New evidence for Darwin’s theory of evolution

Mario A. Lopez, #56

But, parallel gene inactivation in multiple primate lineages is dismissed as a possibility because the author presupposes ancestral relationships.

Parallel gene inactivation was dismissed because each gene exhibited the same disabling sequence difference in all other primates. What are the odds that out of six species, five of them will experience the exact same mutation in three separate strings of about 21 nucleotides each? Ancestral relationship is not a presupposition, it is the only rational conclusion. camanintx

camanintx, Read it again. The presupposition is there. The chimp and macaque do not have the protein-coding genes. According to the author, these genes cannot be explained away by sequencing gaps or annotation errors. Why? Because other primates show the loci in non-coding regions. But, parallel gene inactivation in multiple primate lineages is dismissed as a possibility because the author presupposes ancestral relationships. The major problem I see with this finding is that a gene that supposedly began as non-coding is coding for a protein that causes CLL. Like I said before, this is hardly the type of protein that natural selection can exploit. It is an evolutionary dead end! Mario A. Lopez

Mario A. Lopez, #52

Are you kidding? What this paper demonstrates is 1) the author presupposes ancestral relationships between humans and chimps

The only presupposition I see is yours. The authors started by finding protein-coding genes in the human genome that are absent from the chimp genome. They then found that these DNA sequences in several species of apes and monkeys contained differences that would likely disable a protein-coding gene, suggesting that these genes were inactive in the ancestral primate. So what we have is evidence of common descent along with genetic changes that created new protein machinery, something Joseph said didn't exist. camanintx

Sorry. That last post was intended for: camanintx Mario A. Lopez

Joseph, Are you kidding? What this paper demonstrates is 1) the author presupposes ancestral relationships between humans and chimps and 2) the affected lymphocytes resulted from an up-regulated gene which simply duplicates proteins of the same kind. 3) The abstract does not differentiate between affected lymphocytes (i.e. B, NK, or T) 4) It is not likely that CLL resulted from a non-coding region because the affected cells start off as active lymphocytes affected by a mutation (in this case possibly as a result of being low on a particular receptor protein). 5) CLL is hardly good for vertical evolution. :) Mario A. Lopez

"Joseph" (#46) asked: "What is the genetic evidence that demonstrates such a transformation is possible? (that is to transform a land mammal into a whale)" I am not enough of a biologist to answer such a question about genetics, but I am sure that the well-understood transformation of cetaceans from land animals to sea animals is dependent on interpretation of the fossil record. Fossils in rocks typically do not leave much genetic material, so perhaps there is no direct genetic evidence that would satisfy you. So this may be a trick question with no possible answer. But there is evidence in the genes of today's whales showing their connection to land animals. Have you read the summary at http://en.wikipedia.org/wiki/Evolution_of_cetaceans PaulBurnett

Joseph, #47

Lenoxus, There isn’t any evidence that genetic changes can modify something as to give rise to new protein machinery and new body plans.

Are you sure about that? Recent de novo origin of human protein-coding genes camanintx

Lenoxus: It sounds as if you've exhausted your objections to ID and are now moving on to irrelevant complaints. One second you're unhappy with ID, and now the real problem is that it doesn't have a "successor," or at least doesn't have one right now. Why even answer? You'll just invent another non-scientific requirement. ScottAndrews

Assuming ScottAndrews is correct, and ID specifically is not able or supposed to answer those questions, but those questions are still scientifically answerable… then what scientific movement is ID waiting for?

Why would the doctor look for the cause of the fever without first determining that there was a fever?

