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This is what a reply to an Intelligent Design argument looks like

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Three days ago, I posted a 123-word critique of unguided mechanisms for evolution as an explanation for the genes, proteins and different kinds of body plans found in living things. The critique was taken from Dr. Stephen C. Meyer’s book, Darwin’s Doubt (Harper One, 2013), and I invited skeptics to rebut Dr. Meyer’s case, in 200 words or less. When I didn’t get a satisfactory rebuttal, I re-posted it. The critique read as follows:

“This book has presented four separate scientific critiques demonstrating the inadequacy of the neo-Darwinian mechanism, the mechanism that Dawkins assumes can produce the appearance of design without intelligent guidance. It has shown that the neo-Darwinian mechanism fails to account for the origin of genetic information because: (1) it has no means of efficiently searching combinatorial sequence space for functional genes and proteins and, consequently, (2) it requires unrealistically long waiting times to generate even a single new gene or protein. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious, and (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan.” (2013, pp. 410-411)

In response to an objection from ID skeptic Mark Frank, who wrote that Dr. Meyer “explains perceived weaknesses in his understanding of evolutionary theory but gives no reason why design is a better alternative,” I also quoted another short passage from Darwin’s Doubt, which made a positive case for Intelligent Design:

…[E]ach of the features of the Cambrian animals and the Cambrian fossil record that constitute negative clues – clues that render neo-Darwinism and other materialistic theories inadequate as causal explanations – also happen to be features of systems known from experience to have arisen as the result of intelligent activity. In other words, standard materialistic evolutionary theories have failed to identify an adequate mechanism or cause for precisely those attributes of living forms that we know from experience only intelligence – conscious rational activity – is capable of producing. That suggests, in accord with the method of historical scientific reasoning elucidated in the previous chapter, the possibility of making a strong historical inference to intelligent design as the best explanation for the origin of those attributes. (2013, p. 358)

While Mark Frank answered the first challenge I issued, he and other readers failed to address the second. So let me spell it out.

What I was looking for was a short scientific rebuttal of Dr. Meyer’s arguments, something along these lines (I’m making this stuff up):

Contrary to Dr. Meyer’s claim that the combinatorial sequence space for functional genes and proteins is too large to be searched within the time available, scientists have calculated that functional proteins as short as 50 amino acids could have been generated within the space of 100 million years on the primordial Earth, within proto-cells near hydrothermal vents, and they have recently created artificial life-forms requiring only short amino-acid chains. What’s more, it turns out that the pathways between various proteins domains were in fact much shorter than previously believed, making the origin of the various proteins found in organisms today from a much smaller subset mathematically plausible. Scientists have also created a workable model of a developmentally plastic genome in which early acting mutations are nowhere near as harmful as in modern organisms. Finally, cell biologists have recently sketched a plausible hypothesis as to how the epigenetic information in the cell may have arisen, step-by-step. (Insert references here.)

That is what a proper reply to an Intelligent Design argument looks like. Maybe we’ll see one, in a decade or two. Who knows? But I’m not holding my breath. The case for Intelligent Design is built on cutting-edge science. The case for life having arisen by an unguided natural process is built on conjectures and castles in the air. That’s why we call it “promissory materialism.”

Comments
... it has been of utmost importance to simply ignore or assume the material conditions required for an autonomous self-replicator capable of open-ended evolution...
A gaping lacuna in modern evolutionary theory. There is no theory of evolvable systems.Mung
May 15, 2015
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MatSpirit:
That means that in a one billion base pair genome, 4^(1,000,000,000-1000) combinations will never even be tried. That’s an astronomically large number of genomes that are never searched. If you have one billion base pairs in a genome and change a single base pair, what is the size of your search space? Answer: 4. And one of them is just like the original, known to work DNA.
Your first paragraph contradicts your second paragraph.
... what is the size of your search space? Answer: 4. And one of them is just like the original, known to work DNA.
