anything about it.
 Thus, the pattern that we see is one of always-decreasing biodiversity. Extrapolating this pattern forward and back in time suggests that a very wide variety of life was created at some time in the past, and that without intervention, all of it will eventually become extinct. This supports intelligent design, and not Evolution. [If diversity is eventually going give way to extinction and there is no new speciation, then where is the Precambrian hippo or T Rex or human or house fly? Where did these new species come from after the dinosaurs? Why are there creatures that look like they are between animal types, but don’t have fossil records to show they were there from the beginning nor around long enough to be much more than a transition?
 I didn't mean to imply that all life forms were created at the same time. I just meant that decreasing biodiversity has been observed throughout recorded history. There may have been many points in the past at which the intelligent designer created new forms of life, such as the beginning of the Cambrian, the beginning of the Mesozoic, and the early Cenozoic. If none of these events ever happened again, biodiversity would continually decrease until it completely disappeared. Of course, that might take so long that the sun might run out of fuel before it happens. I'm just saying that recorded history has not observed natural selection creating new information.
 Why is the life in Australia so much different than anywhere else on earth? Evolution says it is because of extreme isolation, but if there was one designer, wouldn’t isolation be irrelevant?
Isolation is definitely relevant. The original ID hypothesis states that organisms are designed with a certain amount of variability so that they can adapt to a limited extent. Humans have demonstrated this variety very well by breeding Chihuahuas and Great Danes. Isolation could certainly have a similar effect, and produce foxes, coyotes, and wolves from the same original dog. The ID prediction is that isolation could not produce a cat from a dog. The marsupials of Australia were probably designed differently from other mammals, because we have never seen breeding produce a marsupial mammal from a placental mammal, or vice versa. And because Australia is isolated from the rest of the world, marsupials have not spread across the globe as many other mammals have.
 Why does the fossil record show a growth of diversification rather than a decline? Why is life more complex the longer life has been on the planet?]
 If the fossil record shows a growth of diversification, it could be because each successive design event introduces a whole lot of new diversity. But the fossil record shows some stunning decreases of diversity, such as the mass extinction at the end of the Mesozoic, and the end of the Paleozoic. The Cambrian Explosion seems to have produced every modern phylum, plus several that have become extinct. So if we measure diversity by the number of phyla, then we do see a decline rather than a gradual growth. As for variations within genuses or species, we would expect those to increase over time if the originally created organisms had variability built in to their genetic code, which the ID hypothesis states.

4. Irreducible complexity

A. Evolution predicts that organisms evolve through long sequences of small mutations. Thus all the complexity and diversity of life that we observe must have arisen through many, many steps, every one of which produced a survival advantage. If any structure or system that we observe is irreducibly complex, meaning that it could not have arisen through this process, then Evolution is falsified. So, obviously, Evolution predicts that no such structure or system will be discovered.

B. Irreducible complexity is very typical of things designed by human intelligence. A computer, for example, must have at least an input device, a processing unit, and an output device in order to serve any purpose. A radio is an even more significant example. Not only does a radio receiver have a certain minimum number of parts, but even a complete receiver is useless by itself. There must be a radio transmitter, which is a completely separate and completely different machine, transmitting a signal for the receiver to pick up. Television is the same way. So, Intelligent Design predicts that we will observe many biological structures and systems, and even inter-special dependencies, that are irreducibly complex.

This seems to me to be one of the ID'ers strongest points. The bacterial flagellum certainly does seem to be an irreducibly complex electric motor. Of course, if it were the only example, we could dismiss it. But we observe apparently irreducible systems everywhere: eyes (of which there are several varieties)[We have both living examples today and fossil evidence that eyes have evolved. Therapsida is a lizard with a double joint jaw. The lower jaw is mammalian and the second joint bones have already begun shaping themselves into the tiny bones of the inner ear. Irreducible complexity is a valid concern if simpler steps are found that cannot have existed. So far, that has not been the case. Not having found all the steps does not mean there are none.
 True, there is not yet a rigorous proof that eyes could not have evolved. But we have zero evidence of the steps that led to trilobite eyes. When a theory requires hundreds or thousands of steps that we cannot even imagine, and we have no evidence for any of those steps, isn't it more reasonable to believe the much simpler explanation that eyes were designed and created just like video cameras were?
