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Michael Behe on the Witness Stand

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As most people are aware, Michael Behe championed the design-inspired ID Theory hypothesis of Irreducible Complexity.  Michael Behe testified as an expert witness in Kitzmiller v. Dover (2005).

Transcripts of all the testimony and proceedings of the Dover trial are available here.  While under oath, he testified that his argument was:

“[T]hat the [scientific] literature has no detailed rigorous explanations for how complex biochemical systems could arise by a random mutation or natural selection.”

Behe was specifically referencing origin of life, molecular and cellular machinery. The cases in point were specifically the bacterial flagellum, cilia, blood-clotting cascade, and the immune system because that’s what Behe wrote about in his book, “Darwin’s Black Box” (1996).

The attorneys piled up a stack of publications regarding the evolution of the immune system just in front of Behe on the witness stand while he was under oath. Behe is criticized by anti-ID antagonists for dismissing the books.

Michael Behe testifies as an expert witness in Kitzmiller v. Dover. Illustration is by Steve Brodner, The New Yorker on Dec. 5, 2005.

The books were essentially how the immune system developed in vertebrates.  But, that isn’t what Intelligent Design theory is based upon. ID Theory is based upon complexity appearing at the outset of life when life first arose, and the complexity that appears during the Cambrian Explosion.

The biochemical structures Behe predicted to be irreducibly complex (bacterial flagellum, cilium, blood-clotting, and immune system) arose during the development of the first cell.  These biochemical systems occur at the molecular level in unicellular eukarya organisms, as evidenced by the fact that retroviruses are in the DNA of these most primitive life forms.  They are complex, highly conserved, and are irreducibly complex.  You can stack a mountain of books and scientific literature on top of this in re how these biochemical systems morphed from that juncture and forward into time, but that has nothing to do with the irreducible complexity of the original molecular machinery. 

The issue regarding irreducible complexity is the source of the original information that produced the irreducibly complex system in the first place.  The scientific literature on the immune system only addresses changes in the immune system after the system already existed and was in place.  For example, the Type III Secretion System Injector (T3SS) is often used to refute the irreducible complexity of flagellar bacteria.  But, the T3SS is not an evolutionary precursor of a bacteria flagella; it was derived subsequently and is evidence of a decrease in information.

The examining attorney, Eric Rothschild, stacked up those books one on top the other for courtroom theatrics.

Behe testified:

“These articles are excellent articles I assume. However, they do not address the question that I am posing. So it’s not that they aren’t good enough. It’s simply that they are addressed to a different subject.”

Those who reject ID Theory and dislike Michael Behe emphasize that since Behe is the one making the claim that the immune system is Irreducibly Complex, then Behe owns the burden to maintain a level of knowledge as what other scientists write on the subject.  It should be noted that there indeed has been a wealth of research on the immune system and the collective whole of the papers published gives us a picture of how the immune system evolved. But, the point that Behe made was there is very little knowledge available, if any, as to how the immune system first arose.

The burden was on the ACLU attorneys representing Kitzmiller to cure the defects of foundation and relevance. But, they never did. But, somehow anti-ID antagonists spin this around to make it look like somehow Behe was in the wrong here, which is entirely unfounded.  Michael Behe responded to the Dover opinion written by John E. Jones III here.  One comment in particular Behe had to say is this:

“I said in my testimony that the studies may have been fine as far as they went, but that they certainly did not present detailed, rigorous explanations for the evolution of the immune system by random mutation and natural selection — if they had, that knowledge would be reflected in more recent studies that I had had a chance to read.”

In a live PowerPoint presentation, Behe had additional comments to make about how the opinion of judge John E. Jones III was not authored by the judge at all, but by an ACLU attorney.  You can see that lecture here.

Immunology
Piling up a stack of books in front of a witness without notice or providing a chance to review the literature before they can provide an educated comment has no value other than courtroom theatrics.

The subject was clear that the issue was biological complexity appearing suddenly at the dawn of life. Behe had no burden to go on a fishing expedition through that material. It was up to the examining attorney to direct Behe’s attention to the specific topic and ask direct questions. But, the attorney never did that.  Read more here.  There is also a related Facebook discussion thread regarding this topic.

