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PZ Myers throws down a gauntlet to ID

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Yesterday, Intelligent Design critic and creationist basher, P.Z. Meyers, posted what he considers to be a real scientific challenge for ID proponents on his Pharyngula blogsite. The main thrust of his challenge is outlined in this Youtube video:

[youtube ZkED8cWRu4Q]

So, has Myers indeed stumbled upon a true significant challenge for ID?  Or, has he simply stumbled, as he so often does, over his own misconceptions and metaphysics?  I vote for the latter.
First off, he stumbles into what Phillip Johnson called Berra’s Blunder referring to Darwinist Tim Berra’s book Evolution and the myth of creationism,1990, pg 117-119, where Berra writes “If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.” As Johnson points out, Berra completely misses the point that similarities between cars are still the result of common design.

“Of course, every one of those Corvettes was designed by engineers. The Corvette sequence – like the sequence of Beethoven’s symphonies to the opinions of the United States Supreme Court – does not illustrate naturalistic evolution at all. It illustrates how intelligent designers will typically achieve their purposes by adding variations to a basic design plan. Above all, such sequences have no tendency whatever to support the claim that there is no need for a Creator, since blind natural forces can do the creating. On the contrary, they show that what biologists present as proof of “evolution” or “common ancestry” is just as likely to be evidence of common design.”
P. Johnson, Defeating Darwinism by opening minds, 1997, pg 63.

In other words, homolgy doesn’t necessarity imply evolution, or exclude design. In his challenge, Myers is relying on the same sort of blunder, as he is assuming that any homology automatically eliminates design. My challenge back to him would be to show scientifically why that is the case.

ID proponent and Darwinism critic, Cornelius G. Hunter points out the hidden metaphysical blunder Myers is making as well. On his Darwin’s God blogspot, Hunter writes “While there are several problems with the challenge, the disguised religion comes around the 1:15 mark, [in the Youtube video], where the criterion of homology is explained. Don’t worry if you are not familiar with the concept of homology. The bottom line is that the challenge uses random design as a test for whether a structure evolved. Specifically, if there is any non random pattern detectable, then it must not have been designed; instead, it must have evolved.” Hunter goes on to say “This is today’s version of a test that dates back to Daniel Bernoulli and Immanuel Kant in the eighteenth century. The idea is that God would not design according to a gratuitous pattern.” In other words, this yet another version of the old “God wouldn’t have done it this way” argument. It would be interesting to see Myers scientific explanation for how he knows what God would or would not do.

Then there’s Myers’s implied Philosophical Naturalism, as he writes in the blog “The argument has long been highly asymmetric. Scientist find a gene, and what do they do? Figure out what it does, and dig into the databases to find its relatives within that organism or in other species. Creationists claim genes can’t be created without the intervention of a designer, and what do they do? Nothing.” In other words, Myers merely assumes evolution is the only explanation for homology, and his criticism of ID is that they aren’t busy digging into databases looking for those homologies, that is to say a naturalistic explanation for the data. Thus, according to Myers, doing “nothing”, means “not looking for only undirected, natural causes” as opposed to actively trying to understand the information content of the genetic code, tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about. All that, per Myers, is doing “nothing”.