 In these examples, we have the steps. Irreducible Complexity also ignores factors such as strong and weak nuclear forces, gravity, chemistry and the atomic structure. Sure there are millions of possibilities if only the combinatorial factor is considered, but hydrogen and oxygen will almost always make water if they get close together. This does not require a designer to make water. Proteins have preferred orientations just as atoms do.],
What do you mean by this? Do you mean that proteins form spontaneously when amino acids get close together? Do nuclear forces, gravity, chemistry, or atomic structure cause molecules to spontaneously form into irreducibly complex machines? I have never heard anyone claim either of these things.
 ears, the digestive system, the cardiovascular system (including the blood clotting mechanism, without which any organism would almost certainly bleed to death before reaching maturity), the musculoskeletal and nervous systems (which I put together because either of them would be useless without the other), wing-powered flight, sexual reproduction, etc. [If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory [of natural selection] would absolutely break down. – Darwin. I do not know the research state of every one of these points, but I do know that there is a lot of money and fame for the person who can point out a system that violates Darwin’s statement. Digestive systems abound of simple types like flies to astonishingly complex like a cow’s. Dinosaurs have been found with stones where their stomachs would be indicating they have the same digestive system birds have. Flying squirrels and snakes may be intermediate steps to flight; ostriches have feathers and wings, but don’t fly. Are they built by design?
Well, as you point out below, ostrich wings do serve a purpose. They don't work for flying, which is what wings are usually for, but they do have a minor purpose. Have human designers ever done anything similar? Yes. Drag racers have a wing which functions similarly to an airplane's wing, but does not allow the vehicle to fly. It serves a different purpose on the drag racer than on the airplane. Also, wings are very necessary for an airplane to fly, but not necessary for a drag racer to drive. It could still drive around without them, just not quite as well.
 What I’ve often wondered, and science is beginning to answer this, did birds learn to fly jumping into a tree, or jumping out of a tree. It turns out to be most likely neither. Feathers are scales with hollows in it. It’s the same stuff. Some dinosaurs developed feathers to keep warm not to fly. As they ran around on the ground chasing prey, they started waving their arms to grab their food. The additional thrust from the feathered arms gave them an edge in feeding over those that did not.
If a bird-like creature ran along the ground, and waved its arms in the same motion birds use to fly, wouldn't the majority of the thrust generated by the wings push it in the opposite direction that it was running, thus slowing it down?
 Those that ate more had more offspring who themselves evolved this flapping motion to catch prey. This edge became more and more powerful until one left the ground all together. Now, Evolution makes this prediction. If birds evolved from lizards trying to catch prey, their wing beat pattern should be one of reaching out to grab something and pulling it in. This is exactly the motion of a bird flap. Flightless birds should also flap their wings to help them run faster and maneuver better, which is exactly what happens. Does this make it the only answer? No, but it shows evolution made a prediction, it was studied in a lab using high speed cameras, and birds flying and animals grabbing are the same motion.]
Have we ever observed any feathered animal flapping its wings to catch flying insects? Many computers have the same chip architecture, the x86 family, for example. This architecture has been shown to be inferior to a RISC architecture, but most personal computers still use it. The repeated use of this same architecture does not show that they all evolved from a common ancestor.
 There are also inter-special dependencies, like bees and flowers, humans and intestinal bacteria, and wasps and figs. Now, in many of these cases, there are examples of similar but less complex things, like bacterial cilia for the flagellum, and the worm digestive system for the human digestive system. But all of these things would require not one or two, but thousands of intermediate steps to be developed through small, random mutations. It is difficult, if not impossible, to even imagine how every one of the thousands of intermediate steps could have provided a selective advantage. [I think the wing example is a good one where, even if it proves to be false, it is a great example of how unrelated advantages combine in the end to be a unique advantage that is greater than the sum. It’s also important to be aware that a change does not have to have any advantage to be there.
I thought changes did have to be advantageous. The mechanism of change in evolutionary theory is natural selection, which selects changes that cause advantages. Any mutations that do not cause advantages will be lost in the random shuffling caused by sexual reproduction. If you put a wide variety of purebred dogs together, the offspring will all tend to look more and more similar in successive generations.
 Why are birds so colorful? There’s no advantage to being colorful except to attract a mate. On top of that, they had to evolve colored vision in order to take advantage of being colorful. I don’t know there is an answer.
