Richard Sternberg on “Junk” DNA

A podcast on the original subject of Sternberg's article - nuclear architecture in rod receptors of nocturnal animals Nakashima

Mr DATCG, No, water does not accumulate for millions or billions of years before being released in a megaflood. Glacial lakes form and drain within the cycle of ice ages of a hundred thousand years or less. Nakashima

Maybe you want to move your eye debate here since no seems to care about the Sternberg proposal about the use of junk DNA. Apparently all eyes appeared in the Cambrian and none have appeared since, though they may have changed a little. So the complexity of the various eyes have to deal with the fact that there is no known predecessor and it was a relatively short time for such complex systems to arise. I can't conceive how an eye could arrise by drift. There has to be a complex history. If this is wrong then it would be of interest to provide different information. jerry

Mr DATCG, Have you heard of the neutral theory and drift? Some traits just happen, they come along for the ride when other traits are selected. The inverted eyes of vertebrates happened way before fish existed. Nakashima

69 Nakashima, "Sorry, no. It is possible to argue for a geophysical catastrophe, such as a large flood, because water is a physical object that can accumulate in one place and then be released." Yes, it can accumulate over millions or billions of years, correct? Its the bursting forth of water through natural dam boundaries that is an event, you might even say an explosion of forces. "The source of evolutionary saltation cannot be accumulated in one place and then released. Mutations are events, not objects." Umm, I'm a little confused by your use of the world "saltation." Can you expand? How do you explain the Cambrian Explosion of Information? Why do fossils appear fully formed, developed in a short time period relative to the proposed 4.8 billion years of earths existence? Didn't Oxygen accumulate before life could explose onto the scene? In fact, water had to accumulate. And many other natural features before life exploded in diversity so grand that we are all in awe of it today? Whether telic or atelic supporters? What else had to accumulate? What other ingredients? Still not sure about your use of saltation. But, if mutations gradually, step by step accumulate before a change occurs that leads to speciation. How is it not a fundamental accumulation to a physical construct until suddenly an advantage is selected for in one place of organic life that then is spread through populations rapidly? For example say Flu virus? DATCG

Nakashima, Regarding dinosaurs, my statement was concerning findings by an evolutionist regarding a specific turnover of theory in Uniformitarianism. He points to many other regions around the globe that are now being identified as a result of the work by Bretz that was once scoffed at and mocked. Once cherished and firm beliefs that were considered factual have now been overturned. The review by Baker serves good purpose as warning to complacency to follow consensus thinking. I think it a very significant finding and review. It certainly not the geology record I learned in limited academic studies on the subject. As to story telling, your conflating my points. I'm saying one good story is as good as another. It is my poor attempt at satire. But the observed experimental data that can be repeated in regards to rapid changes for Cave Fish eyes being restored is not something I discovered. Evolutionist did and it surprised the heck out of them when it happened. It was a very good test of evolution and it actually supports rapid changes, not long millions of years. You stated that Cave Fish are younger than Caves earlier. Well, how much younger? The first fish supposedly evolved 500 million years ago, correct? So, while a Cave may be older than a fish, that is hardly an argument the fish has not changed rapidly in time in Caves since their appearance in the fossil records. It could be that fish have been switching off/on eyes in caves for 300 million years. How can you possibly know? My final statement in regards to the geological time record is one of trust in the end. I'm beginning to seriously doubt what I was taught since new research is now turning up megafloods all over the world. The next question is how does, or can such cataclymic events effect dating methods? I'm not sure. But it certainly changes the landscaping theory. I'd guess the next grand place that might fall into the category of Bretz's Megafloods model, is a canyon in Arizona. What do you think? If the Grand Canyon does eventually succomb to Bretz's model, how does it effect different longstanding theory about the geologic column? I'm in the... I don't know category right now. But I think story-telling is very good on both sides. DATCG

Allen, In response to your argument about fish having inverted eyes. I'd ask some questions about why? Is there an advantage to the fish? What is the advantage? Next, I contend that evolution itself argues it is an advantage for the fish. I then ask, if it is not an advantage, why was it selected according to evolution theory? Is it an adaptation? And finally, if evolution is not selecting for advantages in fish, but inferior selection to weaken a species, then what has happened to the theory? Now, that doesn't mean Design theorist are let off the hook. They must come up with answers too. But at this point, I am reminded of a favorite statement by evolutionary dogmatist in unguided processes. Just because we do not have all the answers today, does not portend an answer in the future. Let science work. Scientist may discover the reason. As the appendix is no longer seen as a vestigial organ, there may be good reason inverted eyes exist in fish. DATCG

Forgetting the minutia concerning whether or not there is 'junk DNA', the whole argument of life being 'suboptimal' or 'shoddy design' has always failed to impress me. According to our grand cultural visions of what a 'superior being' would be, we are poorly made, powerless, unintelligent, and otherwise quite primitive. If many of those who have such complaints were to design humanity, should we believe it would be glorious? No wonder a God who comes as a weak little baby born in a stable eludes us for so long. We cannot complain about the design that exists without inferring our own conceptions of what 'optimal design' is. So tell us, those of you who are discontent, what would that be? This may seem unrelated but it's not... ...A guy told me once that he was appalled at the preaching of a God who would condemn us for the way He made us (ie. weak, powerless, and sinful). I asked him if he was implying that a 'real God' would take the responsibility upon Himself for all that? And what would happen to those who insist upon bearing that cross themselves? Is their condemnation God's choice or theirs? Naturally, there was no comment... Lock

After "inverted eye", it should read: "might not be so much.... I left out the "not". Sorry. PaV

Allen in #48:

To do what you suggest (i.e. reverse the orientation of the vertebrate retina so that the photoreceptor cells face outward) would require the complete inversion of the entire vertebrate nervous system (see my comments, above, for the reason). This is precisely the problem with the design hypothesis: to truly optimize a design, one can “start from scratch” and completely redesign the characteristic in question. In evolution, you can’t do this; evolution is completely restricted to building on already existing structures. This is what we mean by “historical contingency” in evolution (especially macroevolution).

I don’t see any basis for your statement that an “inversion of the entire vertebrate nervous system” is required to form a cephalapod eye. The cephalapod eye, as you know, forms when the ectoderm forms a special layer which then curves round itself to form the equivalent of the optic cup, and to which the optic nerve later attaches, whereas in vertebrates, a vesicle from the brain induces the formation of the eye’s outer layer, while the vesicle invaginates to form the optic cup. If the ectoderm were to form the “optic cup” (as in the cephalapod) instead of the optic vesicle, then inversion wouldn’t need to take place. So I don’t see why the entire nervous system needs to be inverted.

Evolution cant’ do this. From a purely design standpoint, it makes absolutely no sense to have the ventilatory and ingestive pathways cross in the pharynx. This “design” results in an irreducible frequency of choking deaths.

Everyone dies, Allen. If the Designer wanted to design us so that we wouldn’t die, He’s obviously done a poor job of it. Now we’re into the theological question as to why the Designer/Creator would want to act in such a way. But this is strictly theological; not scientific/philosophical.

An intelligent designer would have completely separated the respiratory and digestive systems, to completely rule out the possibility of choking due to food lodging in the opening of the trachea. Natural selection can’t do this. It cannot be prospective, and can only work with structures and functions that already exist. This meant adding an epiglottis to the otherwise badly designed pharynx. This reduced to a minimum the frequency of deaths due to choking.

. . . etc. Maybe I’m wrong, Allen, but if a Designer exists, then He has chosen to “evolve” forms rather than bring them directly into existence, because that’s what the fossil record suggests (confirms). If that’s the case, then, as you say further down in your post, “This almost always means that the resulting arrangements of structures and functions represents compromises in which negative side-effects are irreducible beyond a certain point.” Why would the Designer choose to do such a thing? Well, maybe He intends for there to be a significance to the fact that all life is related. Maybe not. But, again, we’re now discussing theology. As to the “lensing” of rod cells in nocturnal animals, I don’t think that’s the best argument for ‘design’. vjtorley has a link to a 1998 article by Michael Denton that I read for the first time a couple days ago. His argument---which is the very one I suggested in post #27---is that the blood system, in particular the choriocapillary system, assist in providing oxygen and nutrients to the photorecptor cells, and that the ‘inverted eye’ might be so much as ‘bad design’ as a ‘preadaptation’. I think this is a much stronger argument for design. As to the use of “junk-DNA” in providing for density differences in the nucleus of the rod cells, and your view of this as a bit ridiculous, well maybe all this points out is ‘one’ use of such ‘repetitive elements’ in the genome. Maybe scientists will now find that such repetitive elements have similar functions in different type cells, or that the ‘backbone’, if you will, that they provide, might facilitate regulation of gene transcription. Then it might not seem so laughable a proposition. We await. I don’t think that anyone can prove ‘design’ doesn’t exist in nature. Maybe no one can prove that it does exist. But if we want to ascertain which is the most ‘reasonable’ proposition, we are then immediately faced with theological arugments. We see this in the Origins. But let us then admit that we have left behind the realm of the strictly scientific. PaV

Allen MacNeill #28

The inverted arrangement of the vertebrate retina is a consequence of its embryological development: the vertebrate retina forms from an outpocketing of the hollow embryonic cerebrum, in which the cell bodies of the cells that will become the bipolar and retinal ganglial cells face outward toward the surface of the cerebrum, while the cells with which they synapse (i.e. the cells that become the rod and cone cells) are underneath them (the “hollowness” of the embryonic cerebrum is important - see Inference # 2, below).

#48

To do what you suggest (i.e. reverse the orientation of the vertebrate retina so that the photoreceptor cells face outward) would require the complete inversion of the entire vertebrate nervous system (see my comments, above, for the reason). This is precisely the problem with the design hypothesis: to truly optimize a design, one can “start from scratch” and completely redesign the characteristic in question. In evolution, you can’t do this; evolution is completely restricted to building on already existing structures. This is what we mean by “historical contingency” in evolution (especially macroevolution).

You seem to be assuming that any Designer worth His or Her salt should be willing to "start from scratch," in order to optimize the function of some organ. But isn't that asking a bit much? Why should we expect a Designer to make continual interventions of this kind, in evolutionary history? I would argue that a truly Intelligent Designer should be able to foresee the emergence of vertebrates, with their own distinctive pattern of embryonic development, and endow the first living cell with the genetic and evolutionary wherewithal for its vertebrate descendants to "figure out" a way around their developmental constraints, so that they could eventually come up with a visual system which, even if it is somewhat rigged, still out-performs that of other animals - for as I pointed out in an earlier post (#34), vertebrate eyes see better than invertebrate eyes. It is surely a contingent fact that vertebrates were in fact able to evolve eyes as sophisticated as the ones they possess. One can easily imagine worlds inhabited by living creatures, where that kind of evolution simply couldn't have happened. Thus even if a step-by-step explanation of the vertebrate eye's evolution were discovered, the successes that evolution has achieved to date would suggest to me that the first cell, whatever it was, must have possessed an enormous evolutionary potential - which indicates some kind of front-loading. That doesn't mean the genes for vertebrate eyes had to be there from the start; but it does mean that DNA was designed to evolve its way around almost any engineering problem. As I'm not a biologist, I'm not competent to speculate how the first cell could have been designed to evolve so magnificently well, or what kind of pre-packaging it might have had, but this is what I would like to see future research focus on. I am also unable to comment on Sterberg's article, as what I know about mice could be written on the back of a postcard. vjtorley

Mr Vjtorely, I'm glad you enjoyed the small humor there, and found in it some cause for further discussion! ;) I think any Intelligence aware of the internal dynamics of the Earth could well have been aware of the paths of various large rocks in space. Certainly any Intelligence capable of manipulating supervolcanoes could divert asteroids as well. So Intelligently Designed volcanoes, meteors, gamma rays from nearby supernovae - it is all the same for me. However, it cannot be denied that the K-T boundary exists and does demarcate a catastrophic change in the species distribution of the planet. In that sense, our ancestors are indeed lucky. I have read Rare Earth, and I'd like to recommend also Ward's Out of Thin Air though it is irritating in places. I agree with the Rare Earth position that life is probably common, while complex life is probably much rarer. This rarity depending upon the existence of plate tectonics, axial tilt, moon, magnetic field, etc. I'm not as bought into the thesis of Conway Morris that intelligence is inevitable. I'd like to believe that intelligence is like eyes and flight - so useful that it is strongly selected for. So if we rewound the tape, could we see intelligent rheas stomping around the pampas, or intelligent komodo dragons, or intelligent brown bears? Sure we could, but to me human level intelligence is still far from inevitable. Nakashima

Mr. Nakashima You write, tongue firmly in cheek:

We happen to be the beneficiaries of an intelligently designed meteor that hit the Earth 65 million years ago. Without the meteor, we would still be mice, and some intelligent dinosaur would be thinking self important thoughts about how the Intelligent Designosaur had fashioned the universe for his benefit.