Comments
OT: It is interesting to note that the Darwinists hardly raised an eyebrow in the following article that just came out,,,
Family Ties: Completion of Zebrafish Reference Genome Yields Strong Comparisons With Human Genome - Apr. 17, 2013 Excerpt: Researchers demonstrate today that 70 per cent of protein-coding human genes are related to genes found in the zebrafish,,, http://www.sciencedaily.com/releases/2013/04/130417131725.htm
Excuse me, but should not 70% protein coding similarity between humans and a fish cause at least some concern for Darwinists? The preceding study is reminiscent of this following study:
Kangaroo genes close to humans Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 First Decoded Marsupial Genome Reveals "Junk DNA" Surprise - 2007 Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,, The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off. http://news.nationalgeographic.com/news/2007/05/070510-opossum-dna.html
Now if I were a Darwinist trying to explain widely divergent phenotypes on the basis of changes to genotypes, the preceding would not be comforting to me at all. But perhaps there is a way out for our reductive materialistic friends. Recently, ENCODE researchers, as well as others, have been arguing that the definition of 'gene' is fraught with difficulty and that RNA should actually now be considered the fundamental unit of inheritance,,,
The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video http://www.metacafe.com/watch/8593991/ Further Thoughts on the ENCODE/Junk DNA Debates - James Shapiro - Sept. 18, 2012 Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of "DNA Elements" rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries. Diogenes and like-minded people argue that we knew enough in the 1970s to understand the basic principles of genome organization. They do not accept that the flood of new information from genome sequencing and the kind of methodologies exemplified by the ENCODE project will fundamentally alter our genetic concepts. While they are certainly entitled to these opinions, I think we have to recognize that they are nothing more than that -- simply opinions that fly in the face of scientific history. http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html Landscape of transcription in human cells – Sept. 6, 2012 Excerpt: Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene. http://www.nature.com/nature/journal/v489/n7414/full/nature11233.html
But alas, RNA’s are found to be far more difficult to align into presupposed evolutionary relationships than Genes are/were:
Phylogeny: Rewriting evolution - Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. - Elie Dolgin - 27 June 2012 Excerpt: “I've looked at thousands of microRNA genes, and I can't find a single example that would support the traditional tree,” he says. "...they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist - Kevin Peterson) Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says. Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong. http://www.nature.com/news/phylogeny-rewriting-evolution-1.10885 micro-RNA and Non-Falsifiable Phylogenetic Trees - (Excellently Researched) video http://www.youtube.com/watch?v=qv-i4pY6_MU
Music and Verse:
Brooke Fraser - Day is Dimming http://www.youtube.com/watch?v=qI-Szg6TPRQ 1 Corinthians 15:53 For the perishable must clothe itself with the imperishable, and the mortal with immortality.
bornagain77
April 18, 2013
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A True story Once Upon a time there were a bunch of dinosaurs that lived happily in the valley, these dinosaurs were special because each one of them had mutations happening in them! They were so happy with these mutations that each one decided to keep these mutations so that one day they could combine them to become something. They did not know what yet but they did so anyway! Every once in a while they would dream about getting feathers, wings and a lung system that could make them soar high in the sky so that they could cope with the requirements of flight! With each passing generation they used unguided blind evolutionary processes to assemble their dream of flight, bit by small bit. Things went slow for the dinosaurs but they were patient because they had time on their side and given enough time anything is possible! After millions of years little dinosaurs started being born with all these pieces in themselves to transform into the dream of becoming birds. They were so happy that they could not contain their excitement. Every day they climbed trees and jumped out to practice in anticipation for the day when they could finally fly! Then one day, all of a sudden they noticed that they had in fact started evolving proto-feathers! Their plan worked and through perseverance they have built their own body plans from the ground up without even knowing what was required for flight! The Dinosaurs were so proud of their ancestors for the dream of flying one day without ever knowing what flight even is, but they did it and so overcame everything despite the odds!Andre
April 18, 2013
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Hi Nick Yes please can we get a textbook on Macro-evolution's facts! I'll make it easy for you; 1.) I want to see a step by step process of the evolution of the lung system. 2.) Step by step process of the evolution of the heart. 3.) Step by step process of the sexual reproductive system. 4.) When did survival of the fittest kick in? With the first single cell organism or later? How did they know that survival is key? 5.) How does natural selection select? If something is not in the search space how does it find stuff that is not there? Or has everything always been there? 6.) If Random mutations are 90% bad most of the time why are we here? is 1% good enough to go from a single cell to a complex organism such as a human? Is this scientifically possible? 7.) How did the feathers evolve? 8.) How did animals evolve from cold blooded to warm blooded? Your most valuable scientific facts will be greatly appreciated. Good Luck! AndreAndre