You guys have determined the fever, and we're waiting to hear about the cause. What is preventing the successor to ID from appearing — the scientific hypothesis that will examine those questions? Or am I looking at it the wrong way, and there is no successor movement? If not, why not? I thought the questions were scientifically answerable. Lenoxus

Timothy: Read the FAQ. It's very difficult to participate in a discussion of Intelligent Design without knowing what ID is. It will make more sense when you're acquainted with the subject. ScottAndrews

Lenoxus, There isn't any evidence that genetic changes can modify something as to give rise to new protein machinery and new body plans. Joseph

PaulBurnett, What is the genetic evidence that demonstrates such a transformation is possible? (that is to transform a land mammal into a whale) Just how can such a [remise be objectively tested? Joseph

"On the other hand, you might wonder how, when, by what or whom? There’s plenty of room to explore and discover. Do you realize how ridiculous it is to suggest that knowledge might prevent science?" Why then did you, in your last response, act as if ID had nothing to say about anything other than a simple yes or no to the question of design? Why should ID not investigate the implimentation of design? Lord Timothy

Lenoxus: I'll tell myself that I'm re-posting this simple explanation for the benefit of any onlookers. A thermometer can indicate to a doctor that a patient has a fever. A thermometer can never, ever tell the doctor why the patient has a fever. Is it a virus? Some other infection? Which one? Does it logically follow that if the thermometer cannot answer those questions, nothing can? Does that make the thermometer useless? Does that make it a science-stopper? Why would the doctor look for the cause of the fever without first determining that there was a fever? Do you routinely attempt to invalidate other hypotheses by adding your own arbitrary, non-scientific requirements? Do you demand that every theory explain everything beyond what it explains? Or do you think that science should have different standards for theories you don't like? Again, that was for the benefit of other readers. I fully expect you to raise the same weak objection again and again as if you had never read the clear and simple explanation. ScottAndrews

"that ID can’t study those areas, but those areas can be studied. What, if not ID, is supposed to do that studying?" Is anyone saying ID cannot study these issues? They shouldn't be saying that. I see no reason why they cannot be studied and haven't seen anyone make that statement though I haven't seen everything somebody has said. What people have tried to do that are critical of ID is to insist that these must be answered before design can be concluded. That is a non sequitur. Of course if you had the who, what, when and how pinned down, design would be ho hum. I have often said that if there was some evidence that some intelligent race roamed the solar system or galaxy several billion years ago, no one would blink at the conclusion that life was designed. It would be taken for granted by people like Richard Dawkins and the focus would be on why and maybe how and timing and of course speculation as to what they were about and where they came from. jerry

jerry: I didn't think I was jumping on an inconsistency — I just assumed that when you said "There is no evidence it ever occurred", you were indeed referring to bird speciation in general. You may be right — there may indeed be no evidence that all bird speciation occurred naturalistically. As for the whole when/where/who thing, I agree that is a separate issue. In that area, though, I do feel that there is an important inconsistency in what has been said here — that ID can't study those areas, but those areas can be studied. What, if not ID, is supposed to do that studying? Lenoxus

"I’m surprised that ID should have any problem with the natural speciation of birds" What gave you any idea that ID has a problem with bird speciation? I certainly don't. I just pointed out that Darwinists believe it takes over 20 million years for a small difference that prevents inter breeding to arise. I have questions about the origin of birds but not what happened after the first gene pool appeared. In fact I look on birds as a bonanza for investigation, they were the supposed king of the planet, replacing the dinosaurs and having the ability to fly. You appear to be like a raptor ready to pounce on anything you think is a little bit of a morsel but you seem to have bad eyesight and what looks like carrion is dead wood or stone. ID can certainly investigate the who, what, when and how of ID and the evolution of birds. But they are separate issues from whether something is designed or not. They are not necessarily related. And each is definitely difficult since whatever design happened did so a long time ago in what is probably unique events. Doesn't it get a little bit tiresome trying to find some little inconsistency and then leaping for the kill and then find out you have misjudged the situation. Why are you here? Not to learn anything, that is for sure or else you would take a much different tack. If it is to vex us, then what does that say about someone who just wants to antagonize others. jerry

jerry:

These things you hypothesize leave forensic trails.

Of course, neither fossils nor genetic comparisons between bird species would count as those trails. In any case, I'm surprised that ID should have any problem with the natural speciation of birds — don't birds all demonstrate the same body type? Do any of them demonstrate a novel "unevolvable" feature the others don't? ScottAndrews:

ID cannot investigate those questions. Nowhere does it state that those questions cannot be investigated.