An excellent example of irreducible complexity. The system has 3 components:
1. Colorful plumage
2. Colored vision
3. Female instincts find colorful plumage attractive.
Remove any one of these, and the other 2 are useless. By the way, instincts in general are a good example of irreducible complexity. For example, it is hypothesized that the evolution of the eye began with a light-sensitive skin patch. Imagine that you had a light-sensitive skin patch. What would you do with it? Would you try to move toward light? away from light? Wake up when it got light? Wake up when it got dark? The first individual to have a light-sensitive skin patch must also have an instinct that makes it do something beneficial in response to the light, or the light patch is useless and therefore not selected for. While it is extremely unlikely (maybe even impossible) for either of these things to appear all at once, it is exponentially more unlikely for them both to appear at the same time in the same individual. For evolution to be true, history must be full of such impossibly unlikely coincidences.
 On the other hand, other species have adapted to the fact that birds see color. This is easy to imagine. Two salamanders are born, one with red stripes and one with green stripes. The birds eat all the green striped ones and leave the red ones because it looks like this other creature that is poisonous. It doesn’t take long for there to be no more green ones except in rare mutations that try to get that back.]
Actually, this is not as likely as it appears at first glance. If birds saw in black and white at one time, and then evolved the ability to see color, the salamanders would have had only a few generations to evolve coloration similar to the poisonous creature, or they would all be eaten. Unless some of them were already colored like the poisonous creature before there was any advantage to being colored that way, they would probably become extinct. And matching the coloration of a poisonous creature by chance is another highly unlikely coincidence.
Secondly, if the birds couldn't, at one time, tell the poisonous creatures apart from harmless salamanders, then they must not have eaten either one, or they would have all died from eating poisonous creatures. Once they got colored vision, why did they decide to start eating green-striped salamanders? And how did they know which color was safe to eat? Again, it's remotely possible, but seems very unlikely.
And even if we could imagine it, we have not found any fossil evidence of the intermediate steps between wingless mice and winged bats. [Karen Sears, at the University of Colorado Health Sciences Center in Denver, has discovered that the change from mice to bats is only one gene. This discovery was made less than a year ago, but explains why bats evolved so rapidly. Once this gene change occurred, the evolution to bats would have required very few transitions. Very few bat fossils exist at all though there are an enormous number of bats. Small + delicate + forest environments with acidic soils = low possibility of preservation. Many teeth have been found that link bat like teeth to hedgehogs, shrews, and moles, but we only have the teeth.]
 That's a fascinating experiment, thanks for pointing it out. Apparently, an increase of 50 cm in limb length could happen in much less than 10,000 generations.
However, saying that this one gene changes a mouse into a bat is a gross overstatement of the facts. Karen Sears did not make bats out of mice, she made mice with really long fingers. How well do you think a mouse with really long fingers would survive in the wild? It would be at a great disadvantage to other mice, and it still cannot fly, so it would certainly be selected against. Even being able to change much more than we ever expected could happen in one generation, bats almost certainly could not have evolved in this way.
 On top of that, according to the evolutionary tree, many of these systems must have evolved many times. For example, wing-powered flight must have evolved four times, in birds, bats, pterosaurs, and insects. [If there is an intelligent designer, wouldn’t one mode be sufficient? Why create such different methods?
What different methods? I gave four examples of wing-powered flight. I didn't give any examples of combustion-powered flight (like rockets and missiles), or rotary flight (like helicopters). My point is that it seems hard enough to evolve flight once, and it would be exponentially harder to do it four times. For example, if I told you that I won the Powerball jackpot, would you believe me? Probably. Somebody has to win it, right? What if I told you that I won the Powerball jackpot four times? What about 40 times? You would never believe me. Even if I showed you incontrovertible proof, you would assume that I cheated somehow. It's simply too improbable to be believed. And yet, you will believe, without a shadow of a doubt, that eyes evolved independently not just once but 40 separate times?
 Why give these methods to creatures that never use them? Evolution predicts exactly that there will be various ways to do anything. The more possible ways to fly there are, the more likely there will be flying creatures. The forms of motion that are most varied are also most common. There are more ways to walk than fly, and there are more walking creatures than flying. There are more ways to swim and so more swimming. Bats do not fly in a grabbing way. They flap up and down and let the leather wings change shape as they flap doing the work automatically that birds require a complex motion to accomplish. Why make things so hard on the birds?]