Are you serious?Mung
May 15, 2015
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MatSpirit:
Darwinian evolution is very efficient at searching combinatorial space. Its secret is that it only changes one or two base pairs at a time. This means it explores only areas of the search space that are very near to the original DNA, which is known to be functional because it’s successfully reproducing.
Your second and third sentences both contradict your first sentence.Mung
May 15, 2015
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sean at 53
Clearly you don’t like it, but that’s not a requirement of coherence.
I don’t like it or dislike it. It’s just incoherent.
I have some idea, though certainly not a full explanation. But that is not required YET.
Uhm. The physical requirements for one thing to specify another thing have been well-known for quite some time. What is clear here is that you have no idea what they are, and have never thought about it.
To declare that life is irreducibly complex, you need to have disproved all other explanations.
To show that a thing is irreducibly complex only requires you to show that it is irreducibly complex. In this particular instance, that is a simple task. Let me suggest something to you. In the living cell, the translation apparatus organizes proteins by specifying individual amino acids via the arrangement of nucleotides. For instance, the system specifies the addition of leucine by the nucleic arrangement CTA. Here is my suggestion; go find out how CTA specifies leucine. Or, let’s just be frank. As evidenced by your responses here thus far, you have no intentions of engaging any issues in earnest. You seem much more comfortable denigrating people and cheerleading for scientism. As for myself, I have no desire to chase you around trying to get you to stop your attack long enough to learn something of the things you attack – thus, I will limit my involvement. For other readers of this post, I will simply leave a link to a recent comment to another equally-challenged critic. cheersUpright BiPed
May 15, 2015
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Mung @35 asked RDFish if their stated position was that “no known cause that can account for the origin of biological systems”. That question must be assuming something, because on its face it makes no sense. The difference between science and creationism is about what the cause is; both assume something caused the origin of life. RDFish replied @57 that “Nothing that we know of could have existed prior to living things and have been responsible for their creation”. Nothing? Not abiotic chemistry? Not deities? Nothing? Really? Or do you just mean “nothing we can describe specifically”? sean s.sean samis
May 15, 2015
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https://uncommondescent.com/intelligent-design/this-is-what-a-reply-to-an-intelligent-design-argument-looks-like/#comment-565004
"What part of that don’t you understand?
It's likely not that he doesn't understand. It's rather an apologetics thing in disguise. Doesn't want to appear as 'creationist' easy to discredit. Mung is too low on the totem rung for serious scholarly engagement with actual problems as most people around the world. His capitalized Intelligent Design seems to be purposefully divorced from lower-case intelligent design (Craig would crucify his haughty self-righteousness with higher reason). Joking as proponentsist always on behalf of Discovery Institute version Intelligent Design means hard to take seriously such a voice as Mung. RDFish, nevertheless, this doesn't mean no deity or empty universe, lack of soul & spirit. Right? Maybe that anti-theism is your biggest grief, even beyond Intelligent Design? vjtorley's capitalized catholic stain is visible; but that doesn't mean anti-theism worldview perspective is off limits for critique.Dash Design
May 15, 2015
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The part where you use a simple yes or no to answer a question that requires only a simple yes or no.Mung
May 15, 2015
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Mung I've answered your question repeatedly. Nothing that we know of could have existed prior to living things and have been responsible for their creation. What part of that don't you understand?RDFish
May 15, 2015
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Hi Collin,
The point is that Meyer is not using “materialism” to talk about just “matter.” He’s talking about matter, force fields, forces, and other unintelligent “substance.” Your complaint is a quibble that does not go to his real point.
Not really a quibble, no. The point I'm making is that one cannot make blanket statements about "materialistic explanations", because it is not a well-defined category. ID tries to eliminate all possible "materialistic" explanations of origins, which would leave the "non-materialistic" explanation of ID. But we cannot eliminate all possible "materialistic" explanations because we have no idea what other sorts of "materialistic" phenomena there might be that could eventually explain biological systems. In other words, the physicalist might wish to posit that some unknown physical phenomenon might be found someday to be responsible, and the dualist might wish to posit that some unknown non-physical phenomenon might be found someday to be responsible, but since neither can produce any evidence of such a thing, the question is currently open.