So, is ID waiting for some new hypothesis to come along that can examine those questions? Or are those questions (When and how were the ID mechanisms applied?) fundamentally not scientific? I fail to see how it can be something other than those two possibilities — by definition, science explores every question it can, and doesn't every question it can't. I have to say, I still feel kinda bad that I don't know of any genetic study demonstrating an animal species gaining a function that required millions of years and at least, say, three mutations. (That a given feature happened through ordinary genetic change alone remains the null hypothesis, but as far as I know, that's all it is.) Take it as an amateur concession. Lenoxus

Well, WHY is it that ID investigates some things but not others? Common or garden science pokes its inquisitive nose into pretty much everything where there's an observation to be recorded, a measurement taken, an hypothesis to be formulated and tested. I thought ID was supposed to be, in part at least, a science-based idea. Why is it so picky about what it investigates? damitall

New evidence for Darwin’s theory of evolution idnet.com.au The "fact" of Darwinian evolution finally has some support, or so they say at ScienceDaily

Since the opening sentence confuses the scientific concepts of "fact" and "theory", why should I give any credence to the rest of this post? camanintx

Lenoxus, Ay, there’s the rub! Unfortunately, ID seems to hold that it simply can’t investigate those questions until everyone in the scientific community first agrees about design You are correct. ID cannot investigate those questions. Nowhere does it state that those questions cannot be investigated. People explain to you time and again that ID does investigate some things and doesn't investigate others. Then you cheerfully go on as if you forgot what you just read or couldn't comprehend it. So when you repeat an objection that's been answered repeatedly to you specifically, are you forgetful or are you trolling, using other participants for your amusement? ScottAndrews

Outmeal Stout, also known as Sal Gal,

As I have said in other threads, the attempts of ID proponents to soup-up the ancient argument from improbability are going nowhere. The ultimate reason is that there is no way to assign a probability at all to our wondrous universe. We should focus on intelligence as the source of intelligence, not as the source of some fancy sort of information.

If there is no way to assign improbability to our wondrous universe, then the argument that improbability is invalid is itself invalid, for you would never know it, you could never say that it is probable. There is fancy information in the language of the DNA code, and to deny this is, in my opinion, faulty. Especially when you consider that we, as human intelligent agents, by the evolutionists scheme, are the result of non-intelligence, which is faulty in the same way. Clive Hayden

Hey Oatmeal, What you are proposing sounds like a "chance of the gaps" scenario. The universe is indeed finite and there is a limited amount of combinatorial probabilities. To say that there is no limit to resources, time, or success ratios it extremely naive. Mario A. Lopez

Lenoxus: "In any case, I am to this day surprised that (as far as I know) no genetic study has been shown on UD to argue for saltation — only the sparseness of the fossil record has. I know, that’s kind of a tu quoque on my part, but my point is that all the evidence so far suggests that genetic change is gradual, leaving only so much wiggle-room for a designer’s actions. Saltation, including the early-front-loading variety, would have an obvious footprint that we’re not seeing." Me: Well, I am not ready to defend "saltations" (at least not as it is commonly known) or even "punctuated equilibrium" as it is currently articulated. Both ideas are more or less observations, not mechanisms. However, those observations serve as a heuristic to spur scientific discovery. Saltations or punk eek attempt to identify the sudden (in geological terms)appearance of novel body plans; however, lack the biochemical explication that leads one species to diverge morphologically. ID is another piece of the puzzle. We may not know the actual "modus operandi" of a designing intelligence to bring about such changes, but we know that the process requires the infusion of a large amount of novel information. Information that, to date, evolutionists are yet to account for through the process of RM+NS, but which clearly can be accounted for by a designing intelligence. Lenoxus: "Clearly, psuedogene remnants are easier to look for than functional-gene predecessors, because there are many more things the latter could look like. So right now, at least, there does seem to have yet to be a well-recorded genetic record of the million-year development of one function that didn’t come at the cost of another. Of course, even the study in the OP didn’t actually look at something “gradual”, which can be difficult when you only have access to living species — it simply compared a few genomes and looked at the differences. For all we know, those differences arrived saltationally — there’s just no reason to believe that at present, though." Me: Actually, we know of many such events. What do you think a "fitness cost" is? Lenoxus: "One thing I am positive of right now is that no evidence will be found to the natural development of CSI; this is because the definition of CSI is vague enough to retreat elsewhere regardless of what function or complexity is found, in particular because of its subjective standard for determining specification." Me: Please read Dembski's work and get back to us on this one. Lenoxus: "Oh, and why do I think ID predicts zero junk? Articles like a this. I take the phrase “as much as possible” to ultimately mean “100%”, because if some “junk” DNA “has” to be there for the rest of the DNA to work, it’s not really “junk”. The prediction of little/no junk comes from “”Intelligent agents typically create functional things.” However, it is a prediction which appears to clash with “genetic entropy”, which suggests increasing amounts of junk over time. The two can be reconciled, but only with a hypothesis regarding which moments in history the designer intervenes to counteract entropy." Me: I am not sure how you get 100% from "as much as possible."` Actually, the cell has many mechanisms to self-correct damages (another intelligent design);however, you are missing the point altogether. ID has little or nothing to say about "intervening" intelligence. Obviously, human designed artifacts also face the effects of nature. Does that mean that the designer will intervene, let's say, every time it rains? Check you logic. Mario A. Lopez

