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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
franklin:
Why are you asking? Is Nick the only individual who can supply references that will be accepted by you?
I denied that Nick had ever supplied such a reference, You can provide evidence to the contrary?Mung
April 21, 2013
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frankin on the witness stand: No thanks. I'd have to perjure myself.Mung
April 21, 2013
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mung: Did Nick?
Why are you asking? Is Nick the only individual who can supply references that will be accepted by you?franklin
April 21, 2013
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mung, you are correct. I did not supply any reference(s).
Did Nick?Mung
April 21, 2013
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mung, you are correct. I did not supply any reference(s). come now, mung, surely you're aware of all the forums/threads where you've made your now oft repeated request. Perhaps, you should look there.franklin
April 21, 2013
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franklin@68:
you were already given two citations why haven’t you looked at those and why are you still claiming that none exist when they obviously do
Textbooks on Macro-Evolutionary Theory? Really? Where? They certainly weren't provided by you in this thread. You post @689 being the only post you've made in this thread.Mung
April 21, 2013
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Stephen, that might be exactly what I'm looking for. Thanks.Chance Ratcliff
April 21, 2013
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Chance, if you want to get into it at a much deeper level, you can simply Google "articles by Jay Richards." Of special interest would be Catholics and Intelligent Design Parts 1, 2, 3, 4, and 5. The same information can be found at the data base for Evolution News and views. The short video was, of course, just a preview. If you do take time to read all or part the 5-part series, let me know what you think. Jay Richards is my favorite ID luminary.StephenB
April 20, 2013
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Stephen @97, thanks. I found the video you referenced, it's quite informative, but too short! I also found a video for a speech Richards gave to a group at Biola which might be worth watching. I'm taking a peek now: The Central Issues [God and Evolution]. The first few minutes is promotional materal for God and Evolution but then it switches gears to the actual speech. The book is now on my wish list. Thanks much for the explanation and recommendations.Chance Ratcliff
April 20, 2013
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Chance @93, I think the most efficient and entertaining way of introducing yourself to this subject is to view the YouTube presentation by philosopher Jay Richards, entitled “Common Catholic Misunderstandings of Intelligent Design.” Also, if you ever get a chance to read “God and Evolution,” edited by Richards, I encourage you to take advantage of the opportunity. To me, the crux of the disagreement is the misguided belief among neo-Thomists (St. Thomas himself would have never made such a mistake) that ID confuses a thing’s “nature” with its “function, reducing the former to the latter. It just isn’t true. There is much more to it than that, though, so I hope you can follow up with at least the first reference.StephenB
April 20, 2013
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wd400, so is inane ridicule the only 'rational' response, (as if rationality were even possible in the epistemological failure that is the atheistic worldview), to the constraints found for the evolvability of proteins of one function to other proteins of a similar but different function? In case you don't know wd400, again pretending as if you will be reasonable to evidence, the reason why proteins are tightly constrained to any specific sequence of amino acids is because the specific sequences of amino acids are found to be 'context dependent', in that the ‘whole’ of the protein structure takes precedence over how the 'parts' of the amino acids are used in any particular functional sequence thus further severely constraining the ‘evolvability’ of proteins. Dr. Durston relates the 'context dependency' problem of proteins this way:
(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf
Structure is found to take precedence over sequence here as well,,,
Proteins with cruise control provide new perspective: Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.” http://www.princeton.edu/main/news/archive/S22/60/95O56/
And here,,,
Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975
Moreover, besides the ‘context dependency’ as to how proteins are constructed from amino acids, it is now found that proteins are also dependent on the specific context of the particular cellular environment that they may be in. Thus, the sheer brick wall that neo-Darwinian processes face in finding ANY novel functional protein in the first place, (Axe; Sauer), to perform any specific single task in a cell, is only exponentially exasperated by the fact that many proteins are multifunctional and, ‘serendipitously’, perform several different ‘context dependent’ tasks within the cell:
Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought: Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival. Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013 Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.” Explaining how a protein can perform multiple roles – Cell Biology – December 18, 2009 Excerpt: It’s been known for more than a decade that some cell proteins can carry out multiple functions.,, Discovering that the same protein could perform very different roles opened one of the great new chapters in molecular biology. http://scitechstory.com/2009/12/18/explaining-how-a-protein-can-perform-multiple-roles/
Moreover, protein-protein interactions and domain-domain interactions for proteins are tentatively found to be very different in different species
A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,, http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005096
The preceding finding is backed up by the fact that alternative splicing codes are found to be vastly different between different species:
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F
and What is alternative splicing?
