Tuesday, May 11, 2010

Why Ken Miller is Right About Our Backward Retina

In the steady-stream of “not junk after all” findings it was inevitable that our backward retina would be discovered to work quite well, thank you. But if you think it is another icon of evolution that has been shattered, think again. Evolutionary explanations of vision go back to Darwin, and they haven’t changed much in spite of our much improved understanding of how vision actually works. And now new findings that the inverted design of our retina isn’t as bad as it looks, while interesting, are not much more than a yawner for evolutionists.

Darwin’s view of vision

In Chapter six of Origins Darwin addressed what he saw as the chief difficulties with his new theory. A good example to begin with was the eye. “To suppose,” wrote Darwin, “that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.”

But Darwin then abruptly pivoted. Anticipating the twentieth century’s non intuitive findings such as quantum mechanics and chaos theory, Darwin’s justification for evolution was that science is not always intuitive. Does the earth really hurtle at breakneck speed around the stationary sun? Vox populi, vox Dei, advised the sage of Kent, cannot be trusted in science. The next pivot was even easier:

Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated; but I may remark that, as some of the lowest organisms, in which nerves cannot be detected, are capable of perceiving light, it does not seem impossible that certain sensitive elements in their sarcode should become aggregated and developed into nerves, endowed with this special sensibility.

It is incredible that such non scientific conjecture continues to be taken seriously by anyone today. This nineteenth century thought experiment was conveniently oblivious to the biochemistry underlying vision. Even the relatively simple third eye vision cascade dwarfs anything of which Darwin could have dreamt. And it shows no sign of having evolved.

As if sensing a problem Darwin employed a deeply metaphysical argument from one of his favorite authors, David Hume’s anthropomorphic warning:

It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrument, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. Further we must suppose that there is a power, represented by natural selection or the survival of the fittest, always intently watching each slight alteration in the transparent layers; and carefully preserving each which, under varied circumstances, in any way or in any degree, tends to produce a distincter image. We must suppose each new state of the instrument to be multiplied by the million; each to be preserved until a better one is produced, and then the old ones to be all destroyed. In living bodies, variation will cause the slight alterations, generation will multiply them almost infinitely, and natural selection will pick out with unerring skill each improvement. Let this process go on for millions of years; and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?

The Enlightenment supplied the gnosticism and Darwin supplied the just-so story. We must suppose “natural selection or the survival of the fittest” created the eye, our religion depends on it.

Dawkins and our backward retina

But Darwin didn’t have the best argument of all. What Darwin did not know was that our eye’s retina is a kluge—it is backwards. Over and over, as evolutionists such as Ernst Mayr and Elliott Sober have pointed out, Darwin argued that nature’s absurdities mandate evolution. The backward retina would have been a gem for Darwin. Needless to say when the inverted design was found, it became yet another metaphysical mandate for evolution. As Richard Dawkins has explained:

Like any nerve, the optic nerve is a trunk cable, a bundle of separate “insulated” wires, in this case about three million of them. Each of the three million wires leads from one cell in the retina to the brain. You can think of them as the wires leading from a bank of three million photocells (actually three million relay stations gathering information from an even larger number of photocells) to the computer that is to process the information in the brain. They are gathered together from all over the retina into a single bundle, which is the optic nerve for the eye.

Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate retinas. Each photocell is, in effect, wired in backwards, with its write sticking out on the side nearest the light. The wire has to travel over the surface of the retina, to a point where it dives through a hole in the retina (the so-called “blind spot”) to join the optic nerve. This means that the light , instead of being granted an unrestricted passage to the photocells, has to pass through a forest of connecting wires, presumably suffering at least some attenuation and distortion (actually probably not much but, still, it is the principle of the thing that would offend any tidy-minded engineer!).

This much celebrated inverted design has served as a canonical example of why design is false, and evolution true. It isn’t that the design is not complex (indeed it is). It is that the design is not right. No designer would have done it that way. Dawkins must admit that the attenuation and distortion may not be significant, but so what? It is “the principle of the thing.” The retina obviously is not intelligently designed. This is evolutionary metaphysics.

Not junk after all

Now that evolution has been safely established, new research is showing that this icon of dysteleology actually improves vision. As one report explained:

in 2007 researchers analyzing the retinas of guinea pigs reported that the glial cells which nourish and physically support the bed of neurons also act as optical fibers for the rods and cones. These Müller cells are funnel-shaped, with wide tops that cover the surface of the retina and a long slender body that guides light to the receptors below. … findings suggest that sending light via the Müller cells offers several advantages. ... This suggests the cells act as light filters, keeping images clear. … The researchers also found that light that had leaked out of one Müller cell was unlikely to be taken up by a neighbor, because the surrounding nerve cells help disperse it. What’s more, the intrinsic optical properties of Müller cells seemed to be tuned to visible light, leaking wavelengths outside and on the edges of the visible spectrum to a greater extent.