One thing I am positive of right now is that no evidence will be found to the natural development of CSI; this is because the definition of CSI is vague enough to retreat elsewhere regardless of what function or complexity is found, in particular because of its subjective standard for determining specification. To the contrary, the concept of complex specified information is utterly dead, though Dembski will admit this no more than he will admit that he misunderstood the Weasel program. Framing an ancient event for which the antecedents are largely unknown, demanding a probabilistic model of the processes giving rise to the event, and then using the necessarily low probability assigned by the model to rule out an entire class of possible explanations (i.e., materialistic causation), as opposed to concluding that the particular model is inadequate, is bogus. It is even worse logic to treat the logarithm of the probability assigned by the inadequate model as a quantity of physical information, and to say that the putative physical information must have been created out of nothing by immaterial intelligence. Lenoxus you should know by now that it is impossible to predict what the designer should do. We know nothing about its motives or powers. All outcomes are equally possible and probable. Even if the material universe is discrete and finite, its possible configurations may be infinite, in which case there is no uniform distribution on material "outcomes." A huge scientific problem with the "intelligence creates information" proposition that ID cannot sidestep is the question of how much information, be it complex specified information or active information or foobar information. Creation of information is miraculous from the perspective of a physics that is founded on mass-energy conservation, and for there to be no bound on the quantity of information an intelligence can create is unacceptable. (Dembski and Marks avoid talking about searches that never succeed, in which intelligence presumably creates infinite active information that is negative in sign.) As I have said in other threads, the attempts of ID proponents to soup-up the ancient argument from improbability are going nowhere. The ultimate reason is that there is no way to assign a probability at all to our wondrous universe. We should focus on intelligence as the source of intelligence, not as the source of some fancy sort of information. All living systems are intelligent. What do we know from immediate experience about the origins of intelligent systems? Either an intelligent system is the offspring of a self-replicating system, or the device of an intelligent system. Our experience supplies us only one way to resolve the regress of self-replicating intelligences, namely with design. Oatmeal Stout

Example of niche partitioning in bats. In this case, we have variation in harmonic frequecies in calls leading to differences in abilities to distinguish certain kinds of insect prey:

Switching harmonics is likely to have far-reaching consequences for the ecological interactions between morphs by creating a marked discontinuity in the bats' perception of available prey. Low frequencies have longer wavelengths, so they reflect poorly from small prey because of Rayleigh scattering12, 13, 14. Consequently, the large morph is likely to encounter difficulties in detecting insects with wing lengths of less than 12.8 mm (wavelength 27.2 kHz under local conditions), and experimental evidence suggests that insects smaller than 5.0 mm might be undetectable to bats echolocating at 27 kHz13, 14. In contrast, prey almost half the size should still be detectable by the small morph (wavelength 6.5 mm) and possibly by the intermediate morphs (8.9 mm). However, low frequencies are less subject to environmental attenuation15, conferring greater detection ranges. We modelled prey detection distances for the three morphs from Buton for small (5 mm) and large (25 mm) prey. Backscattering reduces the target strength of small prey so severely at low frequencies that the detection distances differ little between morphs and are uniformly low (1.6–2.5 m). By comparison, atmospheric attenuation is the key factor influencing detection ranges of the large prey, with detection distances of 9.6 m for the large morph, 7.3 m for the intermediate morph and 5.5 m for the small morph. The large morph therefore samples more than five times the volume of potential 'large-prey space' than the small morph, over twice that of the intermediate, and, most importantly, more than 90 times the volume of its own 'small prey space'. Switching harmonics could therefore create a marked shift in 'apparent resource distribution'; to the large morph, large insects appear more numerous than they are in absolute terms, and small prey (if detected) appear less abundant. Conversely, the small morph will detect almost nine times as many small insects as the large morph. This perceptual ecological discontinuity provides a novel opportunity for natural selection to initiate divergence within the population2; 54 kHz bats detect more small prey, but 27 kHz bats are at a competitive advantage in taking large insects.