It may interest you to know that the latest research casts serious doubt on the meteor theory. See New Blow Against Dinosaur-killing Asteroid Theory, Geologists Find in Science Daily, April 28, 2009. An excerpt:

The enduringly popular theory that the Chicxulub crater holds the clue to the demise of the dinosaurs, along with some 65 percent of all species 65 million years ago, is challenged in a paper to be published in the Journal of the Geological Society on April 27, 2009. ...... The newest research, led by Gerta Keller of Princeton University in New Jersey, and Thierry Adatte of the University of Lausanne, Switzerland, uses evidence from Mexico to suggest that the Chicxulub impact predates the K-T boundary by as much as 300,000 years. "Keller and colleagues continue to amass detailed stratigraphic information supporting new thinking about the Chicxulub impact, and the mass extinction at the end of the Cretaceous," says H. Richard Lane, program director in the National Science Foundation (NSF)'s Division of Earth Sciences, which funded the research. "The two may not be linked after all." ...... Keller suggests that the massive volcanic eruptions at the Deccan Traps in India may be responsible for the extinction, releasing huge amounts of dust and gases that could have blocked out sunlight and brought about a significant greenhouse effect. (Emphases mine - VJT.)

What does all this have to do with Intelligent Design? Plenty. If volcanism caused the extinction of the dinosaurs, then it is perfectly legitimate to view their extinction as a designed event. Volcanic eruptions are a consequence of plate tectonics. Plate tectonics are essential for the life on a planet. "It may be that plate tectonics is the central requirement for life on a planet" according to Peter Ward and Donald Brownlee, authors of Rare Earth, New York: Copernicus, 2000, p. 220. According to Guillermo Gonzalez, co-author of The Privileged Planet, plate tectonics drives the Earth's carbon dioxide-rock cycle, regulating the balance of greenhouse gases and keeping the planet at a livable temperature, by recycling rocks such as limestone down into the mantle, where the Earth's heat releases carbon dioxide from these rocks, which then gets vented to the atmosphere through volcanoes. If the Intelligent Designer who created the first living cell also designed the Earth, with its system of plate tectonics, then this Designer could well have foreseen - and indeed, ordained - the fact that the India would be subjected to massive volcanic eruptions at a time when the dinosaurs were flourishing, thereby pushing them over the edge and enabling the mammals to emerge from the shadows. If you think this a trifle far-fetched, I would like to add that not only dinosaurs but many other kinds of animals were experiencing a reduction in species numbers, millions of years before the K-T extinction event, according to Dr. Norman MacLeod of the Natural History Museum in London:

Six million years prior to the KT boundary there were about twenty species of ammonites in the world's oceans. Three million years before the KT boundary there were only fifteen or so and one million years prior to the KT boundary we have less than half of what we started out with, we have less than ten species so the extinction event has already been going on for millions of years. The amazing thing is that we see the same pattern in the fish record, we see the same pattern in the terrestrial reptile record, we even see the same pattern in the mammal record. All of these groups were undergoing an extinction event for millions of years and it would be absolutely amazing to me if dinosaurs weren't undergoing the same sort of extinction and indeed I think they were undergoing the same sort of long term extinction. (Italics mine - VJT.)

In other words, the dinosaurs may well have been on the way out, anyway. Mammals also suffered some losses, but they were relatively small and inconsequential:

In particular, marsupials largely disappeared from North America and the Asian deltatheroidans, primitive relatives of extant marsupials, went extinct. (Wikipedia, article "Cretaceous–Tertiary extinction event.")

It has become fashionable to assert that if the evolution of life were rerun from scratch, it is very unlikely that anything resembling humans would emerge. However, at least one prominent paleontologist disagrees with this view: Simon Conway Morris, author of Life's Solution: Inevitable Humans in a Lonely Universe (Cambridge University Press, ISBN 0-521-82704-3). In the words of a reviewer, Anthony Campbell:

His view is that evolution has been constrained to follow certain paths leading more or less inevitably to the development of intelligence.

Remarkable neurological convergences between intelligent animals as diverse as apes, crows and cephalopods leads Morris to postulate that the evolution of intelligence on Earth was biologically fore-ordained, and that "if we had not arrived at sentience and called ourselves human, then probably sooner rather than later some other group would have done so, perhaps from within the primates, perhaps from further afield, even much further afield" (quote from Campbell's review). Although Campbell (who wrote his review in 2005) raises the "meteor issue" (as you do) as an objection to Morris's theory that the emergence of intelligent life on Earth was inevitable, he is fair-minded enough to acknowledge:

[I]t can hardly be denied that the book provides an impressive array of evidence to support its author's contention.

The upshot of all this is that we humans are not just a lucky fluke, as some atheistic materialists would have us believe. vjtorley

Mr DATCG, That quote is exquisitely interchangeable between biological and geological gradualistic processes over long periods of time. Sorry, no. It is possible to argue for a geophysical catastrophe, such as a large flood, because water is a physical object that can accumulate in one place and then be released. The source of evolutionary saltation cannot be accumulated in one place and then released. Mutations are events, not objects. Nakashima

Mr DATCG, in re your comment 58, you seem to be seriously arguing that humans and dinosaurs walked the earth at the same time. This view is shared by no one. From Wikipedia: But the Triassic takeover may have been a vital factor in the evolution of cynodonts into mammals. The cynodonts' descendants were only able to survive as small, mainly nocturnal insectivores.[12] As a result: The therapsid trend towards differentiated teeth with precise occlusion accelerated, because of the need to hold captured arthropods and crush their exoskeletons. Nocturnal life required advances in thermal insulation and temperature regulation to enable the ancestors of mammals to be active in the cool of the night.[16] Acute senses of hearing and smell became vital. This accelerated the development of the mammalian middle ear, and therefore of the mammalian jaw since bones that had been part of the jaw joint became part of the middle ear. The increase in the size of the olfactory and auditory lobes of the brain increased brain weight as a total percentage of body weight. Brain tissue requires a disproportionate amount of energy.[17][18] The need for more food to support the enlarged brains increased the pressures for improvements in insulation, temperature regulation and feeding. As a side-effect of the nocturnal life, discerning colors became less important (they lost two out of four opsins), and this is reflected in the fact that most mammals have poor color vision, including the "lower primates" such as lemurs.[19] Nakashima

Nakashima, This is off-topic in regards to billions of years or a Uniformitarian view. See review of Bretz's MegaFloods hypothesis below as valid scientific reasoning by Victor Baker. He reviews Bretz's original fight for a cataclymic event in the East Washington Scablands. It is an eye opener for how scientist can be lethargic or stubbornly refuse to think outside of established doctrine since it may challenge their worldviews. See: The Channeled Scabland: A retropective His review from what I have access to questions the established doctrine that did not allow for any other perspective for decades simply because it went against Uniformitarianism. It now turns out, Bretz's model is no anomaly, but rich in scope around the world. Original Abstract and paper... Original Abstract - Baker, Author Subscription is required for full text. Baker states...

"Uniformitarianism is a regulative principle or doctrine in geology that unfortunately sometimes conflates (a) the pragmatic application of modern process studies to understanding the past (actualism) with (b) substantive presumptions that deny effectiveness to cataclysmic events. As recognized by William Whewell, who invented the term, meaning b is contrary to the logic of science (Baker 1998).2"

I agree with Baker's remarks. The doctrines presumptions interfere at times and is contrary to the logic of science. It has taken 50 years for this to slowly be overturned and has still not made adequate ripples into the uniformitarian brethren. Although, Bakers restrospective is a good start.

"Indeed, one can envision a kind of investigation that inverts the usual reasoning process whereby studies of common, small-scale processes are extrapolated to the domain of less common, unobserved large-scale processes."

Where has this practice been seen before? Traditional and neo-Darwinist appropriate small-scale processes and extrapolate them "to the domain of less common, unobserved large-scale processes." That quote is exquisitely interchangeable between biological and geological gradualistic processes over long periods of time. Extrapolations to "unobserved" processes being key. In the end, it leads to considerable myth and story-telling. Whereas actual observations today as Baker points out from the Bretz model are applicable today on smaller scales in other locations.

" In addition to stimulating discoveries of cataclysmic flood landscapes, studies of the patterns, forms, and processes evident in the Channeled Scabland have informed understanding of processes that occur at smaller scales in modern bedrock channels that are impacted by extreme, high-energy floods (e.g., Baker 1977, 1984; Baker & Pickup 1987; Baker & Kochel 1988; Baker & Kale 1998)."

Bretz's model is applicable across modern day events that are factually categorized, analyzed and repeatedly observed "in modern bedrock channels." This can lend added weight to rapid depositories and captured life in small or megadeath flood events around the world. As indeed large buriel grounds of dinos and other assorted life are found to exist. Instead of "usual extrapolations" of uniformitarianism, there are "cataclysmic flood landscapes" that can capture dinosaurs rapidly preserving tissue and bones, as opposed to millions or billions of years of gradual sedimentary layering. The paper goes on to describe large flood events around the world, including the English Channel. The point I'm trying to make is that gradual, billions of years processes are not written in stone as the only known mechanism for shaping our planet. Neither does the fossil record agree with gradualistic theory. That being the case, we cannot determine if our ancestors lose or gain information over long time periods. Gould recognized this and tried to correct the problems with Punctuated Equilibrium. I think appealing to time is no longer valid as a throw away point by evolutionist for what may or may not occur as an unobserved past-event horizon(nocturnal vs diurnal). There is observable evidence of what does happen rapidly today in biological processes, catastrophic events and observable fossil records. These are undeniable facts, with the latter fossil record still open for remote possibilities and disagreements if transition fossils do appear. But what we have today is scant evidence for gradualism. Within the biological realm, evolutionist of the old paradigm are now appealing to more mechanisms and tossing off natural selection as a strong force. HGT for example may appear at first to strengthen the case for unguided evolution, but it also weakens the data collection points and trail tracking to an absurd guessing game. This is one reason why I believe Koonin, Baptiste, Doolittle, et al., are arguing for a plurality of multiple trees, bushes, or a forest. Even admitting we may never know the beginning points. LUCA is in serious trouble if the original tree of life is so available to wholesale information swapping. HGT also lends weight to rapid variation as well. Natural Selection, the hallmark of Darwinism becomes weaker as Gradualism is exposed as an unsupportable model in modern research. And billions of years to lose or gain information in my opinion becomes weaker too. I don't think its overturned, but certainly weaker. DATCG

A commenter at evolution engineered states:

Simply put ...RNA polymerases bind DNA non-specifically. They have to, in order to be able to transcribe all sequences without falling off midstream. It is this non-specific binding, an unavoidable aspect of the fundamental nature of the enzyme, that is the source of much (most?) of the junk RNA that Sternberg et al. are so captivated by. One can increase the specificity of RNA polymerases by many mechanisms, but it is impossible to avoid the need for the enzyme to bind DNA non-specifically.

