Home » Intelligent Design » Could the eye have evolved by natural selection in a geological blink?

Could the eye have evolved by natural selection in a geological blink?

It is commonly believed that Dr. Dan-Eric Nilsson and Dr. Susanne Pelger of Lund University in Sweden demonstrated in a scientific paper written back in 1994 that a fully-developed vertebrate eye could have developed from a simple light-sensitive spot by a process of unguided natural selection, in “less than 364,000 years.” That, at any rate, is the popular myth. What’s the reality?

Nilsson and Pelger certainly made a convincing case for gradualism in their paper, but they failed to bolster the case for Darwinism. Looking at the eye from a purely anatomical standpoint, they showed how a vertebrate eye could have developed from a patch of light-sensitive skin by the accumulation of numerous tiny modifications over the course of time – in other words, gradual change, or evolution. But what very few people realize is that Nilsson and Pelger used intelligently guided evolution to transform their flat, light-sensitive spot into a focused camera-type eye. What’s more, Nilsson – who is a convinced Darwinist – has recently acknowledged as much! (I’ll have a lot more to say on that surprising story, below.) Additionally, Nilsson and Pelger’s claim that the eye could have evolved in “less than 364,000 years” turns out to be a hypothetical estimate, which (as we’ll see) only applies to an intelligently designed fitness landscape.

In this post, I’m going to critically examine Nilsson and Pelger’s 1994 paper, A Pessimistic Estimate of the Time Required for an Eye to Evolve (Proceedings: Biological Sciences, Vol. 256, No. 1345, (April 22, 1994), pp. 53-58). Before I continue, I would like to personally thank Professor Dan-Eric Nilsson for having responded to my queries regarding his paper. Dr. Nilsson was also kind enough to send me a copy of his new paper, entitled, “Eye evolution and its functional basis” (forthcoming in Visual Neuroscience, 2013, 30, doi:10.1017/S0952523813000035), which addresses the evolution of the eye in much greater depth than the 1994 paper which he co-authored with Dr. Susanne Pelger. I’m going to discuss Nilsson’s new paper in my next post. I’d also like to thank Dr. Anders Garm, a colleague of Dr. Nilsson, for having taken the time to answer my queries about vision in box jellyfish, in relation to the evolution of the eye.

Does Nilsson and Pelger’s model lend support to Intelligent Design or Darwinian evolution, or both?

It is my contention that Nilsson and Pelger’s model of the evolution of the eye is in fact a striking example of Intelligent Design, rather than Darwinian evolution. Readers may be surprised to learn that Nilsson and Pelger deliberately selected each of the 1,829 steps in their model leading from a light-sensitive spot to a camera-type vertebrate eye, by choosing which features they wanted to vary at every step along the way. That makes their model intelligently designed. And although the pathway created by Nilsson and Pelger was indeed a gradual one, their model lacks a key ingredient that would, if present, turn it into a powerful argument for Darwinism: probability calculations, showing how likely it was that Nature would have chosen the pathway they selected. I conclude that while Nilsson and Pelger’s model can be viewed as an Intelligent Design hypothesis regarding how the eye might have emerged over time through a process of guided evolution, it cannot be legitimately invoked as an argument for accepting Darwinism.

Some readers might object that Nilsson and Pelger’s 364,000-year estimate of the time required for the vertebrate eye to have developed does make it a truly Darwinian model, since it shows that the eye could have evolved relatively quickly. However, it turns out that Nilsson and Pelger’s estimate is based on a host of simplifying assumptions which render it useless for practical purposes. Nilsson and Pelger have left us with a theoretical model of how the eye could have evolved gradually, but without a realistic estimate that would demonstrate the feasibility of their model, over geological time.

Darwinism and the epistemic bar

Gold medal winner Ethel Catherwood of Canada scissors over the bar at the 1928 Summer Olympics. Image courtesy of Wikipedia.

For some time now, Darwinists have been fighting – and generally winning – arguments against critics who contended that Darwinian evolution was impossible. They have won these arguments in two ways: firstly, by identifying a scientific flaw in their critics’ assumptions, which either invalidates their anti-Darwinian arguments or calls them into question; and secondly, by constructing theoretical models showing that a step-by-step evolutionary sequence from a hypothetical ancestor to its modern-day descendants would have been viable at each and every stage, and that each step along the way would have conferred a fitness advantage on the creature possessing it. (Nilsson and Pelger’s 1994 paper falls into the second category.) Both of these tactics have served well to establish the theoretical possibility of Darwinism, as a scientific theory.

These tactics by Darwinists certainly make for splendid PR coups, but what do they actually prove? At the very most, all they prove is that Darwinism is theoretically possible: it might (in a very weak sense of “might”) have happened. But theoretical possibility and scientific plausibility are two very different things. In order for a hypothesis to attain the status of a respectable scientific theory, the mechanisms to which it appeals have to clear a certain threshold of probability, before that hypothesis can be deemed scientifically plausible.

What I’m arguing here is that Darwinism has secured public (and scientific) acceptance by lowering the epistemic bar from the standard usually required of a scientific theory. Most theories gain acceptance only after it has been shown that they are scientifically plausible, in addition to being supported by powerful evidence in their favor. For Darwinism, however, this requirement was waived. After making a strong scientific case that his theory of evolution was supported by converging lines of circumstantial evidence, Darwin managed to win acceptance for his new theory, simply by mounting an argument showing that its mechanism (natural selection) was theoretically possible. This was due in no small part to Darwin’s rhetorical skills: in terms of sheer eloquence, his Origin of Species was unmatched in the annals of scientific literature.

Now, there are a couple of significant exceptions to the requirement that a scientific hypothesis should invoke a plausible mechanism before it can be taken seriously as a scientific theory. Newton’s theory of gravity gained acceptance despite the fact that it lacked a known mechanism, for the simple reason that it could be experimentally verified, at scales ranging from falling apples to the movement of the planets in the solar system. And in our own day, no geologist doubts the reality of continental drift, even though the underlying mechanism – plate tectonics – remains poorly understood. After all, scientists can actually measure the continents drifting, at the rate of several centimeters a year. It is easy to extrapolate back in time and show that at one point, they would have all been together. Unfortunately, neither of these exceptions is of any help to Darwinism.

First, the parallel with Newton’s theory of gravity fails. While there is evidence in the fossil record for large-scale evolutionary change, this evidence tells us nothing about the mechanism involved. Hence it cannot be adduced as evidence for Darwinism.

That leaves us with extrapolation. Darwinian evolutionists have long argued that their theory can be validated by extrapolating from observed evolutionary changes, such as those wrought by artificial selection. As Professor Jerry Coyne put it in Nature magazine in 2001:

When, after a Christmas visit, we watch grandma leave on the train to Miami, we assume that the rest of her journey will be an extrapolation of that first quarter-mile. A creationist unwilling to extrapolate from micro- to macroevolution is as irrational as an observer who assumes that, after grandma’s train disappears around the bend, it is seized by divine forces and instantly transported to Florida. (Nature 412:587, 19 August 2001.)

A Southbound Amtrak 139 train on the Siver Star route crosses Central Boulevard in downtown Orlando, Florida. Image courtesy of Wikipedia.

What this analogy overlooks is that there is only one railway track taking Grandma to Florida. Macroevolution, on the other hand, is a multi-forked path with an astronomically large number of possible branches, and additionally, there is no intelligent driver and no pre-programmed destination, in Darwin’s theory. Thus in order to demonstrate the feasibility of a vertebrate eye evolving from a light-sensitive spot by a Darwinian mechanism, it is necessary to show first that the probability of its arriving at a vertebrate eye within the time available exceeds a certain threshold, rendering the theory plausible and hence worthy of scientific credence. In other words, proponents of Darwinian evolution have to come up with some “hard numbers.”

Historically, Darwinists have usually resisted this demand for “hard numbers” by arguing that the mathematical calculations verifying the ability of natural selection to transform a light-sensitive spot into a camera-type eye over millions of years were just too hard to do, and that the skeptics’ demand for “hard numbers” was an epistemically unreasonable one. “We’ve got the fossils, as well as the evidence from homology, embryology, vestigial organs and biogeography, and we’ve got a mechanism which has been shown to work on short time-scales,” say the Darwinists. “That should be enough to convince you.”

Nilsson and Pelger’s 1994 paper is therefore highly significant, because it represents a genuine scientific attempt to engage the Darwin-skeptics on their own turf. The authors examine the vertebrate eye – a complex organ often cited by Darwin-skeptics as beyond the power of natural selection to explain – and argue that a step-wise sequence of anatomical changes, occurring one at a time, could have transformed a light-sensitive spot into a fully fledged camera-type eye over a period that they calculate – using conservative assumptions – as “less than 364,000 years,” which means that there was enough time for eyes to evolve 1,500 times over, during the 540 million years since eyes first appeared, back in the Cambrian period. Darwinism wins by a knock-out, right?

Not quite. Unfortunately for Darwinists, the evolution that Nilsson and Pelger describe in their paper is intelligently guided evolution. And I have the evidence to prove it.

Why the model described in Nilsson and Pelger’s 1994 paper is really an example of intelligently guided evolution

The evidence for my contention that Nilsson and Pelger’s model is really an example of intelligently guided evolution comes from two sources: a recent communication sent to me by Professor Nilsson, and the original 1994 paper authored by Nilsson and Pelger.

(a) What Professor Nilsson said recently about the model he and Dr. Pelger created

I claimed above that Professor Nilsson had recently acknowledged that the step-by-step sequence from a light-sensitive spot to a camera eye, which he and Dr. Pelger described in described in their 1994 paper, was actually an intelligently guided evolutionary sequence. I’m now going to supply “chapter and verse” to back up that claim. I recently contacted Professor Nilsson, and asked him about the 1994 paper he co-authored with Susanne Pelger, and he was kind enough to respond. In his response, he patiently explained to me exactly what he and Pelger were trying to establish with their model:

If there is random and heritable variation separately controlling a large number of different parameters, then selection would, for each generation, choose the route that causes the largest improvement of whatever selection was set to favour (e.g. acuity). So, if there is more than one parameter that can vary, evolution can be expected to follow different routes depending on how much the different parameters vary, and how much impact they have on acuity. In real eye evolution, there would be numerous different parameters that express heritable variation in the population, and the amount of variation could itself be modified by selection. Real eye evolution has also resulted in many different end products, using different ways to form images, and different cellular organizations to obtain particular structures. These are all interesting questions, but the Nilsson and Pelger 94 paper does not address these questions. Instead the paper asks the much more tenable question: is there a continuous route from a flat, non-imaging light detector to a focused camera type eye, where each little modification, no matter how small, would generate an improvement in acuity. The important answer we find is yes, there is at least one such route. Although this route was devised by us (by deciding which parameters were to change during different phases along the route) the important result is that there is at least one route where acuity continuously improves at each new generation. Real evolution may find an even shorter route, where acuity improves more for each generation, but that would not change the important conclusion that an eye can evolve from a patch of light sensitive skin by numerous tiny modifications.

Referring to his model of how the eye evolved, Nilsson admits that “this route was devised by us,” in order to generate “a continuous route from a flat, non-imaging light detector to a focused camera type eye, where each little modification, no matter how small, would generate an improvement in acuity,” and that it was constructed “by deciding which parameters were to change during different phases along the route.” That’s intelligently guided evolution. No two ways about it. Case closed.

(b) What Nilsson and Pelger said about their model in their 1994 paper

The fact that Nilsson and Pelger relied on intelligently guided evolution to generate a vertebrate eye from a flat light-sensitive spot shouldn’t be news to anyone who has taken the trouble to read their 1994 paper, A pessimistic estimate of the time required for an eye to evolve (Proceedings: Biological Sciences, Vol. 256, No. 1345, April 22, 1994, pp. 53-58). The clues were there all along. Here’s what Nilsson and Pelger wrote about their mathematical model, in their paper:

Estimates of the number of generations required to make a change to a simple quantitative character are easily made if the phenotypic variation, selection intensity and heritability of the character are known (Falconer, 1989). The evolution of complex structures, however, involves modifications of a large number of separate quantitative characters, and in addition there may be discrete innovations and an unknown number of hidden but necessary phenotypical changes. These complications seem effectively to prevent evolution rate estimates for entire organs and other complex structures. An eye is unique in this respect because the structures required for image formation, although there may be several, are all typically quantitative in their nature, and can be treated as local modifications of pre-existing tissues. taking a patch of light-sensitive epithelium as the starting point, we avoid the more inaccessible problem of photoreceptor cell evolution (Goldsmith 1990; Land and Fernald 1992). Thus if the objective is limited to finding the number of generations required for the evolution of the eye’s optical geometry, then the problem becomes solvable.

We have made such calculations by outlining a plausible sequence of alterations leading from a light-sensitive spot all the way to a fully-developed lens eye. The model sequence is made such that every part of it, no matter how small, results in an increase in the spatial information the eye can detect. The amount of morphological change required for the whole sequence is then used to calculate the number of generations required. Whenever plausible values had to be assumed, such as for selection intensity and phenotypic variation, we deliberately picked values that overestimate the number of generations. Despite this consistently pessimistic approach, we arrive at only a few hundred thousand generations!…

The first and most crucial task is to work out an evolutionary sequence which would be continuously driven by selection. The sequence should be consistent with evidence from comparative anatomy, but preferably without being specific to any particular group of animals. Ideally we would like selection to work on a single function throughout the sequence. Fortunately, spatial resolution, i.e. visual acuity, is just such a fundamental aspect and it provides the role reason for the eye’s optical design (Snyder et al., 1977; Nilsson 1990; Warrant and Macintyre 1993)…

The refractive index of the vitreous lens is assumed to be 1.35.… The aperture size in Stage 6 was chosen to reflect the typical proportions in real eyes of this type.

A graded-index lens can be introduced gradually as a local increase of refractive index…

Based on the principles outlined above, we made a model sequence of which representative stages are shown in figure 2. [The enclosed figure shows eight distinct stages, out of a total of 1,829 in their model - VJT.] The starting point is a flat light-sensitive epithelium, which by invagination forms the retina of a pigmented pit eye. After the constriction of the aperture and the gradual formation of a lens, the final product becomes a focused camera-type eye with the geometry typical for aquatic animals (e.g. fish and cephalopods).

To sum up: Nilsson and Pelger started out with a flat, light-sensitive spot, whose dimensions and thickness they were able to describe with the aid of a few mathematical parameters. They then planned a continuous route from a flat, non-imaging light detector to a focused camera-type eye, such that each little modification, no matter how small, would generate an improvement in visual acuity. The evolutionary sequence was not generated by some random process; it was planned in every detail, at every step by Nilsson and Pelger. They decided “which parameters were to change during different phases along the route.”

Schematic diagram showing the evolution of the eye. Image courtesy of Matticus78 and Wikipedia.

Nilsson and Pelger’s model certainly is a gradualistic model, but it cannot be called a Darwinian model, because although the model’s authors created “an evolutionary sequence which would be continuously driven by selection,” they made no attempt to quantify the likelihood of those changes occurring, in that particular sequence, without intelligent guidance. Without that probability calculation, Nilsson and Pelger cannot claim to have shown that their hypothetical model supports Darwinian evolution. As Nilsson himself put it in his recent communication to me, “this route was devised by us.”

While Nilsson and Pelger can rightly claim to have demonstrated in their 1994 paper is the theoretical possibility of the eye evolving in a Darwinian fashion, at the morphological level, the claim the authors make in the final sentence of their paper, that “the eye was never a real threat to Darwin’s theory of evolution,” remains a doubtful one. Theoretical possibility is not enough to render a theory scientifically plausible.

How Nilsson and Pelger’s 1994 paper has been mis-reported by evolutionists over the last two decades

Left: Professor Richard Dawkins at the 34th American Atheists Conference in Minneapolis, on 21 March 2008. Image courtesy of Mike Cornwell and Wikipedia.
Right: Professor Jerry Coyne. Image courtesy of Wikipedia.

Ever since Nilsson and Pelger’s paper was published, Darwinian evolutionists citing the paper have almost invariably mis-reported its findings. Two great myths have been recycled in the literature again and again: the fiction that Nilsson and Pelger’s model was a computer simulation, and the fiction that the variations in the model were random, like the variations in Darwinian evolution. We now know – thanks to the indefatigable research of Dr. David Berlinski – is that Nilsson and Pelger’s model didn’t even use a computer. And now we also know that the variations introduced into the model were deliberately designed, rather than random.

(a) The myth of the computer simulation – how it all got started, and how it continues to be perpetuated

The reader may be wondering: how did these myths get propagated in the first place? The answer is that they originated from an eminent scientist whom no-one dared to publicly contradict when he got it wrong. I’m referring, of course, Professor Richard Dawkins, who completely mis-read what Nilsson and Pelger said in their 1994 paper. (I wish to state here that I am not accusing Professor Dawkins of acting in bad faith; it is entirely possible that he misconstrued Nilsson & Pelger’s study. In that case, Dawkins is guilty of incompetence, rather than deceit.) In a jubilant review of Nilsson and Pelger’s paper, “The Eye in a Twinkling” (Nature Vol. 368, 21 April 1994, pp. 690-691), Dawkins claimed that their model was based on not one but two computer simulations, and that the mutations occurring in their model were random:

“Nilsson and Pelger’s task was to set up two computer models of evolving eyes to answer two questions. First, is there a smooth trajectory of change, from flat skin to full camera eye, such that every intermediate is an improvement? (Unlike human designers, natural selection can’t go downhill, not even if there is a tempting higher hill the other side of the valley.) Second, how long would the necessary quantity of evolutionary change take?

“Nilsson and Pelger worked at the level of tissue deformations, not at the level of cellular biophysics. The existence of a light-sensitive cell was taken as a given…

“Nilsson and Pelger began with a flat retina, atop a flat pigment layer and surmounted by a flat, transparent layer (see figure). The transparent layer was allowed localized random mutations of its refractive index. They then let the model deform itself at random, constrained only by the requirement that any change must be only 1% bigger or smaller than what went before. And, of course, in order for a change to be accepted, it had to be an improvement on what went before.

The results were swift and decisive. A trajectory of steadily improving acuity led unhesitatingly from a flat beginning through a shallow cup to a steadily deepening cup. The transparent layer thickened to fill the cup and smoothly curved its outer surface. And then, almost like a conjuring trick, a portion of this transparent filling condensed into a local, spherical subregion of higher refractive index – not uniformly higher, but a gradient of refractive index such that the spherical region functioned as an excellent graded-index lens. Best of all, the ratio of the focal length of the lens to its diameter settled down at a close approximation to Mattiessen’s ratio, long known to be the ideal value for a graded-index lens.

“Turning to the question of how long the evolution might have taken, Nilsson and Pelger had to make some plausible population-genetic assumptions. They chose values of heritability, coefficient of variation and intensity of selection from published observations in the field. Their guiding principle in choosing such numbers was pessimism. For each assumption they made, they wanted to err in the direction of overestimating the time taken for the eye to evolve. They even went so far as to assume that any new generation differed in only one part of the eye: simultaneous changes in different parts of the eye, which would have speeded up evolution, were banned. But even with these conservative assumptions, the time taken for a fish eye to evolve from flat skin was under 400,000 generations. Assuming typical generation times of one year for small animals, the time needed for the evolution of the eye, far from stretching credulity with its vastness, turns out to be too short for geologists to measure. It is a geological blink.”

Professor Richard Dawkins’ egregious misreading of Nilsson and Pelger’s paper has been roundly criticized by mathematician David Berlinski. Berlinski is the author of several articles exposing the scientific mis-reporting of Nilsson and Pelger’s paper, including A Scientific Scandal (Commentary, March 31, 2001), The Vexing Eye (Commentary, February 12, 2003), and A Scientific Scandal? David Berlinski & Critics (Commentary, July 8, 2003):

Nilsson and Pelger’s paper has gained currency in both the popular and the scientific press because it has been misrepresented as a computer simulation, most notably by Richard Dawkins. Word spread from Dawkins’s mouth to any number of eagerly cupped but woefully gullible ears. Subsequent references to Nilsson and Pelger’s work have ignored what they actually wrote in favor of that missing computer simulation, in a nice example of a virtual form of virtual reality finally displacing the real thing altogether…

In a more recent paper entitled, The Vampire’s Heart, Berlinski took up the issue again, in an online response to James Downard:

The facts: Nilsson & Pelger’s study, which was widely considered a computer simulation, contained no computer simulation whatsoever. It contained, in fact, no computer analysis at all, perhaps because it contained no analysis at all. It was Richard Dawkins who conveyed the widespread impression to the contrary, writing about a computer simulation that did not exist with the excitement of a man persuaded that he had seen a digital vision. As, indeed, he had. Commentators at the time came to Dawkins’ defense with a gratifyingly prompt display of personal generosity, so that what was, in fact, a complete fabrication took on the aspects of an understandable but trivial error. Any man, after all, might mistake nothing for something.

The “computer simulation” myth continues to be propagated, right down to the present day. In a recent blog article on Nilsson and Pelger’s paper, entitled, Evolution of the Eye: Nilsson & Pelger and Lens Evolution (January 22, 2011), the neo-Darwinist blogger Francis Smallwood (who is also a good friend of ID proponent Joshua Gidney) referred to an “evolutionary simulation” created by Nilsson and Pelger, which was “not programmed to progress in ever-improving stages,” but which “allowed mutation” from which the fittest variation was selected – in other words, “true natural selection”:

Nilsson and Pelger postulated there being three types of tissue of which the eye was comprised: an opaque shield which covered the back of the eye; photocells; and a transparent film or substance (an example of this would be the vitreous mass which we looked at in the previous post.) An eye endowed with the previous constitution formed the basis from which their evolutionary simulation would begin…

So, how did N&P [Nilsson and Pelger] intend their computer eyes to evolve? They treated a genetic mutation as a percentage change in a certain part of the eye, for example, a decrease in the thickness of the transparent layer. A mutation would affect the size of part of the eye, or the functional quality of a part of the eye, such as the refractive index (which we will come to later). And, importantly, the simulation was not programmed to progress in ever-improving stages, as if the whole evolutionary progression was pre-programmed and they simply divided the one long evolutionary phase into lots of small phases, chopping up a pre-selected evolutionary progression into small quantifiable, arbitrary units. Instead, they allowed mutation from which would be selected the variations (mutations) which improved the computer eye – true natural selection…

By allowing mutation in the refractive index of the computer eye, and thus allowing variation which selection could then act upon. The single criterion which selection solicited was improved eyesight. If this criterion was met, however fractionally, selection would harness it and further “act” upon it.

Unfortunately, Smallwood has mis-read Nilsson and Pelger’s paper. Nilsson and Pelger clearly indicate in their paper that the mutations occurred in a planned order (folding mutations first, followed by aperture construction mutations, followed by mutations that varied the refractive index of the lens, followed by mutations that varied the shape and size of the lens), and in his recent communication to me, Professor Nilsson added that “this route was devised by us (by deciding which parameters were to change during different phases along the route).” Whichever way you slice and dice it, that’s not natural selection. That’s intelligently guided evolution.

(b) The myth of the randomly varying parameters

The second great myth which I drew attention to above was the mistaken notion that the variations introduced into Nilsson and Pelger’s model were random ones, when in fact they were all painstakingly designed. This myth also goes back to Professor Richard Dawkins’ review of Nilsson and Pelger’s paper, “The Eye in a Twinkling” (Nature Vol. 368, 21 April 1994, pp. 690-691), in which he wrote:

Nilsson and Pelger began with a flat retina, atop a flat pigment layer and surmounted by a flat, transparent layer (see figure). The transparent layer was allowed localized random mutations of its refractive index. They then let the model deform itself at random, constrained only by the requirement that any change must be only 1% bigger or smaller than what went before. And, of course, in order for a change to be accepted, it had to be an improvement on what went before.

Dawkins went on to breathlessly inform his readers that the results of these random variations were magical: “almost like a conjuring trick, a portion of this transparent filling condensed into a local, spherical subregion of higher refractive index – not uniformly higher, but a gradient of refractive index such that the spherical region functioned as an excellent graded-index lens.”

The myth that Nilsson and Pelger’s model employed random variations was deftly taken apart by the mathematician Dr. David Berlinski in his paper, A Scientific Scandal? David Berlinski & Critics (Commentary, July 8, 2003), from which I shall quote a brief excerpt:

“…[T]he flaw in Nilsson and Pelger’s work to which I attach the greatest importance is that, as a defense of Darwinian theory, it makes no mention of Darwinian principles. Those principles demand that biological change be driven first by random variation and then by natural selection. There are no random variations in Nilsson and Pelger’s theory. Whatever else their light-sensitive cells may be doing, they are not throwing down dice or flipping coins to figure out where they are going next…

Regrettably, Professor Jerry Coyne (who should know better) continues to propagate this myth in his best-selling 2009 book, Why Evolution Is True:

“We can, starting with a simple precursor, actually model the evolution of the eye and see whether selection can turn that precursor into a more complex eye within a reasonable amount of time. Dan Nilsson and Susanne Pelger of Lund University in Sweden made such a mathematical model, starting with a patch of light-sensitive cells backed by a pigment layer (a retina). They then allowed the tissues around this structure to deform themselves randomly, limiting the amount of change to only 1% of size or thickness at each step. To mimic natural selection, the model accepted only mutations that improved the visual acuity, and rejected those that degraded it.

Within an amazingly short time, the model yielded a complex eye, going through stages similar to the real-animal series described above. The eyes folded inward to form a cup, the cup became capped with a transparent surface, and the interior of the cup gelled to form not only a lens, but a lens with dimensions that produced the best possible image.

“Beginning with a flatworm-like eyespot, then, the model produced something like the complex eye of vertebrates, all through a series of tiny adaptive steps – 1,829 of them, to be exact. But Nilsson and Pelger could also calculate how long this process would take. To do this, they made some assumptions about how much genetic variation for eye shape existed in the population that began experiencing selection, and how strongly selection would favor each useful step in eye size. These assumptions were deliberately conservative, assuming that there were reasonable but not large amounts of genetic variation and that natural selection was very weak. Nevertheless, the eye evolved very quickly: the entire process from rudimentary light-patch to camera eye took fewer than 400,000 years.

- Coyne, Jerry A. Why Evolution Is True, 2009, Oxford University Press, p. 155.

In the above passage, Coyne carefully avoids repeating Dawkins’ ridiculous assertion that Nilsson and Pelger’s model was created by a computer simulation, referring only to a “mathematical model.” However, he perpetuates a popular misunderstanding of that model when he claims that Nilsson and Pelger “allowed the tissues … to deform themselves randomly,” and that these random variations, coupled with the culling action of natural selection in rejecting mutations that diminished visual acuity, yielded “a complex eye” within “an amazingly short time.”
What Coyne overlooks here is that the mutations in Nilsson and Pelger’s model were anything but random: each and every one of them was designed by the model’s authors. The authors did indeed manage to trace a viable morphological path from a flat light-sensitive spot to a vertebrate eye, but they failed to show that unguided natural selection had a reasonable probability (within the time available) of finding and successfully traversing this lucky path, without getting side-tracked down an evolutionary blind-alley. For this reason, Nilsson and Pelger’s model, by itself, proves nothing about the ability of natural selection to bring about macroevolutionary transformations.

How did Nilsson and Pelger arrive at their 364,000-year time estimate for the evolution of the eye?