 I can't find anything that says that bat flapping is that different from bird flapping. According to the Department of Zoology at the University of Cambridge, "Birds and bats shorten their wing span by drawing them toward the body during the upstroke and extend their wings during the downstroke." That makes it sound like they both fly basically the same way. If they are different, it could be because bats tend to fly differently than birds. It seems like birds spend more time soaring, and bats spend more time flapping and quickly changing direction. Are the feathered wings of birds better for soaring, and the leathery wings of bats better for maneuverability? Yes, check out this great list of praises of the superb design of birds. (Funny how he praises the design of birds, even though he believes in evolution) Especially note the part where he says that they are better than bats. Clearly, what is 'best' depends on how you look at it.
 There are at least five types of sexual reproduction. Eyes, according to one evolutionist, must have evolved between forty and sixty times. [and is still evolving. This is true with everything.]There are 300 known species of fig wasps, almost all of which pollinate one and only one species of fig tree! (The whole fig wasp thing is a truly astonishing story that deserves more discussion later.) [yeah, and fleas that only infest rabbits and reproduce at the same rate. There’s a lot of cool and astonishing things out there. I definitely share your awe.]
 It's amazing to me that you can see such incredible designs all around you, and be awed by them, and still be positive that they arose randomly. It is far more likely that the heads on Mount Rushmore were created by random wind and rain than that life was created by random processes and natural selection, yet you are sure that Mount Rushmore was intelligently designed, and at the same time sure that life was created by random processes and natural selection. That must take a lot of faith in natural selection.
So, because irreducible complexity appears to be astonishingly common, it supports intelligent design much better than Evolution. [Irreducible Complexity turns out to be not so irreducible.
 Really? You haven't presented any plausible explanation of how any of the systems that I mentioned could have evolved through tiny steps. The explanation of how birds evolved feathers and flight seems implausible and contradictory.
 Doesn’t the enigma of bats speak more for evolution than for Intelligent Design?
 By the enigma of bats, are you referring to the following, from an article about Karen Sears?
Bats have been an evolutionary enigma. That’s because the oldest fossil bats look remarkably like modern ones, each having wings formed from membranes stretched between long fingers, and ear structures designed for echolocation. No fossils of an animal intermediate between bats and their non-flying mammal ancestors have been found.
Only an incredibly dogmatic belief in evolution could possibly think that those things speak more for evolution than Intelligent Design. As far as the evidence shows, bats are marvelously well-designed for maneuverable flying, and for tracking insects in the dark, and have always been so. But I may be misunderstanding your meaning, because your next question doesn't make sense to me at all. Please elaborate on what these two questions are referring to.
 Why aren’t all creatures like bats in the fossil record? Wouldn’t a designer capable of such incredible complexity get things right the first time? Why have inferior stepping stones of digestive systems and eyes if you can just make a good one? Why do birds have to eat rocks to digest food? That’s incredibly primitive.]
 Primitive? What is more abundant and easy to find than rocks? Don't we wish we could fuel our cars with something as abundant as rocks or garbage, like Doc Brown does in Back to the Future 2? Unfortunately for us, we can only use a highly purified form of a substance that we don't know how to produce. If we don't invent engines that can run on a more abundant or renewable fuel source, we could be in trouble.
Inferior digestive systems? A cow's digestive system is much more complicated than ours, does that make it superior? I'm sure glad that I don't have to spend most of my day re-chewing grass that I've already eaten. Still, if we did have to live only on grass, we'd be pretty jealous of a cow's digestive system. As we saw before with birds and bats, what is superior and inferior is relative. It all depends on how you look at it.


Alright, I'll leave it there for now. If these points are scientific, then ID'ers do know at least something about science. [To my knowledge there is only one peer reviewed scientific paper on ID vs. Evolution. It has been shredded. The paper didn’t even support ID, just attacked Evolution. Two books have been written by scientists and have likewise been shown to have little basis. Irreducible complexity has been discredited in both the scientific community and the philosophy of science community. I didn’t even know the last community existed.]
 You ignored the criteria that I proposed for determining whether ID'ers know anything about science. Why is it not a valid criteria? As for peer-reviewed journals, how many papers did Copernicus publish in peer-reviewed journals? There might not have been any at the time, but suffice it to say that his ideas were shredded, discredited, and rejected. Does that mean he didn't know anything about science? More significantly, did that mean that his theory was incorrect?