While I look into this, I will also submit it here for any other comments. William Wallace

Allen, Quick note. I saw your response(s). Thanks. I'll have to respond this weekend to you. You made a good argument that I expected in one area. As to editing functions at UD, lol... we can agree :) DATCG

Allen_Macneill, Furthermore, I believe that the artificial distinction between “science” and “philosophy” that developed during the 20th century has done great injury to both science and philosophy. After all, science used to be called “natural philosophy”, a term that I believe is much more accurate. As you and several others here have pointed out (and I agree with them), one cannot do science without also doing philosophy. That's not clear, nor is that what I said. I said that people have a habit of passing off their philosophy as science irresponsibly. Absolutely there are certain fundamental metaphysical assumptions that underscore modern science. The existence or non-existence of a designer(s) is not one. One does have to regard nature as rational, however. Make of that what you will. That is, doing science means making a set of metaphysical assumptions about what is and isn’t legitimate in scientific investigation. And I agree that assuming that teleology exists in nature has been considered illegitimate since the middle of the 19th century. By the way, Darwin wasn’t responsible for this change. Rather, he was responding to it, as a close reading of his autobiography, correspondence, research notebooks indicates. I never said that Darwin was. I said that this view - the idea that science proceeds with a certain method that sharply limits what can be investigated or proposed and still be considered purely "scientific" - has been the front and center objection to ID for years now. And it's routinely violated by ID critics and anti-theists who love to hijack science in precisely the way ID proponents are accused of doing. You could have simply said “You’re conflating the two” and then pointed out how. That would have been educational, both for me and for others reading your comment. However, you preferred to impute (without justification) motives, about which you are clearly and completely uninformed. Why did you do this, and then continue to do so (and, indeed, “ramp up” your accusations in the rest of your comment)? Do you think attacking another person’s character and motives strengthens your argument? If so, you are sadly mistaken. Spare me, Allen. I said your presentation was duplicitous - and it was. I didn't bother speculating about your motivations for providing such a presentation, nor do I care to. If you want to pull back and say you were merely confusing the issue and I'm a big, bad meanie for using the D-word, so be it. Please note: I do not expect an apology Good, because you're not getting one. Again, if you want to play the poor e-puppy with a wounded ASCII paw routine, so be it. I stand by my deep criticisms of your depiction of this topic, and reiterate that I could really care less to speculate about your motives. All I care about is the presentation itself, and I directed my criticisms at that. I have known many scientists in my time, and only a very few of them made any effort to try to understand the underlying philosophy in their chosen avocation. I think you and I would both agree that this has led to no end of confusion, and to unwarranted conclusions in both science and philosophy. If someone wants to devote themselves to science and care not a whit about philosophy, I consider that unfortunate - but it doesn't concern me so much. What does concern me is the habit of *confusing* science and philosophy, particularly confusing philosophical conclusions based on skewed readings of scientific evidence as a purely scientific conclusion. That it keeps on happening, despite one of the most up-and-center arguments against ID being that it's 'philosophy masquerading as science', is a curious thing. Here is perhaps the root of our disagreement. On the basis of this quote, it seems clear to me that there is a fundamental difference between science and philosophy of science. I agree that this is has been the case since the 19th century, and I believe that this artificial distinction between the two has had unfortunate consequences for both science and philosophy. First, the pertinent philosophy is not limited to philosophy of science. Second, if you want the get rid of this "artificial distinction" - meaning, you want to be able to say your speculations about metaphysics, the existence of a D/designer(s), the actions of said agents, etc are "really science" rather than "philosophy and metaphysics, but making reference to science" - good luck. Because the moment that happens is the moment ID because science. It will merely be a minority scientific position. So will idealism. And panpsychism. And Nick Bostrom's simulation argument/"speculation". And various dualisms. And much more than that. If you're merely saying that you think scientists should take philosophy more seriously, I've responded to that. So long as they know the difference between one and the other, my concern is minimal. nullasalus

Once again, could the designers of this site please consider some kind of post editing function, such as the one at Telic Thoughts? I can't easily read html with all of the tags visible, and this results in my repeatedly making the kind of mistake I have made here. Indeed, it would be nice to be able to delete one's own comment at some later date (after tempers have cooled and rationality reasserted itself). It's hard to replace a broken window, especially when one can't "unthrow" the rock that broke it... Allen_MacNeill

Damn! What I meant to write in the previous comment was this: "On the basis of this quote, it seems clear to me that you believe that there is a fundamental difference between science and philosophy of science." I wish my fumblefingers would stop doing that! Allen_MacNeill

nullasalus (once more):

"Did you even read what I said? I said that the line between science and philosophy is clear in this case, and respect that line. Not “make sure you give a pseudoscientific and hackneyed examination of both philosophical claims”. Do all the philosophy you want, brother - just realize you’ve left the science realm when you do it."

Here is perhaps the root of our disagreement. On the basis of this quote, it seems clear to me that there is a fundamental difference between science and philosophy of science. I agree that this is has been the case since the 19th century, and I believe that this artificial distinction between the two has had unfortunate consequences for both science and philosophy. Allen_MacNeill

nullasalus: Lest you conclude that I am still being "duplicitous in stating that "doing science and philosophy of science are two very different activities" while also stating that I think that the separation of science and philosophy that took place in the 19th century was unfortunate, let me clarify: In the first case, I was simply pointing out the way science and philosophy of science are done today, not asserting that this is a good thing. On the contrary, as my second quote implies, I think this is a bad thing; bad for both science and philosophy. I have known many scientists in my time, and only a very few of them made any effort to try to understand the underlying philosophy in their chosen avocation. I think you and I would both agree that this has led to no end of confusion, and to unwarranted conclusions in both science and philosophy. Allen_MacNeill

In #57 nullasalus asserted:

"You know my view - that there is no “design” hypothesis under MN, just as there is no “no design” hypothesis. Not if you want to remain within the realm of science..."

nullasalus, we have corresponded at Telic Thoughts as well as here, and I admit that I did not know (or at least understand) that this was your position. Having you state it in this way clears up some confusion I have had about your views on the difference between doing science and doing philosophy of science (they are, of course, very different activities). Furthermore, I believe that the artificial distinction between "science" and "philosophy" that developed during the 20th century has done great injury to both science and philosophy. After all, science used to be called "natural philosophy", a term that I believe is much more accurate. As you and several others here have pointed out (and I agree with them), one cannot do science without also doing philosophy. That is, doing science means making a set of metaphysical assumptions about what is and isn't legitimate in scientific investigation. And I agree that assuming that teleology exists in nature has been considered illegitimate since the middle of the 19th century. By the way, Darwin wasn't responsible for this change. Rather, he was responding to it, as a close reading of his autobiography, correspondence, research notebooks indicates. You then assert:

"...it’s still outside the realm of science, and into philosophy and metaphysics. Admit that much, or admit that ID claims are truly scientific claims, even if minority in view."

And I have done so, both here and elsewhere. You then quoted me:

"One can (indeed, one must) multiply virtually to infinity the necessary conditions for the design hypothesis for it to be fully consistent with the empirical data."

and then jumped to the conclusion that I was applying this to all teleological (i.e. "design") hypotheses, when I thought it was clear that I was applying it specifically to Dr. Sternberg's teleological hypothesis for the evolution of night vision in nocturnal mice. You seem extremely eager to conclude that my views, as expressed here and elsewhere, are the result of malfeasance on my part:

"I’m an ID critic and even I’m stunned by just how duplicitous your presentation is here."

You could have simply said "You’re presentation confuses several issues" and then pointed out how.

"You’re conflating the two irresponsibly." [Emphasis added]

You could have simply said "You’re conflating the two" and then pointed out how. That would have been educational, both for me and for others reading your comment. However, you preferred to impute (without justification) motives, about which you are clearly and completely uninformed. Why did you do this, and then continue to do so (and, indeed, "ramp up" your accusations in the rest of your comment)? Do you think attacking another person's character and motives strengthens your argument? If so, you are sadly mistaken. Please note: I do not expect an apology, as you were clearly as mistaken about my motives as I was confused about some of my points (or, at least, presented them in a way that fostered confusion). However, I would like to humbly point out that I try as much as possible to stick to arguments using evidence and logic, and avoid ad hominem attacks. Sometimes I am tempted to use sarcasm, and in this sense I do apologize to all if in doing so I insulted anyone. Perhaps the tendency to use sarcasm is one of those minor sins, for which academics in particular should do penance? Allen_MacNeill

Nakashima, OK, we are talking apples and oranges. I expanded the subject because I thought it necessary. It is not a simple process of inverting the rods. There is a whole support network that must match that change. Sternberg limits his argument to one specific area. But the support mechanisms must also align in the retina. These networks cannot be idly tossed away. So the number of steps, complexity and coordinated events between development pathways and overlapping genes for transcription factors makes it an unlikely, unguided process. Time is not an explanation. It is a story telling overarching plot line, but still not a fact. Only a mythical device inserted for imagination and day dreaming. It appeals to the small probability of anythings possible over time. You said, "Yes, cave fish are probably pretty young species. They have to be younger than the cave they live in! But the examples I was giving stretch across the entire mammal lineage of hundreds of millions of years, plenty of time for color vision to decay." Well, again, this is a story of ifs, mights and maybes. What we observe however is rapid developmental recovery or a switching network turned on through simple recombination. These are actual experimental, repeatable observations by scientist today. I'm not arguing against the loss of information through mutations. I think this is the epic truth established that mutations lead to loss of information, not gain. But, I am not able to relate to story telling possibilities of ancestors living nocturnally due to avoidance of dinosaurs. Historical records show tribes band together and hunt larger, more dangerous predators either as protective measures or for food, pelts, leather, oils, clothing, jewelry, utensils, tools, etc. You assume a scared ancestor, weak, anemic and unable to survive except through hiding. Yet all evidence shows our ancestors travel across great mountain ranges, across oceans, hunting and killing the most brutal predators in the past. Many died in these hunts, but the strong survived to hunt more. I guess we will agree to disagree on story telling. If we're into myths, I'll consider with equal weight King Arthur or the slaying of dragons as realistic as any billion year old mythical tale forced to fit a doctrine or ideology. Countering that while the majority of city dwellers today would not know the first thing about how to track, capture or kill a dangerous beast. Our ancestors certainly did. And they did it routinely without the aid of guns very succesffully to the point of extinction. I think the nocturnal argument fails for many reasons, not the least of which is why our ancestors came out of the trees in the first place if only to hide in caves. Yet we know they domesticated wild horses to ride and attack and lived in tribes. The complex weaving of story telling is insurmountable over time. The contradictions add up to a heap of inconclusive fables. I'm losing faith in the billions of years argument to solve all problems of a materialist argument. DATCG

Allen Macneill, In #33 nullasalus points out that I have not ruled out the “design” hypothesis “on principle”. That is correct; No, Allen, that's not what I said at all. You know my view - that there is no "design" hypothesis under MN, just as there is no "no design" hypothesis. Not if you want to remain within the realm of science (or at least what the NCSE, Ken Miller, and others have repeatedly claimed is that scope.) If you want to talk philosophy, talk philosophy. Don't engage in a shell game where you say you're doing science when you're really doing philosophy. In this sense, the design (i.e.. teleological) hypothesis serves as the null hypothesis for the evolution (i.e. non-teleological) hypothesis. This is a perfectly valid procedure, and is in fact the procedure that Darwin himself followed in several chapters of the Origin of Species. Allen - Darwin's writings contain both (scientifically) superfluous metaphysics, and more purely scientific observation and consideration. Aristotle wrote about both empirical observations and philosophical considerations. You're conflating the two irresponsibly. Let's see how you word it all. • that non-coding DNA be inserted in the genomes of all eukaryotes “in order to” make non-coding DNA available for co-option as light pipes in the retinas of nocturnal mice To these and all the rest of your quaint rephrasing of teleological hypotheses: No, Allen. There can be vast applications of non-coding DNA in eukaryotes in order to serve a vast number of purposes, of which that is one. What you're doing here is akin to me describing the ASCII coding standard as "including colons and parentheses in order to allow Uncommon Descent posters to make a smiley face in a post." Awkward phrasing to make the suggestion seem more outlandish than the basic hypothesis (In this case, "The ASCII coding standard was designed") really is. And it's still outside the realm of science, and into philosophy and metaphysics. Admit that much, or admit that ID claims are truly scientific claims, even if minority in view. One can (indeed, one must) multiply virtually to infinity the necessary conditions for the design hypothesis for it to be fully consistent with the empirical data. No, Allen. Not by a longshot. Not every single act in the nature or the universe needs to be "designed" for there to be design in the universe. Just as not every particular outcome of a procedural content generation program needs to be specifically foreseen by the programmer for the program to be designed. I'm an ID critic and even I'm stunned by just how duplicitous your presentation is here. By contrast, the evolutionary hypothesis (i.e. that non-coding DNA was co-opted by natural selection in the optimization of light-gathering in low-light environments. Furthermore, the evolutionary explanation avoids the contradiction inherent in the observation that the retinas of cephalopods are not optimized for light-gathering in the same way. There is no contradiction, Allen. And furthermore, everything you just wrote is easily squared with a design hypothesis. Vastly more easily than the (still ignored) third option of 'Gosh, we just keep getting lucky, don't we?' Ergo, I believe that my evaluation that the design hypothesis in this case “strains credulity” in that it requires an almost infinite set of preconditions, and necessarily includes a contradiction in its required preconditions. And I believe that your evaluation of the design hypothesis strains credulity. :) I honestly think that’s precisely what I’m doing, by not ruling out any hypotheses a priori (except, perhaps, for hypotheses that have never been given any credence by any scientist, such as the hypothesis that angry thunder deities are responsible for lighting and thunder, etc.) Did you even read what I said? I said that the line between science and philosophy is clear in this case, and respect that line. Not "make sure you give a pseudoscientific and hackneyed examination of both philosophical claims". Do all the philosophy you want, brother - just realize you've left the science realm when you do it. nullasalus

Hi Allen MacNeill, This is a little OT for this thread but you made an admission above that I would like for you to clarify. As I mentioned, I use you as a reference in ID arguments and want to make sure I know what you are saying. You made a claim about Darwin and teleology:

In this sense, the design (i.e.. teleological) hypothesis serves as the null hypothesis for the evolution (i.e. non-teleological) hypothesis. This is a perfectly valid procedure, and is in fact the procedure that Darwin himself followed in several chapters of the Origin of Species.