For those who are mathematically inclined, Nilsson and Pelger’s 364,000-year estimate of the time required for the eye to evolve was derived as follows. After identifying the mathematical principles governing the camera eye (which is found in vertebrates and many cephalopods), Nilsson and Pelger constructed a model sequence, starting with “a flat patch of light-sensitive cells sandwiched between a transparent protective layer and a layer of dark pigment” and finishing with a camera eye possessing a spherical graded-index lens, a flat iris and a focal length that allowed it to focus images sharply. Eight of the steps in Nilsson and Pelger’s model sequence are illustrated in Figure 2 of their paper. However, there were in fact 1,829 steps altogether, owing to the constraint imposed by the authors, that the amount of change in size or thickness at each step would be limited to only 1%. Now, Nilsson and Pelger’s model of the eye described it in terms of about ten features which could be measured mathematically: corneal width, corneal thickness, upper retinal surface width, lower retinal surface width, upper pigment surface width, lower pigment surface width, central refractive index, iris width, lens width and lens height. The fact that there are no less than ten mathematical parameters might appear to make modeling very difficult, but in fact, if there is more than one parameter that changes, it is possible to treat the changes in the different parameters as if they were all changes in a single parameter, and then sum the number of 1% steps for the different kinds of changes taking place, in order to arrive at a total measure of change. Now if we take a 1% change and cumulate it 1,829 times we get something roughly equivalent to an 80 million-fold change, as (1.01)^1829 equals 80,129,540. In other words, the total amount of change in the ten different mathematical parameters describing the eye is equivalent to an 80 million-fold change in just one of these parameters. For those readers who are accustomed to thinking in visual terms, Nilsson and Pelger provided a helpful analogy:

“In terms of morphological modification, the evolution of an eye can thus be compared to the lengthening of a structure, say a finger, from a modest 10 cm to 8,000 km, or a fifth of the Earth’s circumference” (p. 56).

Quite some change, one might think! So how long would it take to accomplish? At this point in their paper, Nilsson and Pelger referred to an equation which is commonly used to calculate the observable change in each generation:

R = (h^2).i.V.m

where R is the response, or the observable change in each generation, (h^2) is the heritability (i.e. the proportion of phenotypic variance which is genetically determined), i is the intensity of selection, V is the coefficient of variation (i.e. the ratio between the standard deviation and the mean in a population), and m is the mean in a population. Nilsson and Pelger assigned a value of 0.50 to (h^2), which they say is a standard value. They then (pessimistically) assumed that i = 0.01 and V = 0.01, making the right hand side of their equation equal to 0.5 times 0.01 times 0.01 times the mean, m, or in other words 0.00005 times the mean, m.
It follows that even though the genetic changes occurring in mutated individuals are 1% changes, the observed changes occurring in the population as a whole is only 0.005% per generation (or 0.00005 times the mean, m). Nilsson and Pelger then reasoned as follows:

The number of generations, n, for the whole sequence is then given by 1.00005^n = 80,129,540, which implies that n = 363,992 generations would be sufficient for a lens eye to evolve by natural selection.… (p. 57)

If we assume a generation time of one year, which is common for small and medium-sized aquatic animals, it would take less than 364,000 years for a camera eye to evolve from a light-sensitive patch. (p. 58)

Eight reasons for taking Nilsson and Pelger’s time estimate for the evolution of the eye with a grain of salt

There are several good reasons for refusing to take Nilsson and Pelger’s 364,000-year estimate seriously, as a calculation for how long it would take for the vertebrate eye to evolve. In the absence of a credible estimate, Nilsson and Pelger’s model can no longer be said to buttress the case for Darwinism. All it establishes is that the eye could have developed from a much simpler structure, via a gradual process – and the only gradual process which the authors have shown to be capable of generating an eye is an intelligently guided one.

Here, then, are my eight reasons for skepticism, regarding the 364,000-year estimate.

(a) The 364,000-year figure is a “nice round number,” which appears to have been deliberately chosen in order to provide Darwin’s theory with some good publicity

Mask of Tutankhamun’s mummy at the Egyptian Museum in Cairo. Image courtesy of Bjorn Christian Torrissen and Wikipedia.

My first reason for skepticism is that the 364,000-year figure cited by Nilsson and Pelger in their paper is what I would call a “nice round number.” It sounds even better when you express it in approximate terms, as “a few hundred thousand years,” as Nilsson and Pelger do in their summary. It’s a number which gives every indication of having been carefully crafted in order to impress laypeople with the creative power of natural selection, without exciting their incredulity. Most people think of evolution as a long process that takes millions of years. When we are told that the eye evolved in only 300,000 years, it sounds fast, because it’s well under the “magic million” mark. At the same time, it doesn’t sound too fast, as a figure of, say, 3,000 years would be. Nobody would believe a figure like that.

However, what the evolutionists who cite Nilsson and Pelger’s 364,000-year estimate overlook is that it was deliberately intended to be a conservative figure. That’s why the title reads: “A Pessimistic Estimate of the Time Required for an Eye to Evolve.” As we saw above, Nilsson and Pelger assigned a value of 0.01 to the intensity of selection i, and they also selected a value for 0.01 for the coefficient of variation V. However, each of these figures could have been plausibly chosen to be 10 times higher. Setting the intensity of selection i to 0.01 means that a randomly chosen organism in the general population would have a chance of survival that’s 99% as high as that of an organism possessing the favorable mutation – a very weak selection effect indeed. By comparison, this table, which is taken from the online notes for a university course in population genetics, lists values for the selection intensity i ranging from 0.00 to 2.67. Thus Nilsson and Pelger could have easily assigned a value of 0.10 to i, instead of 0.01.

Likewise, Nilsson and Pelger’s estimate of 0.01 for the coefficient of variation V is very modest: according to some online course notes on Fitness, Adaptation, and Natural Selection in Real Populations by Dr. Steven Carr (Department of Biology, Memorial University of Newfoundland, Canada) a value of 5% to 10% (0.05 to 0.10) for V is typical “for many traits in many organisms.” Had Nilsson and Pelger used a value of 0.10 for the intensity of selection i and the coefficient of variation V, their calculation would have shown that the eye could have evolved in just 3,650 years, which is roughly equivalent to the time that has elapsed since the death of Pharaoh Tutankhamun, who ruled Egypt from 1332 to 1323 B.C.

Here’s my challenge to Darwinian biologists: try telling the man-in-the-street that the vertebrate eye could have evolved from a light-sensitive spot in the time since King Tut died, and see what kind of reaction you get. I wouldn’t mind betting that it will weaken, rather than strengthen, his belief in Darwin’s theory of evolution.

Left: An okapi at Marwell Wildlife, Hampshire, England. Image courtesy of Cahrles Miller and Wikipedia.
Right: A giraffe at Mikumi National Park, Tanzania. Image courtesy of Muhammad Mahdi Karim and Wikipedia.

But there’s an even simpler way to illustrate the biological absurdity of Nilsson and Pelger’s 364,000-year estimate of the time required for the eye to evolve. Let’s go back to what Nilsson and Pelger said in their paper about the changes that occurred in the evolution of the vertebrate eye, from a light-sensitive spot:

In terms of morphological modification, the evolution of an eye can thus be compared to the lengthening of a structure, say a finger, from a modest 10 cm to 8,000 km, or a fifth of the Earth’s circumference” (p. 56).

Let’s now consider a much smaller change: the lengthening of the giraffe’s neck. Above is a picture of a giraffe, next to its closest living relative, the okapi. The structure we are considering here is the giraffe’s neck, which is less than 10 times as long as an okapi’s. Ask the man-in-the-street how long it took for the giraffe to get its long neck, and he’ll probably say, “A few million years.” And yet, we are supposed to believe that the changes involved in transforming a light-sensitive spot into a vertebrate eye, which are equivalent to an 80 million-fold lengthening of an animal’s neck, could have taken place in 364,000 years?

(b) Nilsson and Pelger admit that their estimate is a purely hypothetical one

Second, Nilsson and Pelger explicitly acknowledge in the final paragraph of their paper that their 364,000-year estimate was never meant to be a realistic one, and applies to a hypothetical situation in which “selection for eye geometry and optical structures imposed the only limit.” As they put it:

Because eyes cannot evolve on their own, our calculations do not say how long it actually took for eyes to evolve in the various animal groups. However, the estimate demonstrates that eye evolution would be extremely fast if selection for eye geometry and optical structures imposed the only limit. This implies that eyes can be expected to respond very rapidly to evolutionary changes in the lifestyle of a species. (p. 58)

However, the only situation in which selection for eye geometry and optical structures are likely to impose the only limit on the rate of evolution is one in which all of the other complex organs of the body have already evolved – which of course begs the question. And that brings me to my next point.

(c) Nilsson and Pelger’s estimate isn’t anatomically realistic: it leaves out the brain

The occipital lobe of the human brain (pink). The occipital lobe is the visual processing center of the mammalian brain, containing most of the anatomical region of the visual cortex. Figure 728 from Gray’s Anatomy, with labels removed. Image courtesy of Wikipedia.

Third, Nilsson and Pelger acknowledge in their paper that their 364,000-year estimate for the time required for the evolution of the eye was arrived at by focusing on the evolution of the optical structures of the eye only, in isolation from the brain. But as the authors readily acknowledge, an eye “makes little sense” without an advanced brain, and the complex vertebrate eye of a fish requires a fish brain in order to process the information it conveys to the nervous system:

If advanced lens eyes can evolve so fast, why are there still so many examples of intermediate designs among recent animals? The answer is clearly related to a fact that we have deliberately ignored, namely that an eye makes little sense on its own. Although reasonably well-developed eyes are found even in jellyfish (Piatigorsky et al., 1989), one would expect most lens eyes to be useless to their bearers without advanced neural processing.. For a sluggish worm to take full advantage of a pair of fish eyes, it would need a brain with large optic lobes. But that would not be enough, because the information from the optic lobes would need to be integrated in associative centres, fed to motor centres, and then relayed to muscles in an advanced locomotory system. In other words, the worm would need to become a fish. (p. 58)

Insofar as Nilsson and Pelger’s estimate is derived by focusing on one organ of the body to the exclusion of all others, it cannot be regarded as anatomically realistic.

(d) Nilsson and Pelger’s estimate isn’t ecologically realistic

Fourth, Nilsson and Pelger readily admit in their paper that their 364,000-year estimate deliberately confines its attention to one organism, and ignores changes occurring in other species, and in the organism’s environment:

Additionally, the eyes and all other advanced features of an animal like a fish become useful only after the whole ecological environment has evolved to a level where fast visually guided locomotion is beneficial. (p. 58)

In other words, Nilsson and Pelger’s 364,000-year estimate for the evolution of the eye is not ecologically realistic. It considers one organism in isolation from its surroundings.

(e) Nilsson and Pelger’s estimate isn’t computationally realistic

A surface with two local maxima. (Only one of them is the global maximum.) If a hill-climber begins in a poor location, it may converge to the lower maximum. Image courtesy of Wikipedia.

Fifth, Nilsson and Pelger’s 364,000-year estimate for the time required for the optical structures of the eye to evolve assumes a very smooth fitness landscape, as Dov Rhodes demonstrated in a 2007 physics thesis which addressed their 1994 paper. Using a genetic algorithm, Rhodes calculates that Nilsson and Pelger have under-estimated the time required by a factor of at least five, and more realistically fifty. Rhodes’ thesis, which is entitled, Approximating the Evolution Time of the Eye: A Genetic Algorithms Approach, makes for fascinating reading. I’d like to quote a few brief excerpts:

“A paper published in 1994 by the Swedish scientists Nilsson and Pelger [6] gained immediate worldwide fame for describing the evolution process for an eye, and approximating the time required for an eye to evolve from a simple patch that sense electromagnetic radiation. Nilsson and Pelger (NP) outlined an evolutionary path, where by minute improvements on each step a camera type eye can evolve in approximately 360,000 years, which is extremely fast on an evolutionary time scale.… (p. 1)

“The main problem with the NP model is that although the evolutionary path that it describes might be a legitimate one, it neglects consideration for divergent paths. It is easy to construct a situation in which the best temporary option for the improvement of an eye does not lead towards the development of the globally optimal solution. This idea motivates our alternative approach, the method of genetic algorithms. In this paper we use the genetic algorithm with a simplified (2-dimensional) version of NP’s setup and show the error in their approach. We argue that if their approach is mistaken in the simplified model, it is even farther from reality in the full evolutionary setting. (p. 2)

“Although the paraboloid landscape guarantees convergence, the GA [genetic algorithm] is still a probabilistic algorithm and thus will not always converge quickly. As in evolution, the most efficient path is not necessarily the one taken. This fact suggests that our already conservative value of lambda = 5.41 would be even larger if compared with a real deterministic algorithm such as the NP (Nilsson-Pelger) model. Even though their computation accounts to some extent for the average probability of evolutionary development over time, it fails to consider the countless different evolutionary paths, and instead chooses just one.

Rather than 360 thousand generations, a reasonable lower bound should be at least 5*360,000 = 1.8*10^6 generations, and if our previous speculations have merit, an order of magnitude higher would ramp up the estimate to around 18 million generations. Future experiments that would be useful for improving the accuracy of our results might involve varying the mutation parameter, and most importantly letting algorithms run for longer, allowing the lower bound for convergence to be pushed even higher.” (p. 15)

That was in 2007. I recently emailed Dr. Anders Garm, a collegue of Dr. Nilsson’s, with whom he co-authored a 2011 paper entitled, Box Jellyfish Use Terrestrial Visual Cues for Navigation by Anders Garm, Magnus Oskarsson and Dan-Eric Nilsson (Current Biology 21, 798-803, May 10, 2011. DOI 10.1016/j.cub.2011.03.054). Most of my questions related to vision in jellyfish and other animals, but I also referred in passing to the genetic algorithm described in Dov Rhodes’ 2007 thesis and asked Dr. Garm: “Have any more sophisticated algorithms been developed?” Dr. Garm is a very busy man, but he was gracious enough to issue a brief response that was straight to the point: “No, we do not have such plans at the moment.”

(f) Nilsson and Pelger’s estimate isn’t genetically plausible

Sixth, Nilsson and Pelger say nothing in their paper about the genetic changes required to produce an eye. At the morphological level, the changes look plausible enough; but we have no idea whether continuity at the morphological level translates into continuity at the genetic level. It may, and it may not. We simply don’t know.

The reader will recall that each of the “mutations” in Nilsson and Pelger’s model involved changes of up to 1% in one of ten or so features of the eye: corneal width, corneal thickness, upper retinal surface width, lower retinal surface width, upper pigment surface width, lower pigment surface width, central refractive index, iris width, lens width and lens height. What this assumes, of course, is that there is some gene inside the organism’s DNA which will vary each of these properties, without varying anything else. That’s a convenient simplifying assumption, to be sure, but it’s not realistic at a genetic level. It’s more likely that changes to one of these features will impact – perhaps adversely – on the other features, rendering the organism less viable.

(g) Nilsson and Pelger’s estimate isn’t plausible at the embryological level

Zebrafish embryos. The image at the top is that of a wild-type embryo, while the image at the bottom is that of a zebrafish pigment mutant, which lacks black pigment. Image courtesy of Adam Amsterdam (MIT), J. Bradbury (Small Fish, Big Science) and Wikipedia.

Seventh, Nilsson and Pelger fail to address the question of how the changes required to produce an eye would have impacted the embryonic development of organisms that were evolving this eye. Organisms’ developmental pathways are extremely fragile, especially in the early stages. The idea that changes to these pathways are highly heritable – Nilsson and Pelger suggest a heritability of 50% in their 1994 paper – is biologically implausible. As we’ll see, a more realistic figure for the heritability in such a case would be zero.

The reader will recall that in their paper, Nilsson and Pelger posited the occurrence of no less than 1,829 mutations leading from a creature with a flat light-sensitive spot to a creature with a camera-type vertebrate eye. In estimating the time required for an entire population of organisms to acquire all these mutations, one at a time, they used the following equation to calculate the observable change in each generation:

R = (h^2).i.V.m

where R is the response, or the observable change in each generation, (h^2) is the heritability (i.e. the proportion of phenotypic variance which is genetically determined), i is the intensity of selection, V is the coefficient of variation (i.e. the ratio between the standard deviation and the mean in a population), and m is the mean in a population. Nilsson and Pelger assigned a value of 0.50 to the heritability (h^2), which they said was a common value: in normal cases, they claimed, the heritability is greater than 0.50. They then (pessimistically) assumed that i = 0.01 and V = 0.01, and arrived at a figure of 364,000 years.

I recently emailed a biologist – I won’t reveal his name, as he wishes to preserve his privacy – asking him for his comments on Nilsson and Pelger’s 364,000-year estimate. He replied that for him, speaking as a developmental biologist, the most serious problem with Nilsson and Pelger’s hypothesis was their estimate of the heritability (h^2), for the sort of variation that would be required to transform a flat patch of light-sensitive cells into a hemisphere over many generations.

The biologist whom I contacted argued that while different animals form eyes in various ways, in every case the developmental pathways that culminate in a functional eye are highly constrained. Although there are minor variations in normal eye morphology between individuals in any given species, there is no evidence that the developmental noise represented by those variations is genetically determined. In general, developmental pathways are specified by many more factors than DNA sequences. While DNA is necessary for generating
morphology and physiology, it is far from being sufficient. DNA isn’t everything: there is a lot of other information in the developing embryo that is arguably much more important than the information contained in its DNA. Heritability estimates based on genetic variation simply ignore all these other factors.

The biologist who advised me also pointed out that while heritable genetic mutations are sometimes responsible for some eye defects, none of them came anywhere close to accounting for the elaborate cumulative folding needed for Nilsson and Pelger’s hypothesis to work. In any case, since such defects are harmful, their selection coefficient would actually be negative. He concluded:

So the most realistic value for heritability in this case is 0.00, not 0.50. Zero times anything is zero, so Nilsson & Pelger’s hypothesis is dead from the start.

(h) Nilsson and Pelger’s model isn’t plausible at the biochemical level

Eighth and finally, Nilsson and Pelger fail to address the biochemical changes that must have occurred in the eye, during its evolution from a light-sensitive spot to a vertebrate eye.

Why biochemistry matters, when you are talking about the evolution of the eye

Visual phototransduction is a process by which light is converted into electrical signals in the rod cells, cone cells and photosensitive ganglion cells of the retina of the eye. The image above depicts an outer membrane disk in a rod cell. Image courtesy of Jason J. Corneveaux and Wikipedia.

Why, the reader might ask, is biochemistry such fundamental importance, when discussing the evolution of vision? Professor Michael Behe explained why in his 1996 article, Molecular Machines: Experimental Support for the Design Inference:

The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, or digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant.

To illustrate his point, Professor Behe described the process whereby the human eye sees:

Let us return to the question, how do we see? Although to Darwin the primary event of vision was a black box, through the efforts of many biochemists an answer to the question of sight is at hand. When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein’s metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin.

The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water.

A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision.

If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon.

Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete.

The three-dimensional structure of rhodopsin. Image courtesy of Wikipedia.

The “explanation” that doesn’t explain

At just one point in their paper do Nilsson and Pelger make any attempt to grapple with the underlying biochemistry of the eye, and that is in their discussion of the evolution of the lens. They write:

The development of a lens with a mathematically ideal distribution of refractive index may at first glance seem miraculous. Yet the elevation of refractive index in the lenses of both vertebrates and cephalopods is caused by proteins that are identical or similar to proteins with other cellular functions (Doolittle 1988; Goldsmith 1990; Winstow and Kim 1991; Land and Fernald 1992). Selection has thus recruited gene products that were already there. Assuming that selection operates on small but random phenotypic variations, no distribution of refractive index is inaccessible to selection.

Now, I don’t wish to contest Nilsson and Pelger’s claim that “Selection has thus recruited gene products that were already there.” Indeed, it turns out that the lenses of both vertebrate and cephalopod eyes are made of a protein called crystallin, and as this paper shows, crystallin is a protein which can be found even in simple sponges. Problem solved, right?

Not so fast. What this simplistic approach overlooks is the fact that crystallin comes in various forms – alpha, beta and gamma crystallin – each of which is strikingly different the others in the way it folds up, as these pictures illustrate. What’s more, the Wikipedia article on crystallin acknowledges that the crystallins used in the lens of the eye are quite different from one another, for different classes of animals:

“The crystallins of different groups of organisms are related to a large number of different proteins, with those from birds and reptiles related to lactate dehydrogenase and argininosuccinate lyase, those of mammals to alcohol dehydrogenase and quinone reductase, and those of cephalopods to glutathione S-transferase and aldehyde dehydrogenase. Whether these crystallins are products of a fortuitous accident of evolution, in that these particular enzymes happened to be transparent and highly-soluble, or whether these diverse enzymatic activities are part of the protective machinery of the lens, is an active research topic.

A box jellyfish has a nerve net, but no brain. Despite this, box jellyfish have no less than 24 eyes, of four different kinds, including true eyes, complete with retinas, corneas and lenses, although their visual resolution is poor. Box jellyfish also display complex, visually guided behaviors such as obstacle avoidance and fast directional swimming. They can also use terrestrial landmarks for navigation. Image courtesy of Wikipedia.

There’s more. The Wikipedia article on crystallin omits to mention cubozoan jellyfish, which also have complex eyes with crystallin lenses, although their resolution is much poorer than the vertebrate eye. A 1993 paper entitled, J1-crystallins of the Cubomedusan Jellyfish Lens Constitute a Novel Family Encoded in at Least Three Intronless Genes by Piatigorsky, Horwitz and Norman (The Journal of Biological Chemistry, Vol. 2643, No. 16, Issue of June 5, 1993, pp. 11894-11901), refers to three different families of proteins in the eyes of these jellyfish, and then goes on to discuss three particular proteins from the first of these families:

“The transparent cellular eye lens of the jellyfish (Tripedalia cystophora) contains three major proteins called J1-, J2-, and J3-crystallins. Here we have isolated cDNAs encoding three novel 37-kDa Jl-crystallin polypeptides (JlA, JlB, and J1C) sharing 84-98% identity in amino acid sequences among themselves.”

The J1-, J2-, and J3-crystallins found in cubozoan jellyfish represent families of proteins. By contrast, the JlA, JlB, and J1C crystallins described in the article above represent three very similar proteins belonging to the same family. (For the benefit of readers who are not familiar with chemical jargon, the 37-kDa figure in the above quote means that the molecule in question is about 37,000 times heavier than a hydrogen atom, or about 3,000 times heavier than a carbon atom. – VJT)

More recent work has shown profound chemical affinities between the J3-crystallin and vertebrate saposins, which are multifunctional proteins that bridge certain enzymes (called hydrolases) to fatty acids called lipids, and which also activate enzyme activity. This striking fact can be readily explained if we suppose that jellyfish and vertebrates share a common ancestor. (See J3-crystallin of the jellyfish lens: Similarity to saposins by Piatigorsky et al., Proceedings of the National Academy of Sciences, Vol. 98, no. 22, October 23, 2001, www.pnas.org/cgi/doi/10.1073/pnas.231310698.)

But while there are indeed surprising similarities between proteins of the same family that may be found in different groups of animals, there are also considerable differences between the various families of proteins which may be found within the same animal. We need to ask: can Darwinian processes account for these differences? For instance, how can we be sure that the J1-, J2-, and J3-crystallins found in cubozoan jellyfish all share a common chemical origin?

Is the inter-conversion between the different kinds of crystallin found in animals’ eyes likely to occur, via Darwinian processes?

At this point, a Darwinist might point to the 84-98% similarity figure between the three versions of J1-crystallin found in cubozoan jellyfish (JlA, JlB, and J1C) and argue, “It’s pretty easy to imagine one form of J1-crystallin converting into another, isn’t it? And given enough time, what is there to prevent inter-conversion between the J1-, J2-, and J3-crystallins found in cubozoans?” However, even a similarity of 84% between two proteins of the same family is not as impressive as it sounds. What it means is that these two proteins, each of which contains several thousand atoms, have hundreds of chemical differences between them. [Update: The differences I'm speaking of here are at the atomic level; in a comment below, Nick Matzke helpfully points out that an 84% similarity would mean about 42 differences in amino acid sequence, or about 21 on each sister lineage - which, as I argue below, still appears to be beyond the reach of unguided evolution.] And this is the point where the numbers really start to matter.

Dr. Douglas Axe’s and Dr. Ann Gauger’s research on the question, “How hard would it be for evolution to produce a different function for a protein?” suggests that it would be virtually impossible (see this video), because six changes is the maximum that evolution can accomplish, during the history of the Earth.

There are good grounds for believing that Darwinian evolution is incapable of transforming a protein that performs one biological function into a different protein which is able to perform a brand new biological function. A recent paper by Dr. Ann K. Gauger and Dr. Douglas D. Axe, entitled, The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway (BIO-Complexity 2011(1):1-17. doi:10.5048/BIO-C.2011.1) suggests that such transformations seldom, if ever, occur:

Abstract

Enzymes group naturally into families according to similarity of sequence, structure, and underlying mechanism. Enzymes belonging to the same family are considered to be homologs — the products of evolutionary divergence, whereby the first family member provided a starting point for conversions to new but related functions. In fact, despite their similarities, these families can include remarkable functional diversity. Here we focus not on minor functional variations within families, but rather on innovations — transitions to genuinely new catalytic functions. Prior experimental attempts to reproduce such transitions have typically found that many mutational changes are needed to achieve even weak functional conversion, which raises the question of their evolutionary feasibility. To further investigate this, we examined the members of a large enzyme superfamily, the PLP-dependent transferases, to find a pair with distinct reaction chemistries and high structural similarity. We then set out to convert one of these enzymes, 2-amino-3-ketobutyrate CoA ligase (Kbl2), to perform the metabolic function of the other, 8-amino-7-oxononanoate synthase (BioF2). After identifying and testing 29 amino-acid changes, we found three groups of active-site positions and one single position where Kbl2 side chains are incompatible with BioF2 function. Converting these side chains in Kbl2 makes the residues in the active-site cavity identical to those of BioF2, but nonetheless fails to produce detectable BioF2-like function in vivo. We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. Considering that Kbl2 and BioF2 are judged to be close homologs by the usual similarity measures, this result and others like it challenge the conventional practice of inferring from similarity alone that transitions to new functions occurred by Darwinian evolution.

Excerpt from the paper:

The extent to which Darwinian evolution can explain enzymatic innovation seems, on careful inspection, to be very limited. Large-scale innovations that result in new protein folds appear to be well outside its range [5]. This paper argues that at least some small-scale innovations may also be beyond its reach.

Given these biochemical constraints on what Darwinian evolution can accomplish, it is by no means a foregone conclusion that the alpha crystallins present in the crystalline lens of the vertebrate eye could ever have naturally evolved into beta-gamma crystallins, which belong to an entirely different family. Likewise, it is doubtful whether the three families of crystallins (J1, J2, and J3) found in the eyes of cubozoan jellyfish could have developed from a common molecule without intelligent guidance.

These are the “nitty-gritty” questions that Nilsson and Pelger’s 1994 paper fails to address. Even if we grant for that a Darwinian account of the evolution of the eye might work at the anatomical level, it still needs to be shown that it can work at the biochemical level.

I conclude, then, that the 364,000-year estimate proposed by Nilsson and Pelger for the evolution of the eye is not a biologically realistic one: it applies only to a “toy” world where one structure can simply transform itself by imperceptible degrees into another. But without this estimate, the whole foundation for the Darwinian claim that the evolution of the vertebrate eye from a light-sensitive spot is a plausible occurrence collapses. All we are left with is theoretical possibility. And that, as we have seen, isn’t enough to make Darwin’s theory of evolution by natural selection a proper scientific theory.

At the beginning of this post, I posed the question: “Does Nilsson and Pelger’s model lend support to Intelligent Design or Darwinian evolution, or both?” We are now in a position to answer this question fairly definitively. The model was intelligently designed at every step. And while it shows that the eye might well have developed in a gradualistic fashion, it fails to show that natural selection could have accounted for this process. Therefore it provides no support whatsoever to Darwin’s theory of evolution.