Comments
Thunderf00t replied to this post on YouTube. Challenging the Discovery Institute to Discover: Part 2 http://www.youtube.com/watch?v=Sq3mKJxxZggyqbd
May 23, 2009
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"I know the feeling." Then maybe you should ask. Essentially I asked what your statement was about and you failed to provided an answer.jerry
May 21, 2009
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"If I had a clue what you were talking about, I might respond to this." I know the feeling.derwood
May 21, 2009
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Correction to previous post: ...this type of lipid metabolism proved Archea are not direct ancestors of bacteria (or, for that matter, direct descendants either--they are looking for a Last Unknown Common Ancestor).womanatwell
May 21, 2009
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Nakashima, The gene I put in my post has to do with lipid metabolism in an Archaea. For a while, biologists thought Archaea were direct ancestors of bacteria. Then they found that their cell membranes are composed of phospholipids with different composition than those of bacteria. So this type of lipid metabolism proved Arachaea are not direct descendents of bacteria. This is in contrast to the challenge of this post that wants to prove evolution through genes. I again put the link to this article “Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world,” by Eugene V. Koonin* and Yuri I. Wolf of the National Center for Biotechnical Information (NCBI). It was published October 2008. http://nar.oxfordjournals.org/cgi/content/full/36/21/6688 The article is very important. It talks about how a vast majority of genes being found in the newly sequenced whole genomes are unique to one or, more often, a very small number of organisms. Several paragraphs from this article include:
Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution. The paradox of today's state of the art is that, despite the tremendous progress—but also owing to these advances—the emerging complexity of the prokaryotic world is currently beyond our grasp. We have no adequate language, in terms of theory or tools, to describe the workings and histories of the genomic network. Developing such a language is the major challenge for the next stage in the evolution of prokaryotic genomics.
Please see the graphs of genes from sequenced organisms (they are very colorful). They show how the genes sit separately in isolated islands. I do not understand why the standards of the NCBI are inadequate for the challenger or for many posters in this website. Also, Casey Luskin has spoken for Discovery Institute at: http://www.evolutionnews.org/2009/05/does_any_critic_out_there_unde.html#more .womanatwell
May 21, 2009
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tragic mishap: letting us in on these “tests” Yes, thats pretty much it. If the evidence doesnt support an idea, the idea is discarded. This is how science works. Evolution is no exception. Poking into the genetic makeup shows all the similarities/differences that have been described over & over and which support the evolutionary model. The use of the word 'test' is figurative. Its not a formal process like a school test, just a constant accumulation of evidence that supports an idea. This is why the biology community supports evolution and mocks ID.Graham
May 20, 2009
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Diffaxial: "Your test smuggles its conclusions..." Really? So you are saying the test is unfair because it smuggles in its conclusions? Huh. Sounds almost exactly like the objections to Myers' test from ID proponents, that it smuggles in the conclusion that homology refutes design. Graham: "No, it sounds like every test that every piece of science has faced (and passed)." Really? "Every piece of science" has passed tests like this? Anything that has failed these "tests" does not qualify as a "piece of science"? Than you should not have trouble letting us in on these "tests" that ultimately validated evolution. Please help a poor student understand this concept.tragic mishap
May 20, 2009
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"I was unaware that it was a human’s ability to ‘know’ something that rendered it the product of ‘intelligence.’ A rather odd definition/application, to be sure." If I had a clue what you were talking about, I might respond to this.jerry
May 20, 2009
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Jerry: The answer was provided far above. They all are designed. Each gene encodes proteins through a process only known to exist through intelligence. I was unaware that it was a human's ability to 'know' something that rendered it the product of 'intelligence.' A rather odd definition/application, to be sure.derwood
May 20, 2009
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Joseph: derwood, I was a technical advisor in Iraq (and Colombia, Saudi, Egypt, Ireland, Mexico- well a lot of different countries- but that is another story). I have worked with companies that supply technology to militaries around the world. And that means I have also worked with militaries around the world. Sure, but you claimed to have been injured seeing if you can 'outrun an RPG'in March, 204, near Balad Iraq. I did some searching and found that in 2004 in or near Balad the only non-military injuries were from vehicle attacks - one an RPG attack in which all the occupants of the vehicle were killed, one in which the vehicle was hit by a roadside bomb. Neither took place in March. But anyway the point of Behe’s claim is that not any mutations will do the trick. In terms of the specific issue he was looking at. Did Behe establish that this two-sequential -mutation requirement is widespread? With gene dupication that new gene needs a binding site. And not just any binding site will do- it has to be specific to that gene. During gene duplication events, it is quite common for the binding sites to be duplicated as well. In the beta globin cluster, for example, where in humans there are 5 duplicates, all of the duplicates retained their promoter and enhancer sites. Did Behe