April 18, 2013
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Behe via BA77 @33:
Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.
Exactly. Another example that ID proponents have for years been giving Darwin more credit than he deserved.Eric Anderson
April 17, 2013
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Box, I'll admit, I fail to see a point in much of the above. Do you want to let me know what I'm missing?wd400
April 17, 2013
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#40 Some people miss the point entirely.Box
April 17, 2013
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But seriously, this seems like a real money-making opportunity for you. Why don’t you write a textbook on Macro-Evolutionary Theory? Mung, I'd afraid you have a very warped idea of the way academia works if you think there is much money to be made in writing text books! Especially for topics as specific as macro-evolution, which would only be used by grad students.wd400
April 17, 2013
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@38, seconded. 8)Chance Ratcliff
April 17, 2013
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bornagain77 @33, I continue to be amazed at your ability to examine the skeleton of the best ideas and fill them in with flesh, blood, and bone.StephenB
April 17, 2013
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nightlight @32, thanks for your response. I'll go through it more carefully when I'm able. I might have some additional comments to offer with regard to contingent/random/designed.Chance Ratcliff
April 17, 2013
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Nick, Since you seem somewhat reluctant to establish your bona fides, why should I contribute any of my hard-earned cash to your meeting with Dr. Tour? Assume you wanted Dr. Tour to be prepared for your meeting. What textbook on Macro-Evolutionary Theory would you send him if you were paying for it?Mung
April 17, 2013
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BA77 @33, no problem. Thanks for another post rich in material to distract, fascinate and educate. :DChance Ratcliff
April 17, 2013
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Hi Nick, We're still waiting on that textbook on Macro-Evolutionary Theory. You know, the field that you are in. Yeah, that one. If there is no such textbook, why not just say so and end the charade? But seriously, this seems like a real money-making opportunity for you. Why don't you write a textbook on Macro-Evolutionary Theory? End the dearth.Mung
April 17, 2013
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Thanks Chance and Stephen for bringing this point out about how the limits for Darwinian processes have been tightened. It was at first assumed by the ID community, at least as far as I am aware, that the plasticity of proteins was far greater than it is now found to be. And as such far more leeway was granted to Darwinian explanations at that time. With ID, at that time, focused mainly on the origin of proteins and IC molecular machines and systems. But now, in the past few years, the limits for what Darwinian processes can actually accomplish has been found, empirically, to be much greater than what was originally granted to them. Dr. Behe relates that sentiment here:
Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html
In 2010 Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke came along and found:
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/index.php/main/article/view/BIO-C.2010.2
Then in 2011 Douglas Axe and Ann Gauger came along and found:
The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway - Ann K. Gauger and Douglas D. Axe - April 2011 Excerpt: 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. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1
But what does all this mean as to the constraints for neo-Darwinian processes? Well Dr. Gauger lays out the implications here:
More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012 Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population. You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect. Facing Facts But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes. https://uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/
Moreover, while ID was doing the dirty work that Darwinists refused to do, finding out what the limits to Darwinian processes actually were, from the other end of the spectrum it was becoming more and more evident that the supposed genetic similarity between species, particularly between man and apes, was far greater than Darwinists had originally misled the general public to believe. Falling from approximately 99% similarity to now around 85% to 70% or even lower genetic similarity:
Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% - by Jeffrey P. Tomkins - February 20, 2013 Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor. http://www.answersingenesis.org/articles/arj/v6/n1/human-chimp-chromosome Ten years on, still much to be learned from human genome map - April 12, 2013 Excerpt:,,,"What's more, about 10 percent of the human genome still hasn't been sequenced and can't be sequenced by existing technology, Green added. "There are parts of the genome we didn't know existed back when the genome was completed," he said.,,, http://medicalxpress.com/news/2013-04-ten-years-human-genome.html