Conclusion

As we have seen, there are good reasons for believing that the 364,000-year figure put forward by Nilsson and Pelger for the time required for the eye to have evolved is a fictitious estimate, which has no relevance to biology. However, I don’t wish to sound unduly critical of Nilsson and Pelger’s work: their demonstration that a series of sequential changes, occurring one at a time, could have transformed a light-sensitive spot into a vertebrate eye, was no mean feat, and the acclaim it received was well-deserved. I would also like to add that Dr. Nilsson’s new paper, entitled, “Eye evolution and its functional basis” (forthcoming in Visual Neuroscience, 2013, 30, doi:10.1017/S0952523813000035), marks a major advance on the 1994 paper he co-authored with Dr. Pelger, as it provides a comprehensive account of the evolution of vision in nearly all phyla of animals. Additionally, the new paper attempts to address the evolution of the eye at the biochemical and embryological levels, as well as the morphological level. I intend to discuss Nilsson’s new paper in my next post.

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

176 Responses to Could the eye have evolved by natural selection in a geological blink?

  1. Dr. Torley, the elaborate vision cascade describe by Dr. Behe reminded me of this video by Dr. Benjamin Carson in which he describes the elaborate process going on just to raise your hand:

    Ben Carson – Thought Process to raise your hand – 2:39 mark of video
    http://www.youtube.com/watch?v=Qdo6rT064KA

    And Dr. Craig Hazen in the following video relates how he demonstrated, to academics, how raising your hand is actually, by all rights, a miracle,,

    The Intersection of Science and Religion – Craig Hazen, PhD – video
    http://www.youtube.com/watch?f.....qlE#t=746s

    Dr. Hazen’s example really brings the burning question home, that is all too often missed by academics, as to “what is actually doing the raising the arm and the seeing in the brain?”,, If a person says that it is merely the brain that is raising the arm and is what is doing the seeing then one runs headlong into the argument from divisibility; i.e. the ‘I’ of ones-self is indivisible:

    Case for the Existence of the Soul – (Argument from Divisibility) – JP Moreland, PhD- video
    http://www.youtube.com/watch?v.....ge#t=2304s

    And the argument from divisibility has empirical validation:

    Miracle Of Mind-Brain Recovery Following Hemispherectomies – Dr. Ben Carson – video
    http://www.metacafe.com/watch/3994585/

    Removing Half of Brain Improves Young Epileptics’ Lives:
    Excerpt: “We are awed by the apparent retention of memory and by the retention of the child’s personality and sense of humor,” Dr. Eileen P. G. Vining; In further comment from the neuro-surgeons in the John Hopkins study: “Despite removal of one hemisphere, the intellect of all but one of the children seems either unchanged or improved. Intellect was only affected in the one child who had remained in a coma, vigil-like state, attributable to peri-operative complications.”

    Strange but True: When Half a Brain Is Better than a Whole One – May 2007
    Excerpt: Most Hopkins hemispherectomy patients are five to 10 years old. Neurosurgeons have performed the operation on children as young as three months old. Astonishingly, memory and personality develop normally. ,,,
    Another study found that children that underwent hemispherectomies often improved academically once their seizures stopped. “One was champion bowler of her class, one was chess champion of his state, and others are in college doing very nicely,” Freeman says.
    Of course, the operation has its downside: “You can walk, run—some dance or skip—but you lose use of the hand opposite of the hemisphere that was removed. You have little function in that arm and vision on that side is lost,” Freeman says. Remarkably, few other impacts are seen. ,,,
    http://www.scientificamerican......than-whole

    Moreover there is also “consistent” empirical validation as to the fact that it is not the brain, or some part thereof, that is doing the seeing of your body, but that it is ‘you’, your soul, which is doing the actual seeing of your body:

    Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This ‘anomaly’ is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).)
    http://www.newdualism.org/nde-.....-147-1.pdf

    Blind Woman Can See During Near Death Experience (NDE) – Pim von Lommel – video
    http://www.metacafe.com/watch/3994599/

    And of course there is that whole ‘conscious observer’ enigma at the root of quantum mechanics that refuses to be swept under the rug by materialists (although they certainly try):

    Quantum physics says goodbye to reality – Apr 20, 2007
    Excerpt: They found that, just as in the realizations of Bell’s thought experiment, Leggett’s inequality is violated – thus stressing the quantum-mechanical assertion that reality does not exist when we’re not observing it. “Our study shows that ‘just’ giving up the concept of locality would not be enough to obtain a more complete description of quantum mechanics,” Aspelmeyer told Physics Web. “You would also have to give up certain intuitive features of realism.”
    http://physicsworld.com/cws/article/news/27640

    Verse and music

    John 1:9-10
    The true light that gives light to everyone was coming into the world. He was in the world, and though the world was made through him, the world did not recognize him.

    Brandon Heath – The Light In Me – video
    http://www.youtube.com/watch?&v=VdAKabU3nOM

  2. VJ I think you are far far to generous as to what they have ‘shown’. These exercises in imagination are hardly impressive, more amusing than anything.

    For some time now, Darwinists have been fighting – and generally winning – arguments against critics who contended that Darwinian evolution was impossible.

    Winning somewhere, but not in reality.

    …by constructing theoretical models showing that a step-by-step evolutionary sequence from a hypothetical ancestor to its modern-day descendants would have been viable at each and every stage, and that each step along the way would have conferred a fitness advantage on the creature possessing it.

    Flights of fancy – I just don’t think that can be taken seriously

  3. Great article, mr. Torley. The emperor has no longer any clothes. Looking forward to your review of Nilsson’s new paper.
    I’ve gotta hand it to Dawkins, he did fool me big time back in 1994.

  4. When, after a Christmas visit, we watch grandma leave on the train to Miami, we assume that the rest of her journey will be an extrapolation of that first quarter-mile. A creationist unwilling to extrapolate from micro- to macroevolution is as irrational as an observer who assumes that, after grandma’s train disappears around the bend, it is seized by divine forces and instantly transported to Florida.

    I am embarrassed for Coyne. That has got to be one of the stupidest things I have ever heard anyone say. And in a professional magazine to boot.

    Facepalm.

  5. Neither Nilsson nor Pelger know how many mutations it takes to get an eye from an eye-spot. No one knows.

  6. To suppose 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. – Charles Darwin

    Yes, Mr. Darwin, it IS absurd to think such a thing.

  7. However, I don’t wish to sound unduly critical of Nilsson and Pelger’s work: their demonstration that a series of sequential changes, occurring one at a time, could have transformed a light-sensitive spot into a vertebrate eye, was no mean feat, and the acclaim it received was well-deserved.

    You are far too generous. Their paper may have contained some interesting ideas about a potential incremental pathway, but it is deceptive in its attempt to explain anything by Darwinian processes. Further, the authors have basked in almost 20 years of undeserved praise, somewhat like the guy whose resume contains an unearned degree — who when caught lamely says his secretary accidentally added it to the resume and he just never got around to correcting the record. The authors should have come out and corrected the record, rather than standing by and letting clueless people like Dawkins and Coyne propagate myths about what the paper demonstrated.

    I have a hard time being as charitable and sanguine about this whole intellectual fiasco.

  8. When, after a Christmas visit, we watch grandma leave on the train to Miami, we assume that the rest of her journey will be an extrapolation of that first quarter-mile. A creationist unwilling to extrapolate from micro- to macroevolution is as irrational as an observer who assumes that, after grandma’s train disappears around the bend, it is seized by divine forces and instantly transported to Florida.

    It is really hard to know if grandma will ever arrive at Miami when she is laying the track, randomly directed, one rail at a time, as she goes.

  9. Hi sterusjon,

    I like the analogy you proposed. It’s very apt.

  10. Hi Eric Anderson,

    Thank you for your post. I don’t know why Nilsson and Pelger didn’t correct the scientists who propagated myths about their paper, earlier on. But I’m very grateful for the clarification which Professor Nilsson sent me, as it unambiguously contradicts what many Darwinist biologists have been saying about Nilsson and Pelger’s 1994 paper. For that reason alone, it’s enormously useful. Some day, the myth surrounding the paper will be punctured, and it will be properly appreciated for what it is.

  11. taking a patch of light-sensitive epithelium as the starting point, we avoid the more inaccessible problem of photoreceptor cell evolution (Goldsmith 1990; Land and Fernald 1992). Thus if the objective is limited to finding the number of generations required for the evolution of the eye’s optical geometry, then the problem becomes solvable.

    Emphasis mine
    How convenient. It’s always easy to climb Dawkins’ Mount Improbable when you’re starting on step #10,837.

  12. It is really hard to know if grandma will ever arrive at Miami when she is laying the track, randomly directed, one rail at a time, as she goes.

    Might I also add that there is no Miami in the Darwinian scenario, either. To imply that is to impart teleology to the whole shebang.

  13. Oh, and those rails that are being laid? How were they made? From what materials? How was the underlying support structure put into place? How does the proper gauge appear so that the distance between tracks is exactly the same every time? That’s not even talking about the train!

    There is an absolute wealth of pro-ID material that can be mined from Coyne’s words that he, ironically, meant as an attack on the same.

  14. Semi OT: Another phylum gets pushed back to the Cambrian:

    Strange Phallus-Shaped Creature Pushes Fossil Record Back 200 Million Years – Mar. 12, 2013
    Excerpt: The fossils were found in an area of shale beds that are 505 million years old .
    “Our description of Spartobranchus tenuis, a creature previously unknown to science, pushes the fossil record of the enteropneusts back 200 million years to the Cambrian period, fundamentally changing our understanding of biodiversity from this period.”,,,
    “It’s astonishing how similar Spartobranchus tenuis fossils are to modern day acorn worms, except that they also formed fibrous tubes.” The tubes provide a key missing link that connects the two main hemichordate groups. “The explosive radiation of graptolites in the Paleozoic planktonic ecosystems is known only from the diversity of their tubes. Our findings suggest that the tubes were lost in the lineage leading to modern day enteropneusts, but elaborated on in graptolites and retained to the present day in pterobranchs” added Cameron.,,
    http://www.sciencedaily.com/re.....141450.htm

  15. I gather from the OP that the end product of the evolutionary sequence that Nilsson and Pelger present is an eye that is stationary within the organism. Mammalian eyes, however, come in pairs that move within their eye sockets in a coordinated fashion. I would love to see a proposed evolutionary sequence, designed or otherwise, that could produce the detachment of the eye from its socket, the musculature required to move it, the nervous structure required to control those muscles, and the brain processing required to interpret nerve signals from those eyes into bicameral images and generate appropriate muscular responses from that information. And of course, each small step would have to confer a fitness advantage.

    The reason Nilsson and Pelger’s scheme worked at all is because they were dealing with a relatively simple system (when one ignores the biochemistry)—a cornea, a lens, a retina, and a space that contained them. This made it easy to make small changes each of which improved the system’s functioning (visual acuity). In order to accomplish this sleight of hand, however, they had to ignore the rest of the organism in which the eye functioned, in particular the concomitant changes that would be required to the nervous system. As soon as one begins to consider realistically complex biological systems, it rapidly becomes impossible to imagine how major modifications can come about through a series of small incremental changes, each of which has to improve fitness.

    I agree with Eric Anderson—Jerry Coyne’s train analogy is truly, monumentally stupid.

  16. Bruce David @15:

    Excellent point about the authors ignoring much of the detail of the real system as it functions in the real world (including RexTugwell’s observation @11). What they “evolved” in their paper was a caricature of real biology.

    I’ve said it before and will say it again as it relates to macroevolutionary changes (like the mammalian eye):

    The perception of evolution’s explanatory power is inversely proportional to the specificity of the discussion.

  17. This is a great article, vjtorley.

    I didn’t really read it, but I scrolled through it, and saw the pictures, which gave me all the info I needed to be able to determine that evolution could never have produced the eye:

    - A train: which is a human made thing.
    - Diagrams of the eye, which has complexity/FSC/DFSCI/CSI.
    - Dawkins and Coyne, Athesist Materialist Darwinists (we know they’re always wrong)
    - Some dice, which shows how unlikely it is that the thing that already happened could happen.
    - More biology, which has so much FSC/DFSCI/CSI.

    Well written. Looking forward to learning more about the impossibility of evolution.

  18. RexTugwell,

    How convenient. It’s always easy to climb Dawkins’ Mount Improbable when you’re starting on step #10,837.

    More like using a bulldozer to level out all that rugged terrain, I’d say. Makes the claim to Hillary-an feats rather vacuous.

    Stephen

  19. Semi OT: Complex Arthropod Eyes Found in Early Cambrian – June 2011
    Excerpt: Complex eyes with modern optics from an unknown arthropod, more complex than trilobite eyes, have been discovered in early Cambrian strata from southern Australia.,,, Here we report exceptionally preserved fossil eyes from the Early Cambrian (~515 million years ago) Emu Bay Shale of South Australia, revealing that some of the earliest arthropods possessed highly advanced compound eyes, each with over 3,000 large ommatidial lenses and a specialized ‘bright zone’. These are the oldest non-biomineralized eyes known in such detail, with preservation quality exceeding that found in the Burgess Shale and Chengjiang deposits. Non-biomineralized eyes of similar complexity are otherwise unknown until about 85 million years later. The arrangement and size of the lenses indicate that these eyes belonged to an active predator that was capable of seeing in low light. The eyes are more complex than those known from contemporaneous trilobites and are as advanced as those of many living forms. They provide further evidence that the Cambrian explosion involved rapid innovation in fine-scale anatomy as well as gross morphology,
    http://crev.info/content/11062.....y_cambrian

    ===================

    Evolution vs. The Trilobite Eye – Andy McIntosh
    http://www.metacafe.com/watch/4032589/

    The Optimal Engineering Of The Trilobite Eye – Dr. Don Johnson
    https://docs.google.com/document/pub?id=1TiZcs0eginyh6rijCGd3kwC3CeawjQV1AsC6Xvvnx44

  20. New Fossils Demonstrate That Powerful Eyes Evolved in a Twinkling – June 30, 2011
    http://www.sciencedaily.com/re.....132546.htm

  21. 21

    This is a great article, vjtorley.

    I didn’t really read it, but I scrolled through it, and saw the pictures, which gave me all the info I needed to be able to determine that evolution could never have produced the eye

    LOL!

    UD Editors: Nick, we assume you don’t know that comments like this make you look like an idiot. Otherwise you would not make them. Accordingly, for your dignity’s sake, we are informing you as follows: “Comments like this make you look like an idiot.”

  22. 22

    “I didn’t really read it, but I scrolled through it, and saw the pictures, which gave me all the info I needed to be able to determine that evolution could never have produced the eye:”

    That is funny, in an ironic sort of way. It is unintentional satire of the common Darwinist UD commenter, who, having admittedly not read the article, proceeds to critique it by playfully knocking over straw men and steering well clear of the substance. While the comment was probably intended to mock ID, it almost brilliantly mocks the usual ID critic. The work crescendos with the laughable error that ID attempts to, and must, demonstrate that the neo-Darwinian scenario is logically impossible. Nicely Done.

  23. 23

    Who needs science magazines when you got UD threaqds!
    Well done.
    I do think the eye is a killer point for creationists.
    The big point also being how we all have , almost, the same design for a eye.
    dinosaurs had our eyes.
    Unlikely that such mutation friendly time would of just come up with almost one idea!
    I think creationism could help healing eyesight by a foundation of eyes coming from a single equation.
    So the other eye types are also just a \variety on a single plan.
    insect eyes could be a clue to all eye sight workings and a clue to healing.
    Just speculating.

  24. Eric Anderson @16

    The perception of evolution’s explanatory power is inversely proportional to the specificity of the discussion.

    How To Do It: A Darwinian guide solving materialism’s most difficult challenges.

  25. ‘thus stressing the quantum-mechanical assertion that reality does not exist when we’re not observing it.’

    This, would seem to confirm, Philip, would it not, that the heavenly rebirth of Christ evidenced by the markings of the Shroud of Turin (his birth being implicit, of course) that each birth of a human being, at the point where mindfulness comes into existence, is the creation of a devolved singularity, whereby a whole new personal world is created, a process iterated at our death and resurrection on an overtly preternatural plane, after the pattern of Christ’s Resurrection, as we pass from one world/plane to another.

  26. Anything can evolve in a geological blink if you’re not looking.

    Nick Matzke,

    Did I miss where you supplied me with the name of a textbook on Macro-Evolutionary Theory, or have you remained silent because you really have nothing to offer?

    Did I also fail to see the post where you explained how macro-evolution works in single celled organisms absent any biochemical changes?

    Or are you just another fraud posing as an “educator”?

  27. 27

    How To Do It: A Darwinian guide solving materialism’s most difficult challenges.

    Lol! I didn’t know that playing the flute could be so easy! Tomorrow I’ll take up the cello and violin.

  28. Hi Eric Anderson,

    I loved this comment of yours:

    The perception of evolution’s explanatory power is inversely proportional to the specificity of the discussion.

    That says it all.

  29. bornagain77,

    Thanks very much for the links on Cambrian eyes. I’ll be discussing that topic in my next post.

  30. Dr. Torley, I don’t know if you are interested, but I have various assorted notes (in no particular order) on the eye that I’ve collected for a few years. There may be a few gems in there you might be interested in if you have 5 or 10 minutes to peruse the notes:

    The Miracle Of Eyesight
    https://docs.google.com/document/d/1QpHlMJNngXsGFZAw5hKVYflGFdGl9co0hD6qD3FLY6E/edit

  31. A Pessimistic Estimate of the Time Required for an Eye to Evolve“, is a highly deceptive title. Nilsson and Pelger should have at least added “at the morphological level” and probabably also “which is next to nothing in comparison with the molecular level” and “BTW, we’ve forgotten about the brain”

  32. 32

    21
    NickMatzke_UDMarch 19, 2013 at 1:55 pm

    This is a great article, vjtorley.

    I didn’t really read it, but I scrolled through it, and saw the pictures, which gave me all the info I needed to be able to determine that evolution could never have produced the eye

    LOL!

    UD Editors: Nick, we assume you don’t know that comments like this make you look like an idiot. Otherwise you would not make them. Accordingly, for your dignity’s sake, we are informing you as follows: “Comments like this make you look like an idiot.”

    Hmm. So the person who says he didn’t read something, just glanced at the pictures, and concludes that entire scientific fields are bogus is just fine, and I’m the idiot because I expressed some skepticism about the “just look at the pictures” view?

    Good luck conducting your scientific revolution with that kind of attitude…

  33. 33

    This article is indeed above-average for an ID contribution. Unfortunately, it still has various big problems/oversights. It would take a long post to cover them all. Let’s start with the discussion of crystallins, which is a complete shambles:

    Not so fast. What this simplistic approach overlooks is the fact that crystallin comes in various forms – alpha, beta and gamma crystallin – each of which is strikingly different the others in the way it folds up, as these pictures illustrate. What’s more, the Wikipedia article on crystallin acknowledges that the crystallins used in the lens of the eye are quite different from one another, for different classes of animals:

    “The crystallins of different groups of organisms are related to a large number of different proteins, with those from birds and reptiles related to lactate dehydrogenase and argininosuccinate lyase, those of mammals to alcohol dehydrogenase and quinone reductase, and those of cephalopods to glutathione S-transferase and aldehyde dehydrogenase. Whether these crystallins are products of a fortuitous accident of evolution, in that these particular enzymes happened to be transparent and highly-soluble, or whether these diverse enzymatic activities are part of the protective machinery of the lens, is an active research topic.”

    (removing tendentious bolding)

    Random stuff is bolded, as if these provide reasons to question the standard evolutionary account. In fact, the fact that crystallins in different groups are entirely unrelated to each other, and instead each related to enzymes with totally different functions, is evidence that the “crystallin” function is very easy to evolve, and that a great diversity of enzymes can serve as the starting point.

    Then there is a bunch of bafflegab about how changing protein function is supposed to be virtually impossible, ignoring all of the actual peer-reviewed literature on protein evolution, and instead relying wholly on a single Discovery-Institute-produced paper which looked at one specific system and made basic mistakes like (a) trying to convert protein A into protein B, rather than both from a common ancestor; (b) failing to distinguish between essential, compensatory, and neutral differences; (c) failing to survey the diversity of sequences that could perform each function; (d) failing to survey the diversity of entirely different structures that could perform the same function.

    From this one flawed paper, VJ Torley draws a grand conclusion that one should be skeptical not only of the evolution of the system they studied, but all changes of protein function anywhere in evolution, even the case of crystallin evolution. Never mind that there is no such thing as a “sequence target” or “sequence specificity” for crystallins — completely unrelated proteins and structures are able to serve the role!

    In reality, all you really need for crystallin function is a water-soluble protein that remains clear and soluble at elevated concentrations. A great many enzymes would qualify, since most of them are water-soluble, and many of them are already expressed at high concentration in certain cells. Basically any soluble protein expressed at high concentration in a tissue would increase the refractive index of the tissue, and that’s the only function that is needed to be called a “crystallin”.

    As Nilsson notes, in some cases, “crystallins” are IDENTICAL to enzymes serving enzymatic roles in other cells! I.e., a “crystallin” and an “enzyme” can be the SAME FRIGGIN’ PROTEIN! What name you give it depends only on what tissue you find it in.

    This by itself falsifies Torley’s ridiculous assertions here:

    There are good grounds for believing that Darwinian evolution is incapable of transforming a protein that performs one biological function into a different protein which is able to perform a brand new biological function.

    [...]

    The extent to which Darwinian evolution can explain enzymatic innovation seems, on careful inspection, to be very limited. Large-scale innovations that result in new protein folds appear to be well outside its range [5]. This paper argues that at least some small-scale innovations may also be beyond its reach.

    Given these biochemical constraints on what Darwinian evolution can accomplish, it is by no means a foregone conclusion that the alpha crystallins present in the crystalline lens of the vertebrate eye could ever have naturally evolved into beta-gamma crystallins, which belong to an entirely different family. Likewise, it is doubtful whether the three families of crystallins (J1, J2, and J3) found in the eyes of cubozoan jellyfish could have developed from a common molecule without intelligent guidance.

    Actually, enzymes can apparently be “transformed” into “crystallins” with 0% evolution! Just up-regulate the expression in the eye tissue.

    More evidence, from your very own link on crystallin structures:

    Moonlighting Proteins

    Alpha, beta and gamma crystallins are found in most animals, but they are assisted by other crystallins in different animals. Often, these proteins also have another function elsewhere in the body, and are moonlighting as crystallins. Three examples are shown here: delta crystallin from ducks (PDB entry 1hy1) also acts as the enzyme argininosuccinate lyase, epsilon crystallin from elephant shrew (PDB entry 1o9j) is an aldehyde dehydrogenase that acts on retinal, and lambda crystallin from rabbits (PDB entry 3ado) also acts as the enzyme L-gulonate 3-dehydrogenase.

    Whoops! I guess being a crystallin isn’t so hard after all.

    Also, other mistakes:

    What this simplistic approach overlooks is the fact that crystallin comes in various forms – alpha, beta and gamma crystallin – each of which is strikingly different the others in the way it folds up, as these pictures illustrate. What’s more, the Wikipedia article on crystallin acknowledges that the crystallins used in the lens of the eye are quite different from one another, for different classes of animals

    [...]

    Given these biochemical constraints on what Darwinian evolution can accomplish, it is by no means a foregone conclusion that the alpha crystallins present in the crystalline lens of the vertebrate eye could ever have naturally evolved into beta-gamma crystallins, which belong to an entirely different family.

    Has anyone even claimed that these different crystallins are related? (I haven’t researched it.) If not, you are criticizing a non-existent claim. The usual claim about crystallins is the opposite: they have been repeatedly coopted from different, non-crystallin enzymes.

    And, also:

    There’s more. The Wikipedia article on crystallin omits to mention cubozoan jellyfish, which also have complex eyes with crystallin lenses, although their resolution is much poorer than the vertebrate eye. A 1993 paper entitled, J1-crystallins of the Cubomedusan Jellyfish Lens Constitute a Novel Family Encoded in at Least Three Intronless Genes by Piatigorsky, Horwitz and Norman (The Journal of Biological Chemistry, Vol. 2643, No. 16, Issue of June 5, 1993, pp. 11894-11901), refers to three different families of proteins in the eyes of these jellyfish, and then goes on to discuss three particular proteins from the first of these families:

    “The transparent cellular eye lens of the jellyfish (Tripedalia cystophora) contains three major proteins called J1-, J2-, and J3-crystallins. Here we have isolated cDNAs encoding three novel 37-kDa Jl-crystallin polypeptides (JlA, JlB, and J1C) sharing 84-98% identity in amino acid sequences among themselves.”

    The J1-, J2-, and J3-crystallins found in cubozoan jellyfish represent families of proteins. By contrast, the JlA, JlB, and J1C crystallins described in the article above represent three very similar proteins belonging to the same family. (For the benefit of readers who are not familiar with chemical jargon, the 37-kDa figure in the above quote means that the molecule in question is about 37,000 times heavier than a hydrogen atom, or about 3,000 times heavier than a carbon atom. – VJT)

    [...]

    At this point, a Darwinist might point to the 84-98% similarity figure between the three versions of J1-crystallin found in cubozoan jellyfish (JlA, JlB, and J1C) and argue, “It’s pretty easy to imagine one form of J1-crystallin converting into another, isn’t it? And given enough time, what is there to prevent inter-conversion between the J1-, J2-, and J3-crystallins found in cubozoans?” However, even a similarity of 84% between two proteins of the same family is not as impressive as it sounds. What it means is that these two proteins, each of which contains several thousand atoms, have hundreds of chemical differences between them. And this is the point where the numbers really start to matter.

    For someone claiming that numbers matter, you didn’t try very hard. J1-crystallins are only about 260 amino acids long:

    http://www.ncbi.nlm.nih.gov/pr.....crystallin

    84% similar would mean about 42 differences in amino acid sequence, or about 21 on each sister lineage, not hundreds/thousands of changes! Is this really so hard to accept over millions of years of evolution? Furthermore, the typical situation in proteins is that most changes are basically conservative and neutral, so you can’t even argue that all those changes were required, had to happen at once, or even had to be the product of selection.

    I changed my mind. Actually VJ Torley’s piece isn’t above average, it’s just standard ID blustering-without-doing-the-bare-minimum-to-understand-the-basics. The same low-quality, low-effort, know-the-answer-so-won’t-bother-with-the-research junk that ID puts out every day. Too bad.

    For some time now, Darwinists have been fighting – and generally winning – arguments against critics who contended that Darwinian evolution was impossible. They have won these arguments in two ways: firstly, by identifying a scientific flaw in their critics’ assumptions, which either invalidates their anti-Darwinian arguments or calls them into question

    Well, that part is right at least.

  34. 34

    As for the Berlinski article, Dawkins’s “computer simulation” mistake, etc. — this was all well covered in the responses to Berlinski’s article that were published in Commentary in a subsequent issue:

    http://www.talkreason.org/articles/blurred.cfm

    E.g., my response — see also Nilsson’s response from back then.

    Berlinski’s Blurred Vision
    By Nicholas Matzke
    Goleta, CA

    While Berlinski should be congratulated for pointing out Dawkins’ inaccurate popularization of Nilsson and Pelger’s article on eye evolution as a stochastic computer simulation (it was actually a mathematical model), Berlinski should remove the plank from his own (discussion of the) eye. In “A Scientific Scandal” he asserts that one of the problems for eye evolution that Nilsson and Pelger did not consider was how the skull would be “reconstructed” to include eye sockets.

    But as any decent student who has taken even high school biology would know (at least as long as evolution was not expunged due to creationist political arm twisting), eyes evolved before bones! Cephalochordates, the closest invertebrate relatives of vertebrates, have primitive eyes but no bones. In fact, based on genetic evidence many biologists now think that vertebrate eyes share a common ancestral eyespot with insect eyes, the common ancestor being a perhaps millimeter-long, nearly transparent but eyespot-equipped worm.