Alternative splicing - wikipedia Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within, or excluded from, the final, processed messenger RNA produced from that gene.[1] Consequently the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions (see Figure). Notably, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
And indeed the proteins, even though this following study was severely biased towards a Darwinian viewpoint, are found to be significantly different between chimps and humans,,
Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005: http://www.ncbi.nlm.nih.gov/pubmed/15716009
To put it mildly this huge +80% difference between chimps and humans is more than a slight problem for evolutionary materialists. One problem that immediately pops out is this,,,
“The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.” - Michael Behe – The Edge of Evolution – page 146
Thus wd400, you can continue to make inane comments about crocoducks, or whatever, or you can finally decide to become honest and address these real concerns with integrity. In my opinion, the only one you are fooling with your inane comments is yourself. i.e. It is much easier to see how shallow a person is if you are not that person being shallow wd400! Verse and music:
Proverbs 21:30 There is no wisdom nor understanding nor counsel against the LORD. Not for a Moment - Meredith Andrews - video http://myktis.com/songs/not-for-a-moment-2/
bornagain77
April 20, 2013
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wd400- When your position fails to produce any positive evidence for its claims, yet it still claims dominance, you don't seem to be embarrased by that. Why?Joe
April 20, 2013
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EA et al, I'll ask the question no one has answered again, as it is instructive. When YECs and their unthinking kin claim evolution requires a crocoduck you guys (I presume) laught at them. When Gauger and Axe make fail to create a protein corcoduck you don't seem to be embarrased by your fellow travelers. Why?wd400
April 20, 2013
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Stephen @92,
"Apparently, they are impervious to our multiple correctives, which, for me, calls into question their intellectual honesty."
If one's interpretation of a philosophy disallows the observation of machines in living systems, particularly when one observes machines in living systems, then that person is deluded or dishonest. Incidentally, I once saw a comment somewhere from a young Catholic that went a bit like this: "I'm a Thomist, so I don't accept Intelligent Design." Who are the mainstream promoters of this mischaracterization of Thomism, and where can I get a basic rundown of the issues? I've heard Jay Richards mention that ID is not incompatible with Thomism, but I've never really understood the crux of the disagreement.Chance Ratcliff
April 20, 2013
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Eric Anderson
I certainly would not suggest that, say, humans are just machines. But that we have machines, that our bodies use machines, is indisputable.
Eric, thank you for dramatizing this vital point. The anti-ID neo-Thomists, who outrageously violate the pro-ID philosophy of their master in the name of Catholicism, argue, unreasonably, that recognizing the existence of machines in the human body militates against the idea that the larger organism of which they are a part has a "nature." Apparently, they are impervious to our multiple correctives, which, for me, calls into question their intellectual honesty. St. Thomas, a design thinker par excellence, must be turning over in his grave.StephenB
April 20, 2013
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Incidentally, I just noticed a couple of interesting sessions from the AAAS Meeting in Boston in February 2013. Looks like a very interesting meeting, with some intriguing sessions. Biotechnology and Nanotechnology http://aaas.confex.com/aaas/2013/webprogram/Session5887.html Boy, I hope those guys don't get all confused bringing engineering principles to the table. What a terrible way to approach biology. /sarc Also of interest for this thread: How Macro-Evolutionary Studies Call for an Extended Synthesis http://aaas.confex.com/aaas/2013/webprogram/Session5756.html Note in particular, the fossil record statements.Eric Anderson
April 20, 2013
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wd400:
There will be (and are) intermediate fossils.
Oh, to be sure there are a small handful of fossils that might be viewed as intermediates. In most cases they are subject to question, but even if we assume that the alleged intermediates are in fact intermediates, they are the exception in the fossil record, not the rule. The fossil record is characterized primarily by discontinuity and statis. This is in direct contrast to what Darwin proposed (and what slight, successive change requires), that there would be "innumerable" intermediates, with the fossil record showing organisms merging almost imperceptibly, like colors on a color chart. The fossil record points decisively away from Darwin's expectation. Which is why folks like Gould and Eldridge came up with the clever idea that evolution happens mostly where it can't be observed or preserved. And as for whether gaps between current living organisms are to be expected, that is still completely irrelevant to the question of biological novelty, so it is puzzling why you think the existence of gaps helps us understand biological novelty.