If that was not bad enough for Darwinists, it is now found that a significant percentage of all genomes sequenced, including humans, have completely unique ORFan genes with no traceable evolutionary lineage:
Human Gene Count Tumbles Again - 2008 Excerpt:,, the analysis revealed 1,177 “orphan” DNA sequences.,,, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012 Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics. Genes from nowhere: Orphans with a surprising story - 16 January 2013 - Helen Pilcher Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these "orphan genes" are high achievers (are just as essential as 'old' genes),,, Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing. http://ccsb.dfci.harvard.edu/web/export/sites/default/ccsb/publications/papers/2013/All_alone_-_Helen_Pilcher_New_Scientist_Jan_2013.pdf Orphan Genes (And the peer reviewed 'non-answer' from Darwinists) - video http://www.youtube.com/watch?v=1Zz6vio_LhY
Thus Darwinists have been getting squeezed from both ends over the last few years, for the protein level, the plasticity is just not there for them as it was assumed to be, and on the whole genome level, the gaps are growing wider and wider, to the point of making genetic comparisons completely embarrassing as a Darwinian talking point, as more date comes in.bornagain77
April 17, 2013
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Chance Ratcliff #24: Here I don't find much disagreement (except with the presumed scope of microevolution), so I'm left scratching my head comparing these statement to your comments in #10. The last comment was carefully worded and doesn't imply that neo-Darwinian RM+NS can explain microevolution. I merely say that the counterexamples have no bearing as to whether ND can explain it. Note also that those two responses were aimed at the opposite sides of the debate spectrum, hence disagreements and points made are entirely different. #26 While random mutations may be sufficient to produce certain changes, they are not known to be necessary for those changes, nor sufficient for all observed microevolutionary events. I hope this is clear enough. I still don't think that the 'intelligent agency' is shifting its gears and changing its ways when switching between phenomena based on the level of our current understanding of those phenomena, or our notions du jour of "random" vs "contingent" vs "intelligently guided" -- it does what it does for reasons of its own regardless of how much of it we presently understand. Humans, especially scientists have a habit of labeling everything that is not explained by their theories as intrinsically "unexplainable" a.k.a. "random" (like a void with monsters at the edges of ancient maps). The alternative would be to admit that something which may have an explanation is not explainable by their theory, but that would go against the human nature. As result, we always have the "randomness" monsters beyond the edges of the present scientific theories, regions were one doesn't go, whether in biology or in quantum theory. Note for example, that in human affairs, where we have a better insight into motivations and driving forces, the existence of numerous order preserving mechanisms (laws, police, door locks, bars on ground floor windows,..etc) does not imply that activities violating those mechanisms are "random errors" since we have a good hunch why someone might be breaking into a locked home or having a gunfight with the police. Similarly, if we were beings living at the cellular level or below, those so called "random errors" violating the cellular order preserving (i.e. error correcting) mechanisms might not appear all that "random" to us.nightlight
April 17, 2013
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Footnote to #29, The included link includes a reference for an audio interview in which Jay Richards interviews Ann Gauger about evolutionary adaptive pathways, which is the subject of a paper she coauthored, Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness. P.S. Stephen Re: #26, you're too kind. :)Chance Ratcliff
April 17, 2013
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Chance Ratcliff @26: Your clarity is exceeded only by your precision, which, come to think of it, is the reason for the clarity. Good stuff.StephenB
April 17, 2013
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Thanks for that quote Stephen. There's nothing like hearing directly from someone like Richards, who seems to have a talent for clear and concise statements such as these. He's also a pleasure to listen to in interviews and lectures, as he's very personable and thoughtful. I found a reference for that quote here: Interview With Author of New Paper on the Limits of the Darwinian Mechanism.Chance Ratcliff
April 17, 2013
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For my part, Jay Richards has summed up the ID relationship with Darwin very well, and I certainly wouldn't describe it as Darwin bashing: "Pretty much everyone agrees that natural selection acting on random genetic mutations can explain some things. The really interesting question is, how much can it explain? Since Darwin's mechanism seems intuitively plausible, we're often tempted just to trust our intuitions rather than to look at the hard data. And yet the data increasingly show that, whatever its intuitive attractions, the powers of selection and mutation are surprisingly limited." To me, he gets it exactly right, granting everything that should be granted and pulling back at just the right time and in exactly the right way.StephenB
April 17, 2013
