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Richard Sternberg on “Junk” DNA

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Sternberg needs to write a book debunking junk DNA.

Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye
By Richard Sternberg

www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig

We often hear from Darwinians that the biological world is replete with examples of shoddy engineering, or, as they prefer to put it, bad design. One such case of really poor construction is the inverted retina of the vertebrate eye. As we all know, the retina of our eyes is configured all wrong because the cells that gather photons, the rod photoreceptors, are behind two other tissue layers. Light first strikes the ganglion cells and then passes by or through the bipolar cells before reaching the rod photoreceptors. Surely, a child could have arranged the system better — so they tell us.

The problem with this story of supposed unintelligent design is that it is long on anthropomorphisms and short on evidence. Consider nocturnal mammals. Night vision for, say, a mouse is no small feat. Light intensities during night can be a million times less than those of the day, so the rod cells must be optimized — yes, optimized — to capture even the few stray photons that strike them. Given the backwards organization of the mouse’s retina, how is this scavenging of light accomplished? Part of the solution is that the ganglion and bipolar cell layers are thinner in mammals that are nocturnal. But other optimizations must also occur. Enter the cell nucleus and “junk” DNA.

…[snip]…

Reporting in the journal Cell, Irina Solovei and coworkers have just discovered that, in contrast to the nucleus organization seen in ganglion and bipolar cells of the retina, a remarkable inversion of chromosome band localities occurs in the rod photoreceptors of mammals with night vision (Solovei I, Kreysing M, Lanctôt C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. “Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution.” Cell 137(2): 356-368).

…[snip]…

Why the elaborate repositioning of so much “junk” DNA in the rod cells of nocturnal mammals? The answer is optics. A central cluster of chromocenters surrounded by a layer of LINE-dense heterochromatin enables the nucleus to be a converging lens for photons, so that the latter can pass without hindrance to the rod outer segments that sense light. In other words, the genome regions with the highest refractive index — undoubtedly enhanced by the proteins bound to the repetitive DNA — are concentrated in the interior, followed by the sequences with the next highest level of refractivity, to prevent against the scattering of light. The nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light.

So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell — that the data only point to the lack of design and suboptimality — remind them of the rod cell nuclei of the humble mouse.

Comments
A podcast on the original subject of Sternberg's article - nuclear architecture in rod receptors of nocturnal animalsNakashima
May 6, 2009
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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
May 4, 2009
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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
May 4, 2009
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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
May 4, 2009
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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
May 3, 2009
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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
May 3, 2009
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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
May 3, 2009
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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
May 2, 2009
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After "inverted eye", it should read: "might not be so much.... I left out the "not". Sorry.PaV
May 2, 2009
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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
May 2, 2009
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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
May 2, 2009
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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
May 2, 2009
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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
May 2, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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