. . . it’s hard to imagine a worse [way] to think about the operation of genomes that the lens of computer programming (well, I guess engineering would be worse, but still).
It is very easy to imagine a worse way to think about the origin of biological novelty: particles bumping into each other over aeons. I think you are a bit blinded by your a priori assumptions. It is very facile to hand wave and toss aside the relevant questions about biological novelty by saying that we shouldn't think of biological systems in terms of code, programming, and engineering. But that seems to be more of a debating tactic than a substantive concern. I certainly would not suggest that, say, humans are just machines. But that we have machines, that our bodies use machines, is indisputable. Do you dispute that biological systems are composed of molecular machines? Certainly biological systems depend on coding, algorithms, and engineering principles. There are whole fields that have arisen to take advantage of what can be learned about engineering and systems control by studying biological systems. Indeed, the primary way the workings of biological systems have started to be understood is through reverse engineering, not by sitting around in an ivory tower and imagining how evolution could have produced such and thus. The latter has an incredibly poor track record and has been, frankly, a huge impediment to our understanding over the years. If engineering principles don't apply to biological systems, pray tell, what fantasy principles do you think operate in biology to build systems and keep them functioning?Eric Anderson
April 20, 2013
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wd400 #84:(...) it’s hard to imagine a worse to think about the operation of genomes that the lens of computer programming (well, I guess engineering would be worse, but still)
Wd400, you say that it's hard to imagine anything worse, but I'm willing to give it a go: how about thinking about life as the product of purposeless material forces?Box
April 20, 2013
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wd400, makes an interesting comment here:
it’s hard to imagine a worse to think about the operation of genomes that the lens of computer programming (well, I guess engineering would be worse, but still)
Yes, I can see how looking at life through those particular lens would be quite embarrassing for Darwinists:
Venter: Life Is Robotic Software - July 15, 2012 Excerpt: “All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said (Craig) Venter. http://crev.info/2012/07/life-is-robotic-software/ How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. - Paul Davies http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk “Each cell with genetic information, from bacteria to man, consists of artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction and a capacity not equaled in any of our most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours" Michael Denton PhD. Evolution: A Theory In Crisis pg. 329
Actually, even though the programming in our computers is far simpler than the programming found in genomes,,,
Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information - David L. Abel and Jack T. Trevors - Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8 "No man-made program comes close to the technical brilliance of even Mycoplasmal genetic algorithms. Mycoplasmas are the simplest known organism with the smallest known genome, to date. How was its genome and other living organisms' genomes programmed?" http://www.biomedcentral.com/content/pdf/1742-4682-2-29.pdf The Coding Found In DNA Surpasses Man's Ability To Code - Stephen Meyer - video http://www.metacafe.com/watch/4050638 Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188 Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,,
and contrary to what wd400 would prefer to be true,,,The plain fact of the matter is that computers and engineering principles are, by far, the best tools we have for trying to understand the complexity we are dealing with in life,,
To Model the Simplest Microbe in the World, You Need 128 Computers - July 23, 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ "Complexity Brake" Defies Evolution - August 2012 Excerpt: "This is bad news. Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology speeds up by an order of magnitude each year.",,, Even with shortcuts like averaging, "any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system," Koch said. "It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner." He described the concept of the Complexity Brake:,,, "Allen and Greaves recently introduced the metaphor of a "complexity brake" for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.",,, Why can't we use the same principles that describe technological systems? Koch explained that in an airplane or computer, the parts are "purposefully built in such a manner to limit the interactions among the parts to a small number." The limited interactome of human-designed systems avoids the complexity brake. "None of this is true for nervous systems.",,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html
And wd400 though you may think that "engineering would be worse" than computer programming to look at the genome with, but I can assure you that computer engineers have no such qualms:
Introducing "Bi-Fi": The Biological Internet - October 3, 2012 Excerpt: They already achieved 5 petabits per cubic millimeter! That's 1,000 terabits of data -- nearly twice the entire volume of digital records at the Library of Congress1 -- in a cube the size of the space between your thumb and forefinger when you hold them slightly apart.2 There are more reasons they think DNA storage is the wave of the future: "DNA is particularly suitable for immutable, high-latency, sequential access applications such as archival storage. Density, stability, and energy efficiency are all potential advantages of DNA storage, although costs and times for writing and reading are currently impractical for all but century-scale archives. However, the costs of DNA synthesis and sequencing have been dropping at exponential rates of 5- and 12-fold per year, respectively--much faster than electronic media at 1.6-fold per year. Hand-held, single-molecule DNA sequencers are becoming available and would vastly simplify reading DNA-encoded information." Hand-held? You mean your smartphone might read and write documents in DNA? Why not? Well, if DNA is the ideal storage medium, how about using it for the Internet? In fact, "Bi-Fi: The Biological Internet" is in development at Stanford School of Medicine. (links provided at site) http://www.evolutionnews.org/2012/10/introducing_bi-064781.html Towards practical, high-capacity, low-maintenance information storage in synthesized DNA - January 2013 Excerpt: Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2?×?106 bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11875.html
Supplemental notes:
William Bialek - Professor Of Physics - Princeton University: Quote: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," ExPASy - Biochemical Pathways - interactive schematic http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl
etc.. etc..bornagain77
April 20, 2013
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WD400 #84: (...) it’s hard to imagine a worse to think about the operation of genomes that the lens of computer programming (well, I guess engineering would be worse, but still)
How do you know this?