We could spend a long time debating about whether the journals are biased, but that would be an irrelevant waste of time. I would much rather that we focus on the science, rather than arguing about who is or is not biased.
 In fact, like I said, it seems to me that science is generally (maybe even completely) on their side. [To this, I of course completely disagree. I see it like this. Why is such a powerful being so slow, I mean 15 Million years? That’s a long time.
 In an effort to keep the discussion focused, I have avoided talking about time and dates as much as possible. If you're going to use that as a reason not to believe in intelligent design, maybe we'll have to get into that, as I did above with the Cambrian Explosion. But, in general, why shouldn't an intelligent designer take a long time to do things? If you've got all of eternity, what's the rush?
 Why so many failed experiments? If these things are not intermediary or transitional creatures, they must have been designed to do nothing particularly well.
 What creatures are you referring to? The ostrich is a remarkably good runner. The penguin is a remarkably good swimmer. The walking catfish can " thrive where many fishes cannot. " If these things do nothing particularly well, then natural selection should have eliminated them.
 Why so much waste? Why do I have a tail bone?
 You have a coccyx to "provide an attachment for muscles, such as the gluteus maximus, and also serve as something of a shock absorber when [you] sit down" (from the Wikipedia).
Why do I get goose bumps?
Maybe if we researched them a little more, we would find a purpose for them, just like we have with 'junk DNA'. Maybe they are similar to pain - they warn us that we are getting too cold. Maybe they concentrate blood near the muscles so that we are better prepared to make a quick sprint to escape danger. Maybe they do warm our muscles a little, just not as much as they would if we had fur. If they are left over from our chimp-like ancestor, why don't we get them when we are sexually aroused, like chimps do?
 Why do whales have the remnants of legs?
 Whales have two bones to which their reproductive organs are anchored. It's quite a stretch to call them remnants of legs.
 Why do new creatures appear seemingly randomly?
 Do they appear randomly? In what pattern should they appear, if they are intelligently designed?
 Why do these new creatures get more complicated with time?
 Does the fossil record show monotonically increasing complexity? Is a chimp more complex than a stegosaurus? By what measure are we determining complexity?
 Is this intelligence learning as he goes?
 Maybe. ID doesn't say that he/she/they isn't/aren't. (I personally believe that he isn't.)
 Why do we worry that small pox can evolve from cow pox?
 I don't know. Maybe we have no need to worry.
 Why is some intelligent being messing around with mice on Madeira?
 Is he? Are we sure that all the mice on Madeira started as one species? Are we sure they aren't still one species? The article about them that I found said that they were going to try to interbreed them, but I can't find any info about the results of the interbreeding. The common house mouse species is known to have a variable number of chromosomes, from 22 to 40, and all the mice on Madeira are within that range.
 Why make giraffe necks with the same number of vertebras as us?
 Why not?
Couldn’t an intelligent designer predict that this would cause them problems drinking water?
 Would more vertebra prevent blood from rushing to the head when it is down? It sure is a good thing that giraffes have "One highly specialised vessel near the brain [that] acts as a sponge, slowly absorbing blood to the point where pressure warns the animal to lift its head before damage occurs." That sounds like a very careful design that allows an amazingly tall animal to drink without killing itself.
 More vertebras would have let them bend their necks better.]
Why do they need to bend their necks better? They would have to lower their head just as far to drink no matter how many vertebra they had.
 I know you disagree, so how would you respond to each of these points? And what other points do you think support Evolution better than intelligent design? [There are two aspects of ID that I have troubles with. It makes the assumption that if we don’t know everything and see everything then there must be some designer to fill the gap.
 Evolution makes the assumption that if we don't know everything and see everything then random mutation and natural selection must fill the gap. Why is it any less reasonable to fill the gap with design than to fill it with natural selection?
 The second is the circular and largely negative arguments. For example, I could say that computers must have always existed because they are too complex to design without one.