    Unfortunately, it is a typical creationist strawman to envision eye evolution as occurring on some kind of mythical ancestral eyeless fish with a fully formed skull, brain, etc. On the contrary, biologists (who actually know some biology) know that all manner of gradations of eye complexity exist in extant organisms, from creatures with an “eye” consisting of a single photoreceptor cell, through all of the various stages that Nilsson and Pelger depict, to the “advanced” camera eyes of mammals and cephalopods. Sometimes the whole sequence from eyespot to advanced eye with lens can be seen in a single group (e.g. snails), yet another thing which Berlinski would have known if he’d followed the reference that Nilsson and Pelger gave to the actual classic work on eye evolution, a monster 56 page article by Salvini-Plawen and Mayr in the journal Evolutionary Biology (volume 10, 1977) that reviewed hundreds of papers on eyes across the animal kingdom, and with the fairly clear title “On the evolution of photoreceptors and eyes”. The paper answers many of the questions which Berlinski asserts are unanswered or unanswerable. Complex eyes with lenses have even evolved in single-celled dinoflagellates, which have no blood vessels, brains, or numerous other features Berlinski is concerned about.

    Berlinski on the other hand has a brain as well as eyes, but apparently does not see when it comes to biology. He is not a creationist but he certainly seems to hang out with them and uncritically repeats many of their arguments, unaware of the biological facts that contradict them. If Berlinski is going to declare as bunk the central organizing theory of biology, he should be taking the matter up with biologists in the professional literature, rather than in forums like Commentary, wherein elementary questions like “which came first, skulls or eyes?” can be botched and yet still get published.

    Heck, my response from 10 years ago covers several silly remarks people are making even in this thread.

    1. Skulls came long after eyes. If you are imagining that eyes evolved in a fish or something with a complete skull, skin, etc., you are doing it wrong. Tiny transparent worms would be a lot closer to the truth.

    2. Brains and muscles and the rest are unnecessary for camera eyes, as proven by single-celled critters with camera eyes.

    3. IDists/creationists constantly and irremediably make biology mistakes of the most basic sort, can’t be bothered to double-check before asserting mistaken scientific “facts”, don’t correct each other’s mistakes, and don’t improve over time. Instead it’s “amateur hour” forever failing to even reach mediocrity.

    4. And this is why serious scientists, who do know the facts, won’t ever take IDists seriously. They haven’t earned it.

  35. Nick,

    Thank you for your posts. I was expecting to hear from you. A few quick points:

    1. Pardon my directness, but your posts are a classic example of not seeing the wood for the trees. The two main points about Nilsson and Pelger’s model which I made in my article were that (a) the model was not based on a computer simulation, and (b) each and every one of the 1,829 steps from a light-sensitive spot to a vertebrate eye was planned in painstaking detail, by Nilsson and Pelger. The first point is of course old news: it was made by Dr. Berlinski many years ago, as I acknowledged in my post. The second point, however, is big news: most evolutionary biologists (including Professors Jerry Coyne and Richard Dawkins) are apparently still under the impression that the model employed random variations, when in fact it did nothing of the sort. At the very least, Coyne will have to re-write his textbook, Why Evolution is True, as it makes a factually incorrect claim: “They [Nilsson and Pelger - VJT] then allowed the tissues around this structure to deform themselves randomly, limiting the amount of change to only 1% of size or thickness at each step.” (Emphasis mine – VJT.) That’s not true.

    2. I then put forward no less than eight reasons why the 364,000-year estimate provided by Nilsson and Pelger in their paper could not be taken seriously. You focused on just one of my reasons, relating to biochemistry. (I’ll say more about that below.) Even if you were correct in your criticisms, that still leaves seven good reasons for dismissing the estimate.

    3. I then argued that in the absence of a credible estimate for how long it would have taken an eye to evolve from a light-sensitive spot, Nilsson and Pelger could not be said to have demonstrated that the evolution of the eye by natural selection was scientifically plausible, and that their paper therefore could not be legitimately invoked in support of Darwinism. Rather, it supports a gradualistic version of Intelligent Design, as each their model merely demonstrates that a clever designer could transform a light-sensitive spot into a vertebrate eye, one step at a time.

    4. You spend a great deal of time bringing up points from Berlinski’s 2003 article, A Scientific Scandal? David Berlinski & Critics (Commentary, July 8, 2003), which I never made in my article. Sorry Nick, but we’re in the year 2013 now, not 2003. The fact that I quote from an article like Berlinksi’s does not mean that I endorse it in its entirety. Yes, I am well aware that skulls came long after eyes. (So what?) I’ve read the criticisms of Berlinski on the Internet; that was why I was careful about what I quoted from his article. The quotes which I made from Berlinski’s article in my post related to substantial criticisms of Nilsson and Pelger’s model, which evolutionary biologists have never satisfactorily answered.

    5. You write:

    As Nilsson notes, in some cases, “crystallins” are IDENTICAL to enzymes serving enzymatic roles in other cells! I.e., a “crystallin” and an “enzyme” can be the SAME FRIGGIN’ PROTEIN! What name you give it depends only on what tissue you find it in.

    Nick, why are you shouting? I already know this. Here’s a quote from the Wikipedia article on crystallin, which I cited in my post:

    The main function of crystallins at least in the lens of the eye is probably to increase the refractive index while not obstructing light. However, this is not their only function. It is becoming increasingly clear that crystallins may have several metabolic and regulatory functions, both within the lens and in other parts of the body.

    And here’s a quote from my post, above:

    Indeed, it turns out that the lenses of both vertebrate and cephalopod eyes are made of a protein called crystallin, and as this paper shows, crystallin is a protein which can be found even in simple sponges.

    I’m quite familiar with co-option, Nick. I wasn’t born yesterday, you know. The criticism I made was not about the difficulty of transforming “enzymes” used in other parts of the body into “crystallins” – for as you correctly note, that would require 0% evolution: they’re already there in the body. The real difficulty, as I pointed out, was about converting one kind of crystallin (e.g. alpha-crystallin) into another (e.g. beta-gamma-crystallin). As I wrote in my post:

    There are good grounds for believing that Darwinian evolution is incapable of transforming a protein that performs one biological function into a different protein which is able to perform a brand new biological function.

    Nothing in the foregoing quote rules out the possibility of one protein having two or more biological functions within the human body. My point was simply that proteins that do one or more jobs seem incapable of evolving into new kinds of proteins whose chemical configuration allows them to do different jobs.

    6. You make the following astonishing remark:

    Has anyone even claimed that these different crystallins are related? (I haven’t researched it.) If not, you are criticizing a non-existent claim.

    Let me ask you directly: are you now conceding that it’s impossible for proteins in one family to evolve into proteins from another family, over geological time? Are you saying that J1-crystallin can’t transform into J2-crystallin, and that alpha-crystallin can’t be transformed into beta-gamma-crystallin, over a period of billions of years? That would be quite a concession, Nick. You might want to ask your biochemist friends before making a concession that you subsequently regret.

    7. In my post, I wrote:

    However, even a similarity of 84% between two proteins of the same family is not as impressive as it sounds. What it means is that these two proteins, each of which contains several thousand atoms, have hundreds of chemical differences between them.

    When I said “hundreds of differences,” I was talking about atoms. As I pointed out in my post, the J1-crystallin molecules weigh 37,000 daltons each, which is about the weight of 3,000 carbon atoms. So a 16% difference would still mean a difference of a few hundred atoms: hardly a difference to be sneezed at.

    You wrote:

    For someone claiming that numbers matter, you didn’t try very hard. J1-crystallins are only about 260 amino acids long:

    http://www.ncbi.nlm.nih.gov/pr…..crystallin

    84% similar would mean about 42 differences in amino acid sequence, or about 21 on each sister lineage, not hundreds/thousands of changes!

    We’re both correct here, but on different levels. You’re talking about amino acids; I’m talking abut atoms. But let’s go with amino acids, as the changes involved would have occurred on that level. You argue that that 21 amino acid changes on each sister lineage isn’t such a lot. But the article by Drs. Gauger and Axe, entitled, The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway (BIO-Complexity 2011(1):1-17. doi:10.5048/BIO-C.2011.1) which I cited above claims that even “seven or more nucleotide substitutions” in an enzyme may be beyond the reach of Darwinian evolution. (And before you start putting words into my mouth, I’m well aware that a nucleotide isn’t the same thing as an amino acid.)

    Note too that we’re just talking here about two proteins belonging to the same family: the J1-family of crystallins, found in jellyfish.

    Note also that I avoided dogmatism in my article: I did not say that inter-conversion between J1A and J1B-crystallin was impossible, as I was well aware that they belong to the same family. I merely claimed that its possibility had not been demonstrated. I then argued that if even this inter-conversion was difficult for evolution to accomplish, then a fortiori, conversions between proteins of different families would be all the more difficult.

    8. You dismiss the paper I cited by Drs. Gauger and Axe in one paragraph:

    Then there is a bunch of bafflegab about how changing protein function is supposed to be virtually impossible, ignoring all of the actual peer-reviewed literature on protein evolution, and instead relying wholly on a single Discovery-Institute-produced paper which looked at one specific system and made basic mistakes like (a) trying to convert protein A into protein B, rather than both from a common ancestor; (b) failing to distinguish between essential, compensatory, and neutral differences; (c) failing to survey the diversity of sequences that could perform each function; (d) failing to survey the diversity of entirely different structures that could perform the same function.

    Nick, Dr. Douglas Axe has published in the Journal of Molecular Biology and the Proceedings of the National Academy of Sciences. Dr. Ann Gauger has published in the Journal of Biological Chemistry. They’re no slouches, and they don’t make stupid mistakes. You’re a doctoral student; with all due respect, I think their credibility on protein evolution is considerably greater than your own.

    May I also point out that the criticisms you raise have been answered already, in the following tow posts at Evolution News and Views:

    On Protein Evolution, PZ Myers Is Way Off the Mark and On Enzymes and Teleology, both by Dr. Ann Gauger. Here’s an excerpt from the second post (emphases mine), written in response to criticisms by Paul McBride:

    Our results indicated that a minimum of seven mutations would be required to convert or reconfigure one enzyme toward the other’s function. No one disputes that part of our research. What Paul McBride and others claim is that because we didn’t start from an “ancestral” enzyme, our results mean nothing. They say something like, “Of course transitions to new chemistries between modern enzymes are difficult. What you should have done is to reconstruct the ancestral form and use it as a starting point.”

    Have you noticed the assumption underlying this critique? The assumption is that genuine conversions can be achieved only if you start from just the right ancestral protein. Why is that? Because conversions are hard.

    McBride said as much in his post, tacitly acknowledging the legitimacy of our results, in the following quote:

    Any biologist or biochemist could imagine useful new molecules in a given species that would aid their survival. Little imagination is needed, as many examples are found in other species. A simple example: an enzyme that breaks down cellulose into simple sugars would be immensely beneficial for virtually any heterotroph, yet such cellulases are only found in a handful of organisms, restricted to certain clades. Evolution is not a process that is capable of producing anything and everything, at all times in all species. It is, conversely, a greatly constrained process. A developmental biologist such as PZ Myers knows the minutiae of this constraint in particular models. Much of the process of evolution is guided by purifying selection – pruning those mutants that are at relative disadvantages to the general population – and most of the genomic change that does spread through populations is neutral and escapes selection altogether. Yes, transitioning between different enzyme functions is hard, but this is evidenced by it being relatively uncommon. In a broader sense, and to reiterate, many of the possible variations on life that we could imagine to exist do not exist. [Emphasis added.]

    The problem then becomes, where did the diverse families of enzymes come from, if transitions are so hard, evolution is so constrained, and selection is so weak? Were the ur-proteins from which present families sprang so different from modern ones, so elastic that they could be easily molded to perform multiple functions? If so, how did they accomplish the specific necessary tasks for metabolism, transcription, and replication?

    More than that, how did the proteins necessary for replication, transcription, translation, and metabolism arrive at all, if evolution is so constrained? Those processes are much more complicated that a cellulase enzyme. We have ribosomes, spliceosomes, photosynthesis, and respiration. We have hummingbirds and carnivorous plants and even cows who make use of cellulose-degrading symbionts. The things that have not arrived or arrived very rarely, like cellulases, seem trivial by comparison to the things we see around us.

    If I were you, Nick, I’d think again, before dismissing what Drs. Gauger and Axe wrote as “one flawed paper.”

    More to the point, the key issue which I raised on this post is whether Nilsson and Pelger’s post could be legitimately used to argue in support of Darwinism. You have utterly failed to show that it can be. My criticisms still stand.

  36. 36
    englishmaninistanbul

    A Pessimistic Estimate of the Time Required for a Non Sequitur to Evolve

  37. Incredibly Mr. Matzke appeals to the already present multifunctionality of proteins as proof that proteins can evolve into new functions. This is simply completely ludicrous for him to do so.,,,

    Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein – Cornelius Hunter – December 1, 2012
    Excerpt: Simply put, evolution either must have evolved two independent designs simultaneously in the same protein, or it must have been a two-fer, evolving the one design and getting the second for free. Either way the evidence does not bode well for evolution.
    http://darwins-god.blogspot.co.....olved.html

    Moonlighting Proteins: Proteins with Multiple Functions – Online Publication date 2009

    Introduction

    Moonlighting proteins, also referred to as ‘gene sharing’, refer to a subset of multifunctional proteins in which two or more different functions are performed by one polypeptide chain, and the multiple functions are not a result of splice variants, gene fusions, or multiple isoforms [1]. In addition, they do not include proteins with the same function in multiple locations or protein families in which different members have different functions, if each individual member has only one function. A single protein with multiple functions may seem surprising, but there are actually many cases of proteins that ‘moonlight’.

    Examples and mechanisms of combining two functions in one protein:

    The current examples of moonlighting proteins include enzymes, DNA binding proteins, receptors, transmembrane channels, chaperones and ribosomal proteins (Table 4.1). In general, there are several different methods by which a moonlighting protein can combine two functions within one polypeptide chain. A single protein can have a second function when it moves to a different cellular location; when it is expressed in a different cell type; when it binds a substrate, product, or cofactor; when it interacts with another protein to form a multimer, or when it interacts with a large multiprotein complex. In addition, a few enzymes have two active sites for different substrates (Figure 4.1). The methods are not mutually exclusive and sometimes a combination of methods is employed.
    http://ebooks.cambridge.org/ch.....546310A013

    Moreover, even though the cell is permeated with multifuctional proteins, neo-Darwinian processes are shown to grossly inadequate to account for even a simple function:

    It is interesting to note, in contrast to Axe’s 1 in 10^77 estimate, that the 1 in 10^12 (trillion) estimate for functional proteins (Szostak), that some Darwinists cite from time to time, though still very rare and of insurmountable difficulty for a materialist to use in any evolutionary scenario,,,,

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

    ,,, is detrimental. Szostak’s ‘evolved’ 1 in 10^12 ATP binding protein (although the binding protein was arrived at by intelligent guidance) is shown to be detrimental to life:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells – 2009
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    Strange Behavior: New Study Exposes Living Cells to Synthetic Protein – Dec. 27, 2012
    Excerpt: ,,,”ATP is the energy currency of life,” Chaput says. The phosphodiester bonds of ATP contain the energy necessary to drive reactions in living systems, giving up their stored energy when these bonds are chemically cleaved. The depletion of available intracellular ATP by DX binding disrupts normal metabolic activity in the cells, preventing them from dividing, (though they continue to grow).,,,
    In the current study, E. coli cells exposed to DX transitioned into a filamentous form, which can occur naturally when such cells are subject to conditions of stress. The cells display low metabolic activity and limited cell division, presumably owing to their ATP-starved condition.
    The study also examined the ability of E. coli to recover following DX exposure. The cells were found to enter a quiescent state known as viable but non-culturable (VBNC), meaning that they survived ATP sequestration and returned to their non-filamentous state after 48 hours, but lost their reproductive capacity.
    Further, this condition was difficult to reverse and seems to involve a fundamental reprogramming of the cell.
    http://www.sciencedaily.com/re.....143001.htm

    Thus Mr. Matzke, why in blue blazes do think that multifunctional proteins are proof of evolution when you can’t even demostrate the evolution of a single protein that would be beneficial to life?

  38. Nick Matzke,

    Neither you nor anyone else on this planet knows whether or not any eye can evolve from an eyespot via accumulations of genetic accidents. IOW tere aren’t any serious scientists who support that claim that it could.

    Do you even have any way to test your position’s claims? Obvioulsy not, so why don’t you focus on your position’s shortcomings as opposed to trying to bash ID with your ignorance?

  39. VJTorley,

    This looks like an interesting paper:
    Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

    http://link.springer.com/artic.....-3?LI=true

  40. BTW Nick Matzke- Berliski responded to your bit of spewage from 10 years ago.

    You do realize that humans have skulls, fish have skulls, well many organisms with eyes have skulls, Nick. Right? You do know that?

  41. kuartus,,, and how is the ‘narrative’ that you cited, that uses ‘tree thinking’ to try to establish neo-Darwinian evolution as legitimate, any different from the multitude of ‘just so’ stories we have seen thus far from Darwinists that have ZERO empirical confirmation as to their plausibility?

    Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution – 2008
    Eyes provide a rich narrative for understanding evolution, having attracted the attention of preeminent scientists and communicators alike. Until recently, this narrative has focused primarily on the evolution of eye structure and far less on biochemistry or genetics. Although eye biochemistry was once likened to an unknown “black box;” the flood of discoveries in biochemistry is now allowing an increasingly detailed understanding of the processes involved in vision. As a result, evolutionary comparative (“tree-thinking”) analyses that use these data currently allow a new and still unfolding narrative, both richer in detail and more comprehensive in scope. Rather than toppling evolutionary theory by finding irreducibly complex molecular machines, eye evolution provides detailed accounts of how natural processes tinker with existing genetic components, duplicating and recombining them, to yield complex, intricate, and highly functional eyes. Understanding the new biochemical narrative is critical for researchers and teachers alike, in order to answer anti-evolutionist claims, and to provide an up-to-date account of the state of knowledge on the subject of eye evolution.
    http://link.springer.com/artic.....-3?LI=true

    If I wanted ‘narrative story telling’ that presupposes ‘tree thinking’ to arrive at its conclusion I would buy a Tarzan novel! :) But alas we are dealing with science, (not with narrative story telling), the goal of which is not to assume your conclusion into the premise of your argument, as Darwinists continually do, but which is to prove your premise true by empirical demonstration independent of the ‘narrative’ so that the ‘narrative’ may be supported or not. And that is exactly what Darwinian story tellers do not have!:

    Is gene duplication a viable explanation for the origination of biological information and complexity? – December 2010 –
    Excerpt: The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. © 2010 Wiley Periodicals, Inc. Complexity, 2011
    http://onlinelibrary.wiley.com.....5/abstract

    The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations Douglas D. Axe*
    Excerpt: In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes—genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here (d ? 2 for the maladaptive case, and d ? 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large.
    http://bio-complexity.org/ojs/.....O-C.2010.4

    An Insurmountable Problem for Darwinian Evolution – Gene Duplication – And Minor Transformation of Protein Function – May 2011
    http://intelligentdesign.podom.....1_43-07_00

    “Biologist Douglas Axe on Evolution’s (non) Ability to Produce New (Protein) Functions ” – video
    Quote: It turns out once you get above the number six [changes in amino acids] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
    http://intelligentdesign.podom.....5_14-07_00

    Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness – May 2010
    Excerpt: Despite the theoretical existence of this short adaptive path to high fitness, multiple independent lines grown in tryptophan-limiting liquid culture failed to take it. Instead, cells consistently acquired mutations that reduced expression of the double-mutant trpA gene. Our results show that competition between reductive and constructive paths may significantly decrease the likelihood that a particular constructive path will be taken.
    http://bio-complexity.org/ojs/.....O-C.2010.2

    Why Proteins (Protein Domains) Aren’t Easily Recombined – Ann Gauger – May 2012
    Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
    http://www.biologicinstitute.o.....recombined

  42. 42
    William J Murray

    I think that what most anti-ID advocates fail to understand is that when an ID advocate states that there is no evidence for “evolution”, what they usually mean is that there is no evidence that necessity and chance (in terms of natural selection and chance mutation) are sufficient explanations for all that we see in biology and in the fossil and molecular record.

    ID theory doesn’t claim that natural selection doesn’t select; or that chance mutation doesn’t occur; it doesn’t claim that common descent-with-modification didn’t occur; in fact, I don’t know of any hard, scientific facts in evolutionary theory that are not fully compatible with ID theory.

    If anti-ID advocates claim that there is no metric (such as IC, FSCO/I, semiotic systems) by which something can be determined to (at least provisionally) require intelligent design as part of the sufficient explanation, then they admit they cannot have any evidence that chance and necessity (operating evolutionary mechanisms) are sufficient explanations for what we see in the biological world – because they have just admitted they have no metric for making such a determination.

    This makes the “chance and necessity” theme that runs throughout the evolutionary narrative nothing more than a metaphysical assumption for which Darwinists themselves claim there is no evidence (i.e., no metric that can make such a determination).

  43. Mr. Matzke, it is interesting to note that in your vein attempt to defend the purely materialistic evolution of the eye that you have presupposed that the universe is materialistic. But that materialistic presupposition is shown to be, due to advances in quantum mechanics, false!

    Quantum Evidence for a Theistic Big Bang
    https://docs.google.com/document/d/1agaJIWjPWHs5vtMx5SkpaMPbantoP471k0lNBUXg0Xo/edit

    The Galileo Affair and the true “Center of the Universe”
    Excerpt: because of advances in Quantum Mechanics, the argument for God from consciousness can now be framed like this:

    1. Consciousness either precedes(ed) all of material reality or is a ‘epi-phenomena’ of material reality.

    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.

    3. Consciousness is found to have a special, even central, position within material reality. [14]

    4. Therefore, consciousness is found to precede material reality.

    I find it extremely interesting, and strange, that quantum mechanics tells us that instantaneous quantum wave collapse to its ‘uncertain’ 3D state is centered on each individual conscious observer in the universe, whereas, 4D space-time cosmology (General Relativity) tells us each 3D point in the universe is central to the expansion of the universe. These findings of modern science are pretty much exactly what we would expect to see if this universe were indeed created, and sustained, from a higher dimension by a omniscient, omnipotent, omnipresent, eternal Being who knows everything that is happening everywhere in the universe at the same time. These findings certainly seem to go to the very heart of the age old question asked of many parents by their children, “How can God hear everybody’s prayers at the same time?”,,, i.e. Why should the expansion of the universe, or the quantum wave collapse of the entire universe, even care that you or I, or anyone else, should exist? Only Theism, Christian Theism in particular, offers a rational explanation as to why you or I, or anyone else, should have such undeserved significance in such a vast universe. [15]

    Psalm 33:13-15
    The LORD looks from heaven; He sees all the sons of men. From the place of His dwelling He looks on all the inhabitants of the earth; He fashions their hearts individually; He considers all their works.
    https://docs.google.com/document/d/1BHAcvrc913SgnPcDohwkPnN4kMJ9EDX-JJSkjc4AXmA/edit

    Moreover Mr. Matzke, it is peculiar that you would try to defend the purely materialistic, ‘random’, origin of the eye. The reason I find this ‘peculiar’ is that conscious observation, which includes ‘seeing’ with the eye,,,

    What does the term “measurement” mean in quantum mechanics?
    “Measurement” or “observation” in a quantum mechanics context are really just other ways of saying that the observer is interacting with the quantum system and measuring the result in toto.
    http://boards.straightdope.com.....p?t=597846

    ,,,is exactly what falsifies your ‘necessary’ random variable postulate at the base of your materialistic/atheistic philosophy. To illustrate this falsification Mr. Matzke, bear with me as I give some background,,

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter”.
    J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

    In the following experiment, the claim that past material states ‘randomly’ determine future conscious choices (determinism) is falsified by the fact that present conscious choices effect past material states:

    Quantum physics mimics spooky action into the past – April 23, 2012
    Excerpt: The authors experimentally realized a “Gedankenexperiment” called “delayed-choice entanglement swapping”, formulated by Asher Peres in the year 2000. Two pairs of entangled photons are produced, and one photon from each pair is sent to a party called Victor. Of the two remaining photons, one photon is sent to the party Alice and one is sent to the party Bob. Victor can now choose between two kinds of measurements. If he decides to measure his two photons in a way such that they are forced to be in an entangled state, then also Alice’s and Bob’s photon pair becomes entangled. If Victor chooses to measure his particles individually, Alice’s and Bob’s photon pair ends up in a separable state. Modern quantum optics technology allowed the team to delay Victor’s choice and measurement with respect to the measurements which Alice and Bob perform on their photons. “We found that whether Alice’s and Bob’s photons are entangled and show quantum correlations or are separable and show classical correlations can be decided after they have been measured”, explains Xiao-song Ma, lead author of the study.

    According to the famous words of Albert Einstein, the effects of quantum entanglement appear as “spooky action at a distance”. The recent experiment has gone one remarkable step further. “Within a naïve classical world view, quantum mechanics can even mimic an influence of future actions on past events”, says Anton Zeilinger.
    http://phys.org/news/2012-04-q.....ction.html

    In other words, if my conscious choices really are just the result of whatever ‘random’ state the material particles in my brain happen to be in in the past (determinism) how in blue blazes are my choices instantaneously effecting the state of material particles into the past?,,

    To add significantly more weight that the ‘randomness’ of material states does not determine conscious choices, here is another piece of evidence that solidly demarcates the randomness of the material particles of the universe from the randomness that would be necessarily inherent within ‘conscious’ creatures that were created by God, in His image, with free will:

    Quantum Zeno effect
    Excerpt: The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay.
    http://www.uncommondescent.com.....ent-445840

    Since material particles are held to ‘randomly’ decay by entropic processes, why in blue blazes is conscious observation putting a freeze on ‘random’ entropic decay, unless consciousness was/is more foundational to reality than ‘random’ entropic decay is? This point that consciousness is found to take precedence over the ‘random’ entropic processes of the universe, is really driven home when we realize that the initial entropy of the universe was 1 in 10^10^123, which is, by a far, far, amount the most finely tuned of initial conditions of the universe. (As well as in realizing that these extremely finely tuned entropic processes of the universe are ubiquitous in scientific explanations,,)

    Roger Penrose discusses initial entropy of the universe. – video
    http://www.youtube.com/watch?v=WhGdVMBk6Zo

    The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose
    Excerpt: “The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).”

    How special was the big bang? – Roger Penrose
    Excerpt: This now tells us how precise the Creator’s aim must have been: namely to an accuracy of one part in 10^10^123.
    (from the Emperor’s New Mind, Penrose, pp 339-345 – 1989)

    Shining Light on Dark Energy – October 21, 2012
    Excerpt: It (Entropy) explains time; it explains every possible action in the universe;,,
    Even gravity, Vedral argued, can be expressed as a consequence of the law of entropy. ,,,
    The principles of thermodynamics are at their roots all to do with information theory. Information theory is simply an embodiment of how we interact with the universe —,,,
    http://crev.info/2012/10/shini.....rk-energy/

    But if entropy can explain ‘everything’, why in blue blazes does conscious observation put a freeze on ‘random’ entropic decay unless consciousness is more foundational to reality than the initial entropy of the universe is?

    “It will remain remarkable, in whatever way our future concepts may develop, that the very study of the external world led to the scientific conclusion that the content of the consciousness is the ultimate universal reality” -
    Eugene Wigner – (Remarks on the Mind-Body Question, Eugene Wigner, in Wheeler and Zurek, p.169) 1961 – received Nobel Prize in 1963 for ‘Quantum Symmetries’

    “The impossibility of conceiving that this grand and wondrous universe, with our conscious selves, arose through chance, seems to me the chief argument for the existence of God.”
    Charles Darwin to Doedes, N. D. – Letter – 2 Apr 1873

    Supplemental note:

    LIVING IN A QUANTUM WORLD – Vlatko Vedral – 2011
    Excerpt: Thus, the fact that quantum mechanics applies on all scales forces us to confront the theory’s deepest mysteries. We cannot simply write them off as mere details that matter only on the very smallest scales. For instance, space and time are two of the most fundamental classical concepts, but according to quantum mechanics they are secondary. The entanglements are primary. They interconnect quantum systems without reference to space and time. If there were a dividing line between the quantum and the classical worlds, we could use the space and time of the classical world to provide a framework for describing quantum processes. But without such a dividing line—and, indeed, with­out a truly classical world—we lose this framework. We must ex­plain space and time (4D space-time) as somehow emerging from fundamental­ly spaceless and timeless physics.
    http://phy.ntnu.edu.tw/~chchan.....611038.pdf

    Music and verse:

    Phillips, Craig & Dean – When The Stars Burn Down – Worship Video with lyrics
    http://www.youtube.com/watch?v=rPuxnQ_vZqY

    Genesis 2:7
    And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul.