address any actual cases? Also that gene needs to activated and/ or repressed and at specific times. Then there are enhancers which dictate how many times that gene is transcribed and translated. That is not exactly what enhancers do, but see above. All of that has to be specific to that gene. Transcription factor binding sites are actually pretty common, even in noncoding DNA. Not that it matters, since as I indicated, in the instances in which gene duplications have been investigated, such sequences are partof the duplicated region. Then there needs to be something for that new product to do such that it does not arbitrarily bind to already functioning cellular systems and mess them up. In a new duplicate, the product would be the same as the old, at least initially. Additional product can, in some cases, produce phenotypic or physiological change. So I would say that gene duplication followed by rapid integration and mutation to allow for a differing function, would be a sign of evolution by design- What Dr Spetner calls the “non-random evolutionary hypothesis”. So, everything and anything count as pro-ID 'evidence.' Spetner's hypothesis is fairly weak, even when it was first concocted.derwood
May 20, 2009
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Graham, ID does not even attempt to refute evolution. All ID says about that is that non-telic processes are NOT the sole driver. IOW ID argues against the blind watchmaker as having sole dominion over the variation and diversity.Joseph
May 20, 2009
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To tragic mishap sounds more like a taunt from some professional wrestler No, it sounds like every test that every piece of science has faced (and passed). True, it is expressed in a melodramatic way, but it is basically asking to dig into the evidence and see if the evidence supports ID or evolution, or maybe neither. This is exactly what scientists do all the time, challenge science with difficult questions. Assuming that the resources were available to pursue it, what possible objection could you have ? The worst case seems to be an inconclusive result, but it is possible that it may support ID and refute evolution.Graham
May 19, 2009
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If a protein requires more than two non-selectable mutational steps from any other functioning protein, it was designed. That would be a test to apply to nature.
Your test smuggles its conclusions, secreted in the word "non-selectable" (and "functioning.")Diffaxial
May 19, 2009
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Diffaxial @ 122: If a protein requires more than two non-selectable mutational steps from any other functioning protein, it was designed. That would be a test to apply to nature. If you want a single all-encompassing test to determine forever if ID is true or false, you won't find it because science doesn't work that way. As you guys are so fond of reminding us, evolution has 150 years of science behind it. If your definition of a scientific theory is that it has passed a fair test, then what test did evolutionary theory pass that led to its acceptance? Perhaps if you show me how this process works by giving examples, I can answer your question better. Until then, I'm not willing to discard all scientific knowledge other than that which pertains to this so-called "test", which actually sounds more like a taunt from some professional wrestler. Besides which, there probably are genes which will pass the test as any sensible person would be willing to admit. But PZ Myers is not such a person, and therefore I reject his little test.tragic mishap
May 19, 2009
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Ms Womanatwell, If you are proposing genes that meet the challenge stated in the video, post them in the comments on the original YouTube video. The creator of that video (C0nc0rdance) will reply. This video was created by C0nc0rdance, then a beginning and ending were added by Thunderf00t, then it was blogged about on Pharyngula, then here at UD. Please copy us on any reply you receive! Thanks!Nakashima
May 19, 2009
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Correction & clarification of my previous entries @130 & 132: the genome number (not gene number) of the archea, M. janaschii, is NC 000901.1 and the organism has 1,664,970 nucleotide bases. The GeneID number 1451590 is for the enzyme I mentioned and has about 1000 nucleotide bases. For comparison, another Methanocaldococcus janaschii GeneID is # 1451939 for one protein segment of RNA polymerase RNA polymerase copies DNA to RNA. (The protein sequence is at Uniprot #Q58445): http://www.uniprot.org/uniprot/Q58445 The gene is sequenced at: http://www.ncbi.nlm.nih.gov/nuccore/15668172?content=5&v=974405:978832&report=graph from 974406 to 978834 (over 4000 nucleotide bases). Press the sequence button on top left of toolbars to see the sequence.womanatwell
May 19, 2009
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"Is there any point to which you would wish to draw my attention?" "To the curious incident of the dog in the night-time." "The dog did nothing in the night-time." "That was the curious incident," remarked Sherlock Holmes. ..."Before deciding that question I had grasped the significance of the silence of the dog, for one true inference invariably suggests others. So what do we conclude by the silence of the Darwinists here and in the press both popular and academic. A curious incident. What are the inferences?jerry
May 19, 2009
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Scot.David, So you understand my point completely.jerry
May 19, 2009
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GeneID (ncbi) for sn-Glycerol-1-phosphate dehydrogenase is 1451590: http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=1451590 and covers 645966-644959 .womanatwell
May 19, 2009
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jerry: In "Silver Blaze" The dog did nothing in the night... ps: Please pm Erasamus ASAP!Scot.David
May 19, 2009