The cumulative results show with piercing clarity that life is based on machines — machines made of molecules! Molecular machines haul cargo from one place in the cell to another along «highways» made of other molecules, while still others act as cables, ropes, and pulleys to hold the cell in shape. Machines turn cellular switches on and off, sometimes killing the cell or causing it to grow. Behe, p.4, Darwin's Black Box.
Box
April 20, 2013
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WD400: Could you enlighten us as to the exact nature of the observed evidence that decisively shows the origin of life by spontaneous physics and chemistry i some warm little pond, then shows the formation of major body plans (the several dozens of them) by incremental branching,t hen shows onward the detailed diversification into the claimed tree of life? Failing such, you are papering over a major set of gaps and are denying or dismissing without adequate evidence, the professional summary by expert sources that the dominant feature of the fossil record is that it is one of suddenness in appearance, stasis of basic form, and disappearance rather than OBSERVED incremental transformation into novel forms. Were the incrementalist branching account true, the record should rather be one dominated by transitionals, which just is not so. I suggest a cf. here on. KFkairosfocus
April 20, 2013
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If we want to have some grasp of how biological novelty can come about, we’d be a lot better off understanding programming, systems design (switches, relays, distributed networks), engineering and the like, than spending our time imagining how particles bumping into each other over time can result in biological novelty. We should study biology to understand biology, and if we can borrow from other fields we should. But we shouldn't make metaphors our masters. I'm a computer programmer, it's hard to imagine a worse to think about the operation of genomes that the lens of computer programming (well, I guess engineering would be worse, but still)wd400
April 19, 2013
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Well, that’s a pretty convenient story isn’t it? Have you ever been willing to stop and ask whether the intermediates aren’t forthcoming because they in fact don’t exist? You mistook me. There will be (and are) intermediate fossils. What I mean is if you are looking only at the tips of trees, then evolution creates gaps. ID types (presumably) laugh at creationists when the talk about evolution requiring a croco-duck, why didn't you laugh at Axe and Gauger when they tried to make a protein croco-duck?wd400
April 19, 2013
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And by the way:
I’d make the point that to really understand those fields [biological novelty] you have to get one of the central themes of macroevolution – that the branching nature of evolution means it is fundamentally a gap-forming process (once lineages split they evolve apart, and intermediate forms are lost to us).
is simply not correct. Holding to the (highly questionable and thoroughly anti-Darwinian) idea that we shouldn't expect to see the intermediate forms that show the slow, slight, successive building blocks of biological novelty certainly doesn't tell us anything about how biological novelty actually arises. If we want to have some grasp of how biological novelty can come about, we'd be a lot better off understanding programming, systems design (switches, relays, distributed networks), engineering and the like, than spending our time imagining how particles bumping into each other over time can result in biological novelty.Eric Anderson
April 19, 2013
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wd400 @79:
. . . the branching nature of evolution means it is fundamentally a gap-forming process (once lineages split they evolve apart, and intermediate forms are lost to us).