This can lead to reproductive isolation:

Divergent ecological selection can, in turn, lead to reproductive isolation if the trait under selection also influences mate recognition and results in assortative mating1, 2, 3. Selection for a clear communication channel has been implicated in acoustic divergence in cryptic bat species16, and in horseshoe bats, intraspecific communication seems to involve the temporal and phasic arrangement of the constant-frequency (CF) component of the call17, 18, with a repertoire of oral emissions below the fundamental19. Harmonic switching will not only shift the constant-frequency signal of each morph out of the sensitive foveal region of the other, but into areas of response minima. An acoustic 'blind spot' (auditory threshold maximum) at the fundamental frequency18, 20 will greatly reduce the sensitivity of the small morph to the large morph's 27 kHz calls. Similarly, the large morph will be unresponsive to constant-frequency calls at 54 kHz because of a rapid decrease in sensitivity to frequencies above the auditory fovea20. The large and small morphs are thus functionally deaf to each other's constant-frequency calls. Although the intermediate morph should be able to hear frequencies used by the large morph, and be heard by the small morph, in neither case is this receptivity reciprocal. Similarly, the response minima at the fundamental frequency are likely to disrupt the perception of low-frequency vocalizations among morphs. Thus, if we assume that acoustic communication is important for mate recognition, as occurs typically in bats21, harmonic-hopping could provide an intrinsic mechanism of instantaneous pre-mating isolation.

Kingston T & SJ Rossiter (2004). Harmonic-hopping in Wallacea's bats. Nature 429: 654-657 Dave Wisker

One factor that may facilitate echolocating bat speciation is their ability to partition niches by using different frequencies in their calls. Niche partitioning is driven primarily by competition. Bat populations that acquire different frequencies can specialize by "seeing" different food sources, and thus avoid competition with each other. Dave Wisker

But it takes over 20 million years to form a new species of birds says the Grants of Galapagos Finch fame. Needless to say bats are not birds, and as the source the Grants used for the bird figure tells us (and which I pointed out here before), it takes only 2-3 million years for mammals to develop hybrid sterility/imviability. ompatibility Dave Wisker

"Since multiple speciations can occur simultaneously in different parts of the world, that number (assuming it is even universally accurate) is not too big an obstacle to a large amount of diversification happening." There is one little problem. There is no evidence it every occurred. These things you hypothesize leave forensic trails. If there were any evidence, and believe me we have asked, there would be people all over it to shut us up. It just hasn't happened and it still avoids the real issue of the development of novel complex capabilities. Good try though. jerry

ScottAndrews:

On the other hand, you might wonder how, when, by what or whom?

Ay, there's the rub! Unfortunately, ID seems to hold that it simply can't investigate those questions until everyone in the scientific community first agrees about design. At least, that's a sense I've gotten from answers to questions about that here on UD; an example given was Stonehenge, and that you can't say who the designers are until you've established the structure's design. Also, earlier on this thread, someone named ScottAndrews said "If you’ve read the glossary or done any cursory reading about ID, you should know that its purpose is not to answer such questions." jerry:

But it takes over 20 million years to form a new species of birds says the Grants of Galapagos Finch fame.

