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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
In other words, natural selection is not "weak". Rather, it is ultimately constrained by historical contingency. Weakness ? contingency does it?Allen_MacNeill
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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"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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
May 1, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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[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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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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
April 30, 2009
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