Would you confirm whether or not by teleology you mean: "Teleology (Greek: telos: end, purpose) is the philosophical study of design and purpose." Wiki and/or: "1 a: the study of evidences of design in nature b: a doctrine (as in vitalism) that ends are immanent in nature c: a doctrine explaining phenomena by final causes 2: the fact or character attributed to nature or natural processes of being directed toward an end or shaped by a purpose 3: the use of design or purpose as an explanation of natural phenomena" Miriam Webster. This seems to be a change in your position concerning what Darwin wrote and what students might find in On Origin Of Species . Has your opinion changed on this matter in the last year? Charlie

supporters of ID are moving in the opposite direction, asserting that all characteristics of living organisms must be designed, Allen, where do you get this stuff from? I think just about everybody on this board understands that undirected genomic changes occur and that they can at times be fixed by natural selection. The problem is the dogmatic insistence of the institutional establishment that these forces form a conclusive explanation for biodiversity, and design must not be considered in the mix. tribune7

Allen, You are spouting nonsense interspersed with good reasoning so it is hard to understand sometimes what you are actually saying that makes sense. Natural selection as a process, result or whatever you want to call it is not something that ID says does not happen. But if you want to use the word select (in any fashion you say it happens) then where did the thing that was selected for come from. If it was Darwin's theory then it would leave a trail because his theory which is also in most of the text books presupposes according to Darwin numerous steps along the way. If you are abandoning Darwin's small change scenario which I assume you are doing then there would not necessarily be a trail. But then you have to explain how all this marvelous ordered complexity arose. The 50+ engines of variation fall short here too or you would be all over us with examples and not just with plausible models. We all can make up just so stories as well as the evolutionary biologists but just so stories don't cut it. Unlike evolutionary biologist we like empirical data. No one at ID is saying that every little feature was designed but ID is saying that natural processes have never shown the ability to build organized complexity. It is the question that evolutionary biology begs away by saying it was selected for or it evolved or it emerged or it was exapted. Until you or your colleagues can show how this organized complexity arose, then all you will have are interesting assertions no matter how plausible sounding they are. A lot of things sound plausible till examined closely. Darwin's small change scenario makes good sense to most people till looked at closely. You engines of variation are interesting till looked at closely and we find they too cannot build the organized complexity seen in life either. They can account for small changes but that is it. I have read Brosius' article and know what is out there on the table as the cutting edge of what caused the changes and it is specious to think that it resulted in more than an occasional additions to the functioning genome let alone the construction of anything as complicated as an eye. All this blustering here in the last few weeks by a lot of people has answered exactly nothing. When evolutionary biology is able to answer where all the information came from they can put ID aside but they are nowhere on that issue. Which is why after thousands of comments on numerous topics the basic issue still lies on the table untouched. It lies untouched because you and no one else on this planet has an answer. jerry

PaV in #38:

"I hope you appreciate the point I’m attempting to make."

I believe I understand the point you are trying to make. I simply do not agree with it. Allen_MacNeill

In other words, natural selection is not "weak". Rather, it is ultimately constrained by historical contingency. Weakness ? contingency does it? Allen_MacNeill

I find that I must clarify my position on the importance of natural selection in evolution. I have not asserted that natural selection does not happen, nor that it is not a reasonable ()and empirically consistent) explanation for the evolution of some of the characteristics of living organisms. What I (and an increasing number of evolutionary biologists) have asserted (on the basis of the empirical evidence) is that natural selection is not the only explanation for all of the characteristics of living organisms, nor is it the underlying driving force for macroevolution. Furthermore, as I have pointed out many times, natural selection is an outcome, not a cause of evolutionary change. The underlying causes of evolutionary changes are the "engines of variation" that I have cited and described many times in many different venues. In other words, evolutionary biologists are increasingly accepting more and different mechanisms for evolution, not just natural selection (which was the premier engine of change in the "modern evolutionary synthesis"). To put it as succinctly as possible, I am not a "pan-adaptationist", and I believe (based on the available evidence) that macroevolution is at least partially driven by fundamentally different mechanisms than microevolution. I find it ironic that, just as evolutionary biology is moving away from "pan-adaptationism" and "single overarching mechanisms", supporters of ID are moving in the opposite direction, asserting that all characteristics of living organisms must be designed, and that "intelligent design" is the "single overarching process" by which everything in biology has come about. Allen_MacNeill

in #47, jerry asserts:

"...one hypothesis presumes a trail and the trail is never found."

I'm not sure what you mean by this, but I will assume you mean that we don't know the "trail" which leads from the ancestral to the derived forms (such as the ancestral to derived forms of the cephalopod and vertebrate retinas). This is manifestly untrue. As I have pointed out repeatedly in this thread, evolutionary biologists have not only a plausible evolutionary and developmental explanation for the macroevolution of the two kinds of retinas, we are also now in the process of analyzing the underlying developmental biology that explains how this happened over deep evolutionary time. Allen_MacNeill

Allen writes:

This is precisely the problem with the design hypothesis: to truly optimize a design, one can “start from scratch” and completely redesign the characteristic in question. In evolution, you can’t do this; evolution is completely restricted to building on already existing structures. This is what we mean by “historical contingency” in evolution (especially macroevolution)

Precisely. This was why I posted the paper showing that the origins of insect wings, trachea, and spinnarets could all be explained as modifications of the same structure: the arthropod gill. Dave Wisker

PAV in #38: To do what you suggest (i.e. reverse the orientation of the vertebrate retina so that the photoreceptor cells face outward) would require the complete inversion of the entire vertebrate nervous system (see my comments, above, for the reason). This is precisely the problem with the design hypothesis: to truly optimize a design, one can "start from scratch" and completely redesign the characteristic in question. In evolution, you can't do this; evolution is completely restricted to building on already existing structures. This is what we mean by "historical contingency" in evolution (especially macroevolution). For example, once automotive engineers realized that the only reason that engines were in the front of the car was because that's where horses used to be, they engineered cars with the engine in the back, between or over the drive wheels. But then, some bright engineers realized that, for reasons of optimizing torque in the drive wheels, it makes more sense (and makes for a much simpler drive train) to put both the engine and the drive wheels in front. Evolution cant' do this. From a purely design standpoint, it makes absolutely no sense to have the ventilatory and ingestive pathways cross in the pharynx. This "design" results in an irreducible frequency of choking deaths. But the lungs of vertebrates evolved from an outpocketing of the esophagus (that's why the lining of the lung consists of endodermal epithelium, just like the lining of the digestive system). When our ancestors got all (or most, in the case of amphibians) of their oxygen from someplace besides the lungs/swim bladder, this was not a problem. However, with the invasion of the land environment and the subsequent switch to air breathing, this situation drastically changed. An intelligent designer would have completely separated the respiratory and digestive systems, to completely rule out the possibility of choking due to food lodging in the opening of the trachea. Natural selection can't do this. It cannot be prospective, and can only work with structures and functions that already exist. This meant adding an epiglottis to the otherwise badly designed pharynx. This reduced to a minimum the frequency of deaths due to choking. Among our ancestors that walked and ran (and ate) in a horizontal posture, gravity assists in keeping the epiglottis closed. But, with the evolution of bipedalism and the modification of the larynx as an exaptation for speech, the frequency of deaths due to choking went back up. Once again, an intelligent designer at that point could easily have completely re-engineered the respiratory and digestive systems to prevent all of the many millions of humans that would have died from choking from doing so (yes, I see the teleological "for" in that sentence, but I'm in a hurry). But reorganizing the structure of the vertebrate respiratory and digestive systems would require the entire "re-engineering" of the entire embryological development of the entire vertebrate body. So, natural selection "tinkered a solution to the problem". Note that the evolutionary explanation is inherently utilitarian. That is, it optimizes structures and functions by reducing negative outcomes to a minimum, relative to positive outcomes. This almost always means that the resulting arrangements of structures and functions represents compromises in which negative side-effects are irreducible beyond a certain point. Allen_MacNeill

"And so here we are, right back to multually exclusive dueling world views, with no way to distinguish between the validity of the different hypotheses on the basis of the empirical evidence upon which it is based." Except the one hypothesis presumes a trail and the trail is never found. So that would disqualify the natural selection hypothesis and leave the "appearance of" as most likely "actual." Allen, you have said that Darwin is dead and yet here you are arguing like a cornered rat for Darwin as the supreme force in evolution. Which is it? Natural selection is supreme or it is the weak force so many evolutionary biologists say it is? jerry

And in #36 DATCG wrote:

"Remember though, the eye must not be inverted and must cool itself from the sun and heat. And your process must happen by accidental mechanisms, mutations, evo-devo, etc. I’m not sure how you do it without externalizing some components features like we find for the inverted eye. But you seem to have all the answers. I’m not a scientist, so maybe you’re right."

Once again, you completely ignore the simple fact that the vertebrate retina evolved in exactly the same environment as the cephalopod eye: underwater, under low-light conditions. And you ignore the underlying fact that the vertebrate retina develops as an evagination of the surface cells of the brain, whereas the retinas of cephalopods develop from epithelial cells derived from an invagination of the outer integument. In other words, the underlying orientation of vertebrate versus cephalopod eyes is historically contingent upon the orientation of the tissues that eventually evolved into the retinas, rather than as the optimization of design for vision in underwater low-light environments. Otherwise, why would there be two fundamentally different designs for the same structures that evolved in the same environments? Allen_MacNeill

In #35 DATCG wrote:

"For example, back to the cephlapod eye that Allen mentioned. Its verted eye is inferior to that of the human. It only needs to judge motion, is simplified, including only two neural components and does not include the Foveola. It is not exposed to extened daylight either. Thus the more complex inversted design is not required."

Except that the arrangement of the vertebrate retina originally evolved in fish that lived in exactly the same environments as cephalopods. Ergo, this argument holds no water at all (pun intended, of course). Allen_MacNeill

As for Richard Dawkins not knowing the explanation for the inversion of the vertebrate retina, that's only an indication that he knows very little vertebrate evolutionary embryology, not that no one has an explanation for this inversion. As I pointed out in comment #28, the reason for the inversion of the vertebrate retina is directly attributable to its embryological derivation. Allen_MacNeill

In #34 vjtorley wrote:

"I would venture to say that any structure found in nature which gives human engineers some new ideas for improving their designs is a strong prima facie candidate for having been designed itself."

And,in the same vein, I could assert that

"...any structure found in nature which gives human engineers some new ideas for improving their designs is a strong prima facie candidate for having been optimized as the result of natural selection."

And so here we are, right back to multually exclusive dueling world views, with no way to distinguish between the validity of the different hypotheses on the basis of the empirical evidence upon which it is based. Once again, the mere fact that something in nature looks designed is not acceptable evidence that it is designed. If that were the case, then snowflakes would be considered to be designed, but my two-year-old's Playdoh "sculpture" would not. Allen_MacNeill

nullasalus concludes comment #33 with this:

"If you’re going to restrict science to a narrow topic - and I believe it’s right to do so, for reasons of practicality - then restrict it. Don’t just chase out all the unnecessary stipulations you dislike. Get rid of them all."

I honestly think that's precisely what I'm doing, by not ruling out any hypotheses a priori (except, perhaps, for hypotheses that have never been given any credence by any scientist, such as the hypothesis that angry thunder deities are responsible for lighting and thunder, etc.) Allen_MacNeill

In #33 nullasalus points out that I have not ruled out the "design" hypothesis "on principle". That is correct; I do not rule out "design" as an alternative hypothesis. Indeed, if one is to do science correctly (according to the generally accepted principles worked out by scientists over the past few centuries), then one needs an alternative hypothesis with which to contrast one's own hypothesis. In this sense, the design (i.e.. teleological) hypothesis serves as the null hypothesis for the evolution (i.e. non-teleological) hypothesis. This is a perfectly valid procedure, and is in fact the procedure that Darwin himself followed in several chapters of the Origin of Species. What we are seeking, in other words, is to distinguish which of the possible hypotheses is most consistent with the empirical data available. And, if both hypotheses are possible, then we must take the further step of determining which of the possible hypotheses requires the smallest number of a priori assumptions (i.e. we apply Occam's Razor). Finally, we look to see if there are any internal contradictions between the various conditions that must be met for the various hypotheses, and settle on that hypothesis that: • shows the closest fit to the empirical data available, • requires the fewest a priori assumptions, and • has the fewest internal contradictions between a priori assumptions and inferred implications (ideally none). I believe that, given the foregoing, the non-teleological hypothesis is more reliable, for the reasons I have laid out in comment #28. To be specific, the teleological hypothesis requires the following assumptions: • that non-coding DNA be inserted in the genomes of all eukaryotes "in order to" make non-coding DNA available for co-option as light pipes in the retinas of nocturnal mice • that all of the mechanisms by which non-coding DNA is produced and inserted into the genomes of eukaryotes must be created and utilized "in order to" make non-coding DNA available for co-option as light pipes in the retinas of nocturnal mice • that all of the various eukaryotic chromosome assembly, replication, division, and segregation mechanisms must have been created and utilized "in order to" make non-coding DNA available for co-option as light pipes in the retinas of nocturnal mice und so weiter (see comment #28)... Furthermore, the example of the cephalopod retina clearly indicates that the arrangement of the non-coding DNA in the nuclei of the bipolar and retinal ganglion cells of eukaryotes is not a prerequisite for the optimization of light-gathering in low-light environments. One can (indeed, one must) multiply virtually to infinity the necessary conditions for the design hypothesis for it to be fully consistent with the empirical data. By contrast, the evolutionary hypothesis (i.e. that non-coding DNA was co-opted by natural selection in the optimization of light-gathering in low-light environments. Furthermore, the evolutionary explanation avoids the contradiction inherent in the observation that the retinas of cephalopods are not optimized for light-gathering in the same way. Ergo, I believe that my evaluation that the design hypothesis in this case "strains credulity" in that it requires an almost infinite set of preconditions, and necessarily includes a contradiction in its required preconditions. Allen_MacNeill