Since multiple speciations can occur simultaneously in different parts of the world, that number (assuming it is even universally accurate) is not too big an obstacle to a large amount of diversification happening. Lenoxus

"I asked this same question in a comment here on UD a few months ago. Allen MacNeill answered that their ability to fly allowed them to reach new niches." But it takes over 20 million years to form a new species of birds says the Grants of Galapagos Finch fame. jerry

Mr Joseph, Can you provide any genetic data which demonstrates the transformation required are even possible? I thought that was what the research discussed in the OP was all about, a demonstration of fossil and genetic evience reinforcing each other. Nakashima

Timothy: If that’s really the case, then ID’s critics would be right about ID as an end of inquiry wouldn’t they? That depends entirely upon you. If you found out that a thing was designed, would you be all out of questions? If so, then that would be the end of inquiry. On the other hand, you might wonder how, when, by what or whom? There's plenty of room to explore and discover. Do you realize how ridiculous it is to suggest that knowledge might prevent science? How, on the other hand, does arbitrarily excluding a valid possibility advance science rather than stifle it? ScottAndrews

Ms O'Leary, An interesting question is why speciation happens so readily among bats and beetles. I asked this same question in a comment here on UD a few months ago. Allen MacNeill answered that their ability to fly allowed them to reach new niches. Nakashima

"Why? If you’ve read the glossary or done any cursory reading about ID, you should know that its purpose is not to answer such questions. " If that's really the case, then ID's critics would be right about ID as an end of inquiry wouldn't they? Lord Timothy

Cabal, with regard to the implementation of design throughout history, I think that inquiring about Frontloading is the direction you may want to go. You may find this interesting. https://uncommondesc.wpengine.com/intelligent-design/front-loading-passes-peer-review-in-cell-cycle/ As for the knowledge of people you are discussing with, it may depend heavily upon where you go. If for example you were trying to discuss ID on myspace, you should be prepared to be disappointed. Lord Timothy

"Joseph" (#14) asked: Anyone who thinks such a transformation (tetrapod land animals to whales) is even possible is living in fantasy-land anyway so what does it matter? Are you serious? Do you not accept the summary of cetacean evolution at http://en.wikipedia.org/wiki/Evolution_of_cetaceans ? Are you saying that accepting that Pakicetus and Ambulocetus are ancestors to today's whales is a fantasy? What alternative hypothesis do you propose? PaulBurnett

Joseph:

“Descent with modification”?- what gets modified- no specifics, never anything we can test.

What's modified is the phenotype, largely as a result of mutations to the genotype, the mixing that results from sex, and the occasional HGT. Every once in a while, a UD post (such as this one) argues that a new piece of evidence suggests a strong genotype-phenotype disconnect — this is what we can test for. I'm now extremely curious — why do you keep saying "even possible", when that phrasing rules out the possibility of even a designer causing the changes? Of course the changes are "possible" — they happened! (Assuming that intermediate organisms had DNA, there was a "change".) The question is, how did the changes occur? Lenoxus

Cabal, What I miss from all this is an answer to how design is implemented throughout history. Why? If you've read the glossary or done any cursory reading about ID, you should know that its purpose is not to answer such questions. It addresses a specific question. Why confuse the issue by asking why it doesn't explain something else? Do you ask your thermometer where the heat comes from? ScottAndrews

Lenoxus, You have a few possible transitionals out of what 50,000 or more? Can you provide any genetic data which demonstrates the transformation required are even possible? Next you claim that CSI is vague. Yet it is more clearly defined than anything your position has to offer. "Descent with modification"?- what gets modified- no specifics, never anything we can test. Joseph

Cabal:

What I miss from all this is an answer to how design is implemented throughout history.

That is what science is for- to help us make that determination. However that won't happen until you and your ilk are locked up or kicked out.

Is the designer present all the time, performing his magic at each speciation event observed throughout billions of years?

Do design engineers also use magic? I digress- it is YOUR position which relies on magical mystery mutations.

I find it a problem, though, that almost all design proponents I find on the web seem to know less about evolution than I do.