The cells also seem to help keep colors in focus. Just as light separates in a prism, the lenses in our eyes separate different colors, causing some frequencies to be out of focus at the retina. The simulations showed that Müller cells’ wide tops allow them to “collect” any separated colors and refocus them onto the same cone cell, ensuring that all the colors from an image are in focus.

“It suggests that light-coupling by Müller cells is a crucial event that contributes to vision as we know it,” says Kristian Franze, a neurophysicist at the University of Cambridge and co-author of the 2007 study.

Optical fibers, light filters, autofocus, light-coupling? Is the evolution of such design not in question? Is this another just-so story? Is this not absurd in the highest degree?

It isn’t right

Of course not. It may have a fancy function, but the design still isn’t right. It must have evolved. There remain the blind spot and the wires going off in the wrong direction. Whatever enhancements we discover to the retina are just that, enhancements. It surely could have been done better.

As evolutionist Ken Miller cautions, none of this means that the backwards retina itself helps us to see. Rather, it emphasizes the extent to which evolution has fixed the problem:

The shape, orientation and structure of the Müller cells help the retina to overcome one of the principal shortcomings of its inside-out wiring.

This is evolution. A genre rich in metaphysical pronouncements that otherwise are enshrined in scientific terminology. Miller isn't making any new claims. He is simply being consistent with the traditions of evolutionary thought to which he subscribes. Religion drives science and it matters.

40 comments:

  1. I'm so glad the evolutionists know what is right in designing biological systems and what isn't. Whewh.

    At some point, won't evolution "die the death of 1000 qualifications" as exemplified by another ad hoc explanation by Ken Miller?

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  2. It's not speculation to say we know it can be done better. Cephalopod eyes are also high-precision, color-sensing camera eyes. But they are built out of different tissues, and they don't have the wires sticking out the front, or any blind spot. Creationists always elide this crucial comparative point, basically because they have no answer to it.

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  3. Does the cephalopod eye work as well as the vertebrate eye? And maybe cephalopods have other equally complex ways to solve the problems?

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  4. Actually, from my reading, it's never been shown that cephalopods have the eyes you claim. In fact their eyes only "approach some of the lower vertebrate eyes in efficiency" (Mollusks, Encyclopædia Britannica 24:296-322, 15th ed., 1992; quote on p. 321.), and are probably color blind (Roger T. Hanlon, John B. Messenger. Cephalopod Behaviour. Cambridge University Press, Cambridge, New York, p 19, 1998).

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  5. Cornelius' argument here seems to be "It is complex, therefore it could not have evolved." Don't bother doing a phylogenetic analysis, or cladistic tree, or anything. Just say it's too complex.

    Of course much more is known about the evolution of eyes, particularly at the molecular level, but Cornelius wants you to think scientists know nothing.

    But, more on the molecular interactions later.

    As for invertebrate eyes, the eyes of the Mantis shrimp are far superior to ours; they can see infrared and ultraviolet and distinguish different components of linearly and circularly polarized light.

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  6. Diogenes said..."Don't bother doing a phylogenetic analysis, or cladistic tree, or anything. Just say it's too complex."

    Are all biologists this lazy? The approach of using a cladistic tree, phylogenetic analysis as evidence for Darwinian processes boils down to a fancy why of using pictures of rocks organized from very big to very small and claiming that to be proof of the mechanism that caused the big rock to be broken into smaller rocks. It actually says nothing of the mechanism that achieved this proposed change / evolution.

    You need to buckle up and give come scientific proof of the Darwinian mechanisms being responsible for any evolutionary progress. This was the challenge that William Lane Craig put to Francisco_J._Ayala in their debate about intelligent design. I would like to see you help prof. Ayala out because he only used your argument and had nothing to support the efficacy of Darwinian mechanisms.

    Good luck there...

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  7. "Religion drives science and it matters."

    In Ken Miller's case, Roman Catholicism!

    "No designer would have done it that way."

    And done it differently for the cephalopod.

    Darwin's original argument was simply that if a gradient exists, evolution will be able to follow it as selective pressures change populations. Dawkins et al. are arguing from dysteleology and comparative anatomy.

    The dysteleology continues at the molecular level. A broken opsin gene leaves most mammals color blind. What is the design just-so-story for this?

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  10. Once again, Cornelius clings to the erroneous position to which he has committed himself:


    It isn’t that the design is not complex (indeed it is). It is that the design is not right. No designer would have done it that way... The retina obviously is not intelligently designed. This is evolutionary metaphysics.


    The fact that the retina is backwards is indeed an apparent problem for the design hypothesis. It also makes sense when explained as a product of evolution. But that does not mean that evolution's explanation is BASED ON the failure of design to explain it.

    This is a wall Cornelius simply bangs his head against time and time again.

    At no point does the explanation provided by evolution boil down to 'well design can't explain it, therefore it must have been evolution'. Much as Cornelius and other Creationists/ID proponents might peddle this fallacy.

