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A Darwinian Enigma: Defending The Preposterous After Having Been Informed

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Michael Behe and I had the same reaction after reading Michael Denton’s Evolution: A Theory in Crisis. Our reaction was, “Why haven’t we heard any of this stuff before?”

The answer is simple. All criticisms of Darwinian orthodoxy were successfully branded by Darwinists as the mindless fantasies of religious fanatics whose purpose was to destroy “science.”

But let us ask, Who are those who have engaged in mindless fantasies concerning origins?

In the information age, the notion that random errors can produce highly sophisticated biological information, information-processing machinery, and the associated error-detection-and-repair mechanisms and algorithms, is so preposterous that I conclude that Darwinists have either lost their minds, are pathetically uninformed, or have chosen to deny evidence, rationality, and the discoveries of modern science in order pursue a thoroughly irrational commitment to materialistic philosophy.

In an attempt to defend the clearly preposterous, Darwinists have become the preeminent enemies of science concerning origins.

Comments
Hey everyone, I have been doing some reading and have a question concerning evolution and the beliefs that serve as its underpinnings. Specifically I wanted to explore something the atheist Michael Ruse said: "evolution, akin to religion, involves making certain a priori or metaphysical assumptions, which at some level cannot be proven empirically.” In your opinion, what are these articles of faith that evolution rests upon?above
December 2, 2011
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You mean details like thse?
Ab initio structure prediction: uses quantum mechanics to model atom by atom – Relatively inaccurate, very slow – The only option for totally novel structures
Petrushka
December 1, 2011
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Petrushka: You can find more details here: http://ocw.mit.edu/courses/biology/7-349-biological-computing-at-the-crossroads-of-engineering-and-science-spring-2005/assignments/pres_kate.pdf Yes, they used iterative computation, as far as I can understand. But it is the best example of a top down protein design based on computation, exactly what you seem to deny. It is true that the protein folds, but has not specific function. But the fact remains that, even with limited computational resources, proteins can be engineered top down.gpuccio
December 1, 2011
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I can't read the article, or any of the related articles, but I'll be interested in the details. From the abstract it appears to use an iterative process, which translates to fecundity and selection, just in software instead of chemistry. Are you changing your pitch regarding the modelling of biochemistry in software? How far do you think this approach will go before it exceeds available computational resources, and what do you think about modelling the next step, which would involve predicting utility?Petrushka
December 1, 2011
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Petrushka: "Design of a novel globular protein fold with atomic-level accuracy. (2003) Science 302: 1364-1368 A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature. "gpuccio
December 1, 2011
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As it is, your argument is based upon the unsupported claim that protein folds can’t be predicted.
My claim is supported by the fact that billions of dollars spent every year on pharmaceutical research and billions of hours of computer time have not produced anything like a formula for protein folding, and folding is just the first step to determining utility. And each step introduces an equivalent level of complexity. I think I understand the claim that the origin of cellular machinery is unsolved. It isn't being ignored. It's just a very hard problem. It's always possible, as Darwin surmised, that first life is a miracle. Even so, evolution doesn't require miracles. It just requires that the functional landscape be traversable, and that's an empirical question.Petrushka
December 1, 2011
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yawn.
Your argument is remarkable postmodernist (no name-calling intended) and seems to rest on the claim that mathematics is anthropocentric
My argument is that the transfer of recorded information from the genome demonstrates the same physical objects and physical dynamics as any other form of recorded information transfer ever observed (no matter whether that information was bound to humans, or human intelligence, or other living things, or non-living machines), and by coherently satisfying these physical entailments (through observation) it confirms a semiotic state.
There are many accepted facts that are based entirely on observation and have no theoretical backing. The laws of thermodynamics, for example. These are purely observational. No one has a clue why they seem to be true. They just are.
Like thermodynamics, the physical observations in this case are unrefuted, and the argument that follows makes no unsupported assumptions or has any internal contradictions.
The fact that protein coding sequences cannot predict folds or functional utility is just as firm. It is always possible that the claim is wrong, just as it is possible that an exception will be found to the laws of thermodynamics.