Mr PaV, Squid eyes in a mouse would be the kind of 'rabbit in the Cambrian" evidence that evolutionists say they could not ignore. Vertebrates the only phylum to experience significant evolution?? But we are still fishes! :) Seriously, all land invading phyla have members that have changed radically to adapt to new environments. We happen to be the beneficiaries of an intelligently designed meteor that hit the Earth 65 million years ago. Without the meteor, we would still be mice, and some intelligent dinosaur would be thinking self important thoughts about how the Intelligent Designosaur had fashioned the universe for his benefit. ;) Nakashima

Mr DATCG, When I said 'development', I meant development of the individual, the mouse embryo, not the evolutionary development of the mouse species. The inversion I mentioned is the inversion of euchromatin and heterochromatin in the rod nucleus, not the inversion of the cell layers of the retina. Yes, cave fish are probably pretty young species. They have to be younger than the cave they live in! But the examples I was giving stretch across the entire mammal lineage of hundreds of millions of years, plenty of time for color vision to decay. Nakashima

Allen: in passum.... Suppose that the Designer decided that the vertebrate eye was, indeed, not well-equiped for low-light situations. He decides he has made a mistake. Now, to correct this mistake, he follows the pattern of the cephalapod eye in the case of night-vision animals. Now, the Designer doesn't normally like to tinker with his Design, but is willing to make an exception here, and so he directly intervenes to bring about a "invertebrate eye" within a line of vertebrates. How would evolutionists react? Would they talk about homology? Would they say: "See. This could only have happened through NS since this is obviously an unguided process"? But, of course, we now have here a case of "special creation"---just the thing that NS inveighs against. I hope you appreciate the point I'm attempting to make. As to any suppossed 'inferiority' of design, I think vjtorley's post above [34] (excellent post, BTW) nicely puts things into perspective (no pun intended). Finally, isn't it the case that the only phylum that experience significant 'evolution' is the vertebrate phylum. IOW, squids don't become dinosaurs, whereas fishes become birds and humans---i.e., they have a long way to go by way of development. Is it then possible that the Designer rejected the invertebrate eye because of future functional needs? If so, then this is truly teleology at work. The point here is that UNLESS the invertebrate eye can be shown to be functionally superior to the vertebrate eye, then the kinds of teleological arguments you've made don't really hold water. Or perhaps I'm not seeing all this correctly (pun intended). PaV

Before the National Center for Darwinian Education started coaching scientists to modify their language, the physics text book I used at a public university included the following passage:

The eye is an extremely complex part of the body, and because of its complexity, certain defects often arise that can cause impairment of vision. In these cases, external aids, such as eyeglasses, are often used. In this section we shall describe the parts of the eye, their purpose, and some of the corrections that can be made when the eye does not function properly. You will find that the eye has much in common with the camera. Like the camera, a normal eye focuses light and produces a sharp image. However, the mechanisms by which the eye controls the amount of light admitted and adjusts itself to produce correctly focused images are far more complex, intricate, and effective than those in the most sophisticated camera. In all respects, the eye is an architectural wonder.(Serway et. al 1986 p. 386) [emphasis added]

I just hope Serway et. al don't get Sternberged by the NCSE-mafia, now that I point this Darwinian heresy out. William Wallace

Allen, Your sarcasm makes it more clear to me. I see large bluffs, then in the end you couldn't help but still insult. I'm curious. These are serious questions. How long do you think it will be before humans design eyes? And when they actually accomplish the engineering feat of designing human eyes, do you think that the engineers might learn why the inverted eye is reasonable? Do you not see a remote possibility there may be a reasonable design feature or compromise? Say, as opposed to the inferior verted eye of the cephlapod(octopus or squid)? Could it possibly be in the design process, engineers discover certain tradeoffs that must be made for overall functional design considerations? Again, for example, as a coolant of heat, or color vision, clarity, air versus water, blood flow, sunlight, etc.? I don't pretend to have all the answers, especially in some evolutionary time frame. But I recognize the appearance of design is quite logical reality as well. What amazes me is how you teach with such great authority without ever having engineered one single eye yourself. I'm use to engineers that have actually designed complex systems speaking with authority. They know all the pitfalls, have great experience from past mistakes. But not one single atheist evolutionist has yet to create a single eye from scratch. Not even the simplest verted eye. And evidently, due to billions of years theory, they'll never be able to. Am I right? Yet design engineers will one day recreate the human eye. Question is only how fast will it happen in the future. At that time, we may all learn some very fascinating aspects about vision, imaging and component structures for the maintenance of human eyes from a very practical standpoint. I'm in awe of these nano-features in the eye. There are over 130 million photo receptors in the human eye, nano structures(see VJTorley's post links). But that is blah, blah to you? Maybe not, but it seems that way. When you have designed a better eye for humans, by all means, you can claim to be the grand designer poobah. :) Forget Nobel Prize, thats small fry. Remember though, the eye must not be inverted and must cool itself from the sun and heat. And your process must happen by accidental mechanisms, mutations, evo-devo, etc. I'm not sure how you do it without externalizing some components features like we find for the inverted eye. But you seem to have all the answers. I'm not a scientist, so maybe you're right. DATCG

22, Nakashima, Thanks for your reply. My statement maybe was not clear about natural selection for eyes of the mouse. There are 8 separate layers in the human retina. I'm making assumptions it is similar to the mouse for inversion purposes. If this assumption is wrong, please point it out. "I’m going to go out on a limb and say very few. It happens in only a very specific cell type, so you are at the end of the line in development." Hmmmm, why at the end of evolutionary development? Some other time maybe. Back to the post. Inversion leads to multiple changes regarding arrangements not only of photo cell receptors but of placement and networking of blood vessels and supply, not to mention other musculature features that must be retained or reorganized from back to front. "That means that what ever we are doing here doesn’t have to get undone in a lot of other places." Hmmm... maybe I'm talking apples to your oranges. Or, not understanding you. 8 or 10 Layers of Retina: Internal Limiting membrane 1) nerve fibre layer 2) ganglion cell layer 3) inner plexiform layer 4) inner nuclear layer 5) outer plexiform layer 6) outer nuclear layer External limiting membrane 7) rods and cones 8) retinal pigment epithelium(RPE) Below the RPE or Retina is the Choroid, the vascular layer that allows for high blood flow for cooling of excess heat. A simple inside/out process for the photo receptors is more than a simple switch or two it appears. Because it is not merely dependent upon what is best line of sight, but what is best overall function. There are tradeoffs made for overall optimal performance including cooling operations when increased light appears. In fact, the Choroid has highest blood flow of all tissues in the body, more than the kidney. Thus the placement forces tradeoffs in design techniques. For example, back to the cephlapod eye that Allen mentioned. Its verted eye is inferior to that of the human. It only needs to judge motion, is simplified, including only two neural components and does not include the Foveola. It is not exposed to extened daylight either. Thus the more complex inversted design is not required. "The essential difference is flipping inside and outside. That might be as simple as modifying one protein from having a slightly positve charge to a slightly negative one, or vice versa." Well, that is the intial switch that may set off a cascade of other developmental processes for other proteins and transcriptions. Or, it is at the end where all other functions must already be in place, right? Otherwise, the switch on/off is null and void. "How easy is it, really? We’ll have to find the sequence differences, and watch mouse eye tissues develop, and compare with other nocturnal vertebrates and all the rest of that sciency stuff. Sounds fun!" Indeed! Fun that all people and scientist can enjoy, including Design theorist! :) I agree there can be some "simple" initial switches. But they would not be simple without other information already available. That makes the case of design, not randomly emergent recreation, multiple times over on different isolated islands for example. Such separate cases make appearance of design arguments a more likely reality to me. That guidance has existed, however imperfect some may think it to be. I do not buy into LUCA anymore. Its possible, but current research is leading toward a plurality of trees, not just one. I think this makes it harder for a purely naturalistic evolution. Multiple tree patterns, instead of one gradual flow is in favor of seedings or design guidance systems. "Yes. For example, if an ancestral species was diurnal, but then tinkered itself into a nocturnal niche, then tinkered back into a diurnal niche, its time spent in the nocturnal niche might cause it to lose valuable traits such as color vision that are only useful in daylight." Thats many ifs, mights, tinkers and oughts is it not? We have a good example of Cave Fish that I mentioned above to Allen as part of known scientific research. "Telic, design foresight would be needed to preserve those modules. Otherwise, they would have to be reinvented at great cost upon returning to a daylight niche." I agree. With the Cave Fish experiments, they retained the proteins and so-called non-coding genes to fully replenish lost eyesight. By your example, telic design, foresight did preserve the modules clusters required to be switched back on for the Cave Fish, including the original switch. Stepping into evolutionary shoes, I'm guessing the argument made is the Cave Fish didn't have billions of years to lose all of the genetic information for eyes? Thanks Mr. Nakashima for taking my questions serious and with good responses. DATCG

Re the inverted retina: Dr. Jonathan Sarfati makes the telling point in an article at http://creation.com/index2.php?option=com_content&task=view&id=5214&pop=1&page=0 that vertebrate eyes, for all their alleged defects, see better than invertebrate eyes:

Interestingly, anyone with excellent eyesight is said to have 'eyes like a hawk', which are 'backwardly wired', not 'eyes like a squid'.

Sarfati provides supporting documentation in footnotes 5 and 6 of his article:

5. Squid eyes are really a 'compound eye with a single lens', and its structure 'is much simpler than in the vertebrate eye'. Budelmann, B.U., Cephalopod sense organs, nerves and brain, 1994. In Portner, H.O., O'Dor, R.J. and Macmillan, D.L., ed., Physiology of cephalopod molluscs: lifestyle and performance adaptations, Gordon and Breach, Basel, Switzerland, p. 15, 1994. 6. Squid eyes are said to merely 'approach some of the lower vertebrate eyes in efficiency.' Mollusks, Encyclopædia Britannica 24:296–322, 15th ed., 1992; quote on p. 321.

In a similar vein, an article entitled Inverted Human Eye A Poor Design? by Dr. Jerry Bergman points out:

Most verted eye types are very simple, although a few types, such as the cephalopod eye (squids and octopus), are almost as complex as the vertebrate eye. Verted eyes tend to be functionally inferior, a conclusion usually determined by measuring performance in response to visual stimuli. Even the better verted eyes are still "overall quite inferior to the vertebrate eye."

Another point which has been overlooked is that vertebrates aren't the only animals that possess inverted retinas. Flatworms do too. (See Richard Dawkins, Climbing Mount Improbable, New York: W. W. Norton, 1996, 170.) Scientific critics of design theory should be able to offer a testable theory as to why both flatworms and vertebrates have inverted retinas. And what is Dr. Richard Dawkins' explanation for why vertebrates have inverted retinas?

I don't know the exact explanation for this strange state of affairs. The relevant period of evolution is so long ago. (Dawkins, R., 1986. The Blind Watchmaker: Why the evidence of evolution reveals a universe without design. W.W. Norton and Company, New York, p. 93.)

Some explanation! Lastly, an article entitled Living optical fibres found in the eye in "The Register" (1 May 2007) comments that the recent discovery that the vertebrate eye contains Muller cells, which work almost exactly like a fibre optic plate, could have useful technical applications for human designers:

The discovery doesn't have any direct medical applications, but it could pave the way for dramatic improvements in various pieces of sensing equipment.... If the technique could be replicated with optical plates, it could mean engineers would be able to fit more into delicate sensors. "They could include lots of other things - computing elements for example," [researcher Andreas Reichenbach] adds.