  44. William J Murray @ 42

    I think that what most anti-ID advocates fail to understand is that when an ID advocate states that there is no evidence for “evolution”, what they usually mean is that there is no evidence that necessity and chance (in terms of natural selection and chance mutation) are sufficient explanations for all that we see in biology and in the fossil and molecular record.

    I would replace the word ‘understand’ with ‘acknowledge’.

  45. Dr.Torley: “Nick, why are you shouting?”
    Yes, why are you shouting Nicky? Is something the matter?

  46. In support of post 43: Besides conscious observation, (through recent breakthroughs in quantum mechanics), falsifying atheistic materialism as the true description of reality (or even the materialistic evolution of the eye in particular), it is also now found that the universe, and planet earth, are ‘suspiciously’ set up for conscious ‘intelligent’ observers, such as ourselves, to ‘observe’ and discovery the deep mysteries of the universe:

    i.e. Visible light is incredibly fine-tuned for life to exist. Though visible light is only a tiny fraction of the total electromagnetic spectrum coming from the sun, it happens to be the “most permitted” portion of the sun’s spectrum allowed to filter through the our atmosphere. All the other bands of electromagnetic radiation, directly surrounding visible light, happen to be harmful to organic molecules, and are almost completely absorbed by the atmosphere. The tiny amount of harmful UV radiation, which is not visible light, allowed to filter through the atmosphere is needed to keep various populations of single cell bacteria from over-populating the world (Ross; reasons.org). The size of light’s wavelengths and the constraints on the size allowable for the protein molecules of organic life, also seem to be tailor-made for each other. This “tailor-made fit” allows photosynthesis, the miracle of sight, and many other things that are necessary for human life. These specific frequencies of light (that enable plants to manufacture food and astronomers to observe the cosmos) represent less than 1 trillionth of a trillionth (10^-24) of the universe’s entire range of electromagnetic emissions. Like water, visible light also appears to be of optimal biological utility (Denton; Nature’s Destiny).

    Extreme Fine Tuning of Light for Life and Scientific Discovery – video
    http://www.metacafe.com/w/7715887

    Fine Tuning Of Universal Constants, Particularly Light – Walter Bradley – video
    http://www.metacafe.com/watch/4491552

    Fine Tuning Of Light to the Atmosphere, to Biological Life, and to Water – graphs
    http://docs.google.com/Doc?doc.....aGh4MmdnOQ

    Moreover, besides light being extremely fine tuned for life,,,:

    The very conditions that make Earth hospitable to intelligent life also make it well suited to viewing and analyzing the universe as a whole.
    – Jay Richards

    Privileged Planet – Observability Correlation – Gonzalez and Richards – video
    http://www.metacafe.com/watch/5424431

    The Privileged Planet – video
    http://www.youtube.com/watch?v=JnWyPIzTOTw

    The Privileged Planet: How Our Place in the Cosmos Is Designed for Discovery – book By Guillermo Gonzalez, Jay Wesley Richards
    http://books.google.com/books?.....38;f=false

    The following site is very interesting;

    The Scale of The Universe – Part 2 – interactive graph (recently updated in 2012 with cool features)
    http://htwins.net/scale2/scale.....olor=white

    The preceding interactive graph points out that the smallest scale visible to the human eye (as well as a human egg) is at 10^-4 meters, which ‘just so happens’ to be directly in the exponential center of all possible sizes of our physical reality (not just ‘nearly’ in the exponential center!). i.e. 10^-4 is, exponentially, right in the middle of 10^-35 meters, which is the smallest possible unit of length, which is Planck length, and 10^27 meters, which is the largest possible unit of ‘observable’ length since space-time was created in the Big Bang, which is the diameter of the universe. This is very interesting for, as far as I can tell, the limits to human vision (as well as the size of the human egg) could have, theoretically, been at very different positions than directly in the exponential middle of all possible sizes;

    A few more notes of related ‘observability correlation’ interest;

    We Live At The Right Time In Cosmic History – Hugh Ross – video
    http://vimeo.com/31940671

    The End Of Cosmology? – Lawrence M. Krauss and Robert J. Scherrer
    Excerpt: We are led inexorably to a very strange conclusion. The window during which intelligent observers can deduce the true nature of our expanding universe might be very short indeed.
    http://genesis1.asu.edu/0308046.pdf

  47. Dr. Ross points out that the extremely long amount of time it took to prepare a suitable place for humans to exist in this universe, for the relatively short period of time that we can exist on this planet, is actually a point of evidence that argues strongly for Theism:

    Hugh Ross – The Anthropic Principle and The Anthropic Inequality – video
    http://www.metacafe.com/watch/8494065/

    Anthropic Principle: A Precise Plan for Humanity By Hugh Ross
    Excerpt: Brandon Carter, the British mathematician who coined the term “anthropic principle” (1974), noted the strange inequity of a universe that spends about 15 billion years “preparing” for the existence of a creature that has the potential to survive no more than 10 million years (optimistically).,, Carter and (later) astrophysicists John Barrow and Frank Tipler demonstrated that the inequality exists for virtually any conceivable intelligent species under any conceivable life-support conditions. Roughly 15 billion years represents a minimum preparation time for advanced life: 11 billion toward formation of a stable planetary system, one with the right chemical and physical conditions for primitive life, and four billion more years toward preparation of a planet within that system, one richly layered with the biodeposits necessary for civilized intelligent life. Even this long time and convergence of “just right” conditions reflect miraculous efficiency.
    Moreover the physical and biological conditions necessary to support an intelligent civilized species do not last indefinitely. They are subject to continuous change: the Sun continues to brighten, Earth’s rotation period lengthens, Earth’s plate tectonic activity declines, and Earth’s atmospheric composition varies. In just 10 million years or less, Earth will lose its ability to sustain human life. In fact, this estimate of the human habitability time window may be grossly optimistic. In all likelihood, a nearby supernova eruption, a climatic perturbation, a social or environmental upheaval, or the genetic accumulation of negative mutations will doom the species to extinction sometime sooner than twenty thousand years from now.
    http://christiangodblog.blogsp.....chive.html

    Supplemental note:

    Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality in the First Place? – Stephen Meyer – video – (Notes in description)
    http://vimeo.com/32145998

    Music:

    Carrie Underwood with Vince Gill How Great thou Art – 720P HD – Standing Ovation!
    http://www.youtube.com/watch?v=pLLMzr3PFgk

  48. Look Nick,
    You may know a lot about biology and evolution, but you’re missing the point. We’re not saying that the eye didn’t evolve. We’re just saying it evolved by intelligent design (and it also didn’t evolve).

    I mean seriously, if the eye is sooo easy to evolve, why hasn’t it been demonstrated in the lab already. I mean you keep saying that your scientists are so smart, right? So what gives. And anyway if scientists demonstrate eye evolution in the lab, that only goes to show you need intelligent design to evolve an eye.

  49. Lizzie chimes in to respond to WJM:

    What most ID (all?) ID advocates fail to understand is that when scientists say that an ID inference is unwarranted, they are not claiming that “necessity and chance.are sufficient explanations” – they are claiming that there is no evidence that they are insufficient explanations.

    LoL! Lizzie, there isn’t any evidence that they are sufficient. Science requires POSITIVE evidence Liz, and your position doesn’t have any. The best you can do is hide behind curtains of time. And that ain’t science.

    Positive evidence Liz. If your position can’t provide any then step aside and let others have a go.

  50. Joe @ 49:

    Lizzie’s comment baffles. How is an ID inference any less a sufficient explanation than chance and necessity?

    So chance and necessity aren’t sufficient. They’re just not insufficient. How does that work?

  51. Nick @34:

    Let’s see. Berlinksi “asserts that one of the problems for eye evolution that Nilsson and Pelger did not consider was how the skull would be “reconstructed” to include eye sockets.”

    Nick says this is not a problem because . . . wait for it . . . the skull did not have to be “reconstructed,” but instead was “constructed.”

    Ooh. Now we see. Reconstruction of a skull might be a problem for evolution, but construction of a skull with just the right measurements and parameters is not a problem, because it came after the eye. So according to Nick, change of an existing structure might be a problem; but formation of a new structure from whole cloth is not a problem.

    Cue laughter . . .

    This is so typical of Nick — ignore the substantive point of the opponent and seize upon some (alleged) deficiency in the claim and then brush aside the real issue. Nick’s response, however, just underscores Berlinski’s point: no-one has a decent explanation of how this entire coordinated system — eye, musculature, skull and socket — could come together by purely natural and material means. It is just bluff and bluster. Another just so story. Way to go Nick.

    What a joke. I hope Nick didn’t include that fine piece of intellectual brilliance in his publications list.

  52. Dr Liddle’s point is also an error. The simple direct chalenge that the atomic and temporal resources available in our solar system or the cosm,os as a whole cannot scratch the surface of the config space for just 500 – 1,000 bits, much less the scope of FSCO/I in cases in question, is strong evidence that blind chance and mechanical necessity will be maximally implausible as explanations of such special configs as we are dealing with. This is of course the underlying analysis that undergirds the second law of thermodynamics, statistical form, but those who believe in informational perpetuum mobiles are unlikely to see the similarity to thinking that one can make a successful perpetuum mobile of the second kind. The point is that the utterly overwhelming bulk of possible configs will be gibberish of no function. KF

  53. Eric-

    Berlinski responded to Nick and provided a clear rebuttal. Either Nick never read it or thinks it best to ignore it.

  54. Kuartus,

    Thanks very much for the link you supplied. The paper looks very interesting.

    Bornagain77,

    Thanks very much for the many useful links. Much appreciated.

  55. Lizzie @49 via Joe:

    Gotta love Lizzie. Always good for a laugh.

    It is good to know, however, that scientists acknowledge chance and necessity are not sufficient explanations. That is an important admission and is a first step in the right direction.

    She is wrong, however, that there is no evidence chance and necessity are insufficient. Every experience we have suggests they are insufficient. Every reasonable calculation of what would be involved in the resources and timeframe of the universe suggests they are insufficient. So there is very good reason to think they are insufficient.

    Now, if what she is really saying is that it cannot be affirmatively proven that they are insufficient, then congratulations, she has just noted that it is not possible to prove a universal negative of this kind. Big deal. Everyone knows that and it is not how science operates. We can’t prove that there aren’t little mice on a treadmill in the middle of the Sun to power it. But we have good reason to think there aren’t. If the lack of a universal negative proof is the foundation on which Lizzie wants to base her materialist creation myth, that is a very shaky foundation indeed.

    Finally, on the positive side of the evidence, we have lots of experience that intelligent beings are capable of producing functional complex systems — in other words, unlike chance and necessity, design is a sufficient explanation.

    So, what was it again that ID advocates fail to understand, Lizzie?

  56. Joe @53:

    Thanks. I skimmed the comments quickly and didn’t notice, so I’ll go read Berlinski’s response now. I expect it will be quite amusing, given Berlinski’s writing style and the way Nick painted a bulls-eye on himself with that intellectual blunder.

    Maybe TalkReason should put a disclaimer on Nick’s article along the following lines: “This article ignores the main substantive issue and relies on an unsubstantiated “just so” story. Cite at your own risk.”

    BTW, I’m sure Nick is aware of Berlinski’s response, but he probably only read the abstract. :)

  57. 57

    What most ID (all?) ID advocates fail to understand is that when scientists say that an ID inference is unwarranted, they are not claiming that “necessity and chance.are sufficient explanations” – they are claiming that there is no evidence that they are insufficient explanations.

    If an ID inference is unwarranted, that necessarily means that chance and necessity are sufficient because those three exhaust all the known possibilities.

    There are only three fundamental descriptions of how phenomena behaves; (1) lawful (regular, predictable), (2) chance (which some would claim is really subsumed by 1, and (3) directed by agency.

    To make the positive claim that (3) is unwarranted, one must be able to show that (1) and (2) are sufficient. But then, this only applies to those that abide by the principles of right reason. Those not so confined can say any foolish thing they want as if they are engaging in reasoned debate.

  58. 58

    If scientists do not know if necessity and chance are sufficient, they cannot say agency is unwarranted. The best they can say is simply “We don’t know if chance and necessity is sufficient, and we do not know if agency is warranted”.

  59. Eric- page 411/12 of “The Deniable Darwin”

  60. Both Eric and William underestimate the power of the evolutionary promissory note, nor the power of the negative proof approach. ;)

    Who needs evidence when you have those in your arsenal?

  61. I have not read all the discussion but just want to say obviously the evolution of the eye has been discussed before. If I am correct the eye first appeared in the Cambrian and has not changed since except in some very minor ways. I believe the term that PZ Myers has used was “tweaked.” Here is a discussion of the eye from 3 years ago starting with a then frequent visitor, Nakashima:

    http://www.uncommondescent.com.....ent-341431

    The discussion got started with how the eye develops during gestation and how the changing of certain proteins affects development on our old friend, the fruit fly. It then evolves into a discussion of the evolution of the eye.

    The conclusion was, no eye before Cambrian, no new eyes after it. At least that is what PZ Myers, Lund University and Wikipedia said.

    http://www.uncommondescent.com.....ent-341449

    Of course that was 3 years ago and all could have changed since then.

  62. First time I’ve looked at Nilsson’s and Pelger’s paper. It underscores the kind of depressing quackery I see on a regular basis in the field of evolutionary biology. The very first step I would have liked to see them take is to supply a list of proteins required for a simple light-sensitive spot and another list of proteins required for a fully developed vertebrate eye. Step two would be to provide a testable method to go from list A to list B. Step three would be to ascertain the regulatory sequence changes in the respective genomes and then present a testable method to go from A to B. Before we can have phenotypic changes, we have to obtain genotypic changes, so their paper, to be taken seriously, should have focused primarily on the genotypic changes to go from A to B. Specifics, not creative story telling or creative story modelling.

  63. WJM, I agree completely. Clearly the Chance and Necessity scientists haven’t proven anything, and there’s no reason to discount Agency.

    I think it’s indicative of a failure to communicate. Case in point: In most high school Science curricula, 10th grade is Chance, 11th grade is Necessity and of course senior year is Agency. But I remember when I went to high school, the Chance teachers never talked to the Necessity teachers, and neither of them spoke with the Agency teachers. If I’m not mistaken, I think they even have their own schools now.

    This is a shame. If they could just learn to get along, at least enough to figure out of the whole evolution thing, we wouldn’t have to argue like this.

  64. Great, Lizzie sez that ID is a universal negative which ignores the fact that it isn’t.

    Earth to Lizzie- ALL design inferences mandate that necessity and chance be eliminated before reaching a design inference. Newton’s four rules of scientific reasoning mandate it. Perhaps that it what has you confused.

    The explanatory filter says that not only do we have to eliminate necessity and chance, there also has to be some specification. Behe lays out that specification in “Darwin’s Black Box”:

    “Our ability to be confident of the design of the cilium or intracellular transport rests on the same principles to be confident of the design of anything: the ordering of separate components to achieve an identifiable function that depends sharply on the components.”

    If we don’t see that then we don’t infer design.

    IOW ID is a universal negative in the same way that archaeology, forensic science and SETI are.

    That said there are scientists who say there is evidence for a designer. Many scientists make that claim. And those who claim there isn’t any evidence for a designer don’t offer any reasoning behind that claim. And they sure as heck don’t offer any positive evidence for necessity and chance being up to the task.

    IOW Lizzie, unguided evolution is unsupported by evidence or argument. Perhaps you should start there.

  65. WJM:

    The best they can say is simply “We don’t know if chance and necessity is sufficient, and we do not know if agency is warranted”.

    Unfortunately they don’t say that. They say “Necessity and chance are sufficient. No designer required. (just give us time and we will show you)”

  66. Lizzie continues:

    We just don’t see any reason to posit mice in the sun without good reason to support the hypothesis.

    ID doesn’t posit mice in the sun. It posits a designer to get the sun in the first place- that is to get matter and energy and all the right parameters so that there would be a sun.

    What is the other option? We exist as a series of fortunate (for us) accidents? We emerged from the chaos?

    And she finishes with a false accusation:

    IDists set up a straw man of evolutionary claims, and then pile fallacy on fallacy by interpreting their demolition of their straw man as support for ID.

    What strawman? Please be specific for once in your life.

  67. Joe:

    I have a problem.

    At least TWICE, I took EL, step by step through the per aspect design inference explanatory filter, in which she had occasion to see that there are indeed two successive defaults.

    First, mechanical necessity leading to lawlike regularity. This fails, once there is high contingency.

    There are two observed mechanisms that can give rise to high contingency outcomes on closely similar starting points.

    Chance, generally giving rise to stochastically distributed contingency.

    On which we know that if we sample a vast config space — population of possibilities — we have every reason to expect the bulk of the distribution to be picked up.

    If we instead see functionally specific outcomes from narrow, unrepresentive zones [aka islands of function -- cf. here for the common sense, simple reason why such is a real, commonly seen and expected phenomenon, contrary to many willfully dismissive and too often closed minded strawman arguments by objectors . . . ], that points to not a blind contingency but one pivoting on purposeful choice. Such as the same design that produces posts in English that are contextually responsive, not gibberish. Where also, such FSCO/I is routinely — and ONLY — observed to come about by such design.

    In short, we have an inference to best empirically grounded explanation on a widely observed causally adequate source, where FSCO/I has long been shown to be an empirically reliable sign of such a source.

    This, is backed up by good empirical and analytical reason to see that the other candidates for causal explanation at this level are not empirically warranted per observation, and per analysis are not credibly causally adequate.

    Why?

    Mechanical necessity does not give rise to high contingency, and blind chance samples within the accessible atomic and temporal resources of our solar system or the observed cosmos (the ONLY observed cosmos) are only adequate to sample such a small fraction of possibilities, that we have no good reason to expect special and unrepresentative clusters isolated in the space of possibilities to be picked up.

    For instance, to illustrate, I have drawn a needle in the haystack comparison on the config space of 500 bits:

    xv: Why should this be so? Let us consider: in the 10^17 or so seconds on its conventional timeline the 10^57 or so atoms of our solar system (our practical “world”) will have gone through maybe as many as some — oops, corrected 12:06:01 — 10^117 Planck-time quantum states. (We note, it takes about 10^30 such for the fastest chemical reactions, and many more for the organic chemistry type reactions relevant to so much of cell based life.) But 10^150 possibilities is 10^33 times as much as that, so our solar system could not search out more than a negligible fraction of 10^150 possibilities. Where, we can see that a string of 500 bits has 2^ 500 = 3.27*10^150 possible configurations. For just 500 bits [[~ 72 ASCII characters], on the gamut of our solar system, there is just too much haystack to reasonably expect to find the proverbial lost needle.

    xvi: To understand this better, let us work back from how it takes ~ 10^30 Planck time states for the fastest chemical reactions, and use this as a yardstick, i.e. in 10^17 s, our solar system’s 10^57 atoms would undergo ~ 10^87 “chemical time” states, about as fast as anything involving atoms could happen. That is 1 in 10^63 of 10^150. So, let’s do an illustrative haystack calculation:

    Let us take a straw as weighing about a gram and having comparable density to water, so that a haystack weighing 10^63 g [= 10^57 tonnes] would take up as many cubic metres. The stack, assuming a cubical shape, would be 10^19 m across. Now, 1 light year = 9.46 * 10^15 m, or about 1/1,000 of that distance across. If we were to superpose such a notional 1,000 light years on the side haystack on the zone of space centred on the sun, and leave in all stars, planets, comets, rocks, etc, and take a random sample equal in size to one straw, by absolutely overwhelming odds, we would get straw, not star or planet etc. That is, such a sample would be overwhelmingly likely to reflect the bulk of the distribution, not special, isolated zones in it.

    Now, all of this has been pointed out to EL and ever so many others, over and over again, and is easily accessible in known sites, if there was need to refresh memory or clarify understanding.

    But, we are not seeing any sign of acknowledging patent facts and cogent analyses, or if there is a lack of clarity, asking questions.

    Nope, we are seeing willful ignoring of such and confident manner, patently false declarations presented in disregard to duties of care to accuracy, fairness and truth. In effect, erecting and knocking over strawman distortions.

    If that is where EL is, after a year in which there was ample time to reflect and set things to rights, that is sadly revealing. I do not want to use the words that fit such behaviour, but those who are indulging such need to think about what I have just had to describe amounts to.

    I must therefore call upon EL and ilk to stop in such a course and do basic duties of care.

    On pain of being willful distorters and dismissers of the patent truth.

    I for one have no intention to chase in circles with those whose attitude to duties of care is like that.

    So, I have spoken just once, for record.

    KF

  68. F/N: I will add, that it is no strawman to say that an adequate evolutionary materialist picture of origin and body plan level diversity of life needs to account for these two phenomena. Just the simplest credible genome for cell based life will have 100,000 to 1 mn bits of genomic info, and major body plans credibly come in at 10 – 100 mn bits each. These are well beyond the FSCO/I threshold of 500 – 1,000 bits, which leads to the sort of needle in haystack searches above. Where also, part of what needs to be explained at OOL is the origin of the metabolising automaton that embeds a von Neumann, kinematic, code using self replicating facility, and so one cannot appeal to differential reproductive success on chance mutations. Where also, this is the very ROOT of the Darwinian tree of life so the convenient excuse that evolutionary theory speaks to the post OOL situation invites the retort, no roots, no shoots or branches etc. Thus, it is fair comment to say that design is a reasonable candidate, whatever the a priori materialist ideologues may think. And if design is at the table at OOL, it remains at the table all the way from microbes to Mozart. And, such issues have been on the table for a very long time. So, the empty assertion of “straw men” — sorry to have to say — is little more than a willful, turnabout false accusation. Let me issue a simple counter-challenge to EL and ilk, or rather remind. For almost six months, there has been an open challenge to provide a comprehensive evolutionary materialist summary case in about 6,000 words [a good feature article length]. There has been a lot of carping and distraction, as well as real cases of strawman distortions. Let me simply invite EL et al to actually present their case, or else accept that they have not got a cogent case to make that is anything materially different from the alleged strawmen we have been said by you to be making up. Put up, or by default lie exposed as willfully making false accusations. KF

  69. 69

    lastyearon, your buffoonery has become tiresome. If you have a comment that addresses the substance of the issues, by all means make it. If all you have is mockery and japing, take it somewhere else. Last warning.

  70. 70

    Look Nick,
    You may know a lot about biology and evolution, but you’re missing the point. We’re not saying that the eye didn’t evolve. We’re just saying it evolved by intelligent design (and it also didn’t evolve).

    What??

  71. Eric Anderson #4:

    I am embarrassed for Coyne. That has got to be one of the stupidest things I have ever heard anyone say. And in a professional magazine to boot.

    Facepalm.

    It is truly embarrassing. And what I find striking in the train analogy is the double standard used by Darwinists who scorn ID arguments that draw analogies between biological systems and mechanical devices (eg. mouse trap), yet they always resort to similar analogies in their pro-Darwinism arguments as they compare Darwinian evolution to this Miami-bound train, gradual evolution of car models, or climbing a mountain called Improbable.

  72. 72

    51
    Eric AndersonMarch 20, 2013 at 10:13 am

    Nick @34:

    Let’s see. Berlinksi “asserts that one of the problems for eye evolution that Nilsson and Pelger did not consider was how the skull would be “reconstructed” to include eye sockets.”

    Nick says this is not a problem because . . . wait for it . . . the skull did not have to be “reconstructed,” but instead was “constructed.”

    Ooh. Now we see. Reconstruction of a skull might be a problem for evolution, but construction of a skull with just the right measurements and parameters is not a problem, because it came after the eye. So according to Nick, change of an existing structure might be a problem; but formation of a new structure from whole cloth is not a problem.

    Cue laughter . . .

    This is so typical of Nick — ignore the substantive point of the opponent and seize upon some (alleged) deficiency in the claim and then brush aside the real issue. Nick’s response, however, just underscores Berlinski’s point: no-one has a decent explanation of how this entire coordinated system — eye, musculature, skull and socket — could come together by purely natural and material means. It is just bluff and bluster. Another just so story. Way to go Nick.

    What a joke. I hope Nick didn’t include that fine piece of intellectual brilliance in his publications list.

    Wow, you are a silly one. You seem to have forgotten that not even all vertebrates have bone skulls — early-diverging groups have skeletons made of squishy cartilage. Bones formed around eyes rather than the reverse.

    Look here and start reading:
    http://neurodojo.blogspot.com/.....-bone.html

    …then ask, why would a scientist who knows these basics take anyone seriously (like Berlinski) who didn’t? It’s a similar issue for the guy in the comments above who imagines that evolution would have had to “detach” the eye from the eye socket and then connect it back up, or something. No, eyes evolved in small squishy guys, vertebrates came later, vertebrates with bone instead of cartilage even later.

  73. 73
    William J Murray

    Dr. Liddle says:

    And awry goes the logic again. Let me repeat: no scientist (qua scientist) is claiming that they have proven there is no little mouse/ID involved in creation. All they are saying is: there is no evidence that there is.

    Dawkins disagrees when it comes to biology:

    “Biology is the study of complicated things that give the appearance of having been designed for a purpose.”

    When a scientist finds marking that appear to be the result of water erosion, or finds markings on a land sonar image that appear to be artifacts of some sort, that appearance offers the first direction on how to go about further investigation. They might find out that the appearance is deceiving, and that what they have found is the result of something else, but what a thing appears to be is the first evidence used in organizing additional scrutiny.

    So we’re not talking about mice on treadmills in the sun that have appeared to no one; we’re talking about an appearance of design that is apparent to virtually everyone, and is so pronounced that atheistic, materialist biologists cannot even talk about it without inserting the language of design and purpose.

    Hawking disagrees with Dr. Liddle’s “no evidence” claim on the cosmic scale:

    “A bottom-up approach to cosmology either requires one to postulate an initial state of the Universe that is carefully ?ne-tuned — as if prescribed by an outside agency — or it requires one to invoke the notion of eternal in?ation, a mighty speculative notion to the generation of many different Universes, which prevents one from predicting what a typical observer would see.”

    Darawinistic scientists have to purposefully turn a blind eye to the apparent design; they virtually all agree that the universe appears to be fine tuned, and that biology appears to be designed for a purpose; but here is Dr. Liddle saying that there is “no evidence” that would even warrant research about whether or not chance and necessity could be sufficient explanations, or if ID is warranted as per the appearance of that which one is attempting to explain.

    If a scientist is going to attempt to truthfully and factually explain something, and everyone agrees that it looks designed, Dr. Liddle would have us believe it is perfectly good science to simply not investigate the possibility that what appears to be designed perhaps necessarily was designed. Dr. Liddle would have us believe that it is perfectly good logic and science to happen upon a scene that everyone agrees looks like murder, but then to simply ignore that possibility and focus completely upon a Darwinistic explanation, no matter how anti-common sense or absurd or mystifying that explanation is (according to Lewontin).

    And so, when the investigators focus entirely upon finding Darwinistic explanations for the “murder” scene, and interpret everything in terms of that heuristic, and set up experiments in terms of that heuristic, she thinks that it is not equivocating for those investigators to say “there is no evidence of a murder”, even though they haven’t looked for it and have a deliberate mindset to explain, describe and interpret everything in “natural death” terms and conclusions.