This will need to be parsed apart. Firstly, protein coding sequences do not "predict" proteins, they physically drive the assembly of proteins within the confines of the system in which they are coordinated to operate. Secondly, for your argument to possibly be wrong it would first need to possibly be right. As it is, your argument is based upon the unsupported claim that protein folds can't be predicted. Your commanding evidence for this claim is that no one know how. So what you end up with is an unsupported assertion backed up by an anthropocentric fallacy which conflates reality with your personal judgement of what is knowable. What principle is at work which would confirm that 'proteins folds cannot be predicted', you do not say.
My point would be that ID requires three things never witnessed: 1. an observed instance of design, 2. a designer, 3. the ability to predict the utility of coding sequences.
Your #1 is a subjective shell game; the observation of immaterial properties instantiated into physical objects (semiosis) is an intractable inference to volitional agency coming from an unrefuted line of examples. You simply ignore it. Your #2 is typical materialist drivel. ID proponents must produce proof of a designer, but materialists needn't produce any material demonstrations of proof at all. This desperate requirement is an open call for training wheels and a safety net for an ideology failed by modern molecular science. Such ultimate requirements are posted for no other reason than to distract from the fact that the evidence for design is already observable and unrefuted. Observable unrefuted evidence (in the present) requires the ultimate distraction, hence the ultimate goalpost. Your #3 is just a little out of place. Are you suggesting that if I produce the designer in your #2, you'd still like him/her/it to falsify your argument about protein folds?Upright BiPed
November 30, 2011
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Your argument stands on the idea that if humans cannot predict the folding of a protein (and therefore design it), then such information cannot be known (and by extention, proteins cannot be designed). This is, of course, an entitrely anthropocentric idea, and a bad one at that.
Your argument is remarkable postmodernist (no name-calling intended) and seems to rest on the claim that mathematics is anthropocentric. There are many accepted facts that are based entirely on observation and have no theoretical backing. The laws of thermodynamics, for example. These are purely observational. No one has a clue why they seem to be true. They just are. The fact that protein coding sequences cannot predict folds or functional utility is just as firm. It is always possible that the claim is wrong, just as it is possible that an exception will be found to the laws of thermodynamics. My point would be that ID requires three things never witnessed: 1. an observed instance of design, 2. a designer, 3. the ability to predict the utility of coding sequences.Petrushka
November 30, 2011
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Name calling? Are you referring to me saying you are "quite an empiricist"? Is that what you refer to as "a lot of name-calling"? If it is, then sure, there was a lot of "name calling" going on. In any case, you know exactly what I am talking about. Your argument stands on the idea that if humans cannot predict the folding of a protein (and therefore design it), then such information cannot be known (and by extention, proteins cannot be designed). This is, of course, an entitrely anthropocentric idea, and a bad one at that.
I’m not discussing why things exist. I’m discussing how a very narrowly defined range of phenomena work.
And I am trying to get you to acknowledge the fact that the way in which your "phenomena works" has already-observable design embedded in it - which cannot be ignored by any empiricist operating with integrity. But because you have demonstrated little interest in evidentiary integrity, your own words and actions fold back upon themselves in contradictions. First you ignore the evidence against you by claiming you are "not discussing why things exist". Then you launch this anthropic deformity in logic. Then you use this silly argument to to do exactly what you said you weren't doing - making claims about why something exist. Why not do the right thing by science, and address the physical evidence instead? How does an physical object become observably instantiated with an immaterial property?Upright BiPed
November 30, 2011
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Petrushka you state you would be 'converted':
if you would show me how to design protein domain sequences without either evolution or magic.