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  11. David vun Kannon said...
    "Darwin's original argument was simply that if a gradient exists, evolution will be able to follow it as selective pressures change populations."

    Are you telling me that you have proof of a gradient existing that "forced/nudged/pushed/coerced" the evolution of the eye, for that is what you imply by gradient... not so? Is this mechanism standing apart from "selective pressures" that allegedly also "forced/nudged/pushed/coerced" the evolution of the eye? I am asking because I can surely live with this kind of "forced/nudged/pushed/coerced" because it sounds much better that aimless random mutation.

    It is almost like saying the universe had the eye in mind all along, evolution just had to achieve the outcome.

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  12. Nothing can falsify the theory of evolution.

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  13. Ritchie: "This is a wall Cornelius simply bangs his head against time and time again."

    Are you really such a hopeless case Ritch?
    You never get it and if you continue to miss the point and skewer the logic you probably never will cause your mind is ALWAYS on hold.

    "The fact that the retina is backwards is indeed an apparent problem for the design hypothesis. It also makes sense when explained as a product of evolution."

    How can you possibly know something in nature is "wired backwards"?

    It isn't wired backwards - unless you've already assumed evolution AND presumed you know far more than you possibly can.

    You fail, as always, to admit the reality of Hunter's points on your "bad design = no design" BS
    -which contrary to your lame denial is still widely used by twit headed Darwieners since you used it yourself!!
    AND, you also fail to admit that claiming anything in nature is "wired backwards" is just plain arrogant presumption based on meager human understanding.

    You reason so poorly in this whole subject -worse, you can't even see that!

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  14. Evolutionists are helplessly lost in the logic department.

    Their own self-generated cognitive dissonance has crippled their brains from reasoning clearly.

    The logical fallacies of Darwinian thinking are right at the root hypothesis.

    They could even serve as classic samples of well defined easy to see logical fallacies - begging the question, undistributed middle, post hoc ergo propter hoc, Gambler's Fallacy, Slippery Slope, ...

    Sad, but true.
    Darwins OOS is full of such fallacious
    reasonings and so are the works of virtually all his fanatical disciples - like Ritch, dio, Rob, et al. the "debaters" that come here every day.

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  15. The point of Ken Miller's commentary, and the point of all
    "bad design" arguments is to point out that from the vantage
    point of design, all of biology is both wondrous and botched.
    The point being is that ID yields self-contradictory, and hence
    useless, pronouncements about biology. Indeed, ID is always about
    metaphysical pronouncements.

    Science, which is to say evolution, tells us
    about processes, not about metaphysics.

    -John

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  16. John Stockwell:

    ===
    ID is always about metaphysical pronouncements.
    ===

    Such as?

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  17. Blogs are not the best place for argumentation as I have observed over the years... but a great place for information!

    If could only count the times I have read exchanges like this:

    Evo proponent: "The eye is a flawed design and it is wired backwards."

    ID: "Actually new research on Muller cells suggest that the "backward wiring" actually helps filter light and color to make vision clearer."

    Evo: "Geez, you and your non-science metaphysics"

    ID: "???. Ummm... Where was the metaphysics?"

    Evo: "This doesn't mean evolution is not true. You guys have no proof and this in no way shows a designer."

    ID: "Umm... I thought we were talking about the backward design of the eye here - how did we get so sidetracked? And more importantly, how come you are ***avoiding*** the inital point and talkign about metaphysics, phylogenetic analysis, and that ID can't be tested? What say you about the eye!?!?! We can talk about the rest another time..."

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  18. I completely agree with "The Predestined Blog." The comments from the evolution camp are simply all over the map.

    For example, everything Diogenes said above is silly.

    Diogenes said:

    “Cornelius' argument here seems to be "It is complex, therefore it could not have evolved." Don't bother doing a phylogenetic analysis, or cladistic tree, or anything. Just say it's too complex.”

    Really? The *point* of this post is that the evolutionists ignore all new evidence that might contradict anything they already believe or have said in the past. Try to pay attention.

    Diogenes said:

    “Of course much more is known about the evolution of eyes, particularly at the molecular level, but Cornelius wants you to think scientists know nothing.”

    Really? Evolutionists “know” how the human eye actually evolved (not to mention other eyes that you have declared as superior to the human eye)? Something other than a “it *could* have happened this way” story? Please link to something that proves your point.

    Diogenes said:

    “As for invertebrate eyes, the eyes of the Mantis shrimp are far superior to ours; they can see infrared and ultraviolet and distinguish different components of linearly and circularly polarized light.”

    Really? Assuming the eye (and anything irreducibly complex) is the result of design, how would you (or anyone) have certainty regarding the designer’s intent? If the eye is the result of design, then your subjective declarations regarding what is superior is meaningless.