But your point about “mind/body” dualism I think is potentially an issue. In fact, it may be “THE” issue for more than just ID, but for our entire culture war. is there something “more” than just this “stuff.”
YES! Thank you for being one of the few people here who understand and are willing to admit this! Dualism (and metphysical libertarianism) is indeed what ID is arguing for. Pretending that there is some scientific way of settling this ancient metaphysical question is ID's big lie. Cheers, RDFish/AIGuyRDFish
May 15, 2015
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https://uncommondescent.com/intelligent-design/this-is-what-a-reply-to-an-intelligent-design-argument-looks-like/#comment-564997 Yes, although new here I agree with that. vjtorley's Intelligent Design is not testable, just some kind of quasi-'catholic' faith seeking validity among scientists or philistines without empirical data. WL Craig intelligent design otoh *is* faith. He says so clearly. So if you don't have it, sean samis, then how could you possibly know what they are talking about & feeling? You are intentionally exclusing yourself from that knowledge life experience. Easy to test human designs made into products, right? Humans designs. But that's not vjtorley's Intelligent Design, which already implies deity. WL Craig says clearly (even creationist self-deception not excused - they normally respect him):
"Obviously, theists, who believe in an intelligent designer of the universe, may not be on board with all the tenets of ID."
The capitalized Intelligent Design of vjtorley is obviously anti-atheist & need not be accepted. So, sorry if you are one of those atheists or anti-theists, sean samis. You don't count to ID movement people like vjtorley except as evil & wrong & inhuman; as enemy. :(Dash Design
May 15, 2015
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Dash Design; You wrote that “SC Meyer says intelligent design is scientific theory ...” That cannot be true unless intelligent design can be tested; how would we do that? sean s.sean samis
May 15, 2015
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Upright BiPedThis statement is incoherent.” Clearly you don’t like it, but that’s not a requirement of coherence. “Do you have any idea ... etc.” I have some idea, though certainly not a full explanation. But that is not required YET. Eventually, yes. But not yet. Science is a process of discovery. To declare that life is irreducibly complex, you need to have disproved all other explanations. You do have some idea of the evidentiary requirements of that, don’t you? Those have not been satisfied. Not yet. The race is on. Of course, it helps that only scientists are doing any actual science on this. sean s.sean samis
May 15, 2015
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sean,
I realize that for creationists, it is of utmost importance to assume that the material conditions required for evolution are refuted, but that assumption is not converted to evidence (much less proof) by mere urgency.
This statement is incoherent. You do realize that in order to organize an autonomous living cell, something must be specified, correct? For instance, if you are going to organize the manufacture of a protein of some particular sequence, the objects that make up that sequence will have to be specified by some method to indicate them among other objects. Correct? Do you have any idea what the material requirements involved in bringing that specification into reality? Or, is strategically dancing around the issue going to be the limit of your involvment here?Upright BiPed
May 15, 2015
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Upright BiPed I realize that for creationists, it is of utmost importance to assume that the material conditions required for evolution are refuted, but that assumption is not converted to evidence (much less proof) by mere urgency. “You should pick some other target for your criticism; IC is a complete loser for you.” I don’t criticize irreducible complexity, I just make note of its requirements which are daunting and as yet unsatisfied vis-à-vis creationism. sean s.sean samis
May 15, 2015
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sean,
concluding that anything actually is irreducibly complex would mean that the requirements have been established by evidence, and not by assumptions
Irreducible complexity is entirely and wholly irrefutable in biology. You cannot organize a heterogeneous living cell without it. You probably are not aware of the evidence surrounding this fact because it has been of utmost importance to simply ignore or assume the material conditions required for an autonomous self-replicator capable of open-ended evolution, but that doesn’t make the evidence go away. You should probably pick some other target for your criticism; IC is a complete loser for you.Upright BiPed
May 15, 2015
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Hello People, What I don't understand is why 2 dressing as 1? Thread started by vjtorley about Intelligent Design. SC Meyer about intelligent design. WJ Craig speaks more clearly: http://www.reasonablefaith.org/should-christians-accept-intelligent-design#ixzz3ZEUvk8mE
"I think it advisable to capitalize “Intelligent Design" (ID) in order to signal that we are using the words in a technical sense, rather than in the sense accepted by every Christian."