Well Petrushka, since evolution, or magic, has NEVER been observed to 'design protein domain sequences', whereas when intelligence is used in concerted effort with 'directed evolution, we can design novel functional proteins, (yet our 'designed proteins still fall short by several orders of magnitude when compared to the 'optimal' proteins found in nature), why in blue blazes do you hold to the position that has zero evidence instead of the position that has some evidence???? Surely you are aware that for man to design functional proteins completely without some refining trial and error process, because of their rarity (1 in 10^77), would require man to have near infinite knowledge in the first place?!? So basically you are saying to us, when you ask us to show you how to design novel functional proteins, that if you had the knowledge of God to do as such then you would believe in God??? But Petrushka, would you not then be God??? Perhaps you should set your sites a little more modestly??? :)
Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681
Dr. Stephen Meyer comments at the end of the preceding video,,,
‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009) A few comments on ‘non-local’ epigenetic information implicated in 3-D spatial organization of Body Plans: https://docs.google.com/document/pub?id=1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY
Verse and Music;
Romans 1:20 For since the creation of the world God's invisible qualities--his eternal power and divine nature--have been clearly seen, being understood from what has been made, so that men are without excuse. Nichole Nordeman - "What If" http://www.youtube.com/watch?v=EUGQFH03apc
bornagain77
November 30, 2011
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To be more specific I'm discussing whether the known kinds of genetic and genomic change can effectively traverse the sequence landscape. I don't know how the cellular machinery originated, and it isn't necessary to know how it originated in order to study its behavior.Petrushka
November 30, 2011
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There seems to be a lot of name-calling embedded in your post, but I'm not able to figure out what you mean. I'm not discussing why things exist. I'm discussing how a very narrowly defined range of phenomena work.Petrushka
November 30, 2011
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...and all the while you wilfully refuse to acknowledge the observable evidence required for your wholly anthropocentric argument to even exist. You are quite an empiricist petrushka.Upright BiPed
November 30, 2011
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I would also be "converted" if you would show me how to design protein domain sequences without either evolution or magic. I'm told 500 bits of functional sequence can only be the work of intelligence. So I'm eagerly awaiting a demonstration that a human or something like a human can assemble an entirely new protein coding sequence without fecundity and selection.Petrushka
November 30, 2011
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P: Pardon, but that is a pretzel-twisty response. The fossil record precisely does not show the dominance of transitionals, as I pointed out. GEM of TKIkairosfocus
November 30, 2011
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Petrushka: Well, we will wait for you!gpuccio
November 30, 2011
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Basically the short answer to your question is yes. If someone like Thornton exhaustively investigates the pathways from a parent sequence to a child sequence and finds no mechanism for traversing the gap, that would be a very serious matter. Let's see one.Petrushka
November 30, 2011
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I'm not sure what you mean by all the investigation. Work like Lenski's takes decades to investigate a simple three step change. Thornton's work is also pretty time and effort consuming. But that is the kind of work that needs to be done.Petrushka
November 30, 2011
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Petrushka: A simple question: if after all the active investigation no incremental way of traversing the functional landscape is found, will you change your mind? Will you come on our side? You would be welcome, everybody needs stubborn fighters like you...gpuccio
November 30, 2011
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Petrushka: It is part of the blindness of Darwinism that its proponents actually believe that the fossil record supports the theory. It does not. Darwin saw that it did not, and 150 years later that hasn't changed. In fact, it is much worse today because orders of magnitude more fossils have been unearthed. You ask, "What exactly do you want?" If Darwinism were true, then we should see millions of examples of slow, incremental change of one species into another. We should see a fish fin slowly morphing, step by Darwinian step, into a pentadactyl limb, or a small rodent's forelimbs gradually elongating and becoming a bat's wings, or reptilian scales changing in small incremental steps into feathers. The time scales on which these changes must occur are vast, and they are universal, if the theory is correct. But there is not one instance of such a pattern. Not one. What do I want? If there were even one such sequence, it would cause me to seriously re-evaluate my position regarding the truth of Darwinism. But there aren't any. That speaks volumes to me.Bruce David
November 30, 2011
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Petrushka asks:
Perhaps you care to address the series leading from jaw bones to inner ear bones.
That particular Darwinian fairy tale is addressed at the 31:49 minute mark of this following video (you have to skip over 31:49 minutes of a 'brief' description of the stunning engineering and design found in the ear to get to the ludicrous, and laughable, Darwinian explanation proffered by evolutionists for this amazing sophistication we find in the ear :) ).
The Hearing Ear by Dr. David Menton http://www.youtube.com/watch?v=HPiXlJ3eIwo
bornagain77
November 30, 2011
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Sorry, the alleged tree of life would lead to a fossil record absolutely DOMINATED by transitional forms, just on the implications of dominance of the most abundant.