    Even though when those investigators more closely examined the scene, it looked even more like murder to everyone involved in the investigation.

    Indeed, what we found by going deeper into the cells was not **less and less** appearance of design, but an appearance of design that is so overwhelming that it would probably shock Darwin himself back into the church.

    That scientists merely claim that there is no evidence that “chance and necessity” are insufficient to explain our observations.

    Apparently, Dr. Liddle is equivocating “not looking for evidence” with “there is no evidence”. The only way to find evidence that chance and necessity are insufficient is to develop a metric of some sort that can (provisionally) make such a determination, such as IC, FSCO/I, or finding a semiotic state.

    Where has any scientist other than ID advocates attempted to develop a metric to test whether or not the apparent design in biology should be dismissed as a false appearance? Most Darwinists that I know claim there is no metric for making such a determination, so according to them there is no means by which to collect rigorous evidence either way – to show N+C sufficient, or to show ID necessary.

    But – there is such evidence; the overwhelming appearance of design, the FSCO/I metric, the presence of irreducibly complex features, and (which is also IC) the existence of a semiotic state.

    Investigators that are admittedly committed to a “natural death” explanation are not trying to find evidence for murder in the first place, and interpret all evidence that might support a finding of murder in terms of natural death in the second place.

    And Dr. Liddle claims to not be equivocating or prevaricating. If you’re committed to conclusion X, and interpret everything in terms of X even to the point of Lewontinian absurdity, what does it mean to say there is no evidence of not-X?

  74. Nick: You seem to have forgotten that not even all vertebrates have bone skulls — early-diverging groups have skeletons made of squishy cartilage. Bones formed around eyes rather than the reverse.

    I can’t tell whether he’s trying to prove or disprove what Eric wrote…

    Eric: This is so typical of Nick — ignore the substantive point of the opponent and seize upon some (alleged) deficiency in the claim and then brush aside the real issue.

    I’m going to guess he’s just giving corroborating evidence?

  75. And so, when the investigators focus entirely upon finding Darwinistic explanations for the “murder” scene, and interpret everything in terms of that heuristic, and set up experiments in terms of that heuristic, she thinks that it is not equivocating for those investigators to say “there is no evidence of a murder”, even though they haven’t looked for it and have a deliberate mindset to explain, describe and interpret everything in “natural death” terms and conclusions.

    Believing is seeing!

  76. Hi everyone,

    I’m seeing lots of comments about skulls on this thread by pro-Darwin contributors, and nothing about brains – which is bizarre, as Nilsson and Pelger acknowledge in their 1994 paper that the evolution of the eye was constrained by the evolution of the brain:

    If advanced lens eyes can evolve so fast, why are there still so many examples of intermediate designs among recent animals? The answer is clearly related to a fact that we have deliberately ignored, namely that an eye makes little sense on its own. Although reasonably well-developed eyes are found even in jellyfish (Piatigorsky et al., 1989), one would expect most lens eyes to be useless to their bearers without advanced neural processing. For a sluggish worm to take full advantage of a pair of fish eyes, it would need a brain with large optic lobes. But that would not be enough, because the information from the optic lobes would need to be integrated in associative centres, fed to motor centres, and then relayed to muscles in an advanced locomotory system. In other words, the worm would need to become a fish. (p. 58)

    “Large optic lobes,” whose information is subsequently “integrated in associative centres, fed to motor centres, and then relayed to muscles in an advanced locomotory system.” That’s what Darwinists need to explain, before declaring the problem of the evolution of the eye solved.

  77. Dr. Torley: “Large optic lobes,” whose information is subsequently “integrated in associative centres, fed to motor centres, and then relayed to muscles in an advanced locomotory system.” That’s what Darwinists need to explain, before declaring the problem of the evolution of the eye solved.

    Is it ok for evolutionists to restrict their scope of conjecture to the morphological ‘evolution’ of the optic lobes? They don’t have to bother themselves with the pesky little molecular details now do they?

  78. Nick Matzke:

    No, eyes evolved in small squishy guys, vertebrates came later, vertebrates with bone instead of cartilage even later.

    That’s the story, anyway. And even if true it doesn’t point to any mechanism.

  79. Lizzie is a lost cause. She actually thinks that Darwin solved the design problem. However she actually thinks she wrote a program that shows natural selection creating CSI. Even though I have explained to her, many times, that it does no such thing (one reason is it start with the very thing that requires an explanation-> the ability to replicate with variation. the other reason is it doesn’t simulate natural selection and it doesn’t even produce CSI. other than that…)

    So when you have someone that firmly believes in something that strongly- 150+ years later and still no evidence that natural selection is a designer mimic- having more (or fewer) offspring doesn’t design anything- then you have no chance of ever convincing them otherwise. They don’t give a damn about any evidence. All she has is faith- blind faith.

    And Lizzie, dearest, this bit of nonsense just proves that you are on an agenda of lies and misrepresenations:

    But the IDist says: “you can’t rule out murder, and people that have been pushed off cliffs look like this, therefore we must infer murder”.

    AGAIN, the EF AND Newton’s four rules of scientific investigation say we have to look at necessity and chance FIRST.

    How many times do I have to tell you that? It’s as if you are just some daft old nannie who thinks that you can just make stuff up and get away with it because you remind people of some old senile relative.

    You have serious issues lady.

  80. Newton, Pasteur, Einstein, all saw evidence for Intelligent Design in the universe. Lizzie Liddle sez there ain’t no such evidence.

    Enough said…

  81. Hi everyone,

    I have had some lively exchanges of opinion with Elizabeth Liddle in the past. While we are poles apart on a variety of issues, I have the greatest respect for her intelligence, and she is the last person I would describe as daft. Mistaken, maybe, but she herself would be the first to admit that.

    The motto for her Website is a phrase of Cromwell’s, taken from a letter he wrote to the General Assembly of the Church of Scotland on August 3, 1650: “I beseech you, in the bowels of Christ, think it possible that you may be mistaken.”

    Who knows? Perhaps Lizzie will one day change her views on design inferences.

  82. 82
    William J Murray

    Dr. Liddle said:

    The appearance of design is not evidence of design – the explanandum cannot also be the explanation – that would be circular reasoning. Which you are allowed to do on this blog, but it remains fallacious.

    Does Dr. Liddle really not understand that I’m using “appearance” in the observation sense, and not in the instantiation sense, after I began my post with repeated references to what biological features and the fine tuning “appear” to be (look like) when observed?

    I mean … really? Surely she doesn’t think I believe observing and interpreting a thing explains that thing?

    In any event, I’m sorry I took your thread so far off course, Dr. Torley. Your posts are always extremely educational and I greatly appreciate the effort you are obviously expending to bring this information to light.

  83. Nick @72:

    Either you are clueless or you are being purposely obtuse (I suspect the latter).

    The point is that the eye doesn’t evolve in some vacuum and then just work. There is a whole coordinated system, including musculature, nerves, brain interpretation of signals, and, yes, in many organisms skeletal structures. All of it has to be coordinated and in place.

    It matters not one whit whether the skull came first or last. You propose this fantasy story that all of this coordination is not a problem because the skull came later, or the skull doesn’t exist in some creatures, or some other equally absurd “reason.” Actually, I suspect you realize full well that there is no decent evolutionary explanation for vision, but you just enjoy BS’ing too much to admit as much.

  84. Joe @79:

    She actually thinks that Darwin solved the design problem. However she actually thinks she wrote a program that shows natural selection creating CSI.

    LOL! I’ll be looking for her name in the list of Nobel laureates soon, if she has managed to write such a program. :)

    Despite Lizzie’s general polite demeanor, I fear you are largely correct about her approach. Either she doesn’t understand ID or she is being purposely deceptive.

    However, I hope vjtorley is right @81 and that somewhere, sometime, she will actually start to examine the design question without the a priori blinders in place.

    Well, enough on that. She isn’t here to defend herself, so probably not appropriate to pile on much more . . .

  85. Eric- it’s good for a laugh, anyway:

    Creating CSI with NS

  86. Back to the topic-

    Until we know what genes are responsible for eyes then we cannot say whether or not they evolved, let alone how.

  87. Strange- Mikey Elzinga really thinks that Matzke has refuted Dr Torley, which proves Mikey doesn’t know anything about biology.

    Nice job Mikey.

  88. Until Matzke actually starts doing science by itemizing the list of proteins required for a simple light sensitive spot, and then itemizing the list of proteins required for fully developed vertebrate eye, and then provides a testable method to go from list A to list B, Matzke hasn’t even begun to refute Thorley, or to defend a darwinian process, or to even do science. Matzke confuses creative story telling, combined with dodging and evading the core issues, with doing science.

  89. Nick,
    What the ID proponents (specifically Eric Anderson and KD) are saying is that evolution isn’t science because it lacks sufficient detail at the molecular level. In order for them to accept that the eye evolved by accident (which is highly unlikely) you need to show exactly how it happened, molecule by molecule.

    However, personally I don’t even think that’s enough. We all know that organic molecules are extremely complex entities that are made of lots of atoms. And we also know that the atoms in those organic molecules are extremely complex themselves, and are made of lots of electrons, neutrons and protons. And protons and neutrons are themselves complex entities made of quarks and gluons. And I’m sure those guys are made of even smaller stuff.

    So basically, what I’m asking is: where is the evolutionary explanation of quarks and gluons? And why should I accept that the eye evolved by accident if you can’t tell me how those quarks and gluons did it?

  90. @lastyearon

    Your shtick is as transparent as it is trying. Do you stick to sniping because you fear you have nothing of substance to contribute? Why don’t you come out from behind your silly pretense and address the issues?

  91. Semi OT, seeing as if we did not have light the eye would be pretty useless for us to have:,,

    Best Map Ever Made of Universe’s Oldest Light: Planck Mission Brings Universe Into Sharp Focus – Mar. 21, 2013
    Excerpt: The Planck space mission has released the most accurate and detailed map ever made of the oldest light in the universe, revealing new information about its age, contents and origins.
    The map results suggest the universe is expanding more slowly than scientists thought, and is 13.8 billion years old, 100 million years older than previous estimates. The data also show there is less dark energy and more matter, both normal and dark matter, in the universe than previously known. Dark matter is an invisible substance that can only be seen through the effects of its gravity, while dark energy is pushing our universe apart. The nature of both remains mysterious.
    “Astronomers worldwide have been on the edge of their seats waiting for this map,” said Joan Centrella, Planck program scientist at NASA Headquarters in Washington. “These measurements are profoundly important to many areas of science,,,
    The cosmic microwave background is remarkably uniform over the entire sky, but tiny variations reveal the imprints of sound waves triggered by quantum fluctuations in the universe just moments after it was born.,,,
    The newly estimated expansion rate of the universe, known as Hubble’s constant, is 67.15 plus or minus 1.2 kilometers/second/megaparsec. A megaparsec is roughly 3 million light-years. This is less than prior estimates derived from space telescopes, such as NASA’s Spitzer and Hubble, using a different technique. The new estimate of dark matter content in the universe is 26.8 percent, up from 24 percent, while dark energy falls to 68.3 percent, down from 71.4 percent. Normal matter now is 4.9 percent, up from 4.6 percent.
    Complete results from Planck, which still is scanning the skies, will be released in 2014.
    http://www.sciencedaily.com/re.....084221.htm

    Planck satellite unveils the Universe — now and then (w/ Video showing the mapping of the ‘sphere’ of the Cosmic Microwave Background Radiation with the satellite) – 2010
    http://phys.org/news197534140.html#nRlv

    The Known Universe by AMNH – video – (please note the ‘centrality’ of the Earth within the CMBR in the universe in the video)
    http://www.youtube.com/watch?v=17jymDn0W6U

    Centrality of Earth Within The 4-Dimensional Space-Time of General Relativity – video
    http://www.metacafe.com/w/8421879

    Of note:

    The curvature of the space time of the universe is ‘flat’ to at least 1 in 10^15 places of accuracy
    http://books.google.com/books?.....38;f=false

    Quotes of note:

    The best data we have [concerning the Big Bang] are exactly what I would have predicted, had I nothing to go on but the five books of Moses, the Psalms, the bible as a whole.
    Dr. Arno Penzias, Nobel Laureate in Physics – co-discoverer of the Cosmic Background Radiation – as stated to the New York Times on March 12, 1978

    “Certainly there was something that set it all off,,, I can’t think of a better theory of the origin of the universe to match Genesis”
    Robert Wilson – Nobel laureate – co-discover Cosmic Background Radiation

    “There is no doubt that a parallel exists between the big bang as an event and the Christian notion of creation from nothing.”
    George Smoot – Nobel laureate in 2006 for his work on COBE

    “,,,the astronomical evidence leads to a biblical view of the origin of the world,,, the essential element in the astronomical and biblical accounts of Genesis is the same.”
    Robert Jastrow – Founder of NASA’s Goddard Institute – Pg.15 ‘God and the Astronomers’

    ,,, ‘And if you’re curious about how Genesis 1, in particular, fairs. Hey, we look at the Days in Genesis as being long time periods, which is what they must be if you read the Bible consistently, and the Bible scores 4 for 4 in Initial Conditions and 10 for 10 on the Creation Events’
    Hugh Ross – Evidence For Intelligent Design Is Everywhere; video
    http://www.metacafe.com/watch/4347236

    It is also very interesting to note that among all the ‘holy’ books, of all the major religions in the world, only the Holy Bible was correct in its claim for a transcendent origin of the universe. Some later ‘holy’ books, such as the Mormon text “Pearl of Great Price” and the Qur’an, copy the concept of a transcendent origin from the Bible but also include teachings that are inconsistent with that now established fact. (Hugh Ross; Why The Universe Is The Way It Is; Pg. 228; Chpt.9; note 5)

    Verse and Music:

    Genesis 1:3
    And God said, “Let there be light,” and there was light.

    DC TALK – IN THE LIGHT
    http://www.youtube.com/watch?v=CWq1XYxtlRs

    The following video and article are very suggestive as to providing almost tangible proof for God ‘speaking’ reality into existence:

    The Deep Connection Between Sound & Reality – Evan Grant – Allosphere – video
    http://www.metacafe.com/watch/4672092

    Music of the sun recorded by scientists – June 2010
    Excerpt: The sun has been the inspiration for hundreds of songs, but now scientists have discovered that the star at the centre of our solar system produces its own music.
    http://www.telegraph.co.uk/sci.....tists.html

  92. Enlarged Image of Cosmic Background Radiation (courtesy Physorg)
    http://cdn.physorg.com/newman/.....ck_cmb.jpg

  93. LYO:

    Perhaps it has not caught your notice that Quantum theory has allowed us long since to understand organic chemistry, inorganic chemistry and polymer/materials science.

    That is not the level of concern we have.

    Developments in molecular biology since the 1940′s and 50′s have allowed us to see the molecular machines at work in the living cell, and that functionally specific complex organisation and associated information, based on what we already know, is what is posing the challenge for the fundamentally pre-quantum, C19 Victorian era theories in biology.

    Just as, the spectroscopic study of black body radiation at end of C19 led to a crisis in physics resolved by the development of quantum theory over the period from 1900 – 1930 in the first instance, the development of our understanding of what is happening at molecular levels in cells is raising serious questions about where such can come from. For, we already have a known capable mechanism for creating FSCO/I, and reason to see that the preferred mechanisms implied in darwinist narratives, do not meet that threshold of known capacity to cause the phenomenon.

    In short we know that FSCO/I is created by designers, directly and indirectly, but the same cannot be said for fundamentally blind forces of chance and mechanical necessity.

    That is what has to be resolved, to arrive at a satisfactory answer.

    And, contrary to your suggestions of closed mindedness, if it can be shown observationally that forces of blind chance and mechanical necessity can and do create FSCO/I relevant to cell based life and to the rise of novel body plans, the whole design theory project in the world of life would collapse because of the decisive impact of such evidence; but — never mind those who project their own make/break anxieties unto others — that is not a critical concern for design thinkers. (Yes, that’s right, just keep on reading to see why.)

    What you are doing, then, is little more than trying to twist about the circumstances, where there is evidence on the table, but it cuts across the a priori materialist ideology, which is evidently being desperately clung to.

    Why do I so freely say such?

    Simple. Ironically, it would not — repeat, NOT — have a fundamental impact on design thought if it were to happen that FSCO/I could be shown to originate by forces of blind chance and mechanical necessity, as there is a world of evidence on the source of a fine tuned cosmos set up to an operating point suitable for cell based life.

    That is, design thinkers do not have a critical worldview issue on the origins of life and body plans; it is the materialists who do. (Yes, I mean exactly what you just read.)

    So, we are free to go with the evidence where it leads; it is simply a matter of what the evidence warrants — currently, strongly, design — not a make/break worldview level issue.

    For us.

    For you, it seems the matter is quite different.

    Per a priori materialist ideology, blind chance and mechanical necessity HAS to account for everything, no exceptions, from hydrogen to humans. No wonder there has been an attempt to redefine science as a search for such blind causes, to ease the pressure by blocking serious consideration of alternatives.

    Which easily explains a lot of the rhetorical patterns we so often, so drearily predictably see.

    So, please think again and do better next time.

    KF

  94. I am a big believer in ID but I never expect that there will be any proof that the universe, life, and all its variations were specifically designed. I doubt that there are few here who believe that ID will ever be scientifically proved. Most, I guess, hope it will be the last man standing and if that happens there would be a big fight within the design supporters for what is true.

    Right now there are multiple hypotheses by various groups as to how it happened. One of them is some intelligence designed and implemented parts or all of the physical universe. And within this framework, it does not necessarily mean that it was the same intelligence for all the elements under consideration. Within the design spectrum, there are many competing explanations and some find other ID explanations as unpalatable as they do purely naturalistic explanations.

    For another group, the very thought of a design explanation is anathema. Their very faith/life choices would be crushed by such a cause and effect scenario. Just as there are many who support ID whose faith is challenged by a purely naturalistic explanation.

    The currently accepted hypothesis supporting a naturalistic explanation is really wanting as we all know (Matzke is surely in the group that knows this) but that does not mean there are not other scenarios that are naturalistic that may prove more plausible. It is not an either/or situation (either being Darwin and or being ID). No naturalistic explanations are on the horizon that they think could replace Darwin’s ideas which is why they are defended so irrationally. But if one came up, they would pivot in a nanosecond.

    And it not without many trying to find such an alternative. That is why people like Matzke go to such lengths to defend an incremental process thought by the average person and average biologist to be plausible because of Darwin’s ideas. He surely knows of the alternative searches. But until something shows a real possibility the current faith must be defended. Some ways to defend this faith is by selective use of evidence and story telling but another way is to mock alternatives. Ever wonder why they even bother to mock ID?

    I would think that Matzke and others in the scientific community know the limitations of whatever the latest synthesis is but cannot admit it because to do so would give credence to an intolerable exegesis. So he comes around here which surprises me. Why spend time with the loonies if what they are espousing is drivel. One cannot be thought of as serious if one talks to the crazies. No, by Matzke showing up here, he is in fact acknowledging the substance of ID and its influence.

    If ID disappeared tomorrow, the entire discussion of the evolution debate would change. Darwin’s ideas would be discredited with the same information provided by ID and there would be a search for an alternative explanation. Such a search is going on but one that cannot be admitted too loudly. But at the moment, the best explanation is that the mechanism behind evolution is a mystery but the modern scientific community cannot admit that.

    It should also be the tack of the ID community. Take the high road. Instead, we mock them, they mock us. It is schadenfreude for both sides and is what fuels blogs on the internet, the belittling of both sides.

  95. Jerry: Science, because of its reliance on inductive methods, is simply not in the business of proof. That means that scientific knowledge claims (especially things like laws and theories) are weak form, provisionally warranted, more or less empirically reliable, but not — as a rule — shown as so beyond all reasonable doubt or possibility of correction. That has been publicly acknowledged to be so since Newton et al. Currently (and for the foreseeable future), when we investigate the remote past of origins, we are unable to directly observe what actually happened. So, at best, we make plausible models based on observed traces from the past, and inference to best explanation on observed causal factors shown capable of creating the relevant effect. When it comes tot he FSCO/I in life forms, Design meets this test, but blind chance and mechanical necessity acting through chance variation and differential reproductive success, has not — and has not after 150 years of trying. KF

  96. KF,

    There is nothing in what you said, I disagree with. In fact I have made the exact same argument here a few years ago expressed a little differently.

    Which is why I said that Matzke must understand it too. He is not dumb.

  97. Hi Jerry,

    Ultimately, it boils down to accident or design. Did life, the universe and everything make itself by accident? Or was it designed? There is no third way. The beauty of ID is that it eliminates the ‘accidental’ explanation at the same time as it supports the ‘designed’ explanation.

    Interestingly, if Nick Matzke is a theistic evolutionist then he is actually on the same side as ID proponents when it comes to this question: all theistic evolutionists believe that life, the universe and everything was the result of Intelligent Design, albeit using an evolutionary method of creation. No theistic evolutionist believes that mankind was an accident and that, somehow God was surprised when mankind emerged!

  98. Chris,

    There an infinite number of permutations within this debate and I am not sure that your explanation sums it up correctly. How much was designed and with what ends are just two unknowns that could lead to all sorts of hypotheses. Others could provide a lot of other issues. I was a daily reader and frequent participant on this site for years so I am very familiar with most of the issues.

    I was very contentious at times and was banned by Dembski once for challenging him. I happen to believe that Darwin’s ideas are true but in a very limited sense. They along with the latest synthesis are the basis for modern genetics which is a very powerful and useful science. For that ID should acknowledge Darwin, otherwise it looks foolish and petulant. But evolution is more than genetics and micro evolution and beyond these areas is where Darwin’s ideas are barren.

    I have no idea what Matzke believes but he has to understand the issues. Why he acts like he does is the curious event. But he has to recognize ID as an influential argument. Otherwise he would ignore the people here.

  99. lastyearon @89:

    I don’t believe I’ve said in this thread that evolution is not science (or that, properly applied, it cannot be science), so your accusation is a misrepresentation of my position. (We could have an interesting discussion about what “evolution” means, but that is a separate issue for now.)

    But I’ll go ahead and call your bluff:

    Are you suggesting that quarks and gluons and atoms contain complex specified information? Do they contain sequences of particles that store a code for construction of an organism? I didn’t think so. So your insincere attempt at analogy fails.

    In contrast, organisms are dependent on the biochemical information stored in, for example, DNA. Indeed, Nick has stated that all the information for an organism is contained in its DNA. So under Nick’s view, by definition, the explanation for something like the eye must be, at the end of the day, a sequence of nucleotides. And it remains true that neither Nick nor anyone else knows precisely what sequence of nucleotides is needed to construct an eye, nor what changes in nucleotides were needed to go from a light-sensitive spot to a camera-lens eye. But we have good reason to believe that a good many changes would be needed and that such changes could not occur within the timeframe of the known universe.

    But I’m not even that picky. I’m not even demanding precise details about what actually occurred in the remote historical past. I’d be happy with an engineering-quality analysis of what is needed and what might have occurred, as long as it is a reasonably complete analysis that can be seen to have a chance of operating in the real biological world.

    Instead, we are treated to hand-waving just-so stories that, even when dressed up in fancy scientific language, go little beyond Kipling’s children’s stories. And when someone like Berlinski makes the perfectly reasonable observation that many coordinated changes, including those in skull structure, are required to get to where we are today, we get the laughable response: “Nuh-uh, because the skull came later; and besides, some creatures don’t have skulls.” Right. And some creatures don’t have arms, so I suppose we don’t need to explain how arms came about.

    What a joke.

    So your comment fails and your attempt at saving Nick & Co. from the hard work of actually coming up with an explanation for vision on the basis of chance and necessity just underscores yet again that they have no such explanation.

  100. Hi Jerry,

    Sometimes the answer is simple, no matter how complicated the question appears to be.

    Tell me, if existence is neither the result of an accident, nor the result of design, then what is it the result of?

    In the absence of a specific response to that question I can only repeat, there is no third way and I put it to you that what you might consider any possible third way will ultimately be reducible to accident or design.

  101. Eric, I don’t understand why you’re arguing with me. Of course I agree that organisms contain complex specified information. It’s obvious to anyone who isn’t an atheist materialist darwinist. And I know it’s been proven mathematically in one of the posts on this blog. I forget where, but I know I saw some sort of formula a while back.

    All I’m saying is this: When molecules get together to build an eye, they know how to do it because of information. That information was obviously put there by a designer, and didn’t just happen by accident. So to, when protons get together with neutrons and electrons to build an atom, they know how to do it because of information. And that information had to be placed there by a designer.

  102. I liked your response to Coyne’s train analogy, but I feel you missed one very vital argument against it. The fact that at any time and any point along Grandma’s trip one can observe her progress. Also, when she gets home she will still be Grandma.

  103. Maybe when combined, chance and necessity developed a mutual urge to design…? And then it became a mania with them, so that they’d designed ever more sophisticated things; perhaps competing with each other.

    Not born of the urge of the flesh or the will of man, or of God, of which latter, scripture imputes to the Word made flesh, but of the will of a kind of tango danced by chance and necessity? I think we should be told.

  104. Axel,

    “Maybe when combined, chance and necessity developed a mutual urge to design…? And then it became a mania with them, so that they’d designed ever more sophisticated things; perhaps competing with each other.”

    All these factors require consciousness. Evolution, or chance and necessity if you will, do not have urges or a need to compete. They do not have manic episodes. They simply plod blindly along with no sense of purpose or direction.

  105. 105
    William J Murray

    Nic,

    You obviously have not accounted for the Darwinian Chance Fairies that sprinkle Magical Emergence Dust on rocks and mud and bake up things like consciousness and complex, self-replicating machinery in the Materialist Easy Bake Oven they call “Deep Time”.

  106. Chris,

    You just narrowed the question to existence. I know of no known way that something could just come into existence. No one does. I also know that it is an issue that goes almost no where in terms of design. For example, someone could tell you that there may be a universe generator out there and we are just one of the zillion universes all with their own big bang. That is how some are explaining it. Hard to support one way or another. I think it a nonsense argument but others will says it makes sense to them.

    As far as design after existence, there are an infinite number of possibilities. An intelligence could design a system that produces many things using a random generator and no one would never know what will be the result. The things created by this process may or may not exhibit characteristics that indicate design. Are they designed? Yes, but it would be hard to support it unless you saw the system that actually generated the objects. An analogy: if the Judeo Christian God created the universe, is each rock, piece of dirt, molecule of gas designed? Yes, because they are the result of a design process but that will get you no where in convincing someone that they are designed.

    There is the basic question of how much is designed. The materialist wants zero design and will reject even one instance of design prior to humans unless it is another randomly constructed intelligence. The ID people want at a minimum, one element of design prior to humans. For example, the fine tuning of the universe may be enough for the TE’s and that is only one instance of design they may accept prior to humans. Though it is an impressive one. The Deist will then come along and say that was it. The rest is just random. And by the way could say, I am history, care less what happens to my creation and don’t expect to ever hear from me again.

    But even here there is lots more possibilities people consider. Some Deist say the god created life and humans and after that nothing or he could have front loaded design into the first cells. Is that design yes.

    Interesting is that Dawkins believes we could be designed, just that it wasn’t a god. He said so in the movie Expelled.

    It may sound simple but it really isn’t. I don’t think anything I said is anti ID. I am actually a big ID supporter but never thought it was an easy sell.

  107. 107

    Jerry, “existence” or “life, the universe and everything”… all amounts to the same thing, when you consider the important stuff, in this discussion.

    A universe generator? Design. That’s as far as the science goes. The anti-ID brigade is wrong. Simple.

    A system that has been designed to use randomness to create everything in existence? Yep, still Design. Pretty much what theistic evolutionists like Francis Collins believe in.

    Zero design? Accident.
    Deistic fine tuning only? Design.
    Dawkins Aliens? Design.

    So simple, that in all cases, you already chose accident or design yourself: no third way needed, no third way available.