Is not this clear & helpful difference? vjtorley seems to suggest Intelligent Design is theological basis - because he is Christian he capitalizes. SC Meyer says intelligent design is scientific theory - he speak not as Christian but as scientist. Proper reply to vjtorley's Intelligent Design not difficult if reject his worldview. To SC Meyer, his science seems like idolatry - human intelligence is like a god.Dash Design
May 15, 2015
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CharlieM, If you believe there is a material difference between “neo-Darwinian mechanisms” and “evolution” which is relevant to this topic, you should say so and tell us what it is. I notice that Vince Torley introduced Dr. Meyer’s paragraph as “a 123-word critique of unguided mechanisms for evolution” so even Torley seems to treat them interchangeably. “From your posts I can only conclude that you don’t seem to understand what ID advocates mean by, ‘irreducibly complex’.” Behe (who I believe did not actually invent the term) defined it as “a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.” By that definition, concluding that anything actually is irreducibly complex would mean that the requirements have been established by evidence, and not by assumptions. “why have you used the term ‘creationist’ where ‘intelligent’ would have been more appropriate?” Because I used the term in a question specifically about creationist inferences. “You do know that creation science and intelligent design are different entities?” I do know that is what creationists claim; I do know it is a difference without great significance. I realize that there are multiple versions of creationism, of which ID is only one, but ID belongs to the general category of creationism. I doubt there’s more than a tiny fraction of IDers who believe we were created by space aliens. God’s the guy the vast majority of IDers affirm. It’s creationism. ID is a modernized form of creationism that at its roots was around when Charles Darwin was born. sean s.sean samis
May 15, 2015
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PS: To make things a bit specific, think about proteins in AA sequence space.kairosfocus
May 15, 2015
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MS, you are making the commonly encountered assumption of working within an island of function and finding incremental changes within that, and/or projecting a vast incrementally accessible continent of function from first life to us, mango trees, molluscs etc. That would have to be justified without begging questions; which predictably you simply cannot. By contrast, the focal problems addressed by ID have to do with initially finding the islands of function in beyond astronomical search spaces. And, islands there will be as the demands of closely co-ordinated correctly placed and coupled parts to achieve function drastically constrain acceptable configs. To get the proper understanding do what is usually skipped over and try to see how a stew of chemicals in Darwin's pond or the like can get by empirically warranted and search-challenge plausible steps, to a gated, encapsulated, metabolic automaton with a code using integral von Neumann self replicator and genome of about 100 - 1,000 bases. Yes, self replication, the usual side-step has to be accounted for as a case of functionally specific complex organisation and associated information, FSCO/I for short. Then, extend to dozens of basic body plans demanding 10 - 100+ mn base prs, including the embryo development program or equivalent. Then, explain why we do not see overwhelming numbers of transitional forms in the fossil record to those basic plans. Finally, account for the origin of the functioning mind we have on the like grounds without self-falsifying self referential incoherence. KFkairosfocus
May 15, 2015
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I meant to answer these assertions when you first posted them. Sorry for the delay. (1) it [Darwinian evolution] has no means of efficiently searching combinatorial sequence space for functional genes and proteins... Darwinian evolution is very efficient at searching combinatorial space. Its secret is that it only changes one or two base pairs at a time. This means it explores only areas of the search space that are very near to the original DNA, which is known to be functional because it's successfully reproducing. For instance, if you change a base pair in a gene that affects nostril width, genes for heart valves, kidneys, livers and every other gene in your body are left in their original, successful form. That also means that DE never even explores large areas of a genome's combinatorial space. You're never going to see a genome starting with one million "C"s because you just can't get there one base pair at a time while remaining viable. That means that in a one billion base pair genome, 4^(1,000,000,000-1000) combinations will never even be tried. That's an astronomically large number of genomes that are never searched. I wonder if Dembski has ever thought of this: If you have one billion base pairs in a genome and change a