I would venture to say that any structure found in nature which gives human engineers some new ideas for improving their designs is a strong prima facie candidate for having been designed itself. Other links for those who are interested in chasing up the debate on the vertebrate eye: http://www.arn.org/docs/odesign/od192/invertedretina192.htm The Inverted Retina: Maladaptation or Pre-adaptation? by Michael J. Denton Denton vs. Squid; the eye as suboptimal design by Dr. Ian Musgrave (a reply to Denton). Is our 'inverted' retina really 'bad design'? by Dr. Peter V. Gurney. An eye for creation (an interview with eye-disease researcher Dr George Marshall, University of Glasgow, Scotland). The Not-So-Intelligent-Design of the Human Eye by Steven Novella. (A reply to George Marshall.) Novella claims that a top-down Designer could have made a better design:

For example, the rods and cones could have been designed so that the photoreceptor discs are produced at the top (meaning the layer closest to the direction of light), with older ones moving backward toward the bottom of the cells where they are absorbed. Below this absorption layer could be the blood vessels and the axons from the rods and cones could also leave from the bottom of the rods and cones through this opaque absorption layer (the RPE).

Inverted Human Eye a Poor Design? by Dr. Jerry Bergman. Bergman argues at length that alternative designs would not work:

A major concern, when critiquing the existing vertebrate retina design, involves speculations on the quality of vision that would result from another design. If the retina were reversed, the RPE or its analog and its cellular support system would have to be placed either in front of the photoreceptors or on their side. These approaches are clearly inferior to the existing vertebrate system that produces superior sight for terrestrial animals. If located in front of the retina, depending on how transparent those cells were, this design could prevent most light from reaching the photoreceptors. If the RPE were located on each side of the rods and cones, as in the cephalopods, primarily only the front of the sensory cells would be able to respond to light. Prince even claims the cephalopods side design "is protective and shields the receptors from excess light." Opaque wastes would accumulate in the path of light, and nutrients would have to be plentiful, thereby further diminishing the amount of light reaching the photoreceptors. Surrounding each photoreceptor RPE retina cell also requires increasing the space between the photoreceptors, further decreasing the amount of light able to strike the photoreceptors, consequently lowering vision resolution.

The Evolution of the Human Eye by Sean Pitman. Scientific article: Muller cells are living optical fibers in the vertebrate retina by Kristian Franze, Jens Grosche, Serguei N. Skatchkov, Stefan Schinkinger, Christian Foja, Detlev Schild, Ortrud Uckermann, Kort Travis, Andreas Reichenbach and Jochen Guck. In PNAS May 15, 2007 vol. 104 no. 20 8287-8292. vjtorley

Allen_MacNeill, Some comments. Definition 2: All non-teleological explanations can be reduced to a sentence that includes the phrase “as a result of”, but do not include the phrase “in order to”. A "non-teleological" explanation is not the same as an explanation that rules out or excludes teleology. We can give "non-teleological" explanations of devices which are obviously designed, event(s) which clearly have intention at work within them by any reasonable standard, or otherwise obviously have teleology of some form at work in them. Not that you were saying otherwise. But it does mean that your list is leaving out a third option: Explanations that utterly rule out teleology. Not 'rule them out as necessary for the strictly limited scientific investigation' but 'rule them out as incorrect and actually void'. Include that third option, and it will look strained and ridiculous compared to the second as well, filled with "by sheer luck" and similar appeals. What that means is... So, which of the two hypotheses - the ID hypothesis or the evolutionary hypothesis - is supposed to be the one that “strains credulity”? ..Is the incorrect question to ask. Everything that makes up the 'evolutionary hypothesis', if it excludes extraneous metaphysics and sticks entirely to the science (and what's more, the known and demonstrated science) can be subsumed under the ID hypothesis (and possibly under the no-ID hypothesis as well.) Indeed, Sternberg here is launching a criticism of that no-ID hypothesis by looking at the data itself in this case, not denying it. Another problem. The outcome of this “natural experiment” is very clear: such an arrangement is not necessary, ergo the Intelligent Designer didn’t need to do any of the things listed in the long list of interventions in comment #28 “in order to” enhance the night vision of some little rodents. Indeed, except for setting the stage for the process of evolution by natural selection (which, once set up, would need no further intervention), the Intelligent Designer didn’t need to do anything to produce night vision in rodents, or any other biological object or process for that matter. The problem is, this statement leaves science aside and rushes full bore into philosophy and metaphysics. I happen to believe that when Sternberg starts to look at junk DNA and declares that he sees design at work, he's into the same realm - I'm the outlier around here. But have a look at what you're doing. If there's a designer, certainly a designer capable of setting up such rules (and then some), you can have no idea what said designer would or wouldn't need to do in order to achieve goals that you are or aren't sure are desired. You're in the dark as to the intentions of the designer, whether a given goal is an end in and of itself, a part of a grander goal, or otherwise. At most, all you can comment on is what results experiments tend to yield, or hypothesize about what pathways and events actually occurred in the past (and of course, gather evidence in favor or against said hypotheses). You can't rule out or in intention of what actually happened, you can't rule out or in whether those events were facilitated by a designer or not. So when you say things like.. The whole point, in other words, is that any kind of design (good, bad, or indifferent) is unnecessary for an evolutionary explanation of the various characteristics of living organisms, as far as we can tell via observation. ..Again, sayonara science, because you've left that realm behind you. Design is "unnecessary for an evolutionary explanation" metaphysically. Scientifically, that question is unknown and unimportant - that field leaves you able to examine nature without having to hypothesize unthinking, unpurposeful, mindless foundations of ultimate reality -or- omnipotent (or maximally potent) God, gods, or designers. If you're going to restrict science to a narrow topic - and I believe it's right to do so, for reasons of practicality - then restrict it. Don't just chase out all the unnecessary stipulations you dislike. Get rid of them all. nullasalus

Mr MacNeill, i am not sure your fact pattern is correct in Fact 8. You seem to have combined two separate issues that have been discussed on this thread. 1 - in the OP, the issue is the ability of the nucleus of the rod cell itself to help focus light, via an inversion of the normal density layers of euchromatin and heterochromatin 2 - in comment 12, Mr JGuy referenced a web page about Muller glial cells acting as light pipes to assist in the transmission of light with less distortion before arriving at the rod and cone cells. The light pipes and the DNA lensing are two separate adaptations to the inverted retina. Neither shows design, merely reaction to the historical contingency of growing our eyes out of our brain tissue in a peculiar way. Nakashima

PaV [26], email me and I can describe what I know. It really won't further the conversation about Sternberg's post, so I won't do it here. Go to the about tab at my home for email address. William Wallace

As for asserting that evolutionary biologists as a group "use 'bad' design as an argument against 'design'", I would have to conclude that any evolutionary biologist who did anything this dumb deserves to be made fun of. After all, "bad" design is still design, as is "sub-optimal design" or any other kind of "design". The whole point, in other words, is that any kind of design (good, bad, or indifferent) is unnecessary for an evolutionary explanation of the various characteristics of living organisms, as far as we can tell via observation. I have in the past politely asked ID supporters to suggest an experiment (using purely empirical methods) that would unambiguously distinguish between explanations incorporating "design" (i.e. teleological explanations) and explanations that do not incororate "design" (i.e. evolutionary explanations). In the case of Dr. Sternberg's hypothesis for the "design" of the eyes of some nocturnal mice "in order to" enhance their night vision, however, such an experiment has already been done in nature. The arrangement of the cephalopod eye is essentially a "control" for the arrangement of the vertebrate eye, testing whether the arrangement of the non-coding DNA in the nuclei of vertebrate bipolar and retinal ganglial cells is necessary for the enhancement of vision in low-light environments. The outcome of this "natural experiment" is very clear: such an arrangement is not necessary, ergo the Intelligent Designer didn't need to do any of the things listed in the long list of interventions in comment #28 "in order to" enhance the night vision of some little rodents. Indeed, except for setting the stage for the process of evolution by natural selection (which, once set up, would need no further intervention), the Intelligent Designer didn't need to do anything to produce night vision in rodents, or any other biological object or process for that matter. Allen_MacNeill

Sorry, that should have been comment #14 in the last paragraph (I forgot to change it from #XX to #14; it's Spiny Norman's fault...) Allen_MacNeill

Re Clive in #19: Mea culpa, I must have channeling Dinsdale's brother Doug when I posted comment #14. And now for something completely different (i.e. a sarcasm-free, "academic" presentation of the same argument): Let us first identify the "facts" (that is, the empirical observations): Fact 1: The majority of the eukaryotic genome consists of non-coding DNA sequences. Fact 2: The rod and cone cells of the vertebrate retina face inward, away from the source of light, which must pass through two layers of cells (the bipolar and retinal ganglial cells) before it reaches them. Fact 3: The inverted arrangement of the vertebrate retina is a consequence of its embryological development: the vertebrate retina forms from an outpocketing of the hollow embryonic cerebrum, in which the cell bodies of the cells that will become the bipolar and retinal ganglial cells face outward toward the surface of the cerebrum, while the cells with which they synapse (i.e. the cells that become the rod and cone cells) are underneath them (the "hollowness" of the embryonic cerebrum is important - see Inference # 2, below). Fact 4: The cells lining the hollow ventricles of the embryonic vertebrate cerebrum are ciliated cells. Fact 5: Cephalopods (i.e. octopi and squids) have eyes that are remarkably similar in structure to vertebrate eyes, with one very significant exception: Fact 6: The light receptor cells of the cephalopod retina face outward, toward the light, and therefore no light is blocked by the secondary cells of the cephalopod retina. Fact 7: The non-inverted arrangement of the cephalopod retina is also a consequence of its embryological development; to make a long story short, the neurons in the brains of cephalopods are arranged differently than the brains of vertebrates. Fact 8: The arrangement of the non-coding DNA in the bipolar and retinal ganglial cells of some (i.e. not all) clades of nocturnal mice focus light in a manner that is very similar to that of "light pipes" (i.e. cylinders with a high internal index of reflection). Fact 9: Both nocturnal mice and cephalopods live in low-light environments. Next, a few direct inferences from empirical observations: Inference 1: The photoreceptor regions of rod and cone cells (based on their embryological development and fine structure) are essentially highly modified cillia. Inference 2: The "inverted" arrangement of the vertebrate retina happens because when the embryonic cerebrum folds outward to form the retina (see Fact #3, above), the ciliated cells are necessarily on the inside of this evagination, facing inward, not outward (this doesn't happen in cephalopods). Next, a few definitions pertaining to teleological versus non-teleological explanations: Definition 1: All teleological explanations can be reduced to a sentence that includes the phrase "in order to". Definition 2: All non-teleological explanations can be reduced to a sentence that includes the phrase "as a result of", but do not include the phrase "in order to". Now, on to the core of the argument: The teleological explanation for the arrangement of the non-coding DNA in the bipolar and retinal ganglial cells of nocturnal mice, as made by Dr. Sternberg in the article quoted, is as follows: Teleological Hypothesis 1: Nocturnal mice have non-coding DNA in the nuclei of their bipolar and ganglion cells that is arranged the way it is in order to function as light pipes, thereby enhancing their ability to see in low-light levels. From this, ID supporters (including the poster of this thread) make the following inference: Design Inference 1: Telological Hypothesis 1 is evidence in favor of the hypothesis that all non-coding DNA exists "in order to" fulfill some specified function, determined by the Intelligent Designer (identity, characteristics, and motivations unspecified); that is, it has a purpose, intended by its Designer. From this, ID supporters derive the following design implication: Design Implication 1: The Intelligent Designer incorporated non-coding DNA into the genomes of all eukaryotes in order to have it function as light pipes in the bipolar and retinal ganglial cells of some clades of nocturnal mice. The non-teleological explanation for the arrangement of the non-coding DNA in the bipolar and retinal ganglial cells of nocturnal mice is as follows: Non-Teleological Hypothesis 1: Nocturnal mice that have non-coding DNA in the nuclei of their bipolar and ganglion cells that is arranged the way it is as a result of natural selection: those mice in which the non-coding DNA in the nuclei of their bipolar and ganglion cells that is arranged the way it is survived and reproduced more often than mice in which it was arrangement in some other way. From this, evolutionary biologists make the following inference: The arrangement of the non-coding DNA in the nuclei of the bipolar and ganglion cells of some nocturnal mice is an evolutionary exaptation that evolved by natural selection. From this, evolutionary biologists derive the following evolutionary implication: Evolutionary Implication 1: The assumption that an Intelligent Designer incorporated non-coding DNA into the genomes of all eukaryotes in order to have it function as light pipes in the bipolar and retinal ganglial cells of some clades of nocturnal mice is unecessary. Here are some other implications that if the Design Inferences and Implications listed above are warranted: Design Implication 2: Since it is possible for retinas to be arranged "the right way out" (see Fact #6, above), then having retinas that are arranged "inverted" is not necessary for the improvement of vision in low light (see Fact #9, above) Design Implication 3: Therefore, the Intelligent Designer must have had some other purpose in mind for the "inverted" arrangement of the vertebrate retina. Design Implication 4: Since the existence of non-coding DNA is a necessary prerequisite for its rearrangement into "light pipes" in the nuclei of the bipolar and retinal ganglial cells of some nocturnal mice, then the Intelligent Designer must have had this purpose in mind when He inserted the non-coding DNA into the genomes of all eukaryotes (including, of course cephalopods, which (oddly enough) don't need it to enhance their vision in low-light environments. Design Implication 5: Since some non-coding DNA sequences are the result of "skip-duplication" of repeated sequences (as in ALU sequences), while other non-coding DNA sequences are the result of transposon duplication/insertions, retroviral cDNA insertions, and RNA retroposition via reverse transcriptases (among other processes), the mechanisms for all of these processes must be considered to have contributed to the ultimate purpose of enhancing the night vision of some nocturnal rodents. Ergo, the Intelligent Designer created these as well, "in order to" bring about such enhanced night vision. Design Implication 6: The mechanisms of eukaryotic mitosis are intimately and necessarily related to the organization of eukaryotic DNA. Ergo, the Intelligent Designer had to also intervene in the origin and evolution of this ubiquitous mechanism of eukaryotic cell reproduction "in order to" ensure that such mechanisms work in such a way as to distribute the non-coding sequences so as to ensure that the night vision of some rodents will, in the fullness of time, be enhanced by the rearrangement of that non-coding DNA. Design Implication 7: Since sexual reproduction in eukaryotes is tied to meiosis, and meiosis uses the same cellular structures and functions as mitosis, then one must assume that meiosis (and therefore virtually all forms of eukaryotic sexual reproduction) are somehow part of the "grand design", the end product of which is enhanced night vision in a few rodents. Design Implication 8: DNA "editing" and repair mechanisms (mediated by dozens, possibly hundreds of different, inter-related enzymes) are essential for the reliable replication of DNA in eukaryotes. This necessarily includes the accurate replication of non-coding sequences in eukaryotes. Ergo, all of these mechanisms are also necessarily somehow part of the "grand design", the end product of which is enhanced night vision in a few rodents. Design Implication 9: The gradual decline in DNA "editing" and repair is strongly implicated in the process of aging in eukaryotes, especially animals. This gradual decline is a necessary consequence of operation of these mechanisms, which means that aging (including the aging of all humans) is necessarily somehow part of the "grand design", the end product of which is enhanced night vision in a few rodents. etc., ad infinitum The point? The soi-dassant "design inference" cited by Dr. Sternberg for the purposeful arrangement of the non-coding DNA in the nuclei of the bipolor and retinal ganglial cells of a few species of nocturnal mice necessarily requires a virtually infinite set of associated assumptions, inferences, and implications, many of them so profoundly counterintuitive as to strike all but the most dedicated ID supporter as absurd. There; that's another way to say the same thing that I said in comment #xx. Granted it's less fun this way, but the content is the same. So, which of the two hypotheses - the ID hypothesis or the evolutionary hypothesis - is supposed to be the one that "strains credulity"? Dinsdale... Dinsdale... Allen_MacNeill