Well, that's a pretty convenient story isn't it? Have you ever been willing to stop and ask whether the intermediates aren't forthcoming because they in fact don't exist? First Darwin told us that the number of intermediates should be "innumerable" and we just needed more time to search the fossil record. When, after decades of diligent search, the fossil record didn't comply, we were told that the fossil record couldn't be trusted because all those soft bodies wouldn't be preserved. Then a bunch of soft bodies were found, but still didn't fit into the slight-successive-changes model. So Gould and Eldridge came up with the brilliant idea that we shouldn't expect to see intermediates because evolution (of that kind anyway) is always happening somewhere just out of sight. wd400 goes one final step and claims that the whole process of evolution is gap-forming and intermediates aren't to be expected. Darwin recognized and acknowledged that his theory would collapse if large numbers of intermediates weren't found. At this point we can pretty safely say that Darwin's idea of slight successive changes has been falsified in the fossil record. "But wait!" comes the cry. "We shouldn't expect to see any intermediates. Evolution creates gaps, not continuities; and in any event, the interesting stuff in the play of life always happens off stage where we can't see it." The thoughtful skeptic asks: "Where is the evidence for all the alleged changes? We don't see it." The evolutionist responds: "Of course not. That is exactly what our theory predicts -- the evidence will be lost to us. So the fact that we don't have any evidence is exactly what we predicted and supports our theory!" Pardon me while the laughter subsides for a moment. OK, I've composed myself. Let's move to the next item . . .
But, for instance, Gauger and Axe either don’t understand evolutionary biology or willfully ignore it when they write their papers.
Not sure exactly what you are referring to here, but hopefully you are not referring to things like Elizabeth Liddle's made-up, biologically-naive, engineering-free a priori assumption of a smooth easily traversable fitness landscape. We've already discussed that here on another thread. Alternatively, if you're concerned with the fact that they are focusing on specific mutations toward a particular gene, that isn't a useful criticism either. But maybe there is something else. What have they written that belies a fundamental misunderstanding of evolutionary biology? BA77 has already addressed your misrepresentation of Behe's position, so I won't add to that point.Eric Anderson
April 19, 2013
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wd400 you state:
If you want to talk about of novelty then evo devo and genome evolution and protein evolution are the fields to dig into
How about we dig directly into the empirics wd400? Can you show me just one molecular machine that was arrived at by purely Darwinian processes?
"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 The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,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
of related note to the fact that Darwinists have ZERO empirical evidence of Darwinian processes EVER producing a molecular machine, here is an example that intelligence can do as such:
(Man-Made) DNA nanorobot – video https://vimeo.com/36880067
And since you can never back up your evolutionary fantasies with empirical evidence why do you, wd400, consider what you are dogmatically doing to be science instead of religiously motivated pseudo-science? Though I take issue with much of what you said, since it is false as to solidly and 'scientifically' supporting your claims, to focus in on your one comment here since it most directly exposes you for the fraudulent person you are,,,
Like wise Behe’s mangling of the Durret & Schmid “waiting time” papers doesn’t paint him in a great light.
Yet Dr. Behe responded as such,,
Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461
Please tell me wd400, in which other modern scientific area are mathematical models allowed to outweigh what the empirical evidence actually says when it conflicts with observational evidence? In any other field the mathematical theory would be scrapped!
“On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003) Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013 Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated? https://uncommondescent.com/intelligent-design/macroevolution-microevolution-and-chemistry-the-devil-is-in-the-details/
bornagain77
April 19, 2013
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If you want to talk about of novelty then evo devo and genome evolution and protein evolution are the fields to dig into ('evolutionary novelty' and, probably more importantly, 'expatation' are the key terms). I'd make the point that to really understand those fields you have to get one of the central themes of macroevolution - that the branching nature of evolution means it is fundamentally a gap-forming process (once lineages split they evolve apart, and intermediate forms are lost to us). As for the relatice sophistication of your garden variety creationists and prominent ID people. Sure, there's a differnce. But, for instance, Gauger and Axe either don't understand evolutionary biology or willfully ignore it when they write their papers.. Like wise Behe's mangling of the Durret & Schmid "waiting time" papers doesn't paint him in a great light.wd400
April 19, 2013
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Is not a number of small steps equivalent to one great leap, both may take you a great distance, from A to B whatever A and B amy be? Even the small steps of atomic clocks take us throught one year to the next...Cabal
April 19, 2013
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Alan, that is nice and vague and totally useless.Joe
April 19, 2013
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For biologists, then, the microevolution/macroevolution distinction is a matter of scale of analysis, and not some ill-defined level of evolutionary “newness.” Studies that examine evolution at a coarse scale of analysis are also macroevolutionary studies, because they are typically looking at multiple species – separate branches on the evolutionary tree. Evolution within a single twig on the tree, by contrast, is microevolution.
From hereAlan Fox
April 19, 2013
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