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Box, thanks for the clarification on that technical point. The flaw only surfaces when you take the sentence out of context. The very next sentence I wrote reads, "These biochemical systems occur at the molecular level in unicellular eukarya organisms, as evidenced by the fact that retroviruses are in the DNA of these most primitive life forms." Cilia and immunity do occur in unicellular eukarya, and all four irreducibly complex systems are required to sustain life in the most primitive multi-cellular eukarya organisms. The point is that the focus of irreducible complexity is the molecular machinery that appears early at the origin and beginning stages of the development of life, and is highly conserved in vertebrates, just as Behe highlighted in Darwin's Black Box. Your point is well-taken and noted. ThanksDennisJones
April 17, 2013
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Footnote to my #24 regarding the scope of microevolution: ID proponents do not suppose that microevolution is synonymous with random mutations in the one-or-two substitution range. It does not suppose that all antibiotic resistance is necessarily in this range, and ID doesn't suppose that all observed morphological/phenotypical changes (microevolution) are achievable by trivial substitutions within the sufficiency of random mutations. Rather, Intelligent Design is perfectly comfortable and compatible with teleological mechanisms of morphological change, such as phenotypic plasticity. To clarify the above, random mutations are accepted as a sufficient cause for certain small-scale events, but this in no way implies a necessity relationship, nor does it associate the phenomena of microevolution exclusively with random mutations. This is unequivocal. While random mutations may be sufficient to produce certain changes, they are not known to be necessary for those changes, nor sufficient for all observed microevolutionary events. I hope this is clear enough.Chance Ratcliff
April 17, 2013
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Dennis Jones: "The biochemical structures Behe predicted to be irreducibly complex (bacterial flagellum, cilium, blood-clotting, and immune system) arose during the development of the first cell."
'Blood-clotting' did not arise during the development of the first cell.Box
April 17, 2013
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nightlight @15,
"The ‘irreducible complexity’ examples by Behe, or CSI examples by Dembski, serve as counterexamples to neo-Darwinian theory of evolution (ND=RM+NS), pointing to some instances where ND’s RM+NS mechanism seems incapable of explaining the particular biological artifacts. The existence of direct counterexamples has no bearing on whether RM+NS mechanism is capable of explaining some other biological artifacts, such as micro-evolution (e.g. bacterial resistance to antibiotics)."
Here I don't find much disagreement (except with the presumed scope of microevolution), so I'm left scratching my head comparing these statement to your comments in #10. Anyway, yes, the random mutation force of change posited by neo-Darwinism has intrinsic limitations, making it sufficiently capable of trivial changes but insufficient to account for large-scale ones; this is no different from general experience with random effects, such as the occasional short word produced by random jumbles of letters, versus the content of a meaningful paragraph of specified text -- at sufficient length unattainable by chance in the entire age of the universe.Chance Ratcliff
April 17, 2013
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Eric, I have probably read everything of relevance concerning ID except I have not read much in the last couple years. Thus, I have read Behe's books and was one of the first ones on this site to state the implications of The Edge of Evolution. I read Meyer's book just after it came out and a lot of Dembski's books and several others by those who are anti ID as well as about a dozen videos I purchased from ARN. There was a point I couldn't consume enough of the stuff. I have also seen the arguments play out in other arenas and think I have a good feel for what the typical educated person knows in the world on this. And what they do not know is that ID has no problem with the source of much of the variation in life forms on the planet. Most species would make it through the legendary filter. What ID has problems with is origins not the on going process of modification that takes place and which creates a lot of the diversity we see. So to restate my position. Use this as a basis for debating the problem. I was not describing isolated instances in my observations. It took me several years to realize that ID wasn't criticizing all of Darwin so why did I have this impression. My first introduction to ID was at a conference with Behe, Dembski, Meyers and some others in 1998. Eight years later I was arguing on this site to stop the Darwin bashing and accept the limited changes that his and the modern synthesis has documented. But be firm in what is accepted or seen as possible by natural process versus what is pure speculation and no way possible through natural processes. Behe put limits on the ability of known naturalistic processes but just where the actual line is is unknown. So the best approach is an honest approach and that it is a mystery. I believe Behe used that term some place. By using such an approach the result will be to take the steam out of Darwin. That should be the objective. Make Darwin trivial. If as you say that was always part of ID then I missed it and so did most of the others here because Darwin trashing was endemic especially on this site. And I never heard it argued out in any of the public forums in any structured way. I brought up the Dembski example because the girl stopped Dembski in his tracks and he did not answer her coherently. If as you say there was always some obeisance to Darwin, then Dembski did not pay it to get rid of his heckler. Most of the commenters here didn't understand it either and as I said it did not play out in the public arena and I listened to dozens of debates or presentations. The Dover trial being just one very visible example. So we will continue to disagree.jerry