    Finally, crying about metaphysics on a post like this shows you aren’t paying attention. As has been said a million times: While ID may have metaphysical implications, those implications are outside the scope of ID. ID does not reach any metaphysical conclusions beyond the inference that biology shows evidence of design. Period. It could be little green men for all ID cares.

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  19. "The Predestined Blog "

    Ha! You wish that was the conversation. The ID advocate in your case comes off quite well. Most often I see comments like Hitch's above.

    In fact, the entire argument here is that evolutionary biology is based on Richard Dawkin's anti-design arguments. Hunter again and again conflated the response to creationism/design with the primary data supporting evolution.

    This is because engaging the primary data is impossible for and ID advocate. I'd love to see this blog use design detection to show us uncontroversial design, to test ID based hypothesis, and we could have a real, scientific debate. But, it is far easier to pick on a single example used by Richard Dawkins, who gets sucked into using anti-design arguments (not that he was wrong).

    But what is the point here? Yes, Dawkins famously made a counter-metaphysical claim that the eye appears undesigned, that it looks tied to its evolutionary past. No one ever claimed it was 'junk,' or non-functional.

    Now we find the 'wiring' helps focus light. Does this undo the overall scheme of the eye? Does it refute everything we know about eye evolution? No. It shows evolution has worked with what it has in producing clear color vision.

    Where is the ID argument?

    Some primary data to share:

    If we hypothesize common descent, we would predict the distinct modern Protostome and vertebrate systems should share some intermediate.

    Confirmed: "The visual cycle systems in ascidians, the closest living relatives of vertebrates, show an intermediate state between vertebrates and non-chordate invertebrates."
    http://www.ncbi.nlm.nih.gov/pubmed/19720652

    If we hypothesize common descent predict a nested hierarchy in the molecular phylogeny of photoreceptors. We would predict key mutations-changes in the protein sequence would govern unique features of the resulting vision.

    Confirmed:
    "Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules"
    http://www.ncbi.nlm.nih.gov/pubmed/19720651

    We might expect molecular and morphological investigations to find common evolutionary routes. We would expect constraints based on history and contingency along the way.

    "...On the basis of molecular and morphological findings, I discuss the functional requirements for vision and how these have constrained the evolution of eyes....A corresponding evolutionary sequence is suggested, starting at non-directional monitoring of ambient luminance and leading to comparisons of luminances within a scene, first by a scanning mode and later by parallel spatial channels in imaging eyes."
    http://www.ncbi.nlm.nih.gov/pubmed/19720648

    Or, and I don't think you'll find God or metaphysics in those articles.

    Religion might drive Dawkins, but it can't touch actual science.

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  20. === Cornelius' Daily Unsupported Statement: ===
    Even the relatively simple third eye vision cascade dwarfs anything of which Darwin could have dreamt. And it shows no sign of having evolved.
    ==============
    Bare assertion unsupported by evidence as usual. Contradicted by evidence below, as usual.

    === Michael: ====
    The approach of using a cladistic tree, phylogenetic analysis as evidence for Darwinian processes boils down to a fancy why of using pictures of rocks organized from very big to very small and claiming that to be proof of the mechanism that caused the big rock to be broken into smaller rocks.
    ===============

    You're ignorant of basic evolutionary theory. First, rocks/mineral types cannot be organized into a *unique* nested hierarchy, *unique* phylogenetic tree etc. Second, forming a phylogenetic tree is only the first step in the use of Darwinian detective tools to construct evolutionary pathways-- no scientist claims that's the end of the analysis-- but if you don't do step #1, you're just blowing smoke.

    First, it is impossible to arrange rocks/mineral types into a *unique* phylogenetic tree. You try it-- there are too many, equally valid phylogenetic trees and the algorithms do not converge to one *unique* tree. Most things cannot be organized into *unique* trees. A well-known example are the biochemical functions that are tabulated in Gene Ontology (GO). Biochemical functions in the GO cannot be *uniquely* nested and cannot expand into a *unique* tree (because one "node" has many parents.)

    Unlike rocks or GO biochemical functions, sequences of protein domains do form phylogenetic trees, as do species, genera, etc.

    That is just step #1 in deducing proposed, testable evolutionary pathways. Like a detective dusting for fingerprints, or digging a bullet out of a dead body. Nobody claims step #1 is the end of the detective work.

    But Michael's creationist logic is: "You say digging a bullet out of the body tells you who committed the crime! But a bullet can't talk!"

    Your rejection of Step #1 does not put limitations on evolutionary theory because you haven't even tried step #1, much less #2, #3...

    Here is a paper on the evolution of the eye, including the biochemistry of interacting proteins:

    "Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup." Trevor D. Lamb, Shaun P. Collin & Edward N. Pugh. Nature Reviews Neuroscience 8, 960-976 (December 2007).

    It's behind a pay wall at the moment. I'll excerpt it later when I can get behing the pay wall.

    For now, I'll recite from memory. The biochemistry of vision starts with opsins which start a cascade of interacting proteins that start with G-protein coupled receptors.