It is. Every fossil ever found is transitional. Every thing that has ever reproduced is transitional. There are plenty of transitional series where the forms are closer to each other than dog breeds. What exactly do you want? Perhaps you care to address the series leading from jaw bones to inner ear bones.Petrushka
November 30, 2011
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APM: I do like the idea of evolved strawmen. That allows us to attribute much of human hypocrisy to a neo darwinian mechanism, after all :)gpuccio
November 30, 2011
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Neil: You are obviously entitled to your opinion. That's free will, indeed. Otherwise, you would not be part of the intelligent people who defend a stupid theory (please, take that as a compliment!) :)gpuccio
November 30, 2011
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P: I find this astonishing. You have been presented, over and over again with the facts and discussion of the cases where incremental small changes will work, within islands of function, and the issue being begged, that on evidence ranging from the implications of discovering complex algorithmic functionality to the issue of integrated embryological body plan development directly connected to that, to the protein fold domains to the sudden appearance, stasis and disappearances that characterise the fossil record, to the Cambrian fossils that so abundantly show this occurring at the TOP-down end of the record, etc. And, your response is that the asserted contiguity of a vast continent of functional life forms that would have to be foundational to the claimed tree of life by increments, is being "investigated." (And that, when you have paused from trying to belittle the expertise of one who has had to write sophisticated algorithmic search into programs.) Sorry, the alleged tree of life would lead to a fossil record absolutely DOMINATED by transitional forms, just on the implications of dominance of the most abundant. The required evidence is not there, and the sampling theory tells us why: credibly, it was never there. That's why Gould et al came up with alternatives to suggest why macro evo could be explained in absence of such evidence. The evidence clearly points to adaptation of body plans per built-in capacity as the variability of food crops, deer, fish, gulls, dogs and humans plainly shows. But it also points to the origin of said body plans being at a completely different order of algorithmic complexity and required explanation. It strikes me that we have been dealing with a grand case of over-extrapolation of very limited evidence, driven by an a priori imposition of materialism, that has led to a warping of the very understanding of science, and to seeing he evidence of limited adaptability as instead illustrations of what is a "must be" because of that controlling a priori. That is what Johnson aptly exposed and rebutted in his November 1997 First Things article:
For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]
But then, those of us who had to deal with true-believer Marxists and their students a generation ago, find all of this grand exercise in worldview-level question begging ever so familiar. Especially when one tried to point out the implications of the overdetermined set of equations implied by the labour theory of value in Marxist hands. GEM of TKIkairosfocus
November 29, 2011
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Graham, There is a difference. You find ghosts, demons, and angels preposterous because there is no place for them in your particular worldview. In other words, their existence would violate your paradigms. Gil, Gpuccio, and I are saying something different, namely that the idea that any combination of natural law and chance could produce the exquisitely subtle, stunningly complex, and sophisticated machinery of the cell is preposterous on its face, no matter what your worldview.Bruce David
November 29, 2011
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gpuccio, I think your experience and feelings are similar to what Behe described. I think he said he felt like he had been "led down the garden path." There are lots of people who think evolution is true because they've been told so, but when you ask them what aspect of the science they find most convincing or what application it has in their field you get blank stares, lots of hemming-and-hawing, or perhaps a weak reference to some evolution talking points: insects and insecticide, finch beaks, vague references to some old fossil and the like.Eric Anderson
November 29, 2011
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Petrushka: Well having mastered checkers using a comprehensive database of moves... It was not just a database, but a sophisticated search algorithm using a human-designed leaf-node evaluation function, crafted tediously with the input of two human grandmaster players. My checkers program employs the following techniques: A minimal-window, principle-variation, alpha-beta search, with iterative deepening to maximize alpha-beta cutoffs based on preliminary searches. Two rapidly accessed hash tables (one for the most valuable moves at the root of the tree in order to minimize tree growth, and one for the base of the tree for recognizing most-recently-seen positions) for quick look-up of previously searched lines of play to avoid search duplication and to modify the search window when the window fails and a re-search is required. My program also includes a maximized-for-efficiency move generator, which is based on CPU register variables, using the most efficient bit-based CPU instructions. This is a short list of what was required to produce WCC. The program is approximately 65,000 lines of tediously designed, tested, and revised C code (with many more lines of code required for all the supporting software, such as the user interface and the database generation, compression, and real-time RAM and disk-based acquisition code.) Yet, the Darwinist expects me to believe that my mind came about by random errors filtered by natural selection. In my view, this epitomizes irrationality driven by an ideological commitment to a demonstrably ludicrous proposition. Engineering real systems that really work in the real world gives one a unique perspective on how out of contact with reality Darwinists have become.GilDodgen
November 29, 2011
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I wouldn't be so quick to attribute the strawman to design. Perhaps it evolved over time from a pile of sawdust that was struck by lightning.APM
November 29, 2011
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OK Neil- what is this alleged strawman?Joe
November 29, 2011
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