    Clearly Jerry, you are seeking details, you have questions about ID specifically that you want answers to. But science cannot provide those answers. Intelligent Design science is only in the business of eliminating accidental explanations and demonstrating Design. Beyond that, ID science can say nothing.

    You need to look elsewhere for the details. Then you can decide whether or not Dawkins Aliens are responsible for existence or not.

  108. Hey Dr. Torley, you’ve gotten a friendly shout out at ENV:

    Evolution of the Mammalian Eye: Ho-Hum, No Big Deal? – Stephen A. Batzer March 21, 2013
    http://www.evolutionnews.org/2.....70331.html

  109. Chris,

    I never said there was a third option between design or non design. It is like Barry’s A and not-A from a recent post. It is either one or the other. But there is the question of just what is meant by design, what is then designed, and what isn’t, how the design is implemented (timing, boundary conditions etc.) and how the design subsequently plays out over time as a result. For example, if some intelligence designed the universe, is the local thunder storm an example of design. It would be the result of the original design but no one would point to a thunder storm as evidence of design in the universe. That would convince no one.

    Or there is the scenario where the universe is designed and every event plays out according to the original plan even to the position or every molecule. But then life is created or happens and the movement of the organism then accidentally causes a change in the disposition of some of the molecules by accident. Is that change designed, especially when it is humans exercising free will in their actions. Certainly some could say the action of the human exercising free will is a design event but is the displacement of the molecules that result from this event part of any design? I am not sure it is a question worth considering but what does the answer mean for what is and isn’t designed?

    I have been following ID since 1998 when I went to a conference in New York City where Behe, Dembski and Meyers and others spoke. I have read most of the books on both sides of the argument and followed the debate on this site for several years. This is a great place to learn but one has to be careful because some here had agendas when I was reading the site every day. I assume it is still true since I have infrequently read or posted anything in the last couple years. Some of the people are the same and some are new but the arguments seem the same.

    I have my opinions and I was never shy at expressing them here but I never saw anyone refute anything I had espoused which I then didn’t agree with their argument. They might not have agreed with me but no one refuted what I said. That doesn’t mean I am always right but it does mean that there are a lot of unanswered questions. Because of this I never found the evolution question a simple argument or that a simple dichotomy explained the design issue.

  110. William,

    “the Materialist Easy Bake Oven they call “Deep Time”.”

    Ah yes, the old ‘if in doubt, re-date, strategy.

    What I find so funny is the fact evolutionists talk about a light sensitive cell as if it’s no big deal. Light sensitive cells can be found floating around just about anywhere. Once you’ve got one it’s just a matter of time till you have an eye.

    And then they call it ‘science’. Mother Goose should be their patron saint.

  111. 111

    Hi Jerry,

    Thanks for your response, which, by the way raises some very valid points. But can I just rewind for a moment?

    We agree that existence can only be the result of accident or design. I think we further agree that, there is a compelling rational and empirical basis to eliminate the possibility that existence was the result of an accident.

    Now, don’t you think that that statement alone – existence is not an accident – is absolutely massive? For starters, it means that everything important that “internet atheists” have ever contributed to this debate is completely wrong. But, much more importantly, it means that the atheists that actually matter in society, the ones who are in a position to influence the education of our children and shape the opinion of the general public, they too have been totally wrong all along. And it should just be a matter of time before the truth is widely established.

    If Intelligent Design science makes no further progress, say because it is derailed by political agendas or religious dogma, then the sole achievement of comprehensively eliminating an accidental explanation for existence, while laying rock-solid foundations for Design, is one that is as great as any scientist has ever achieved… and could be the most important.

    So, while we reflect on this achievement, we can look beyond science for answers to the questions you raise. Personally, I’m no Christian, but I think a thunderstorm is a potent reminder that we are ultimately at the mercy of a Grand Power. And that our immaterial souls will survive when there are no more atoms. Ultimately, no matter where you look, you may never be satisfied with the answers. Indeed, you cannot truly eliminate Descartes Demon Doubt: the possibility that your existence is just an illusion brought on by a demon who is toying with your soul in a jar. But hey, even that is still design!

  112. Chris Doyle, I liked your preceding comment,,, but,,,

    “I’m no Christian”

    Being a Christian, and seeing as you argue very coherently in your posts, I would like to suggest a few lines of evidence in favor of Christianity to perhaps get you to thinking a bit more deeply about it.,,, This study came out a little over a year ago,,,

    Scientists say Turin Shroud is supernatural – December 2011
    Excerpt: After years of work trying to replicate the colouring on the shroud, a similar image has been created by the scientists.
    However, they only managed the effect by scorching equivalent linen material with high-intensity ultra violet lasers, undermining the arguments of other research, they say, which claims the Turin Shroud is a medieval hoax.
    Such technology, say researchers from the National Agency for New Technologies, Energy and Sustainable Economic Development (Enea), was far beyond the capability of medieval forgers, whom most experts have credited with making the famous relic.
    “The results show that a short and intense burst of UV directional radiation can colour a linen cloth so as to reproduce many of the peculiar characteristics of the body image on the Shroud of Turin,” they said.
    And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.”
    http://www.independent.co.uk/n.....79512.html

    Moreover, in Judeo-Christian cultures, in the positive Near Death Experience testimonies you will find mention of an indescribably bright ‘Light’ or ‘Being of Light’ who is always described as being of a much brighter intensity of light than the people had ever seen before.

    Ask the Experts: What Is a Near-Death Experience (NDE)? – article with video
    Excerpt: “Very often as they’re moving through the tunnel, there’s a very bright mystical light … not like a light we’re used to in our earthly lives. People call this mystical light, brilliant like a million times a million suns…”
    – Jeffery Long M.D. – has studied NDE’s extensively
    http://abcnews.go.com/Nightlin....._gydvW8jbI

    All people who have been in the presence of ‘The Being of Light’, while having a deep NDE, have no doubt whatsoever that the ‘The Being of Light’ they were in the presence of is none other than ‘The Lord God Almighty’ of heaven and earth.

    In The Presence Of Almighty God – The NDE of Mickey Robinson – video
    http://www.metacafe.com/watch/4045544

    Near Death Experience – The Tunnel, The Light, The Life Review – video
    http://www.metacafe.com/watch/4200200/

    “The Light was brighter than hundreds of suns, but it did not hurt my eyes. I had never seen anything as luminous or as golden as this Light, and I immediately understood it was entirely composed of love, all directed at me. This wonderful, vibrant love was very personal, as you might describe secular love, but also sacred.
    Though I had never seen God, I recognized this light as the Light of God. But even the word God seemed too small to describe the magnificence of that presence. I was with my Creator, in holy communication with that presence. The Light was directed at me and through me; it surrounded me and pierced me. It existed just for me.” – testimony taken from Kimberly Clark Sharp’s Near Death Experience

    1 John 1:5-7
    “This is the message we have heard from him and declare to you: God is light; in him there is no darkness at all. If we claim to have fellowship with him and yet walk in the darkness, we lie and do not live out the truth. But if we walk in the light, as he is in the light, we have fellowship with one another and the blood of Jesus, his Son, purifies us from all sin.”

    Toby Mac (In The Light)
    http://www.youtube.com/watch?v=5_MpGRQRrP0

    It should also be carefully noted: All foreign, non-Judeo-Christian culture, NDE studies I have looked at have a extreme rarity of encounters with ‘The Being Of Light’ and tend to be very unpleasant NDE’s save for the few pleasant children’s NDEs of those cultures that I’ve seen (It seems there is indeed an ‘age of accountability’). The following study was shocking for what was found in some non-Judeo-Christian NDE’s:

    Near-Death Experiences in Thailand – Todd Murphy:
    Excerpt:The Light seems to be absent in Thai NDEs. So is the profound positive affect found in so many Western NDEs. The most common affect in our collection is negative. Unlike the negative affect in so many Western NDEs (cf. Greyson & Bush, 1992), that found in Thai NDEs (in all but case #11) has two recognizable causes. The first is fear of ‘going’. The second is horror and fear of hell. It is worth noting that although half of our collection include seeing hell (cases 2,6,7,9,10) and being forced to witness horrific tortures, not one includes the NDEer having been subjected to these torments themselves.
    http://www.shaktitechnology.com/thaindes.htm

    Near Death Experience Thailand Asia – video
    http://www.youtube.com/watch?v=Y8M5J3zWG5g

    A few more notes:

    The Day I Died – Part 4 of 6 – The NDE of Pam Reynolds – video
    http://www.metacafe.com/watch/4045560

    “I think death is an illusion. I think death is a really nasty, bad lie. I don’t see any truth in the word death at all” –
    Pam Reynolds Lowery (1956 – May 22, 2010)

    Heaven Is Real: A Doctor’s Experience With the Afterlife – Dr. Eben Alexander – Oct 8, 2012
    Excerpt: One of the few places I didn’t have trouble getting my story across was a place I’d seen fairly little of before my experience: church. The first time I entered a church after my coma, I saw everything with fresh eyes. The colors of the stained-glass windows recalled the luminous beauty of the landscapes I’d seen in the world above. The deep bass notes of the organ reminded me of how thoughts and emotions in that world are like waves that move through you. And, most important, a painting of Jesus breaking bread with his disciples evoked the message that lay at the very heart of my journey: that we are loved and accepted unconditionally by a God even more grand and unfathomably glorious than the one I’d learned of as a child in Sunday school.
    http://www.thedailybeast.com/n.....rlife.html

  113. Dr. Torley, of somewhat related note to the ‘evolution of the eye’: Please note, on the following site, how the sclera (white of the eye), a uniquely human characteristic, was brought in very early on, in the artists’ reconstructions, to make the fossils appear much more human than they actually were, even though the artists making the reconstructions have no clue whatsoever as to what the color of the eyes, of these supposed transitional fossils, actually were.

    10 Transitional Ancestors of Human Evolution by Tyler G., March 18, 2013
    http://listverse.com/2013/03/1.....evolution/

    Evolution of human eye as a device for communication – Hiromi Kobayashi – Kyoto University, Japan
    Excerpt: The uniqueness of human eye morphology among primates illustrates the remarkable difference between human and other primates in the ability to communicate using gaze signals.
    http://www.saga-jp.org/coe_abst/kobayashi.htm

    related notes:

    Paleoanthropology
    Excerpt: In regards to the pictures of the supposed ancestors of man featured in science journals and the news media Boyce Rensberger wrote in the journal Science the following regarding their highly speculative nature:
    “Unfortunately, the vast majority of artist’s conceptions are based more on imagination than on evidence. But a handful of expert natural-history artists begin with the fossil bones of a hominid and work from there…. Much of the reconstruction, however, is guesswork. Bones say nothing about the fleshy parts of the nose, lips, or ears (or eyes). Artists must create something between an ape and a human being; the older the specimen is said to be, the more apelike they make it…. Hairiness is a matter of pure conjecture.”
    http://conservapedia.com/Evolu.....thropology

    “National Geographic magazine commissioned four artists to reconstruct a female figure from casts of seven fossil bones thought to be from the same species as skull 1470. One artist drew a creature whose forehead is missing and whose jaws look vaguely like those of a beaked dinosaur. Another artist drew a rather good-looking modern African-American woman with unusually long arms. A third drew a somewhat scrawny female with arms like a gorilla and a face like a Hollywood werewolf. And a fourth drew a figure covered with body hair and climbing a tree, with beady eyes that glare out from under a heavy, gorilla-like brow.”
    “Behind the Scenes,” National Geographic 197 (March, 2000): 140

    “We have all seen the canonical parade of apes, each one becoming more human. We know that, as a depiction of evolution, this line-up is tosh (i.e. nonsense). Yet we cling to it. Ideas of what human evolution ought to have been like still colour our debates.”
    Henry Gee, editor of Nature (478, 6 October 2011, page 34, doi:10.1038/478034a),

    Paleoanthropologist Exposes Shoddiness of “Early Man” Research – Feb. 6, 2013
    Excerpt: The unilineal depiction of human evolution popularized by the familiar iconography of an evolutionary ‘march to modern man’ has been proven wrong for more than 60 years. However, the cartoon continues to provide a popular straw man for scientists, writers and editors alike.
    ,,, archaic species concepts and an inadequate fossil record continue to obscure the origins of our genus.
    http://crev.info/2013/02/paleo.....hoddiness/

    “most hominid fossils, even though they serve as basis of endless speculation and elaborate storytelling, are fragments of of jaws and scraps of skulls”
    Stephen Jay Gould

    The Fragmented Field of Paleoanthropology – July 2012
    Excerpt: “alleged restoration of ancient types of man have very little, if any, scientific value and are likely only to mislead the public”
    Earnest A. Hooton – physical anthropologist – Harvard University
    http://www.evolutionnews.org/2.....62101.html

  114. Chris,

    When I was a frequent contributor on this site, I tended to keep religion out of the discussion. Mainly, because I thought it got in the way of any discussion on evolution. Those who oppose ID are quick to seize on any religious argument as a basis for one’s position on evolution.

    My personal position is that the best way to defeat Darwinism and get it out of the curriculum is to accurately portray it scientifically. I believe to get ID or some form of it into the curriculum is a mistake. Darwinism on a grand scale has no basis in science, and to hammer that is in my opinion the best strategy. But to do that, one has to support what is known and supported.

    Namely, Darwin’s ideas are reasonable and in fact play out in our world in lots of ways. One is in the world of genetics or micro-evolution and here Darwin’s ideas are very relevant and this science has proved a boon to mankind. It obviously plays out in society and in the world of commerce. Spencer’s term “the survival of the fittest” which Darwin adopted is almost self evident. So self evident that it is hard to see how it cannot play out at a grander level. Which is why I recommend the tact on evolution as science is that “it is a mystery.”

    Since I stopped commenting here I have been commenting on another site mainly about economics and social policy and sometimes religion and occasionally evolution when it came up. This led me to explore philosophy more and economic history and it is interesting to see how philosophy evolved during the last 3000 years.

    The most interesting philosopher of all was Hegel. His ideas dominated the 19th century and some have called the 19th century the century of Hegel. Within certain groups his ideas are still paramount. It is within this framework that Darwin grew up and his ideas are Hegelian and it was one of the reasons they were so well accepted. The economic left are a prisoner of Hegelian thought and the drama plays out in Washington daily and in other capitals around the world and most know nothing of Hegel even though they are believers of his ideas. Darwin is part of that movement which is why Darwinism is an essential element of leftist ideology. Not entirely a clean distribution because Darwin is essential to atheism and atheism has a hold in libertarianism which is the antithesis of the left.

    But a lot of libertarians are culturally liberal and it is interesting to see how they are willing to let progressives reign in cultural and defense policy while wanting them absolutely out of the economic sphere. So ID is out on the perimeter of the main debate but has been a rock of sanity in the total societal debate. But as long as religion is kept out of it because it gets in the way of the message.

  115. “Scientists say Turin Shroud is supernatural – December 2011″

    As one who has seen the Shroud of Turin, I spent a lot of time learning about it. This was in my pre-ID days. There was a site then and it still exists run by a Jew named Barrie M. Schwortz who was part of the official Shroud investigating team in 1978. He was a photography expert.

    http://www.shroud.com/

    It is a very interesting site. The Shroud is certainly not a hoax but what is it? Like evolution, it is a mystery. The last pope as one of his last official acts ok’d a television exhibition of the Shroud next Saturday, the day before Easter.

    http://www.shroud.it/NEWS.HTM

    Also I believe that the painting of “Our Lady of Guadeloupe” is also a mystery. Though I haven’t read anything about it in years. So maybe there is a more scientific explanation today. I did see that too when in Mexico City.

  116. NATURAL SELECTION DOESN’T PRODUCE ANYTHING! It can only “select” from biological variations that are possible and which have survival value. The real issue is not natural selection but what biological variations are possible.

    ONLY LIMITED EVOLUTION POSSIBLE IN NATURE

    All real evolution in nature is within limits. The genes already exist for micro-evolution (variations within a biological kind such as varieties of dogs, cats, horses, cows, etc.), but not for macro-evolution (variations across biological kinds such as from sea sponge to human). The unthinking environment has no ability to design or program entirely new genes. Only variations of already existing genes and traits are possible. A dog will always be a dog no matter how many varieties come into being.

    Evolutionists hope and assume that, over millions of years, random mutations (accidental changes) in the genetic code caused by radiation from the environment will produce entirely new genes for entirely new traits in species so that macro-evolution occurs. It’s much like hoping that, if given enough time, randomly changing the sequence of letters in a cook book will turn the book into a romance novel, or a book on astronomy!

    Another problem for macro-evolution is the issue of survival of the fittest. How can a partially evolved species be fit for survival? A partially evolved trait or organ that is not complete and fully functioning from the start will be a liability to a species, not a survival asset. Plants and animals in the process of macro-evolution would be unfit for survival.

    Imagine an evolving fish having part fins and part feet, with the fins evolving into feet. Where’s the survival advantage? It can’t use either fins or feet efficiently. These fish exist only on automobile bumper stickers!

    In fact, how could species have survived at all while their vital organs were supposedly evolving? Survival of the fittest (aka natural selection) may explain how species survive, due to minor variations and adaptations to the environment, but not how they originated. Natural selection merely “selects” from biological variations that are possible. It’s not a creative force.

    Genetic and biological similarities between species are no proof of common ancestry. Such similarities are better and more logically explained due to a common Genetic Engineer or Designer (yes, God) who designed similar functions for similar purposes in various species. Genetic information, like other forms of information, cannot arise by chance, so it’s more rational to believe that DNA or genetic similarities between species are due to intelligent design.

    What about “Junk” DNA? The latest science shows that “Junk DNA” isn’t junk after all! It’s we who were ignorant of how useful these segments of DNA really are. Recent scientific research published in scientific journals such as Nature and RNA has revealed that the “non-coding” segments of DNA are essential in regulating gene expression (i.e. how, when, and where genes are expressed in the body).

    All the fossils that have been used to support human evolution have ultimately been found to be either hoaxes, non-human, or human, but not human and non-human.

    All species in the fossil record and living are complete, fully-formed, and fully functional. There’s no macro-evolution in nature.

    Visit my newest Internet sites, THE SCIENCE SUPPORTING CREATION and WAR AMONG EVOLUTIONISTS (2nd Edition)

    Sincerely,
    Babu G. Ranganathan
    (B.A. Bible/Biology)

    Author of the popular Internet article, TRADITIONAL DOCTRINE OF HELL EVOLVED FROM GREEK ROOTS

    *I have given successful lectures (with question and answer period afterwards) defending creation before evolutionist science faculty and students at various colleges and universities. I’ve been privileged to be recognized in the 24th edition of Marquis “Who’s Who in The East” for my writings on religion and science.

  117. WJM:

    You obviously have not accounted for the Darwinian Chance Fairies that sprinkle Magical Emergence Dust on rocks and mud and bake up things like consciousness and complex, self-replicating machinery in the Materialist Easy Bake Oven they call “Deep Time”.

    :cool:

  118. 118

    I always thought the NP paper was extraordinarily simplistic, as it left out everything except morphology. Rhodes’s thesis is an interesting attempt to consider a more realistic fitness landscape. Even then he ignores the discretization effect (the “genotype-phenotype mapping”) inherent in using a genetic algorithm – discretization typically introduces a spikier landscape even if you have an underlying smooth “fitness” function. And in reality the genotype-phenotype-fitness mapping is far too complex to uncover, even for the simplest organism. Dawkins’s “Mount Improbable” is really “Mount Fictitious”, yet many otherwise rational scientists are seduced by the metaphor. I just wish they would learn some mathematics.

  119. Nick Matzke:

    What??

    Troll.

    Hmm. So the person who says he didn’t read something, just glanced at the pictures, and concludes that entire scientific fields are bogus is just fine, and I’m the idiot because I expressed some skepticism about the “just look at the pictures” view?

    That’s truly hilarious coming from you.

    How many times now have you been asked two very simple questions, question which someone of your esteemed background and education ought to be able to readily answer, yet you have remained mute?

    In case you missed them:

    Did I miss where you supplied me with the name of a textbook on Macro-Evolutionary Theory, or have you remained silent because you really have nothing to offer?

    Did I also fail to see the post where you explained how macro-evolution works in single celled organisms absent any biochemical changes?

    Or are you just another fraud posing as an “educator”?

  120. 120

    Hi Jerry,

    Thanks again for your additional interesting comments. I must look further into the Hegelian connection with Darwinism. And I do agree with much of what you say. Especially the bit about keeping religion out of the ID debate, it is irrelevant and atheists often have a very unhealthy obsession with religion which goes way beyond using it as a distraction from the undeniable scientific facts that undermine their materialistic convictions.

    If I could just pick you up on the one point I disagree with, you said:

    “…one has to support what is known and supported. Namely, Darwin’s ideas are reasonable and in fact play out in our world in lots of ways.”

    Firstly, I am perfectly open to theistic evolution, the kind that in actual fact, many evolutionists actually believe in. Natural selection and random mutations could easily be part of the ID programme: the mechanism of evolutionary creation. As you know, a number of ID proponents accept common descent, they just reject the neo-Darwinistic mechanism for change because it is unguided and accidental.

    I could take or leave theistic evolution/evolutionary creation without significantly modifying the non-scientific factors that contribute to my worldview.

    But, I just don’t see how “Darwin’s ideas are reasonable”, nor how they “play out in our world”. I’m of the opinion that, from a purely biological perspective, ID proponents are granting an unnecessary concession to neo-Darwinism when they make such comments. I also think the term “micro-evolution” is highly misleading because it is frequently used to refer to pre-existing sub-specific variety.

    Maybe there are things that apply to economics that are reminiscent of Darwin’s ideas. But I don’t really see how “survival of the fittest” is one of them except in the trivial tautological use of that term. “Survival of the luckiest” or “Survival of the cheats” maybe… but those have nothing to do with Darwinism.

    But, let’s focus on science, rather than economics. What would you say, Jerry, is the best example/evidence of Darwin’s ideas in science?

  121. 121

    Hi BA77,

    Thanks for your post and the interesting links. Don’t get me wrong, though I’m not a Christian I have enormous respect for the Judeo-Christian tradition. Funnily enough, I can find a lot of shared ground in the points you raised. I look for the universal aspects that are shared by almost all religions, namely God, Morality and Afterlife. If you’re on board with all three then you’re on the right path. Because ultimately, it’s not about the technical details of a specific religion, it’s about how well you adhere to God’s Commandments, how often you put aside selfishness for selflessness. Despite themselves, atheists often succeed in this all-important respect where supposedly devout believers fail. Faith helps but it is not essential, and if you don’t back up your faith with substantial good works and sacrifice, then faith alone won’t help you on Judgment Day.

    As a great man once said “Whosoever therefore shall break one of these least commandments, and shall teach men so, he shall be called the least in the kingdom of heaven: but whosoever shall do and teach them, the same shall be called great in the kingdom of heaven.”

  122. Chris,

    I can find a lot of shared ground in the points you raised.

    Funny the ‘points’ I raised were on the Shroud of Turin and the ‘Being of Light’ in NDE’s supporting each other, and yet you didn’t even mention those points so as to ‘share’ them with me.

  123. What would you say, Jerry, is the best example/evidence of Darwin’s ideas in science?

    genetics. Most believe this is a very useful and powerful discipline. Medical science depends a great deal on changes to genomes in order to understand and fight disease and genetic problems.

    Dembski and other ID proponents provide instance of the proportion of allele frequency changes over times in populations which have led to obvious but trivial differences from previous populations. This is a commonly accepted definition of evolution, the change of allele frequency over time. It is simple and obvious but meaningless in terms of the over all debate. But it is evolution, and to deny it, is not useful. Give credit where it is due.

    Read Richard Dawkin’s books. He provides lots of examples which I believe most are accurate. No one denies them. What Dawkins, Coyle and the others fail to do is provide any examples of this playing out over time and providing substantial changes to a species in terms of major capabilities. They always appeal to deep time.

    One of the first books I read on this was by Ray Bohlin, titled “The Natural Limits to Biological Change.” Change happens but it is limited.

    The best way to defeat Darwinism is to accept it as a minor but useful player and rob it of its real glory which is based on bad science and bad reason. To do otherwise and dismiss it entirely is to look small. The constant mocking of the other side by both sides in this debate gets in the way of getting ID a more accurate look.

    Another useful book to read is “Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life” by Eva Jablonka, Marion J. Lamb and Anna Zeligowski. You have to know what they know or else one cannot know when they are blowing smoke.

    Hegel died when Darwin was young but his ideas on history progressing to an end dominated much of philosophy in the 19th century. It still is the accepted creed amongst many who look to a managed progress as a way to an earthly paradise. Hegel had some wild ideas but his idea of a geist and the progress of history hit home with people, especially the elites. Darwin grew up in that atmosphere where progress was thought a natural phenomenon. His ideas on evolution are in sync with these ideas which is one of the reasons why they were accepted so easily. Hegel said that the world was evolving/progressing. Darwin said the same thing about life forms and as Dr. Torley so aptly explains his prose was magnificent. The last half of the 19th century was focused on the idea of progress especially in Germany and it later became a major part of US politics.

    Also Marx was caught up in Hegel’s ideas.

  124. 124

    BA77,

    I am entirely open to the possibility that Jesus was nailed to a cross, removed from it and wrapped up in the very cloth that we now know as the Shroud of Turin. In fact, I could go further and say the Shroud of Turin is much more likely to be genuine than fake.

    That’s what I mean by sharing.

    NDEs are compelling evidence for life after death and the dualistic nature of body and mind. The Being of Light could indeed be a sense of the Creator, or something else closer to the Divine.
    That’s what I mean by sharing too.

    Throw in ID and we do indeed share lots of common ground! But, you’re a Christian and I am not… and I’m as sure as you are in my convictions. I perfectly understand why that difference is important to you and I respect your intentions in challenging me on this point. Nonetheless, religious differences are not important to me: there is only One True Source and almost all religions point to it.
    That’ll do for me.

  125. 125

    Jerry, thanks again for the response.

    And thank-you for the sources: you’ve given me a lot to think about, especially when you throw Hegel in with Bohlin and Jablonka et al.

    I have read various articles and books of Richard Dawkins. The most important book, as far as evolution is concerned, has to be one of his most recent “The Greatest Show on Earth” because, by his own admission, this is the first book he has ever written which seeks to “present the actual evidence that evolution is a fact” (meaning, of course, that he simply assumed the truth of evolution in all previous works!)

    After reading the entire book carefully, it is clear to see that this “actual evidence” is very weak indeed. He commits his first error early on: by failing to recognise that artificial selection is much more powerful than natural selection, that artificial selection is, in fact, Intelligent Design and that there are clear and impenetrable barriers to the variety we can achieve with it (or should I say, there are “natural limits to biological change”!) After that, he never really recovers, depending on just-so stories, more assumptions and mere sub-specific variety.

    So, I’m surprised you recommend Dawkins to say the least.

    Unlike some of my fellow ID proponents, I do not accept the “commonly accepted definition” of evolution that it is merely “change of allele frequency over time”. That is just a tiny step up from the even more ridiculous definition that evolution is just “change over time”. When evolutionists started redefining evolution in this way, it was nothing more than a rhetorical device to compensate for the fact that true Darwinian evolution was not supported by observation or experiment. Call it what you like, but “change of allele frequency over time” is not evolution: it is not what Darwin had in mind, nor does it shed any light whatsoever on how microbes evolved into man, by accident.

    Evolution means change, but change does not mean evolution.
    Variety with-in pre-existing gene pools is not evolution either.

    It is completely unnecessary to concede that things like change, variety or even the badly named “micro-evolution” are examples of Darwin’s idea in the real world. Why? Because once we all realise that Darwin was wrong about everything, there will still be change, variety and that-which-will-formerly-be-known-as-Micro-evolution!