Allen McNeil [14]:

Let me see if I get this straight: the Intelligent Designer put all that non-coding DNA into the genomes of every eukaryote in order to make it possible for a few restricted clades of nocturnal mice to be able to see better in the dark, right?

etc...... Allen, why don't you ask how many at UD believe in the "special creation" of species? If the Designer employs 'common descent' in his design of organisms, then this places constraints on what can be done, and not done. My own presumption about the placement of blood vessels in front of the retina is that it has to do with 'sweeping away' the by-products of the chemical reactions involved in sight. IOW, for keen sight, numerous rods and cones are needed, and they need to 'flash' (remember Frick's Flicker Rate?) more quickly; all of this would lead to greater amounts of reaction products. (Squid live in a watery domain, and probably don't have the same needs.)This is just a supposition. If I'm correct, then we can view the focusing of the mouse nuclei as a simple adaptation for 'night-vision'. IOW, the jury is still not out. It's ironic that I complain that the argument used against design is a theological one, and then you come back, in mocking style, with another theological argument. Again, very few people here would defend 'special creation'. In the meantime, are the Darwinists wrong again? Only you can answer that one for yourself. PaV

[7] William Wallace: Yes, you're correct in saying that BIOS is also a program. However, it is embedded, if I'm not in wrong (I'm not a computer geek!), into the motherboard. IOW, the BIOS is not on your hard drive. And when you 'boot-up' from your CD-ROM, the BIOS is presupposed. But, yes, mine wasn't an exact analogy. PaV

Clive:

find your rhetoric to be at a rather junior high level. I think you’re a large repository of information, but a rather small shack of actual argument. I’m baffled that you teach at any college, to be honest. I hope you only present information to the students, and not arguments.

Here we have the moderator himself, charged to discourage personalized comments, himself directly wielding insults from within the secure confines of his moderation box. Go figure. Diffaxial

Mr DATCG, The inverted retina is a trait of all vertebrates. Even fish. Vertebrates evolved in the sea. Their inverted retinas evolved in the sea, before the transition to land. Next to the cephalopods. It doesn't make sense to argue that the inverted retina is better for vision in the air, when vertebrates began in the water. Nakashima

Allen, Is this what accounts for your scientific rebuttal of Sternberg? Or is this the result of reading to many post and comments from angry, bitter atheist bloggers like Pharnygula's PZ Meyers? A blog you link to. Whose self-description is "Evolution, development, and random biological ejaculations from a godless liberal..." Well isn't that special, says the Church Lady? Spoken like a rebellious teenager of arrested development. Great stuff for James Dean followers on the road to oblivion. LOL... Seriously though, usually your comments are more sincere Allen. BTW, are you stating Sternberg is a converted Christian? I thought he was an agnostic structural evolutionist. And this is the postion is he argues from, is it not? Sternberg posted observations to counter obvious problems with the outdated assumptions of a failed theoretical construct. A theory that has lead to false conclusions in the past(i.e. throw away vestigial organs and JunkDNA). In this case the inverted eye of the mouse is opened up for more discussion based upon recent research to rebut past arguments found wanting yet again by a failed model. He does not have to answer the strawman questions you ask with much handwaving about what God would or would not do. That is a theological question Allen. You know this is just a distraction on your part. The billions of years simply does not matter either. We've seen conservation of information of genes, where blind fish from caves rapidly reproduce in as little as one or two generations new offspring that can see with fully developed eyes. Why did fully functional eyes appear so fast Allen? Why didn't it take billions of years? Because the process and genetic information was always there. The transcription factors and information was always available just waiting upon the correct external stimuli. He rebutted accurately the sub-optimal position of past speculation based upon new research. Why don't you rebut his actual arguments? As to your only genuine argument - cephalapods, they live under water. Readers please see... http://en.wikipedia.org/wiki/Cephalopod Doesn't that cause you to ask at least one question? I'd ask about the environmental differences. Does the diffraction of light through water allow for the retina of cephlapods to be designed as they are versus inverted retina of land mamals? Why? Can it be the need for more direct access due to refraction? Or maybe that the water protects the eye from excess heat? Then is this optimal process for underwater life? Whereas, out of water, on land creatures must deal with heat from the sun directly, not diffracted or cooled by water. Stop making this a God issue and start thinking of why something may be designed differently for other reasons. At least try to step in the shoes of a Design theorist instead of attacking Christian theology which has nothing to do with this post. Design can be by the "little green men" that Richard Dawkins or SETI speculates may have seeded the earth. The inversion of a rodent eye or human eye can have to do with protection from the light spectrum of the sun. Most of your arguments OTOH is more of a theological argument Allen. That a Designer would not design an eye like this. But how do you know? Why not make the evolutionary case scientifically against Sternberg's observations? And stay away from PZ Meyers type ridicule and obfuscation? DATCG

Mr DATCG, Next, how many gradual steps by natural selection are required? I'm going to go out on a limb and say very few. It happens in only a very specific cell type, so you are at the end of the line in development. That means that what ever we are doing here doesn't have to get undone in a lot of other places. The essential difference is flipping inside and outside. That might be as simple as modifying one protein from having a slightly positve charge to a slightly negative one, or vice versa. How easy is it, really? We'll have to find the sequence differences, and watch mouse eye tissues develop, and compare with other nocturnal vertebrates and all the rest of that sciency stuff. Sounds fun! Any theory of blind tinkering cannot account for saving any valid core process or data and is utterly unpredictable since inherant to the blind process is non-determination of stability or stasis. Yes. For example, if an ancestral species was diurnal, but then tinkered itself into a nocturnal niche, then tinkered back into a diurnal niche, its time spent in the nocturnal niche might cause it to lose valuable traits such as color vision that are only useful in daylight. Telic, design foresight would be needed to preserve those modules. Otherwise, they would have to be reinvented at great cost upon returning to a daylight niche. Well, did that ever happen? Is the telic design evidence waiting to be found? Perhaps it happened in a special species that the designer cared about more than mice. Actually, no. We privileged humans had an ancestor with tri-chromatic, perhaps even tetra-chomatic vision (like birds). We lost it, probably with a shift to night time living to avoid all those dinosaurs cluttering the planet. Dinos go boom, we take over. Most mammals are still stuck with poor color vision. primates have rebuilt tri-chromic color vision in a variety of ways, and the human way isn't very good. The fairy tale recovery of trichromaticity (old world primate duplication of LWS) is hardly an unmitigated success story. Humans have lost 10 of the 14 ciliary and rhabdomeric opsins present from lamprey to amniote, not to mention oil droplets that refine color vision. The advent of the MWS gene duplicate represents a minor partial recovery of color vision capabilities, though not nearly to that still enjoyed by birds and lizards. However this highly unstable locus experiences chronic non-homologous recombination mishaps, gene conversion erasing critical spectral differences, chimeric single genes, bizarre tandem arrays, leading to dichromatic color vision in perhaps 15% of the population. The locus cannot stabilize itself by translocating away the gene duplication because such an event would not bring along the essential control region, which is tethered upstream to the primary LWS gene. The initial duplication and continuing instability may be driven by flanking Alu units. Recent selective forces acting on the region are difficult to disambiguate from gene conversion homogenization. Howler monkeys independently duplicated LWS and importantly also its LCR control region, perhaps avoiding problems that have plagued anthropoid primates for 35 million years. New world monkeys exhibit a different form of partial recovery (in females) utilizing spectrally significant coding polymorphisms of a single X-linked LWS locus and random X inactivation. So howler monkeys have done a better job than humans, avoiding problems of color blindness. This, my friend, is tinkering. Nakashima

OK, my reading of this goes along these lines: 1. Evolutionists pronounce noncoding DNA is 'junk'/nonfunctional/remnants of evolution. ID proponents argue that it most probably has a function. 2. Another in an increasingly long line of studies shows a case of noncoding DNA having a particular function, in this case for mice. 3. Although the ID prediction is the one supported by this study, the evolutionists claim the evidence supports the 'tinkerbell' of evolution, or is only needed because of supposed bad design. Seems a tad like desparation/shifting of the goalposts. saywhatyouwill

Allen_MacNeill (17) A significant minority of us IDers have looked at the evidence for chimp/human common ancestry and found it to be strong. While I am convinced that some human mutations (such as the HAR1F) are well beyond the reasonable scope of modern evolutionary theory. bFast

Allen, "Sorry, I forgot: the Intelligent Designer works in mysterious ways, and always covers His tracks so that there is never a scrap of empirical evidence that can unambiguously reveal His intervention in nature. After all, if He did, the rest of us would eventually figure out that He cared about some nocturnal mice so much that He arranged the last few billion years of evolution of the eukaryotic genome just for them. My bad." I find your rhetoric to be at a rather junior high level. I think you're a large repository of information, but a rather small shack of actual argument. I'm baffled that you teach at any college, to be honest. I hope you only present information to the students, and not arguments. Clive Hayden

Sorry, I forgot: the Intelligent Designer works in mysterious ways, and always covers His tracks so that there is never a scrap of empirical evidence that can unambiguously reveal His intervention in nature. After all, if He did, the rest of us would eventually figure out that He cared about some nocturnal mice so much that He arranged the last few billion years of evolution of the eukaryotic genome just for them. My bad. Allen_MacNeill

uoflcard in #11: Based on this comment, it is clear that you accept the hypothesis that humans evolved from a simian ancestor, otherwise your comment would make no sense whatsoever. How refreshing! Have you checked out what your fellow ID supporters think about this? Allen_MacNeill

And, while we're at it, stephenB (I know you're out there), were the biologists who discovered the inversion of the vertebrate retina and the cooption of for light pipes in some mice motivated to do so by their Christian convictions that God (aka the Intelligent Designer) must have done something just like this for His favorite clade of mammals? Allen_MacNeill

Just out of curiosity, does anyone here want to hazard a guess as to why comparative anatomists declared that the vertebrate retina was "inverted", and how it probably got that way? After all, the retinas of cephalopods, are strikingly similar, except that their retinas aren't inverted. Once again, was this all part of the Grand Plan to make the world a better place for those cute little rodents? Just curious... Allen_MacNeill