 This is a common misunderstanding of the ID hypothesis. The hypothesis is not that biological life is too complex to have been created by anything but biological life. The hypothesis is that biological life is too complex to have been created without intelligence. Life and intelligence are two entirely different concepts. Humans happen to have both. Intelligence, in this sense, is not anything like IQ, it is more like free will. It is the ability to choose a goal, develop a plan (aka design) to achieve it, and influence matter and energy to implement that plan. ID'ers do not speculate about the origin of intelligence, since they don't know of any scientific ways to verify any such hypotheses. However, if you want my hypothesis, it is that intelligence, just like matter and energy, cannot be created nor destroyed, but has always existed. We don't remember our existence before we had a biological body because memory is a function of our brain, not our intelligence. That intelligence has always existed is not a circular argument, and it is very consistent with what we know about matter and energy.
 Well this is simply ridiculous. Of course we built up computers slowly over time adding complexity as we go. If we do this with things we create like radios and computers and houses, why assume an intelligent designer doesn’t do the same thing? And if there is an intelligent designer manipulating genes and natural selection in order to create a human from a pre-ape creature, it doesn’t make any difference to Evolutionists who is behind this system, just how to understand it and use it.]
 Maybe an intelligent designer does do the same thing we do. But how similar is the 'evolution' of man-made machines to evolution by random mutation and natural selection? How many random changes did it take to get from Quake to Unreal Tournament? The games are admittedly very similar, but if you took the Quake executable (or code) and started randomly changing, adding, and removing bits, there is probably no way to get to Unreal Tournament, or any other game, through a sequence in which every step is also a functioning game. And even if there were some such path, that is most definitely not how Unreal Tournament, or any other game, was written. Human-designed machines (including programs) can be put into a nested hierarchy, like life, and can be seen to progress from less complex to more complex, which is maybe like life, but they were not (and probably could not be) produced by random small changes and natural selection.
 (If any of this sounds accusatory, I really don't mean it to be. I mean it to be calm and scientific. And I know this is another long one, so respond at your convenience.) [No offense taken or meant. I have learned a lot so far from just a few e-mails. I think this is fun.]
 Oh good, I'm glad you think so too. I've learned tons of fascinating stuff.

I'd like to make a quick addendum to my last email. Most of the things I discussed are more like explanations of things that have been observed rather than predictions about things that we will observe. (Of course, Evolution similarly explains rather than predicts most of the time, as do many scientific theories.) [I find the explanations of ID to be more confusing than less. So much evidence that must be ignored,
What evidence must be ignored? ID'ers certainly don't advocate ignoring any evidence. All they advocate is a re-interpretation of the evidence. For example, homology is re-interpreted as evidence of common design rather than common descent. All new scientific theories do the same thing. Einstein's theory still predicts that an apple will fall to the ground, but it reinterprets that as evidence of the earth warping space, rather than evidence of the earth pulling on the apple.
 such inefficient design that must be accepted, a designer that is learning as he goes along, Leftover pieces that have no business in creatures that would never have used them. These do not make sense to me.
 Most vestigial structures have been discovered to have uses. ID makes the prediction that we will eventually find uses for all the other structures that we don't yet know the purpose of.
 There is a lot we do not know, but every time evolution predicts that we will find something at about this age, it’s there. I don’t mean that every time we look, we find, but rather that everything we find is right where it’s supposed to be.
 This is a huge overgeneralization. First, evolutionists are constantly deciding that such-and-such-thing happened earlier than expected, and being surprised by things like living coelacanths. I'll look up some more specific examples if you'd like me to.
Secondly, in many cases, the reason that things are right where they're supposed to be is because of the circular dating methods mentioned earlier. If you have troubles with circular arguments, why doesn't it bother you that evolutionists use circular reasoning to date rock layers and the fossils in them?
 What evidence have we found that fits ID and not Evolution? Where has ID led us to find something not predicted by Evolution? ID and Evolution look at the same thing and agree. We have the same DNA, but the explanation of why is different. But where did Evolution fail to predict or explain a new finding? How did ID explain or, more importantly, predict that finding? I’m really curious because I have only seen proof through the lack of evidence. I have never seen evidence that contradicts Evolution.]
 The evidences that fit ID and not Evolution are what this whole document started as. To recap:
1. The fossil record shows sudden appearances, disappearances, and long periods of stasis.
2. Genetic family trees often conflict with each other and with morphological trees.
3. We have seen loss of information due to extinction, but no information gain.
4. Many biological systems appear to be irreducibly complex.

And some predictions:
5. All DNA will be found to have some purpose.
6. All apparently useless organs will be found to have some use.
7. The sum of genetic information in all organisms will continually decrease, unless the intelligent designer comes back to increase it again, or humans figure out how to increase it. Thus, until we do so, it is important to preserve what we have.