    The G-protein coupled receptor (GPCR) activates G protein, which in turns initiates nerve signals. This system is shared by all sensory mechanisms (that I know of) and that is used to initiate nerve signals. So, the GPCR protein-protein interaction only had to evolve once. After that, gene duplication of the system and point mutations that increase specificity can customize it for specific sensory systems (sight, touch, etc.)

    This system is widely distributed, found in single-celled organisms, and thus presumably first appeared in single-celled organisms. Some single-cell organisms have a light-sensitive spot (the most primitive type of eye, smaller than one cell) which utilizes this chemical cascade, so the chemistry presumably evolved very early.

    In estimating the likelihood of so many protein-protein interactions evolving in the GPCR cascade, you have to set the population size, and time per generation for one-celled organisms, which are enormously higher than for animals like vertebrates, so the evolution of the protein-protein interactions would be enormously faster than it would have been in vertebrate evolution.

    This is what I remember off the top of my head, I have to read the Lamb et al. paper.

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  21. Diogenes, and anyone interested in the real science literature-

    http://www.ncbi.nlm.nih.gov/sites/entrez

    Now has a feature where you click the "Free Full Text" link on the left, which allows your search to be limited to publicly available sources. There are 831 free articles on eye evolution.

    Maybe someone would care to refute them for us?

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  22. Thanks RobertC, I want to reiterate how thoroughly wrong was Dr. Cornelius' statement that visual cascades "show no sign of having evolved"! Utter bunk! As shown above and below.

    RobertC's ref also specifically disproves Michael's statement about how phylogenetic trees are useless! Read this:

    "Opsins are the universal photoreceptor molecules of all visual systems in the animal kingdom. They can change their conformation from a resting state to a signalling state upon light absorption, which activates the G protein, thereby resulting in a signalling cascade that produces physiological responses. ... Recent cloning techniques have revealed the rich and diverse nature of these molecules, found in organisms ranging from jellyfish to humans, functioning in visual and non-visual phototransduction systems and photoisomerases. ... Then we explore the molecular properties of opsins, by analysing site-directed mutants, strategically designed by phylogenetic comparison. This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules. In particular, we will discuss the evolution of the counterion, the reduction of agonist binding to the receptor, and the molecular properties that characterize rod opsins apart from cone opsins. We will show how the advances in molecular biology and biophysics have given us insights into how evolution works at the molecular level.” [Evolution of opsins and phototransduction. Shichida Y, Matsuyama T. Philos Trans R Soc Lond B Biol Sci. 2009 Oct 12;364(1531):2881-95.]

    As I just pointed out, Michael's statement about how phylogenetic trees are useless in deducing evolutionary pathways is disproven above, as forming the phylogenetic tree is Step #1 in evolutionary analysis. After that, they hypothesized an evolutionary pathway, they made testable predictions, they tested those predictions experimentally. They were confirmed.

    You know-- scientific method and all that?

    ID never does this. Your ass is thoroughly kicked!

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  23. Like in this case examples of bad design always run into the risk of being arguments from ignorance. You should only use such examples if you can demonstrate that a different design would be better. In the case of a complex system like the eye this is not a piece off cake.

    Better would be to use examples of nondesign.

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  24. Hi Diogenes,

    You managed to read so much into so little and miss the point completely. My "big rock to small rock" simile still holds valid because its a simple classification according to consecutive stages of rock degradation, as nature does its work on the rock to get it smaller, that should be considered. You see... Nature at work to change the state of something, with rocks we have described and empirically proven the mechanism but with evolution you want us to just look at "big rocks and small rocks" and then conclude Darwinian evolution as the mechanism. (You convoluted the argument with your bio-taxonomy vs. rock classification mambo jumbo).

    After reading your recital of the evolution of the eye I still fail to see proof that it came about by Darwinian processes. Instead you just described the (here starts the simile again) complex edges (features) of the "rock" (eyes of all sorts) where you know the fractures (mutations) caused the big rock(no eye) to become a small rock(whatever eye you prefer). How about telling me how Darwinian processes caused the eye and give some empirical support for this mechanism at work? Just a viable Darwinian starting point will help your case very much.

    Could you also help me by highlighting any creationist argument in any of my writing in this post. If you look carefully my simile never contest common descent, because (here starts the simile again) I never disagreed that the small rock were once part of a big rock.

    P.S. (to highlight the flawed thinking)
    You quote: "...This site-directed mutant approach led us to identify many key features in the evolution of the photoreceptor molecules"

    This should actually read "...key features of the proposed products of evolution". It is very misleading to imply that it actually describes the mechanism by which these features came into being. "...site-directed mutant approach" is simply a way or means to identify features (like a microscope to see the hidden features) not a description of a viable Darwinian mechanism. That is actually what the writer implied.