That you think so is the problem. Ya see if you could just substantiate the claims of your position ID would go away. Joseph

In my reference to studies showing "gradual" genetic changes increasing function, I was probably overreaching. Everyone here is, I'm sure, aware of studies that Mario A. Lopez mentioned and dismissed as not counting, in part, I assume, because (in terms of the amount of time they took) they're not quite gradual, and, of course, digestion and resistance don't count, because even though they're new functions, they're not really FCSI. In any case, I am to this day surprised that (as far as I know) no genetic study has been shown on UD to argue for saltation — only the sparseness of the fossil record has. I know, that's kind of a tu quoque on my part, but my point is that all the evidence so far suggests that genetic change is gradual, leaving only so much wiggle-room for a designer's actions. Saltation, including the early-front-loading variety, would have an obvious footprint that we're not seeing. Clearly, psuedogene remnants are easier to look for than functional-gene predecessors, because there are many more things the latter could look like. So right now, at least, there does seem to have yet to be a well-recorded genetic record of the million-year development of one function that didn't come at the cost of another. Of course, even the study in the OP didn't actually look at something "gradual", which can be difficult when you only have access to living species — it simply compared a few genomes and looked at the differences. For all we know, those differences arrived saltationally — there's just no reason to believe that at present, though. One thing I am positive of right now is that no evidence will be found to the natural development of CSI; this is because the definition of CSI is vague enough to retreat elsewhere regardless of what function or complexity is found, in particular because of its subjective standard for determining specification. Oh, and why do I think ID predicts zero junk? Articles like a this. I take the phrase "as much as possible" to ultimately mean "100%", because if some "junk" DNA "has" to be there for the rest of the DNA to work, it's not really "junk". The prediction of little/no junk comes from ""Intelligent agents typically create functional things." However, it is a prediction which appears to clash with "genetic entropy", which suggests increasing amounts of junk over time. The two can be reconciled, but only with a hypothesis regarding which moments in history the designer intervenes to counteract entropy. Joseph:

Anyone who thinks such a transformation is even possible is living in fantasy-land

Wow… so not even a designer could have done it? (You keep forgetting to insert the "naturalistically" into that "even possible" phrase.) Look, we have the intermediates. What makes the change with those intermediates (naturalistically) impossible? Or are the intermediates themselves such that they would need non-naturalistic forces to keep them alive? Lenoxus

What I miss from all this is an answer to how design is implemented throughout history. Is the designer present all the time, performing his magic at each speciation event observed throughout billions of years? At all locations, creating endemic species all over the planet? I am asking in all seriousness; how can I understand ID if it cannot be explained in terms a layman can understand? I find it a problem, though, that almost all design proponents I find on the web seem to know less about evolution than I do. Cabal

PaulBurnett:

Would anybody suggest that the whales’ distant tetrapod ancestral line that moved from the sea to the land had “devolved” when they later went back to the sea?

Anyone who thinks such a transformation is even possible is living in fantasy-land anyway so what does it matter? Joseph

Lenoxus, Are there any studies which demonstrate a gain in protein machinery? IOW what is the best evidence for something gained? Joseph

O'Leary (9), "and less on trying to prove Darwin’s theory (an increasingly lost cause, given that Darwinian selection may be only one of the actual mechanisms of speciation)." No-one is trying to PROVE Darwin's theory. Science doesn't actually "prove" anything anyway - proofs are for mathematicians. Evolution - by whatever mechanism amongst the Modern Synthesis is so well established by the evidence that the mechanisms - including random mutation and natural selection - are actually being used. Hence the finding of Taktaalik, for instance. Gaz

People who study evolution should, in my view, focus more on the relation between speciation and ecology People who study evolution are well-aware of the relationship. For example, toothed whales occupy a different niche than balleen whales. The variation that resulted in loss of enamel enables the balleen whales to reduce competition by exploiting a food source that toothed whales cannot use. Dave Wisker