April 17, 2013
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nightlight @10,
"As explained in an earlier post, that kind of ‘part time ID’ (term explaned here), which divides the processes into “natural” (those explainable by the known laws of nature, such as ‘micro-evolution’) and the “un-natural” (those not explainable by the known natural laws such as ‘macro-evolution’, where presumably the intelligent agency has to come down to do it the “un-natural” way), is an incoherent position, confusing the map with the territory i.e. projecting into the processes themselves the attributes of our present state of knowledge about those processes."
That paragraph is at least confused, if it doesn't blatantly misrepresent ID. First of all there is a definitional demarcation issue with terms like "natural" and "unnatural". Depending on use, each can include or exclude instances of observed design, such as bicycles and hang gliders. So if you're using "natural" to mean, the result of chance and necessity, then you are excluding instances where contingent and purposeful configurations of matter are required to produce certain effects, such with computer systems, as well as most microevolutionary changes, which rely on purposeful and irreducible arrangements of specific material parts. Additionally, ID does not divide micro and macro evolution into "natural" and "unnatural" categories, as those sorts of distinctions are not only unhelpful, but potentially obfuscatory, such as the case with your above paragraph. Rather ID theory encompasses methodologies for identifying the hallmarks of intelligence, such as those which are present in living systems, as evident by the presence of digital codes and the machinery which those codes specify, and by which the machinery that processes the codes are constructed. It would be best to read ID literature and produce actual quotes, whereby the claims of prominent ID proponents can be meaningfully compared with your criticisms. It's not clear where your disagreement really lies since your conception of ID, as presented in your above paragraph, appears muddled. It's also unclear whether your theory of U-ID encompasses gradualism with respect to OOL and morphological diversification; and if so, through what physical processes, chance and/or necessity does it achieve its result -- and if your conceptual intelligent force doesn't operate through chance and/or necessity gradually to produce teleological configurations of matter, how does it operate, and how does that invalidate the design inference.Chance Ratcliff
April 17, 2013
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nightlight, Sorry, let me be clear. ID explanations are perfectly capable of being scientific and defended in court. It's just that most scientists and judges are atheists, and they've banned from their journals and courtrooms all explanations of anything involving intelligence. I know it sounds silly, but trust me, it's true.lastyearon
April 17, 2013
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Mr. Matzke, though Darwinists have certainly not explained the origin of the immune system or any variations of the immune system between species (besides story telling and hand waving), let's focus in on the main claim of Dr. Behe, one you are very familiar with, a claim that is at the very top of this blog, the bacterial flagellum. Though much has been written on the Bacterial Flagellum, enough to do another theatrical literature bluff if you were so inclined to be deceptive (which I hold you to be), the plain fact of the matter is that if one digs through all that literature there is not a single example of the Bacterial Flagellum arising de novo by Darwinian processes,,,
Michael Behe Hasn't Been Refuted on the Flagellum - Jonathan M. - March 15, 2011 Excerpt: First and foremost, it trivializes the sheer complexity and sophistication of the flagellar system — both its assembly apparatus, and its state-of-the-art design motif… The synthesis of the bacterial flagellum requires the orchestrated expression of more than 60 gene products. Its biosynthesis within the cell is orchestrated by genes which are organised into a tightly ordered cascade in which expression of one gene at a given level requires the prior expression of another gene at a higher level… [P]romoters are akin to a kind of molecular toggle switch which can initiate gene expression when recognised by RNA polymerase and an associated specialised protein called a “sigma factor”. These three classes of promoters are uninspirationally dubbed “Class I,” “Class II,” and “Class III.”