As for positive evidence that contradicts evolution, I'll address that at the very end of this document.
 But in reading through the ID literature, I've found that many ID proponents make a very scientifically testable prediction. We have found that only about 2-5% of DNA encodes for proteins. Evolution theorists have predicted that the other 95-98% of DNA is leftover junk from the haphazard evolutionary process. [That’s not entirely true. Evolutionists say that there is more to our DNA than is needed and posit that introns are necessary to help scramble genes. The introns are believed to be the scratch pad for evolution. This, in turn, allows evolutionary processes to develop that are more complex than just changing one thing at a time. It also allows for storage of a new sequence within the species that allows for transitional species. This has been studied in bacteria. Furthermore, the Center for Advanced Research in Biotechnology last year discovered that life did not begin with introns, but rather picked them up later. Quoting from the press release. “The CARB analysis shows that the probability of a modern intron's presence in an ancestral gene common to the genes studied is roughly 1 percent, indicating that the vast majority of today's introns appeared subsequent to the origin of the genes.” Why did a designer suddenly need a mechanism that aids evolution, was not needed in the beginning, and is seen to have changed over time?
Have they changed over time? That is not what the quote says. What the quote says is that it is very unlikely that all the modern genes they studied inherited their introns from a common ancestor. Their conclusion is that all the modern genes must have evolved introns independently. The logical ID conclusion, on the other hand, is that the modern genes did not inherit their introns from a common ancestor because they don't have a common ancestor. Which conclusion is more likely? How likely is it that all 10 modern families of genes independently stumbled onto the concept of introns? Also, the next post on pandasthumb contends that bacteria actually do have introns, although they are rare. If the CARB analysis can still be trusted, this means that bacteria also must have evolved introns after the split, since eukaryotes did not inherit the introns from bacteria.
 Also, who among Evolution theorists call any DNA junk? I can’t find where that started, just a bunch of scientists saying it’s not junk?
I quote from pandasthumb.org:
An article in May 23, 2003 issue of Science, “Not Junk After All”, by Wojciech Makalowski states:

“Most researchers have assumed that repetitive DNA elements do not have any function: They are simply useless, selfish DNA sequences that proliferate in our genome, making as many copies as possible. The late Sozumu Ohno coined the term “junk DNA” to describe these repetitive elements.”

“Although catchy, the term “junk DNA” for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure.”
So apparently a peer-reviewed journal believes that lots of DNA was called junk, and that the term did stifle DNA research for 'many years.' Fortunately, there were a few scientists who were willing to go against mainstream thought and risk ridicule to prove that mainstream thought was wrong.
We are finding uses for it, and the uses are to enable evolution.]
Are you referring here, to the hypothesis that introns make break and rejoin events more likely to be successful? I saw some discussion of that on pandasthumb, but no links to scientific papers about it. I would be interested to read some if you know of any. I have lots of questions about it. First, how does the introduction of an intron provide a selectionary advantage? If it only provides the possibility that an organism's descendents can break and rejoin their genes more easily, then it does not directly benefit the organism that first got it, and thus will not be selected for. Second, how similar is the number of introns found in modern genes? If they are only padding, the number should vary widely between species, and possibly even between individual organisms. If the number is quite consistent, then introns would make an excellent case for design of something that random mutation and natural selection could not produce. Third, have we observed this breaking and rejoining process? Fourth, how much variation can this process produce? Does it allow the kind of variation that we see between dog breeds, or does it allow the kind of variation that could produce new organs and functions?
 ID proponents predict that the intelligent agent(s) would not have thrown so much garbage into the design. A few portions of DNA may have degraded since they were designed, in accordance with the Second Law of Thermodynamics, such as our broken vitamin C-production system. But since DNA is obviously very good at preserving itself, most of it should still be functional. Therefore, ID predicts that we will discover that most of that junk DNA is actually useful. [If all the DNA is from a designer and some DNA has been lost, shouldn’t IDers predict %100 of DNA is useful?