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  25. I have to put this one also in play:

    I predicted big rocks will become small rock due to random undirected forces of nature and I actually found the small rock as my proof. By this rigorous scientific method I just proofed exactly how the mechanisms of nature caused the small rocks... or did I just state an obvious relationship between big rocks and small rocks and called it a prediction.

    Wake up and see the lack of evidence for the proposed Darwinian processes at work in the evolution of the eye.

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  26. Michael-
    1)"...site-directed mutant approach" is simply a way or means to identify features (like a microscope to see the hidden features) not a description of a viable Darwinian mechanism. "

    Wrong. The site directed mutagenesis is based on molecular phylogeny. When mutants representing nodes of the 'tree of life' are made, and tested it is THE direct testing of proposed pathways of Darwinian evolution. I'm quite sure the authors meant what they said, and their methodology and v backs this.

    You missed this one too, the experimental confirmation of a missing link:

    If we hypothesize common descent, we would predict the distinct modern Protostome and vertebrate systems should share some intermediate.

    Confirmed: "The visual cycle systems in ascidians, the closest living relatives of vertebrates, show an intermediate state between vertebrates and non-chordate invertebrates."
    http://www.ncbi.nlm.nih.gov/pubmed/19720652"

    2) "Wake up and see the lack of evidence for the proposed Darwinian processes at work in the evolution of the eye."

    830 free articles. I see lots of evidence. Convince me there is nothing in the literature. Get refuting.

    3) "The approach of using a cladistic tree, phylogenetic analysis as evidence for Darwinian processes boils down to a fancy why of using pictures of rocks organized from very big to very small and claiming that to be proof of the mechanism that caused the big rock to be broken into smaller rocks."

    False analogy- how is aligning rocks by size anything like sequence alignment? Molecular phylogeny is nothing like that.

    http://en.wikipedia.org/wiki/Molecular_phylogenetics

    As for the rock-if we found a small rock at the bottom of a hill, that can be typed in mineralogy to a rock at the top of the hill-and matched by stress fractures like that caused in the lab by freezing-is not the most parsimonious explanation erosion due to ice? If we saw clear hammer and chisel marks, we could even infer a human did it. But where are the chisel marks in the genome?

    It is telling that your side has to re-frame evidence by false analogies to make it look less than it is.

    We have phylogeny. We can infer the molecular differences. We can test the function. Molecular phylogeny correlates with morphology. We know of random mutation, gene duplication and divergence, and can track those too.

    If a movie of it in progress is what you want, there's some criminal defense attorneys who would like to meet you. We can bring evidence to bear, and make strong conclusions without an eye witness, right?

    4) Where is the functional design detector? Where's the proof? Give me an example of something biological that is designed, not designed and tell me how you know the difference?

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  27. @Michael

    In case of the rocks how would you prove that the small rocks came form the big rocks under the constraint, that you could not reproduce the erosion conditions in the lab?

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  28. Michael, if nothing else, at least refute this one:

    Evolution of vertebrate retinal photoreception.
    Philos Trans R Soc Lond B Biol Sci. 2009 Oct 12;364(1531):2911-24.
    http://www.ncbi.nlm.nih.gov/pubmed/19720653

    Some other favorites:
    Nilsson, D-E; Pelger S (1994). "A pessimistic estimate of the time required for an eye to evolve". Proc R Soc Lond B 256: 53–58

    Simple modelling, invoking small mutations exposed to natural selection, demonstrates that a primitive optical sense organ based upon efficient photopigments could evolve into a complex human-like eye in approximately 400,000 years....

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  29. Mantis shrimp are crustaceans, not cepahlopods. Don't they have compound eyes?

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  30. John Stockwell:

    ===
    ID is always about metaphysical pronouncements.
    ===
    Dr. Hunter:
    Such as?



    Basically what ID does not tell us is how anything
    came into being. ID does not fit in the epistemological
    program of science by describing a process of orgin. Instead, ID is old tyme divination, which is to say the
    the identification of an "ultimate cause", based not on a scientific theory, but on a correspondence principle.

    Once these identiifications are made, there is nothing to test, nor do we know anything more or new about the item identified as "designed". The holy water of "IDentification" once sprinkled, sanctifies the "IDentified" object as "designed".

    That is 100% a metaphysical pronoucnement, and 0% scientific investigation.

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  31. Nice line, Bossmanham.

    Hope you don't mind if I help myself to this one. A handy gadget to add to my toolbox.

    "....."die the death of 1000 qualifications"...

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  32. Nick, has your blindspot give you trouble lately? How is a blindspot a defect if it will allow benefits that a Cephalopod doesn't have, say a sharp image?

    I'm sure you understand that optimal does not mean perfect in every way. Rather it is what characteristics are more suited to each organism.

    If a blindspot is the result of adjustments to allow for sharp focus and this blindspot does not debilitate or inhibit the organism, then it is a beneficial tradeoff any engineer or businessman would accept in a heartbeat.