single base pair, what is the size of your search space? Answer: 4. And one of them is just like the original, known to work DNA. I don't think Dembski realizes any of this. (2) it requires unrealistically long waiting times to generate even a single new gene or protein. Ever hear of alleles? They're different versions of a gene. All genomes, including the human genome, are full of them. It can't take too long to generate a new gene if we already have several versions of most of them. It has also shown that the mechanism cannot produce new body plans because: (3) early acting mutations, the only kind capable of generating large-scale changes, are also invariably deleterious It doesn't take any mysteriously early acting mutations to strengthen and lengthen the bones in a fish's fin to make an early leg. How about a bat whose wing is made from greatly elongated fingers? Just a handful of late acting genes will stretch them. What about the skin stretching from finger to finger? Most animals' hands and feet begin as undifferentiated pads and then the flesh and skin between the bones is absorbed. Just change a few genes to modify the absorption to make a webbed foot or a membranous wing. Not hard at all. (4) genetic mutations cannot, in any case, generate the epigenetic information necessary to build a body plan.” So what? Nobody in Darwin's time even knew about genetics, let alone DNA. It does no damage to Darwin's theory if some information is transmitted without DNA.MatSpirit
May 14, 2015
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Hi Sean, I have a few questions and criticisms of your criticism. You have substituted "neo-Darwinian mechanisms" with "evolution", why? Do you believe that they both mean the same thing? From your posts I can only conclude that you don't seem to understand what ID advocates mean by, "irreducibly complex". You ask about testing "creationist design inferences" and verifying "theistic explanations". Making design inferences is not something that is confined to creationists so why have you used the term "creationist" where "intelligent" would have been more appropriate? And surely you know that the ID movement is not in the business of looking for theistic explanations? You do know that creation science and intelligent design are different entities?CharlieM
May 14, 2015
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Collin, The standard I hold Meyer to is a standard any scientist would accept. As for “an inference to intelligence”, I’m not even sure I know what that means. Inferring that something was created has no special status or rules; it’s just one of many possible inferences. Inferring intelligent creation by creatures or persons we have never observed does have a serious constraint: you have to prove the creating person/species exists. This is why attributing things to space aliens is not well received in the scientific community; no one’ proven they exist, much less have ever visited. Regarding, “if we infer that Stonehenge was designed by intelligent beings, are we just assuming it is unexplained and therefore irreducibly complex and therefore unsuperable?” This seems like a car-wreck of a question. You are right to say it “makes no sense” because it makes absolutely no sense. We regard Stonehenge as man-made because there’s no obvious natural process to create it, there IS evidence of human construction, and the question of “how it was created” already has some pretty solid answers. The explanation that it is man-made is not something we claim for lack of a better answer, we say it because there’s supporting evidence. This I think is Zachriel’s point. So Stonehenge is not “unexplained”. And unexplained phenomena cannot be “irreducibly complex” because irreducible complexity is a positive finding. By that I mean that nothing is logically presumed to be irreducibly complex just because it cannot be explained; something would be logically regarded as irreducibly complex only when we have solid evidence that all other possible explanations have been explored and exhausted. Similarly, a problem is considered insuperable not because we don’t know the explanation, but because we KNOW that we cannot know the explanation. Regarding, “Meyer is not saying we should stop looking at naturalistic explanations about life, but he is saying that we can make design inferences where appropriate. That’s not unscientific imo.” I’m not sure that’s Meyer’s position, but if it is, good. It is perfectly scientific to HYPOTHESIS that something was man-made (the Antikythera mechanism seems a good example here, or Paleolithic stone tools) but such inferences are not even evidence, much less proof. They are often simply guesses (SWAGs as we used to call them in the Navy.) Unless these SWAGs can be verified, they are not even theories, not in science. So the question to you and to Dr. Meyer and others is: how do you propose to test creationist design inferences? How will you verify or falsify them? Your proposed verification need not be something we can do anytime soon, but eventually. Obviously the same question applies to the related scientific, materialist explanations; and any cursory reading of scientific publications provides the answer. Verification may take decades, or centuries, but it’s doable. How will theistic explanations be verified? How will those be tested? Until there’s a realistic answer, they just are not science. sean s.sean samis