Let me see if I get this straight: the Intelligent Designer put all that non-coding DNA into the genomes of every eukaryote in order to make it possible for a few restricted clades of nocturnal mice to be able to see better in the dark, right? Or, the Intelligent Designer put all of that non-coding DNA in the genomes of every eukaryote in order to make it possible for it to eventually be activated as regulatory regions in some eukaryotes (and differently in each major clade), right? And the Intelligent Designer did this by designing DNA polymerase billions of years ago so that it would "skip-duplicate" randomly when it hits certain repeated nucleotide sequences (such as those in the ALU regions of the eukaryote genome), thereby making it possible for a few restricted clades of nocturnal mice a few billion years later to be able to see better in the dark, right? And the Intelligent Designer also crafted some of the non-coding sequences to look exactly like degenerate transposon sequences and retroviral cDNA sequences and randomly retrotransposed RNA sequences, so that at some point He (of course the Intelligent Designer can't possibly be a She; after all, that would mean He has a Vulva, not a Penis)...anyway, so that He could eventually make those sequences work as "light pipes" for a few restricted clades of mice, right? J.B.S. Haldane got it wrong: the Intelligent Designer doesn't have an inordinate fondness for beetles, He has crafted the vast majority of the eukaryotic genome to benefit those little rodents. Holy Mice Eyes, Batman! (Wait, those would be Fledermice, wouldn't they, and the Intelligent Designer crafted the pinnae of mammals so that, in the fullness of time they could be modified into wave-guides for ultrasound, right?) At what point does one stop and ask if all this teleology run wild makes any kind of realistic sense...unless, of course, one is an ID supporter like Richard Sternberg, in which case every single characteristic of every single living organism has been expressly created "in order to" do something or other, regardless of who benefits from such intervention and regardless of whether there is even the tiniest scrap of empirical evidence that this might, indeed, the case. And you criticize evolutionary biologists for practicing "faith-based" science... Allen_MacNeill

Mr JGuy, The inversion applies to all vertebrates, humans, mice, chickens, fish, etc. After having gotten off to a bad start a few hundred million years ago, it is not surprizing that the vertebrate eye has picked up a number of helpful adaptations which it wouldn't need at all if not for the fact that it was inverted in the first place. Turning glial nerves into light pipes is clever tinkering, but unecessary if the glial cells weren't out front getting in the way. Eyes, like flight, have been invented many times. Each time using the cell histories available. Nakashima

Also, I think this topic is a good time to remind everyone of the bad design of the "inverted" human retina that Dawkins touted in some of his writings. Many years later (relatively recently), it wase discovered that there were cells acting as perfect fiber optics transmiting light through the layers of the retina to the photosenesitive cells. Reminiscent of what Sternberg is arguing of regarding mouse eyes. http://www.detectingdesign.com/humaneye.html#Optical Also, this reminds me of Walter ReMine's comments that roughly decalred that the half life of evolutionists latest & greatest evidences of evolution have a half life of about 15 years. Refuted arguments against the supposedly "bad design" of the human retina will be considered one of the classic examples. JGuy

Slightly OT, but interesting: Scientists Revive Dormant, HIV-Fighting Genes Interesting quote:

A group of scientists noticed that our simian ancestors expressed a protein called retrocyclin that essentially renders them immune to HIV. Hoping to find a way to introduce the same immunity to humans, the group discovered that we too had the same genetic ability to create retrocyclin, but that it was turned into junk DNA long ago for no discernable reason.

Whattaya know, our ancestors were "more fit" than us. And there is a very discernable reason, in light of ID or genetic entropy: neo-Darwinian evolution doesn't build proteins, it destroys them. Probably slowly over time, but it is inevitable that small, non-lethal mutations will build up in genes coding for proteins in an entire population, until the genes start to fail universally, not just in select individuals. uoflcard

If one could calculate the information content of the physical architecture of the cell (minus the DNA), and compare it to the staight forward information of human DNA (6 billion nucleotides?)... I suspect the total information content of the cell strucutre dwarfs the information capacity of DNA. That is, if you count the arrangement of molecules or atomic bonds between the two as a type of information. Unless DNA has some kind of "super duper" data compression scheme that hasn't been discovered yet. JGuy

Along the same lines I would really like to hear the evolutionists explain how the scapula of a quadriped animal (which has no body attachment via ligament) migrated from the left and right side of the rib cage to a position where both scapula are now on one side fo teh rib cage? How ddi this happen AND form a body attachement via ligament? The reason I ask is that when scapular dyskenisis occurs in my patients we see everything from impingement to rotator cuff tears to bicep tendon tears to labral fraying all because the position of the scapula isn't where it's suppose to be. It's seems to me that a body part or system would have to go from functional to dysfunctional before going back to functional again IF evolution were true. wagenweg

Nakashima, Not sure I understand all your statements. "What would confirm whether this tinkering was a design choice or a random improvement?" I would consider modularity, compression and shared data space overlapping, a design choice. Why? Because that is what we do in software design on hardware platforms. What we design today by intelligence we discovered in genetic transcription factors. I then ask, what would confirm it is random improvement period without broad speculation? The only thing so far the Darwinist have is "Time" and "Randomness" can produce anything. Anything remotely probable is thus possible. But, if that is true, then design is probable and inherant in their arguments of ramdom tinkering. They are not allowed to shut out intelligent tinkering based upon random mutation because intelligent foresight can allow for random variation based upon external stimuli as input. Next, how many gradual steps by natural selection are required? How many coordinated genes and transcription factors are involved for regulatory processes of such optimal development in this one area for the mouse? How many critical overlaps of data in genes are there that other phenotypic processes share? "This is a better 'evolution the blind tinkerer' story." I'm assuming that statement is sarcasm. But the point of the article is not to blow away the entire process of Darwinian theory. But to show evolutionist were wrong in their previous assumptions and blind tinkerer sub-optimal statements in regards to the mouse eye. In this particular case, Sternberg answered critics succinctly and rebutted accurately the wrong assumptions made by Darwinian materialist. Assumptions based upon the faulty logic of an outdated research methodology enshrined long ago a priori by a materialist-only approach. A now virtually dead theory except in high school textbooks. This dead theory gave rise to many false leads, wasted time and imaginary phylogentic trees based upon false assumptions. As a result, JUNK DNA is becoming, or has become another failed prediction by strict Darwinian materialist. How much critical time has been wasted on dead end predictions? As to your question on confirmation one way or the other. There's an interesting Nature Research Highlight out recently promoting Systems Genetics research on fruit flies I do not have access to the full paper. If someone does, I think it would be fascinating reading and supports the Design position vs the blind tinkerer story. Quotes from the highlight...

There was a high degree of correlation between the variably expressed transcripts. The authors were able to group these transcripts into 241 modules, with each module consisting of a separate cluster of highly interconnected genes." "The systems genetics approach used in this study is a powerful method for identifying novel candidate genes for complex traits and for determining the relationships between these genes. Notably, most of the candidate transcripts identified were unexpected based on previous mutational analyses of the traits.

a key bold point: "... previous mutational analyses of the traits" What failed in past mutational analyses? Could it be the failed Darwinian paradigm? Some quotes of the abstract from original research paper by Aryoles, et al: "Regressions of organismal phenotypes on transcript abundance implicate several hundred candidate genes that form modules of biologically meaningful correlated transcripts affecting each phenotype. Overlapping transcripts in modules associated with different traits provide insight into the molecular basis of pleiotropy between complex traits." For readers, from Wiki:

"'Pleiotropy' is the multiple effects of a single gene. In other words, it is when a single gene controls several phenotype traits. These traits may be seemingly unrelated."

Essentially, this is shared data space using the same data for different outcomes and regulations. Software programmers do this daily. There are core data that does not change and there is mixed fields that can vary dependent upon interaction with input. Random tinkering does not predict this. It predicts JUNK DNA. Design does predict this based upon forethought and knowledge of future events for variable responses and outcomes. Design also inhibits certain change to core processes due to recognizable limitations that lead to catostrophic failure rates. Natural Selection cannot think ahead. Design can. Design leads to a theory of Core Process Design network with designated overflow areas and interchangeable variation fields. Design also leads to highly compressed fields of shared space between other sub-routines, or program calls. Any theory of blind tinkering cannot account for saving any valid core process or data and is utterly unpredictable since inherant to the blind process is non-determination of stability or stasis. Blind tinkering cannot account for highly coordinated instructed programs to share modular data space either. Also, the article seems to account for larger leaps of funtional outcomes(variation) through organized clusters of modular, shared component space. This is favorable to a Design model instead of many small, gradual steps for a Darwinist model. It appears to weaken the gradualist model. If so, it then explains the fossil record for lack of transitionals and rapid appearances of highly complex life forms. I'm curious what Gil would think of this paper. DATCG

Not that I agree or disagree with SalGal, but small correction to Pav: BIOS is itself a program too. The rest of your analogy is a bit off, too, although I think your overall point may be valid despite this. William Wallace

hi jerry,

I have a question. Is Sternberg saying that the DNA in certain cells rearranges itself in the genome after the embryo starts to form.

No. What he is saying is, the DNA is arranged differently within the nucleus in nocturnal vs diurnal mammals. Dave Wisker

jerry: Sternberg is saying that the chromosomes---wherein, of course, the DNA lies---assumes certain shapes (the eucchromatin and the heterochromatin) AND assumes certain positions within the cell nucleus itself. The G-band and the R-band (associated w/"junk DNA") segregate differently, some going to the very center of the nucleus(chromocenters), and some to the very edge of the nuclear envelope. Thus there is a gap between the center and the edge through which the nucleus is ablt to 'focus' photons onto the edges of the rod cells. This discovery (having come sooner than I expected! validates the predictions of ID, which assumes efficiency and purpose to be elements of design. OTOH, evolutionists use the 'bad design' of the vertebrate eye to make an argument that the design hypothesis is foolish. And yet, ID predictions come true, and confound the argument put forth by evolutionists. What will be their reaction? "You see how clever NS is!" Darwinism---a theory that can never be disproved. As to what SalGal wrote, it is not 'science fiction'. The genetic code is exactly that: a code,'programmed' to produce certain molecules and to perform certain tasks. But it is a program which, like all 'programs' has to be 'run' by some kind of machinery. In this case, the machinery is the cell. In particular, if you built your own computer---motherboard, disk drives, memory, power supply, hard drive---unless there was a communication system that allowed these elements to interact, nothing would happen. In your everyday computer, it's called BIOS; that is, 'basic input output system'. The "BIOS" sets up a priority system (roughly speaking what we call the 'registry') for how these various components can, and should interact. Without the BIOS, you could never get your computer program onto your hard disk. Nothing would happen. Most computer users never even fiddle with the BIOS, but it's the backbone of the computer. SalGal's point is that this "BIOS", by necessity, must be located in the cell itself. If it weren't, then simply combining the DNA, as happens at fertilization, would provide for large amounts of information, but information that could not be processed and used. Her's is a perfectly valid point. The cell also happens to be the repositor of all of the 'hardware' that is needed to 'run a program'. Hence, when the proverbial question is asked: 'which came first, the chicken or the egg', the answer has to be the 'egg'. PaV

I have a question. Is Sternberg saying that the DNA in certain cells rearranges itself in the genome after the embryo starts to form. jerry

Hmmm, what would confirm whether this tinkering was a design choice or a random improvement? Dr Sternberg seems to be arguing "old PC as doorstop = design!" This is a better "evolution the blind tinkerer" story. I think he'd be better off arguing that the position of junk DNA in the normal nuclear architecture shows function as some kind of protection for the protein coding DNA. Nakashima

Is Sal Gal looking for a career as a science fiction writer? It looks like a whole lot of new theory is evolving. The DNA is the design of the cell " No, the cell actively operates upon the DNA, and a great deal of what the cell does is not specified in any sense by the DNA." Is it specified by the "Cell Fairy?" jerry

I believe that the notion that the DNA runs the cell is an unfortunate remnant of the neo-Darwinian paradigm. Every organism begins life as a functioning cell, and uses DNA in various ways. One of those ways is as a nonvolatile store of data. As a computer scientist, I cannot see a prokaryotic bud that has just separated from its parent as supplying a "bootstrap procedure" that gets the "genetic program" up and running. (And let's recall that prokaryotes account for most of the earth's biomass.) No, the cell actively operates upon the DNA, and a great deal of what the cell does is not specified in any sense by the DNA. The only sane evolutionary perspective is that relatively simple uses of DNA arose prior to the complex processes of transcription and translation we observe today. I speculate that some of the present functions of DNA predate storage of protein templates. I'm glad to learn that a multicellular eukaryote has evolved a remarkable use for DNA. The finding lends credence to the notion that there was a time when rudimentary organisms used DNA in ways that we cannot guess today. Sal Gal