"I wish someone would publish something with a little more than simple “variation” or “resistance” or the ability to “digest” something new." The thing about the kinds of changes noted above is that they are easily lost or reversed when the ecology changes. No surprise there, because the alternative might be extirpation (extinction within a region). I recall extinction expert Colin Patterson pointing out in his book on extinctions that daughter species tend to go out before parent ones. People lose sight of the fact that speciation comes with that precise cost, so it may not be in the "fitness" interest of the parent species to make the final break. We often hear environmentalists bemoaning the extinction of rain forest species whose range is only a few hectares. Bingo! You can be sure that would not happen to the English sparrow or the Norway rat. An interesting question is why speciation happens so readily among bats and beetles. People who study evolution should, in my view, focus more on the relation between speciation and ecology and less on trying to prove Darwin's theory (an increasingly lost cause, given that Darwinian selection may be only one of the actual mechanisms of speciation). O'Leary

PaulBurnett "Baleen whales are in many ways an evolutionary success, among other things being the largest animals. Suggesting that they are a product of “devolution” is wrong, as they do have enamel in their teeth – as embryos." It is interesting that you make that point. The quotes in my post are from ScienceDaily, they are not my invention. Maybe you shoul ask the authors of the paper. idnet.com.au

Darwin argued that all organisms are descended from one or a few organisms and that natural selection drives evolutionary change. What is the benefit of not having enamel, such that natural selection would select it out for these mammals? AnaxagorasRules

Re #2 Lenoxus And should or should not the designer “clean up” all genetic material “left over” from a change, hence leaving behind exactly zero “junk”? Lenoxus you should know by now that it is impossible to predict what the designer should do. We know nothing about its motives or powers. All outcomes are equally possible and probable. Mark Frank

Baleen whales are in many ways an evolutionary success, among other things being the largest animals. Suggesting that they are a product of "devolution" is wrong, as they do have enamel in their teeth - as embryos. Just as other animals have vestigial organs only in utero, baleen and baleen whales are not products of the discredited biological fallacy of "devolution," but of evolution. Would anybody suggest that the whales' distant tetrapod ancestral line that moved from the sea to the land had "devolved" when they later went back to the sea? Of course not. PaulBurnett

Lenoxus, I am not sure where you get the idea that ID proponents claim or predict that there will be absolutely no "junk" DNA. Stephen Meyer, who has spoken out against Darwinian predictions concerning junk DNA, has made it pretty clear that ID proponents do NOT deny the degradation of an aboriginal design or even that "mutational processes might have degraded or 'broken' some previously functional DNA." (see Signature in the Cell pgs 406-407) BTW--I don't know of anyone that does not believe evolution to be degrading. The article is not telling us anything we didn't already know about evolution. I wish someone would publish something with a little more than simple "variation" or "resistance" or the ability to "digest" something new. None of these minor changes get us anywhere in the grand evolutionary story as told by Darwinists! If you could provide even one example of an increase of CSI in the genome of any organism, I'd love to see it. Note: An example of CSI should exhibit functional divergence. I should point out that functional divergence does not require an increase of information; however, information increase does require functional divergence. Make sense? For example, in gene duplication the "free" duplicate may only be considered an increase of info. if it acquires a novel function (one that diverges from the original). However, The original must also maintain its function, otherwise, you just gained one function to lose another. As you know, vertical evolution requires an increase of biological information and organization. In other words, If you could show how adaptations lead to morphological innovations, I will embrace Darwinism like the fanatics at Pharyngula! No kidding! Mario A. Lopez

Mammals without enamel therefore must have descended from mammals with enamel-covered teeth.

Should it not be the other way around? I mean, according to evolution, organisms evolve from the simple to the complex, right? Mapou

Lenoxus "... studies that show where in the genome a function was gradually gained?" I would be very grateful if you could give me links to those studies. "should not the designer “clean up” all genetic material “left over” from a change, hence leaving behind exactly zero “junk”?" Not if devolution is independant of the designer. mad doc

On a second reading of the OP, I think I see the insinuated point — that because it is "degeneration", this is an example of "devolution". The question is, why accept this study, which looks at a function gradually lost, and reject studies that show where in the genome a function was gradually gained? And should or should not the designer "clean up" all genetic material "left over" from a change, hence leaving behind exactly zero "junk"? Lenoxus

If it's a psuedogene, it's definitely functional, functional, functional! Genetic entropy always removes non-functional pseudogenes from the genome. Wait, I mean the designer does that, but if the designer didn't, then entropy would cause pseudogenes, and that's why pseudogenes exist! Lenoxus