    Nick Matzke said: "It's not speculation to say we know it can be done better. Cephalopod eyes are also high-precision, color-sensing camera eyes. But they are built out of different tissues, and they don't have the wires sticking out the front, or any blind spot. Creationists always elide this crucial comparative point, basically because they have no answer to it."

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  33. " If we saw clear hammer and chisel marks, we could even infer a human did it."

    You could infer, but could not prove. At least if you used the same reasoning used in determining creation. Of course, in the hammer and chisel example everyone would think you are nuts for not believing it. Where with regards to creation the opposite is true....funny.

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  34. Filipe -


    You could infer, but could not prove.


    That's all we can ever do. When considering events in the past, you can never prove what happened with 100% certainty. Only consider what is likely, possible and probable.


    Of course, in the hammer and chisel example everyone would think you are nuts for not believing it. Where with regards to creation the opposite is true....funny.


    In the hammer and chisel case, a natural explanation is obvious - human craftsmanship. With creation, well, what natural explanation is inferred? Bearing in mind the explanation has to take into account the probability of the existence of all agents it incorporates.

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  35. Then if you can only infer and never prove, why is evolution spoken of as a fact? Is that not dishonest?

    Craftsmanship... can you provide me an example of anything that is crafted(or appears to be, whatever) with design and purpose on any scale of human craftsmanship and upwards that was created by nature, random forces, chance, some kind of selection? I can not honestly understand why in every aspect of life when we see something complex and with a specified purpose we KNOW it was designed whereas with life, something far more complex than humans have ever made, the idea of a designer is dismissed out of hand. Really...I don't get it!
    I have no problem with science and continued pursuit of knowledge, that will and should never end, and I don't see how a belief in a designer would do that.

    Ok, that was way too long. Ignore the end and focus on the beginning, sorry.

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  36. Filipe -


    Then if you can only infer and never prove, why is evolution spoken of as a fact? Is that not dishonest?


    The theory of evolution is a theory. It is spoken of as a fact to emphasise the massive amount of supporting evidence. It is like calling gravity a fact. Technically, the theory of gravity is still only a theory, and yet it is so hugely well supported that we may now just consider it true until given reason to think otherwise.

    Though I can sympathise to a degree. Certainly there can never be a specified level of evidence a theory must pass to become a 'fact'. So technically yes, it is accurate to just consider it a theory. Just a massively well supported one.


    can you provide me an example of anything that is crafted(or appears to be, whatever) with design and purpose on any scale of human craftsmanship and upwards that was created by nature, random forces, chance, some kind of selection?


    Okay. How about walls. A brick wall constructed by humans, and a mass of branches and beach detritus washed up on the beach. Both function as walls. Notice, of course, that the mass of branches and beach detritus will be vastly more complex - the exact arrangement of branches, seaweed and general tide junk will be vastly more intricate than the simple brick-and-cement arrangement. So clearly, complexity does not necessarily equal design. Complexity may well indicate functionality arising out of chaos - surely a feature of non-design??


    I can not honestly understand why in every aspect of life when we see something complex and with a specified purpose we KNOW it was designed whereas with life, something far more complex than humans have ever made, the idea of a designer is dismissed out of hand. Really...I don't get it!


    Brushing past my above comment that complexity does not indicate probable design, the idea that life has a designer is dismissed by science because it is not testable. In principle it COULD be a scientific hypothesis but this would involve speculating on the motives and methods of the designer, stating clearly in advance what observations would and would not falsify such claims, and then going out and testing them. Experimenting. That is what scientists do. But most ID advocates seem totally disinterested in doing this. They seem determined to keep the nature and motives of the designer a mystery and his methods likewise. This keeps the whole hypothesis beyond the reach of scientific testing and renders the label of 'designed' effectively a mere miracle claim. Don't understand something in biology? Just say it was designed by some unknowable beings via unfathomable methods and we can all go home.

    Behe came up with the concept of irreducible complexity, but has never written an article in a peer-reviewed scientific journal explaining, or giving examples of it. Jonathan Wells and Stephen Meyer, two leading light of the ID movement can claim only one article in their whole careers, and those where published under rather suspicious circumstances. Real scientists, by comparison, can produce dozens every year.


    I have no problem with science and continued pursuit of knowledge, that will and should never end, and I don't see how a belief in a designer would do that.


    If you label something as designed, though by unknown agents for unkown reasons via unknown methods, you have explained nothing. You have effectively just called it a miracle. And once you do that, why bother investigating further? Don't understand how eyes formed? Easy - it was a miracle. End of mystery. Such a response does not actually answer or explain anything, and yet discourages further investigation. What could be less scientific?

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  37. Ritchie

    No one doubts gravity, since we all feel its effects. There are things about it we don’t understand certainly, but that gravity exists there is no doubt. We cannot feel the effects of evolution. Oh yes, you can say that since we evolved we are feeling them but that is circular. Our existence does not support evolution.