    As for genetics, well, again, I’m surprised that you picked this as the best example/evidence of Darwin’s idea. Surely it is the exact opposite? I mean, if Darwin understood genetics, not to mention epigenetics, surely he would have disowned his theory? You may be aware of James A Shapiro (if not, please obtain his book “Evolution: A View from the 21st Century” it is a very important work) who dispenses with Natural Selection and Random Mutations in favour of Natural Genetic Engineering.

    Call it what you like, but Natural Genetic Engineering is most definitely NOT Darwin’s idea… it is completely different.

  126. Chris Doyle, your comment in 124, in response to my comment at 112, is interesting for on the one hand you admit:

    In fact, I could go further and say the Shroud of Turin is much more likely to be genuine than fake.

    and

    The Being of Light (in Near Death Experiences) could indeed be a sense of the Creator, or something else closer to the Divine.

    But on the other hand you state:

    But, you’re a Christian and I am not… and I’m as sure as you are in my convictions.,,, there is only One True Source and almost all religions point to it.

    That’s just strange Chris. It seems you agree that the Shroud authenticates Jesus triumph over death, and also seem to somewhat agree that the ‘Being of Light’ fits the ‘mechanism’ needed to explain how the image formed on the Shroud. But then you say you are not a Christian. Well Chris, if you think Jesus actually did rise from the dead, as is indicated by the Shroud, I think you may be much more of a “Christian” than you think you are! :) ,,, And not to get into the despondency inherent in Buddhism, or the ‘violence until peace’ apparent in Islam, or any of the major failings of other religions, but Christianity is drastically different from other religions in that Christianity claims exclusivity in successfully reconciling man with God. And the ‘proof’ of that successful reconciliation with almighty God is Jesus’ triumph over death, besides personal testimony, is the Shroud of Turin. The Shroud of Turin clearly points out a fact that sets Christianity completely apart from all other religions of the world. The fact is that, as I’ve heard said by many preachers before, you can go to the graves of all the other founders of all the other major religions of the world and find the remains of a body, yet, as the Shroud of Turin stubbornly testifies, despite many attempts to refute the Shroud’s authenticity, if you go to the tomb of Jesus you will not find the remains of a body because Jesus has risen from the dead just as was prophesied of Him in the OT (Isaiah 53).

    Burial places of founders of world religions
    http://en.wikipedia.org/wiki/B....._religions

    Matthew 28:5-6
    The angel said to the women, “Do not be afraid, for I know that you are looking for Jesus, who was crucified. He is not here; he has risen, just as he said. Come and see the place where he lay.

    Isaiah 53 – video
    http://www.youtube.com/watch?v=SvK4sD3rTU8

    But I would like to focus on another aspect of authentication for Christianity that diametrically sets it in opposition to the ‘religion’ that ID most directly opposes. The ‘religion’ of Darwinism,,,

    Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity, with meaning and morality,,, Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today.
    Darwinian atheist Michael Ruse – Prominent Philosopher

    “for, as we have just seen, the ways of national evolution, both in the past and in the present, are cruel, brutal, ruthless, and without mercy.,,, Meantime let me say that the conclusion I have come to is this: the law of Christ is incompatible with the law of evolution as far as the law of evolution has worked hitherto. Nay, the two laws are at war with each other; the law of Christ can never prevail until the law of evolution is destroyed.”
    Sir Arthur Keith, (1866 — 1955) Fellow of the Royal College of Surgeons – Evolution and Ethics (1947) p.15 (Note the year that this was written was shortly after the German ‘master race’ was defeated in World War II)

    That ‘point’ that most diametrically sets Christianity apart from Darwinism is ‘death’. The unmitigated horror visited on man by atheistic/Darwinistic regimes is hard to exaggerate,,

    “Christian” Atrocities compared to Atheists Atrocities – Dinesh D’Souza – video
    http://www.youtube.com/watch?v=FmrRC6zD4Zk

    If You Thought Religion was a Bad Idea…Check Out Atheism – Kirk Durston – June, 2012
    Excerpt: To summarize why purely atheistic societies are so dangerous, they not only killed for the cause of advancing a purely atheistic society, but their moral guardrail has no grounds. Thus, extraordinary democide can result, because a portable, hand carried moral guardrail is no guardrail at all.
    http://powertochange.com/wp-co.....s-2012.pdf

    Those numbers for murder by one’s own government are just plain crazy! But besides such insanity at that level when atheists get complete control of a government, Darwinists actually believe that ‘differential death and random variation’ is the source for all the variety of life on earth, whereas Christianity claims that God is source of for all life on earth. What’s more if one traces out the maximum source for ‘randomness’ in the universe, which is suppose to be the source for all creativity in the Darwinian scheme of things, then one finds out some very interesting thing. The maximum source for randomness in this universe are Blackholes:

    if one wants to build a better random number generator for a computer program then a better source of entropy is required to be found to drive the increased randomness:

    Cryptographically secure pseudorandom number generator
    Excerpt: From an information theoretic point of view, the amount of randomness, the entropy that can be generated is equal to the entropy provided by the system. But sometimes, in practical situations, more random numbers are needed than there is entropy available.
    http://en.wikipedia.org/wiki/C....._generator

    Thermodynamics – 3.1 Entropy
    Excerpt: Entropy – A measure of the amount of randomness or disorder in a system.
    http://www.saskschools.ca/curr.....rgy3_1.htm

    Evolution is a Fact, Just Like Gravity is a Fact! UhOh! – January 2010
    Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.

    Entropy of the Universe – Hugh Ross – May 2010
    Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.
    http://www.reasons.org/entropy-universe

    Roger Penrose – How Special Was The Big Bang?
    Excerpt: “But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.”

    What Would Happen If You Fell into a Black Hole? – video
    http://www.youtube.com/watch?v=gLMiJQXsmkc

    ,,Not to mention trying to survive the extremely high temperatures present at the event horizon of the black hole:,,

    Scientists gear up to take a picture of a black hole – January 2012
    Excerpt: “Swirling around the black hole like water circling the drain in a bathtub, the matter compresses and the resulting friction turns it into plasma heated to a billion degrees or more, causing it to ‘glow’ – and radiate energy that we can detect here on Earth.”
    http://www.physorg.com/news/20.....-hole.html

  127. Moreover, it can be forcefully argued that this ‘entropic randomness’, instead of being a such a great source of creativity for Darwinism, is in fact the primary reason why things grow old and die in this temporal realm. This following video brings the point personally home to each of us about the very destructive effects of entropy on our own bodies:

    Aging Process – 80 years in 40 seconds – video
    http://www.youtube.com/watch?v=hSdxYmGro_Y

    *3 new mutations every time a cell divides in your body
    * Average cell of 15 year old has up to 6000 mutations
    *Average cell of 60 year old has 40,000 mutations
    Reproductive cells are ‘designed’ so that, early on in development, they are ‘set aside’ and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,,
    *60-175 mutations are passed on to each new generation.
    Genetic Entropy and The Mystery Of the Genome – Dr. John Sanford – video
    http://www.youtube.com/watch?v=GwCu4rh7kUk

    Yet, to bring this back to the Shroud of Turin and Jesus, one of the unique ‘supernatural’ characteristics of the Shroud of Turin is,,,

    THE EVENT HORIZON (Space-Time Singularity) OF THE SHROUD OF TURIN. – Isabel Piczek – Particle Physicist
    Excerpt: We have stated before that the images on the Shroud firmly indicate the total absence of Gravity. Yet they also firmly indicate the presence of the Event Horizon. These two seemingly contradict each other and they necessitate the past presence of something more powerful than Gravity that had the capacity to solve the above paradox.
    http://shroud3d.com/findings/i.....-formation

    Particle Radiation from the Body – July 2012 – M. Antonacci, A. C. Lind
    Excerpt: The Shroud’s frontal and dorsal body images are encoded with the same amount of intensity, independent of any pressure or weight from the body. The bottom part of the cloth (containing the dorsal image) would have born all the weight of the man’s supine body, yet the dorsal image is not encoded with a greater amount of intensity than the frontal image. Radiation coming from the body would not only explain this feature, but also the left/right and light/dark reversals found on the cloth’s frontal and dorsal body images.
    http://www.academicjournals.or.....onacci.pdf

    Turin Shroud: a medical forensic study of its blood marks and image (Body Position) – G.Lavoie – May 2010
    http://www.acheiropoietos.info.....oieWeb.pdf

    ,,,that when the image was made on the Shroud it is apparent that the body was defying gravity, and thus by default the body was defying the entropic randomness inherent in gravity. But an interesting thing is possible if this (defying of gravity) were to occur. The following researcher thinks a ‘theory of everything’ may be possible if one can get away from the effects of the space-time curvature of gravity:

    Testing Einstein’s E=mc2 in outer space – January 4, 2013
    Excerpt: “The most important problem in physics is the Unifying Theory of Everything – a theory that can describe all forces observed in nature,” said Lebed. “The main problem toward such a theory is how to unite relativistic quantum mechanics and gravity. I try to make a connection between quantum objects and General Relativity.” The key to understand Lebed’s reasoning is gravitation. On paper at least, he showed that while E=mc2 always holds true for inertial mass, it doesn’t always for gravitational mass. “What this probably means is that gravitational mass is not the same as inertial,” he said.,,,
    “Space has a curvature,” Lebed said, “and when you move a mass in space, this curvature disturbs this motion.” According to the UA physicist, the curvature of space is what makes gravitational mass different from inertial mass. Lebed suggested to test his idea by measuring the weight of the simplest quantum object: a single hydrogen atom, which only consists of a nucleus, a single proton and a lone electron orbiting the nucleus.,,,
    Lebed suggested the following experiment to test his hypothesis: Send a small spacecraft with a tank of hydrogen and a sensitive photo detector onto a journey into space.,,
    http://phys.org/news/2013-01-e.....space.html

    And indeed,,,

    Acts 13:36-37
    Now when David had served God’s purpose in his own generation, he fell asleep; he was buried with his ancestors and his body decayed. But the one whom God raised from the dead did not see decay.

    Centrality of Each Individual Observer In The Universe and Christ’s Very Credible Reconciliation Of General Relativity and Quantum Mechanics
    https://docs.google.com/document/d/17SDgYPHPcrl1XX39EXhaQzk7M0zmANKdYIetpZ-WB5Y/edit?hl=en_US

    ,,, I am very happy to see that what is considered the number one problem of Physicists and Mathematicians in physics today, of a unification into a ‘theory of everything’ for what is in essence the finite materialistic world of General Relativity and the infinite Theistic world of Quantum Mechanics, does in fact seem to find a credible resolution for ‘unification’ within the resurrection event of Jesus Christ Himself. According to atheistic reasoning this should not even be on the radar scope of reason. Yet, contrary to what their a-priori bias would hold, it seems almost overwhelmingly apparent to me from the ‘scientific evidence’ that we now have in hand that Christ literally ripped a hole in the finite entropic space-time of this universe to reunite infinite God with finite man. That modern science would even offer such a almost tangible glimpse into the mechanics of what happened in the tomb of Christ should be a source of great wonder and comfort for the Christian heart.

    1 Corinthians 15:55
    “Where, O death, is your victory? Where, O death, is your sting?”

    As a footnote; Godel, who proved, within the incompleteness theorem, that you cannot truly have a mathematical ‘Theory of Everything’, without allowing God to bring completeness to the mathematical ‘Theory of Everything’, also had this to say:

    The God of the Mathematicians – Goldman
    Excerpt: As Gödel told Hao Wang, “Einstein’s religion [was] more abstract, like Spinoza and Indian philosophy. Spinoza’s god is less than a person; mine is more than a person; because God can play the role of a person.” – Kurt Gödel – (Gödel is considered one of the greatest logicians who ever existed)
    http://www.firstthings.com/art.....ematicians

    Music:

    Natalie Grant – Alive (Resurrection music video)
    http://www.godtube.com/watch/?v=KPYWPGNX
    Lyric from song:
    “Death has lost and love has won!”

  128. Dr. Torley,

    If you are reading this far down into the comments you might be interested in an essay by John Stuart Mill on intelligent design written in the mid 19th century. He particularly discusses the eye.

    http://www.earlymoderntexts.com/pdf/millthei.pdf

    It is an essay on theism and the part on design and the eye begins on page 13. My guess is that it was written after Darwin’s Origin of Species. He does not mention Darwin or evolution but does talk about the “survival of the fittest.”

    I wonder how Mill would write his essay today with all the current information. He uses the term “designing intelligence,” so does that make him one of the modern creators of intelligent design.

  129. I found a review of Mills essay. It was published one year after his death in 1874.

    http://ndpr.nd.edu/news/24168-.....-religion/

  130. Hi jerry,

    Thanks for the link to Mill’s article, Theism. Although I was deeply gratified to see that Mill had a high regard for the argument from design, despite having evidently read Darwin’s Origin of Species, I could not help noticing that in his presentation of the argument from design, Mill perpetuated three common myths abut the argument itself – namely, that it is an argument from analogy, that it is inductive, and that it is a merely probabilistic argument, rather than a certain and indubitable proof. All of these claims are false, as I pointed out in my recent online post, Paley’s argument from design: Did Hume refute it, and is it an argument from analogy? (December 30, 2012):

    Paley’s argument is not based on any analogy. He doesn’t say that the complex organs found in living things are like artifacts; he says that they are the same as artifacts in certain vital respects. In particular, these complex organs share several common properties with artifacts: “properties, such as relation to an end, relation of parts to one another, and to a common purpose” (Natural Theology. 12th edition. J. Faulder: London, 1809, Chapter XXIII, p. 413), or as he puts it elsewhere, “[a]rrangement, disposition of parts, subserviency of means to an end, [and] relation of instruments to a use” (Natural Theology. 12th edition. J. Faulder: London, 1809, Chapter II, p. 11). Paley refers to the organs of the body as “contrivances” precisely because they share these vital properties with man-made artifacts. (For the benefit of Thomist readers who may be wondering, I should point out that Paley is fully aware of the intrinsic teleology of living things, and that he repeatedly refers to “final causes” in his Natural Theology.)

    Next, Paley argues that intelligence is the only known adequate cause of objects possessing the combination of properties found in artifacts and complex organs. Our experience tells us that that no other cause, apart from intelligence, is capable of producing effects possessing these properties. Paley concludes that the complex organs of living creatures (such as the eye) must therefore have had an Intelligent Designer…

    For Paley, the inference to design, upon seeing a contrivance, is immediate

    Paley himself declares on several occasions that his argument for a Designer of Nature is a deductive argument….

    The premises of Paley’s deductive argument are as follows. First, we know that intelligent agents are capable of producing effects marked by the three properties of (i) relation to an end, (ii) relation of the parts to one another, and (iii) possession of a common purpose.

    Second, no other cause has ever been observed to produce effects possessing these three properties.

    We are therefore entitled to conclude that if there are systems in Nature possessing these same three properties, then the only cause that is adequate to account for these natural effects is an Intelligent Agent.

    Paley explicitly states, over and over again, in his Natural Theology, that he views his argument for a Designer not as a merely probabilistic argument, but as a proof, whose conclusion was certain and indubitable. For example, in his discussion of the ligament of the ball-and-socket joint of the thigh,… Paley declares that it provides us with unequivocal proof of a Creator…

    After describing the circulation of the blood, he writes: “Can any one doubt of contrivance here; or is it possible to shut our eyes against the proof of it?”…

    Paley puts forward one final argument to convince diehard skeptics in his day, who were still inclined doubt the legitimacy of any inference from the numerous contrivances that we find in the natural world to the existence of a Designer of Nature. He offers a reductio ad absurdum: if the skeptics are right, he says, an absurd consequence follows: it would mean that no matter how perfectly ordered the universe was, we could still never be sure that it had an Intelligent Creator. No sane person would accept such a ridiculous conclusion, he says…

    I provide supporting citations in my article (see Myths Two, Three and Four).

    That said, I was heartened to read Mill’s conclusion that the argument from design “has considerable strength,” and that “the adaptations in nature provide a large balance of probability in favour of creation by intelligence.” Mill also notes that the principle of the survival of the fittest “doesn’t claim to account for the origins of sensation or of animal or vegetable life” and that “there’s something very startling and prima facie improbable in this hypothetical history of nature.”

    Thanks once again for the interesting links, jerry.

  131. Nick Matzke’s not a fraud, he’s a member of a cult.

    That’s one possible explanation for why he can’t even refer me to a standard text on macro-evolutionary theory. I’m just not initiated at the proper level.

    Fraud. Cult member. What’s the difference, really?

    Am I just being incredibly unreasonable? Nick whines when we question his “field.” Yet it appears that his field is not taught in any standard university text.

  132. lastyearon @101:

    Apologies for a late reply. I also apologize if I missed your real point. It seemed like you were making a parody of a design argument, as we were discussing biological information and CSI and you started talking about quarks and gluons and so forth and I could see it playing into Nick’s hands as some kind of argument ad absurdam.

    You are right that there are interesting questions relating to the makeup of the very particles themselves. However, I think that is a separate issue from the source and origin of biological information.

  133. Yeah, “364,000 years is too round of a number,” what a great piece of evidence!

  134. Joealtle-

    Evidence is something that unguided evolution does NOT have.

  135. Who’s saying that evolution is an unguided process? Its guided by natural selection.

  136. Who’s saying that evolution is an unguided process?

    Everyone who understands it

    Its guided by natural selection.

    In what way does natural selection guide anything?

    Natural selection is blind, mindless and without purpose.

    38 Nobel Laureates say:

    Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.

    Yeah baby…

  137. No, now youre putting words in everyone’s mouths. Natural selection is not guided in a specific direction, but it does guide the evolution of biology according to the environment. Great job twisting words buddy.

  138. Natural selection doesn’t guide anything.

    Great job being a gullible fool, bubby

  139. According to who? You? Natural selection guides the entire process of evolution. I thought you guys were smart.

  140. Natural selection guides the entire process of evolution. I thought you guys were smart.

    LOL!

    Now I’m sure we’re dealing with a troll. Don’t feed him, Joe.

  141. Or maybe youre dealing with someone who knows what they are talking about, unlike you.

  142. Natuarl selection is just differential reproduction due to heritable random (chance) variation. Whatever is good enough survives to reproduce (Mayr).

    What guidance is that?

    The mutations are not guided. What survives depends on many factors. And having more offspring doesn’t produce anything but more offspring.

  143. Correct, mutations are not guided, but those who survive more often is decided by natural selection choosing from these mutations. Natural selection is the driving force that provides the “decision” between who survives to pass on genes and who doesnt.

  144. Natural selection does not decide. And organisms can survive for reasons other than natural selection.

  145. Uh yes, natural selection is the process by which organisms with advantageous characteristics are selected to survive. This is a “decision” in the most simple sense.
    What other reasons might an organisms survive or not other than natural selection?

  146. 146

    “What other reasons might an organisms survive or not other than natural selection?”

    Organisms “survive” because they are viable. It’s viable fecundity which needs to be accounted for in the first place.

  147. And this isnt natural selection? Why are they viable or not? Beacause they cannot survive in nature.

  148. 148

    Natural selection requires heritable variation, i.e., viable fecundity. Having a reproducing organism logically precedes natural selection acting on the variations.

  149. Hence why evolution does not start until abiogenesis has occurred.
    Do you have a point?

  150. 150

    So it’s abiogenesis that explains viable fecundity then, not natural selection?

  151. Fecundity is the ability to reproduce. Natural selection decides who reproduces and who doesnt.

  152. 152

    Natural selection doesn’t “decide” anything. It’s the result of differential reproductive success, which requires differential reproduction. Therefore, reproduction with variation happens to precede natural selection by logical necessity. If you want to explain reproduction, then yes, you’ll have to invoke another process, which at this time there are no good candidates for, not by a long shot. There couldn’t be a bigger “mystery” in biology right now than how chemicals self-organize to build nano-scale factories and machines.

  153. I told you already, variation in reproduction provides the choices for natural selection. Natural selection then “decides” who survives in specific environments, which changes the gene pool of the next generation. If you disagree with this then you simply do not understand evolution.

  154. 154

    “If you disagree with this then you simply do not understand evolution.”

    That’s correct. I do not understand how random mutations filtered by natural selection builds molecular machines and whole body plans. Neither does anyone else on planet earth. I’m waiting for total enlightenment. Perhaps you’re the promised one.

  155. Then why are you arguing against evolution if you dont understand it. Many people understand how evolution works, we may not know every detail of it and we may never be able to recreate every instance of change that has led to the diversity of species that we see today, but that doesnt change the fact that their is an overwhelming amount of evidence that supports evolution.

  156. 156

    I understand what neo-Darwinian evolution is supposed to do, it’s supposed to create all biological diversity via RM+NS. What I don’t understand, nor do you, is how this putative force actually builds sophisticated systems, molecular machines, and whole body plans. You’re bluffing.

    Anyone can say, “You know, evolution creates all biological diversity from a universal common ancestor by generating random variations and then selecting the good ones over millions of years.” What nobody can do is show how the process works. I’ts easy to engage in imaginative speculation about how something might occur, especially something so outlandish as fashioning intricate and stunning sophistication out of random mutations acting on natural selection. I’ts another matter entirely to demonstrate the process empirically.

    As the adage goes, In theory, there is no difference between theory and practice. In practice, there is.

  157. Yes of course, the old “science cant explain how it came about, therefore it must have been designed.”
    For the last time, this is an argument from ignorance. Science acknowledges how little it knows about the universe, but the fact of the matter is the best we an do is try to explain it in terms of what we do know through scientific experimentation and observation. What the ID movement is, is an attempt to explain things from a lack of scientific evidence.

  158. 158

    Feel free to lay out the entire process for us. Lectures about what science is, do nothing to explain how to build bodies from single-celled self-replicators, nor self-replicators from inanimate matter. As a matter of fact, it’s not uncommon here for those who claim to know how neo-Darwinism fashions biological diversity to fall back to explaining “how science works” when they can’t actually demonstrate anything empirically.

  159. You want me to type you up an entire science education? Ok give me four years and 80,000 bucks. Ive already admitted that there are a lot of holes in abiogenesis as we are not sure about a lot of things, but what we can do is continue to study science and show how it can happen, and thats what weve done from studies of extant species, study of the fossil record, and studies within every field of biology.
    The only evidence for ID is the gaps between evidence in abiogenesis, this is not evidence.

  160. 160

    Joealtle @159

    “Ive already admitted that there are a lot of holes in abiogenesis as we are not sure about a lot of things, but what we can do is continue to study science and show how it can happen, and thats what weve done from studies of extant species, study of the fossil record, and studies within every field of biology.”

    “Holes” suggests a working theory with missing details. Abiogenesis is no such thing. There is nothing but gross speculation as to how life might have arisen. This shouldn’t be confused with a working theory just because experiments are done and papers are published, if the data cannot show us how life arises via blind matter. Likewise with the neo-Darwinian mechanism for producing all biological diversity. It just hasn’t been shown to do what it’s purported to do. Covering NDE with the lab-coat of the stereotypical scientist does nothing to mask the fact that empirical evidence for the supposed wide-ranging powers of RM+NS is entirely lacking. Even the definition of the “gene” is dissolving in the face of new discoveries. And it only gets worse as time goes on.

    So you can keep claiming that “science” is figuring it all out, but until the efficacy of the mechanism can be demonstrated to match the claims, it doesn’t matter how many science labels you stick on NDE, nor how big you write the word SCIENCE upon it. Neo-Darwinian evolution has failed to explain the diversity of life, and is in the process of being scrapped. Abiogenesis is in shambles with regard to explaining how prebiotic conditions produced the first life by chance and necessity.

  161. Funny you claim that, evolution is stronger than ever and abiogenesis as well as evolution are continually being worked on.
    Evolution is far from “being scrapped.” The fact that you would even say that shows what a joke you and every other idiot on here are.

  162. 162

    There is an awkward but illuminating correlation between belief and presumed efficacy with regard to neo-Darwinian mechanisms. Those who believe in its powers of creation understand it, and those who doubt its claims do not.

  163. Uh yes, natural selection is the process by which organisms with advantageous characteristics are selected to survive.

    There isn’t any selecting going on .

    What other reasons might an organisms survive or not other than natural selection?

    Sheer dumb luck.

    And again, according to Mayr, whatever is good enough survives- it isn’t just the organisms with advantageous traits.

    IOW you don’t understand the very thing you are trying to defend.

  164. Really? No selection going on in the process of natural selection? Dont you think they wouldve named it something different if that is the case?
    And good point, while rare, freak incidents like asteroids strikes can wipe out vast members of a populations and change the gene pool of that population forever. This is also taken into account in the theory of evolution in things such as the bottleneck effect.

  165. Darwin called in “natural selection” to fool people. It worked.

    The Origin of Theoretical Population Genetics (University of Chicago Press, 1971), reissued in 2001 by William Provine:

    Natural selection does not act on anything, nor does it select (for or against), force, maximize, create, modify, shape, operate, drive, favor, maintain, push, or adjust. Natural selection does nothing….Having natural selection select is nifty because it excuses the necessity of talking about the actual causation of natural selection. Such talk was excusable for Charles Darwin, but inexcusable for evolutionists now. Creationists have discovered our empty “natural selection” language, and the “actions” of natural selection make huge, vulnerable targets. (pp. 199-200)

  166. Ah yes, he called it natural selection to fool people. Science is some huge conspiracy! He didnt write an entire book explaining his ideas about where new species have come fro in the process of natural selection or anything, did he?
    Look up sickle cell disease. It is a perfect example of natural selection at work.

  167. Joe, CR, EA … you guys must be quaking in your boots. The arguments being put forward by Joealtle are some of the best I’ve ever seen.

    It really is game over for ID ;)

  168. Ah yes, sarcasm. One of the best weapons for you guys, right next to ignorance and scientific illiteracy.

  169. 169

    PeterJ,

    “The arguments being put forward by Joealtle are some of the best I’ve ever seen.”

    Yes it’s been a cold hard dose of reality for us here over the last 24 hours. I’ve never seen the evidence laid out like that. Abiogenesis happens, the evidence is clear, then some indeterminate single-celled organism evolves by RM+NS into complex life by gradual incremental shifts from lower complexity into every type of creature imaginable; and here they all are for everyone to see. We don’t have all the details yet, such as exactly how it happens, or what steps are involved, or how the transitions are made, but those pesky details will become clear over time because science has shown that random mutations can engineer complex life forms from simpler ones, once those simpler forms come into existence, as is obvious from the evidence that exists somewhere. I guess we’ve just been too blinded by intelligence here to see it. Who would have guessed — twenty-four hours ago I thought that only intelligence was known to produce coding and information processing systems, manufacturing systems, quality control, and power converters, and that only intelligence could put all those pieces together into a stable configuration; but now it’s clear that it happens at random. How could I, how could we all, not have seen it before? Perhaps because we were never exposed to the actual evidence until now. And the evidence is that neo-Darwinism is science, and science shows us how things work, and provides the gritty details that would otherwise be easy to just gloss over in favor of creative story telling.

  170. Yes more sarcasm! Belittle me all you want, but just remember you guys have still failed to provided a single scientific article that supports ID. I was just told that many of the people on here have high degrees and teach, certainly some of you have done some scientific research to back up your claims, no?

  171. Humans with sickle-cell anemia are still humans.

  172. What an incredibly insightful and intelligent comment! You must be the brains behind things here!
    Bye now!

  173. Oh please don’t leave us JoeA. How will we ever learn the truth about this issue.

    You have given us insights into this topic that we never knew before.

    Things will never be the same ;)

  174. JoeA,

    At least allow me to point you to a blog where I’m sure your level of expertise will be very much appreciated.

    http://humanextension.wordpress.com/

  175. 175

    Now that’s funny. Two peas in a pod.

  176. Have I missed something here? This article talks about evolution of a vertebrate eye, suggesting a mammal type eye, but the Nilsson & Pelger paper appears to discuss only a fixed camera type eye, not the swiveling type in mammals. The evolution from a fixed to a swiveling eye would surely take much longer.

Leave a Reply