No, because any particular gene can be rendered useless by just a few incorrect nucleotides. But the entire gene will be still be copied by the transcription process. Just like if a single bit in an executable became corrupted by a bad copy, it might render an entire function useless. If the program was well designed, the program could continue to run without that function, but future copies would continue to copy the now-useless function. This is what appears to have happened with our gene that should allow us to produce vitamin C:
Recently, the L-gulano-γ-lactone oxidase gene, the gene required for Vitamin C synthesis, was found in humans and guinea pigs (Nishikimi et al. 1992; Nishikimi et al. 1994). It exists as a pseudogene, present but incapable of functioning (see prediction 4.4 for more about pseudogenes).
If natural selection works, shouldn't it have prevented guinea pigs from losing that functionality? Or helped them regain it?
Also, the second law of thermodynamics is often misused in this context. I could no more say that a mountain erodes due to thermodynamics. The closed system would have to encompass the entire universe, but at that scale the equations would be so complicated and chaotic as to be meaningless.]
 You certainly could say that mountains erode due to thermodynamics. I thought all scientists believed that. Stones do not fall up mountains when wind or water dislodge them, they fall down, tending towards the most uniform arrangement (flat plains). Yes, it's true that the earth is not a closed system, but it generally radiates as much heat into space as it gains from the sun, so overall, it very closely approximates a closed system. We observe ancient buildings and mountains crumbling all the time, but we do not observe rocks building either of them up. (Well, mountains do get pushed up, but that is by other processes that are evening out the energy in the Earth's core, which is still in accordance with the Second Law.) The Second Law would be entirely useless if it only had any applicability to closed systems, since no such system exists (except maybe the entire universe, but as you said, that's too complicated to analyze). The reason that the Second Law is useful is that if we observe any arbitrarily chosen system, it will usually apply, even though the system is open. The two notable exceptions to this are the products of human intelligence (i.e. factories), and organisms, which both routinely create localized pockets of uneven heat distributions. (There are lots of minor cases where order arises, such as snowflakes and convection currents, but the order created in these cases is orders of magnitude less than in factories and living things, so they really don't belong in the same category.) Now, since we know that one of the major anomalies (factories et. al.) is the product of intelligent design, Occam's razor would suggest to us that the best conclusion is that the other major anomaly (life) is also the product of intelligent design. That conclusion would give us one concept (intelligence) that explains all the systems that can routinely create large amounts of localized order.
I would also like to point out that ID is often accused of trying to stifle scientific research by simply declaring that 'God did it,' but this is an example of ID suggesting avenues for further scientific research. All sorts of DNA experiments are going on right now, and I can't wait to find out what they discover. [Uses for so called junk DNA have been found, but since Evolution does not predict how much is used or not, Evolutionary microbiologists and cellular scientists are happily researching this area. Junk is a misnomer, but there is a lot of DNA that is not used as the blue print for a creature. It doesn’t mean it is junk, just used for something else. If there were a designer, wouldn’t all DNA be used for replication and any other use evidence that there is not a static design? ]
 I'm not sure what you mean by this question. DNA does get replicated, but that is not its purpose. Its purpose is to encode the information necessary to build an organism. What other uses are you referring to? Please elaborate.
 If it turns out that most of our DNA really is useless junk, I'd be ready to abandon ID as a scientific theory. But if it turns out that most of it is useful, I think it would be strong evidence for the truth of ID. [How about if introns are found to be the mechanism behind many of the complexities in Evolution that have IDers puzzled?]
 Sure, if it can be shown to be likely that all or most of the information in DNA was created by random mutations, natural selection, and introns, then I would concede the argument. Showing this would involve answering all of my above questions about introns, and proposing at least one possible pathway that could lead to something that is apparently irreducibly complex, like the bacterial flagellum, analyzing the probability of each step in that pathway, and showing that, given the number of organisms and the time that has passed, there is at least a 1 in 10 chance that such a pathway would have been followed. I know that's asking a lot, but there a lot of reasons to believe in intelligent design, so I think it's fair.

Now, I mentioned above that I would address your request for positive evidence that contradicts evolution. I have shown at least 4 general topics that I think fit Intelligent Design better than Evolution, but apparently those are not what you are looking for. So, besides inventing a time machine and going back and observing what happened, what would you consider to be positive evidence that, if found, would effectively falsify evolution? I just gave an example of something that would cause me to cede the argument. What would cause you to concede?

That’s all for now. If you’re interested, I found www.pandasthumb.org very interesting.
Yes, I've read through several pages on pandasthumb. I generally don't like it because it involves a lot of flaming. Here is my favorite ID site.