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This article by Koga and Morii contains info on 3 ORFan enzymes in Archaea which regulate ether-type lipid biosynthesis: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17347520 . These enzymes are part of the pathway that makes cell membrane lipids different in Archaea than other domains (bacteria and eukaryotes). One mentioned is: sn-Glycerol-1-phosphate dehydrogenase, from Methanocaldococcus janaschii, found at Uniprot # Q58122 at: http://www.uniprot.org/uniprot/Q58122 . Picture of protein is at Swiss Model Repository, enter Q58122 and search (it’s worth the trouble) here: http://swissmodel.expasy.org/repository/ . Gene number is NC_000909.1, sequence of 1,664,970 nucleotide bases found: http://www.ncbi.nlm.nih.gov/nuccore/15668172?content=5&v=644909:646016&report=graph&flip=true Online book discussing criteria for Comparative Genomics, Sequence-Evolution-Function: Computational Approaches in Comparative Genomics by Eugene V. Koonin Michael Y. Galperin found here: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef Discussion of non-orthologous genes, “Chapter 7. Evolution of Central Metabolic Pathways: The Playground of Non-Orthologous Gene Displacement,” found: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef.chapter.371 . A very interesting paper by Koonin and Wolf about the emerging data of comparative genomics is “Genomics of bacteria and archaea” found here: http://nar.oxfordjournals.org/cgi/content/full/36/21/6688 . Many genes are unique to one or a few species.womanatwell
May 19, 2009
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Cabal: simple - religion, belief, faith: the BEST definition is what it actually is - what one thinks is true which automatically is what one puts ones faith, trust, belief in - right forget the dictionaryalan
May 19, 2009
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I base nearly all my conclusions on Behe's Edge of Evolution. To me that is the definitive work so far. I also base a lot of my conclusions on Sherlock Holmes and the story of Silver Blaze and one of the most famous insights in history. Namely, of the dog barking in the night. Both these works support/prove my conclusions about the design of genes.jerry
May 19, 2009
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I don't know, Mr Nakashima, you'll have to ask Dr Behe...Adel DiBagno
May 19, 2009
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Mr DiBagno, I hadn't read that statement of Dr Behe's before, and I find it surprising. I thought he accepted that birds are special kind of fish? :) I'm not sure why Dr Behe thinks this level of diversity is beyond the scope of evolution. Back in the Mississipian era, when some amniote differentiated into amniotes with 0, 1, or 2 holes in the skull, the developmental changes to create holes wasn't that great, was it?Nakashima
May 19, 2009
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Graham, Small changes to what, exactly, led to the evolution of vertebrates from invertebrates? That seems to be the million dollar question. And so far the ONLY answer I have ever receieved is "the DNA gets modified" (or the genome). However the people who accept that answer are not interested in science.Joseph
May 19, 2009
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derwood, I was a technical advisor in Iraq (and Colombia, Saudi, Egypt, Ireland, Mexico- well a lot of different countries- but that is another story). I have worked with companies that supply technology to militaries around the world. And that means I have also worked with militaries around the world. But anyway the point of Behe's claim is that not any mutations will do the trick. With gene dupication that new gene needs a binding site. And not just any binding site will do- it has to be specific to that gene. Also that gene needs to activated and/ or repressed and at specific times. Then there are enhancers which dictate how many times that gene is transcribed and translated. All of that has to be specific to that gene. Then there needs to be something for that new product to do such that it does not arbitrarily bind to already functioning cellular systems and mess them up. So I would say that gene duplication followed by rapid integration and mutation to allow for a differing function, would be a sign of evolution by design- What Dr Spetner calls the “non-random evolutionary hypothesis”.Joseph
May 19, 2009
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jerry [119]:
The answer was provided far above. They all are designed. Each gene encodes proteins through a process only known to exist through intelligence.
Is that The Answer, or jerry's answer? Does everyone in the ID movement agree? How does jerry's special creation of every gene square with Behe's The Edge of Evolution: The Search for the Limits of Darwinism? It was my understanding, subject to correction, that Behe granted naturalistic mechanisms the ability to generate a whole lot of biological variation up to his edge. In 2007, Behe said,
I would suggest that Richard Dawkins re-read my book. In it I clearly state that random evolution works well up to the species level, perhaps to the genus and family level too. But at the level of vertebrate classes (birds, fish, etc), the molecular developmental programs needed would be beyond the edge of evolution.
http://calitreview.com/260 And if I recall correctly, hasn't jerry himself characterized a whole lot of examples of biological variation as "microeveolution, which is no threat to ID"?Adel DiBagno
May 19, 2009
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Tragic @ 117:
Well I have no doubts that you actually read my post, but to make it more clear a fair test would at least include the possibility of the proctor allowing you to pass it.
Fine. You get to be the proctor. Describe your test, and the proctoring by means of which you would decide the outcome. What test?Diffaxial
May 19, 2009
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"non-belief" is a belief. But hey, this thread has nothing to do with religion and in the past 6 weeks some have spent nearly a couple thousand comments of belief on their non beliefs.jerry
May 19, 2009
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