May 14, 2015
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Collin: But in order to explore this issue we should ask ourselves if the methods we use to make a design inference in one scientific domain is applicable in another scientific domain. In science, claims have testable entailments. For instance, Collin: if we infer that Stonehenge was designed by intelligent beings, are we just assuming it is unexplained and therefore irreducibly complex and therefore unsuperable? No, we're claiming there is a chain of causation between the artifact, the art, and the artisans, and that the links of the chain can be tested. For instance, we might look for evidence of humans in the vicinity and time that Stonehenge was built.Zachriel
May 14, 2015
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Sean, I believe that you are holding Meyer to a standard that you do not hold other scientists. You accuse him of pseudoscience for doing something that many other scientists do: make an inference to intelligence. I admit that it is a different thing to assume a human intelligence rather than a non-human intelligence. But in order to explore this issue we should ask ourselves if the methods we use to make a design inference in one scientific domain is applicable in another scientific domain. That is totally legitimate imo. So I ask: if we infer that Stonehenge was designed by intelligent beings, are we just assuming it is unexplained and therefore irreducibly complex and therefore unsuperable? No, that makes no sense. Trying to explain Stonehenge by appealing to wind and water and chemistry alone would be inadequate. Meyer is not saying we should stop looking at naturalistic explanations about life, but he is saying that we can make design inferences where appropriate. That's not unscientific imo.Collin
May 14, 2015
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Collin, Try again. You are pursuing a non sequitur. First, the assumptions I wrote about (which you quoted incompletely) are not assumptions I agree with, they are the mistaken and implicit assumptions of Dr. Meyer which I called out. Reread the entire sentence and you’ll see. Or at least you should. Second, even Dr. Meyer’s assumptions don’t exclude consideration of “intelligent people we cannot see, hear or touch”. sean s.sean samis
May 14, 2015
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Sean, You said, "anything which is currently unexplained is assumed unexplainable, all unresolved complexity is assumed irreducible, and any problem currently known is assumed insuperable." Please explain Stonehenge without resorting to claims about intelligent people we cannot see, hear or touch.Collin
May 14, 2015
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Collin, Nothing in my paragraph supports such an assumption. Nowhere in my paragraph are the words ‘natural’ or ‘process’ used. Nothing in it relies on or asserts a bias toward explanations from “natural processes”. sean s.sean samis
May 14, 2015
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RDFish, The point is that Meyer is not using "materialism" to talk about just "matter." He's talking about matter, force fields, forces, and other unintelligent "substance." Your complaint is a quibble that does not go to his real point. But your point about "mind/body" dualism I think is potentially an issue. In fact, it may be "THE" issue for more than just ID, but for our entire culture war. is there something "more" than just this "stuff." Sean Samis, I think that by your logic, we must assume that Stonehenge was brought about by a natural process. Just because we don't know what that process was, we can't assume that people with brains designed and constructed it.Collin
May 14, 2015
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The paragraph from Dr. Meyer’s book presents a poor case. Point (1) is not a necessary function of evolution. Points (2), (3), and (4) assert unproven claims. Like most pseudoscientific arguments against evolution, the underlying (and illogical) assumption Dr. Meyer makes is that anything which is currently unexplained is assumed unexplainable, all unresolved complexity is assumed irreducible, and any problem currently known is assumed insuperable. There you go; 66 words. And it’s at least as scientific as Dr. Meyer’s paragraph, if not much more so. You may object that it leaves a lot unexplained, but of course there’s only so much one can do within a 200 word limit, and Dr. Meyer appears to have preceded his paragraph with 400+ pages of typing. sean s.sean samis
May 14, 2015
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RDFish, There is therefore no known cause that can account for the origin of biological systems. That’s your stated position?Mung
May 14, 2015
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