…Those genes which are involved in the synthesis of the filament are controlled by the Class III promoters. …The sigma factor sigma-28 is required to activate the Class III promoters. But here we potentially run into a problem. It makes absolutely no sense to start expressing the flagellin monomers before completion of the Hook-Basal-Body construction. Thus, in order to inhibit the sigma-28, the anti-sigma factor (FlgM) alluded to above inhibits its activity and prohibits it from interacting with the RNA polymerase holoenzyme complex. When construction of the Hook-Basal-Body is completed, the anti-sigma factor FlgM is secreted through the flagellar structures which are produced by the expression of the Class II hook-basal-body genes. But it gets better. The flagellar export system (that is, the means by which [regulatory gene] FlgM is removed from the cell) has two substrate-specificity states: rod-/hook-type substrates and filament-type substrates. During the process of flagellar assembly, this substrate-specificity switch has to flick from the former of those states to the latter. Proteins which form part of the hook and rod need to be exported before those which form the filament… The rod structure is built through the peptidoglycan layer. But its growth isn’t able to proceed past the physical barrier presented by the outer membrane without assistance. So, the outer ring complex cuts a hole in the membrane, so that the hook can grow beneath the FlgD scaffold until it reaches the critical length of 55nm. Then the substrates which are being secreted can switch from the rod-hook mode to flagellin mode, FlgD can be replaced by hook-associated-proteins, and the filament continues to grow. Without the presence of the cap protein FliD, these flagellin monomers become lost. This cap protein is thus essential for the process to take place. My description, given above, has really only scratched the surface of this spectacular item of nano-technology… I have not, for the sake of brevity, even discussed the remarkable processes of chemotaxis, two component signal transduction circuitry, rotational switching, and the proton motive force by which the flagellum is powered… But the bottom line is that modern Darwinian theory — as classically understood — has come no where close to explaining the origin of this remarkably complex and sophisticated motor engine. Just as Darwinian “explanations” of the eye may, at first, appear convincing to the uninitiated, largely unacquainted with the sheer engineering marvel of the biochemistry and molecular basis of vision, so too do the evolutionary “explanations” of the flagellum rapidly become void of any persuasiveness when one considers the molecular details of the system… It seems that the bacterial flagellum is as much a — and perhaps a greater — challenge to Darwinism as it was when Behe first wrote Darwin’s Black Box in 1996. http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.html
The assembly of the flagellum is a nothing less than a wonder to behold:
Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video http://www.metacafe.com/watch/3994630/
Indeed so advanced is the assembly process of the Flagellum that it was recently noted:
The Bacterial Flagellum: A Paradigm for Design - Jonathan M. - Sept. 2012 Excerpt: Indeed, so striking is the appearance of intelligent design that researchers have modelled the assembly process (of the bacterial flagellum) in view of finding inspiration for enhancing industrial operations (McAuley et al.). Not only does the flagellum manifestly exhibit engineering principles, but the engineering involved is far superior to humanity’s best achievements. The flagellum exhibits irreducible complexity in spades. In all of our experience of cause-and-effect, we know that phenomena of this kind are uniformly associated with only one type of cause – one category of explanation – and that is intelligent mind. Intelligent design succeeds at precisely the point at which evolutionary explanations break down. http://www.scribd.com/doc/106728402/The-Bacterial-Flagellum
Indeed Biologist Howard Berg at Harvard calls the Bacterial Flagellum
“the most efficient machine in the universe."
And that comment was made way before Dr. Berg discovered this:
Souped-Up Hyper-Drive Flagellum Discovered - December 3, 2012 Excerpt: Get a load of this -- a bacterium that packs a gear-driven, seven-engine, magnetic-guided flagellar bundle that gets 0 to 300 micrometers in one second, ten times faster than E. coli. If you thought the standard bacterial flagellum made the case for intelligent design, wait till you hear the specs on MO-1,,, Harvard's mastermind of flagellum reverse engineering, this paper describes the Ferrari of flagella. " Instead of being a simple helically wound propeller driven by a rotary motor, it is a complex organelle consisting of 7 flagella and 24 fibrils that form a tight bundle enveloped by a glycoprotein sheath.... the flagella of MO-1 must rotate individually, and yet the entire bundle functions as a unit to comprise a motility organelle." To feel the Wow! factor, jump ahead to Figure 6 in the paper. It shows seven engines in one, arranged in a hexagonal array, stylized by the authors in a cross-sectional model that shows them all as gears interacting with 24 smaller gears between them. The flagella rotate one way, and the smaller gears rotate the opposite way to maximize torque while minimizing friction. Download the movie from the Supplemental Information page to see the gears in action. http://www.evolutionnews.org/2012/12/souped-up_flage066921.html
Now Mr. Matzke, seeing as you guys can't even demonstrate the origination of a single protein by purely Darwinian processes (Axe, Sauer), nor the transformation of a existing protein into a similar protein of different function if it requires greater than 7 mutations (Axe, Gauger), then why in the world do you guys pretend as if you have all this evidence showing the origination of this fascinating molecular machines? i.e. Why can't neo-Darwinists be honest like James Shapiro is?
"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/
Instead of honestly admitting what the evidence is telling us, we get this from Darwinists:
Taking on Behe's Challenge: Evolve Me a Cilium - April 15, 2013 Excerpt: "Once upon a time, a complete, working cilium with all the correct components, and with all the right genetic assembly instructions, just "emerged" in some mythical common ancestor. Maybe evolution "repurposed" some protein-coating genes after a mistake duplicated them. However it happened, all those parts were "conserved" the rest of the way, from simple one-celled Chlammy to complex trillion-celled Sammy. During evolution, some branches of the eukaryotic tree lost some parts, but the ones that didn't die are getting along OK. " http://www.evolutionnews.org/2013/04/taking_on_behes071121.html