    I agree that that your example would be complex. However, I said design and purpose. Your example of branches and beach detritus fails because there is no specific design or purpose to that arrangement. It is purely random and common. Now, if the stuff that washed up on a beach created a house full stocked with food and a burning fireplace then I would agree with you. Even if I saw a snowstorm build an igloo I would have to agree with you. But it will never happen.

    When it comes to scientific papers, I have no doubt that community is as politically motivated as any other. Many are simply concerned with covering their own ass. People are people. Even scientists.

    As to your last comment, are you saying it is evolutionary belief that has driven all scientific knowledge since the beginning of recorded human history?

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  38. Filipe -


    No one doubts gravity, since we all feel its effects. There are things about it we don’t understand certainly, but that gravity exists there is no doubt.


    I was not exaggerating when I compared the certainty of the theory of evolution to that of gravity. Your genetic code is a map of your evolutionary history. We use it in forensics every day - we can estalish paternity of children and establish the degree of relatedness between any two given people. Exactly the same methods establish the common ancestry of family members, strangers, all human beings and even different species. Doubt, if you so choose, that the theory of evolution is correct, but then you must also doubt the entire field of genetics (among others).


    I agree that that your example would be complex. However, I said design and purpose. Your example of branches and beach detritus fails because there is no specific design or purpose to that arrangement.


    Oh okay, that's me misunderstanding what you were asking for then. I thought you wanted me to compare similar structures - one (apparently) designed and the other (apparently) not designed.


    Now, if the stuff that washed up on a beach created a house full stocked with food and a burning fireplace then I would agree with you. Even if I saw a snowstorm build an igloo I would have to agree with you. But it will never happen.


    Such metaphors are totally inaccurate in describing how evolution functions, for four main reasons:

    1) The house/igloo would be built by nothing but random chance. Evolution is not chance! It operates according to a fixed law - natural selection - which favours some assemblages over others. Tides and snowstorms just rend and bash things together indiscriminately. To accurately represent natural selection, they would have to be capable of recognising assemblages which could form parts of a house/igloo and selectively NOT tear them apart.

    2) A house is made up of component parts which are pretty functionless when taken alone. Irreducibly complex, if you will. The tide, when it came across an assemblage that would be useful for a house, would have to preserve it, not because it is functional in and of itself, but because it WOULD LATER BE functional when taken as a whole in the end product. Such would demonstrate forward planning. This is not how evolution funtions. At every tiny step in an incremental change, features have to be functional or lost.

    3) The tide/snowstorm examples are examples of single-step, rather than cumulative processes. Evolution builds up complex features slowly over time in a repetative process guided at each step by selective forces. It would be more accurate to imagine not one snowstorm, but thousands of consecutive ones - and each one selectively preserving the igloo-like assemblages of the previous snowstorms.

    4) The tide/snowstorm produces, in a single event, a product totally unlike the beginning product. No animal ever gives birth directly to an animal totally dissimilar to itself. Evolution works as a series of tiny steps - each child is barely distinguishable from its parent, but the beginning and end of the continuum may be significantly different.

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  39. (cont)

    When it comes to scientific papers, I have no doubt that community is as politically motivated as any other. Many are simply concerned with covering their own ass. People are people. Even scientists.


    I don't doubt you are right. But the great scientists are not the ones who meekly towed the line - they are the ones who made the revolutionary discoveries. Scientists as a general rule do not discourage radical thinking - as long as you are willing to do the work to back it up. I'm sure there are politics behind the scenes as in all industries, but to imagine certain people with genuine scientific work are being systematically excluded is little short of a conspiracy theory.


    As to your last comment, are you saying it is evolutionary belief that has driven all scientific knowledge since the beginning of recorded human history?


    Umm, no. Not at all. That would be daft. But it was formed using the principles of modern science - principles such as the scientific method and methodological naturalism - principles which have fundamentally underpinned science since at least the Enlightenment (though doubtless you could trace unofficial versions of these principles back much further). ID is not crafted using these principles. Ergo, it is not science.

    Consider, I have a mystery. I write every possible explanation of that mystery down - each on a seperate post-it note. Then I put those notes on a (very big) wall and blindly throw a dart at it. Basically, I have randomly selected an answer. And it just so happens that the answer I selected, co-incidentally, is the correct one. Have I performed science in obtaining my explanation? No. Just because I happened to arrive at the correct answer does not mean my methods of getting there were scientific. The same is true of ID - even if it does give us the correct answer (and I have a great deal of confidence it does not, but then again, I cannot show that absolutely) that would not necessarily make it science.

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  40. No matter which side of the issue you fall on (to be clear, I'm a creationist), quoting abstracts of studies which supposedly support evolutionary claims does not prove anything at all. We would have to be able to read the actual study to determine if the claims in abstracts are of any value, which probably none of us are going to do as they are pay-per-view documents (I'm certainly not going to pay to read them).

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