bornagain77
April 17, 2013
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Of note: Judgment Day: Intelligent Design on Trial - Phillip E. Johnson - podcast http://www.youtube.com/watch?v=Rpp5TEB3NEg PBS, Darwin and Dover: an Interview with Phillip Johnson. On this episode of ID The Future, CSC's Casey Luskin interviews Phillip Johnson (Jefferson E. Peyser Professor of Law, emeritus School of Law University of California, Berkeley) author of the bestseller Darwin on Trial, and one of the founders of the modern intelligent design movement.bornagain77
April 17, 2013
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Eric Anderson @7
"I think most prominent ID proponents, certainly in their writings and in their documentaries, give Darwin more credit than he deserves. They are often willing to assume for purposes of discussion that Darwin’s mechanism explains microevolutionary events just fine. However, we’re learning more and more that many of those microevolutionary processes may not even be driven by the alleged mutation+selection mechanism."
I agree. The term "microevolution" does little more than reference the observed result of phenotypic change, much like natural selection references the results of survival. Neo-Darwinism posits the driver of change to be random mutation. To reference Koonin:
"Undirected, random variation is the main process that provides the material for evolution. Darwin was the first to allow chance as a major factor into the history of life, and this was arguably one of his greatest insights. Darwin also allowed a subsidiary role for directed, Lamarckian-type variation, and he tended to give these mechanisms more weight in later editions of Origin. Modern Synthesis, however, is adamant in its insistence on random mutations being the only source of evolutionarily relevant variability. Koonin, Eugene V. The Logic of Chance: The Nature and Origin of Biological Evolution (FT Press Science) (Kindle Locations 394-398). "
So while Darwin, according to Koonin, did allow some room for Lamarckian-type inheritance, neo-Darwinism has been insistent that the main driver of change is random mutations. I think it's wise to be cautious about what is credited to the mechanisms of neo-Darwinism, while perhaps offering clarification about what actually causes observed microevolutionary changes. For instance, phenotypic plasticity apparently has significant powers with regard to morphological changes, which are the product of preprogrammed responses to environmental cues rather than the result of mutation and selection. Ultimately we must be cautious about where to credit Darwin. His insistence on random variation and gradualism are not exactly panning out in all respects. Phenotypic plasticity, as well as what James Shapiro calls "natural genetic engineering" are bringing to light the non-random nature of morphological changes, which can also be non-gradual. Random mutations on the other hand, tend to break more than build, and cause disease rather than innovation.Chance Ratcliff
April 17, 2013
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jerry @4:
One way of doing this is to say that the micro-evolutionary process is a very real one but also one that is remarkably limited. Give Darwin his due but then show that what Darwin observed and wrote about does not and can not explain all of life’s complexities. Make them do the explaining. That is one of the major failures of ID.
Have you read Darwin's Black Box, Signature in the Cell, Edge of Evolution? Or seen Unlocking the Mystery of Life? ID proponents have been giving Darwin his due -- probably a lot more than his due -- for years. Johnson in Darwin on Trial gave Darwin credit for helping explain microevolutionary phenomena. Paul Nelson has also made similar statements. I am not sure why you think there is some deep seated reluctance to acknowledge microevolutionary processes. If anything, Darwin has gotten way more credit than he should have from ID proponents. Precisely because as a debating tactic it sometimes helps to just accept, for purposes of discussion, that microveolutionary processes can be explained by a Darwinian mechanism, so that the real meat of macroevolutionary change can be focused on. Now if you happened to be sitting in one live seminar in which Dembski didn't answer an audience question just the way you would have liked, fine. I have taught a lot of classes and given many live presentations and there is hardly a single time I don't come home thinking, "What I should have said was x" or "I could have explained y better." That certainly doesn't speak to any larger systemic failure by major ID proponents to acknowledge microevolutionary changes that can be reasonably explained by purely natural processes. Your suggestion of "Give Darwin his due but then show that what Darwin observed and wrote about does not and can not explain all of life’s complexities" is precisely the approach taken in Darwin's Black Box, Signature in the Cell, Edge of Evolution, etc. I know you have some good exposure to ID, so I am a little perplexed as to why or how you have missed this obvious approach in the ID literature. On the other hand, if someone happens to think that RM+NS or similar processes can explain a great deal more than they have ever been shown to explain, then they might end up feeling that Darwin is getting short shrift. But that is an evidentiary question, not a tactical one.Eric Anderson
April 17, 2013
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