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Michael Behe on the Witness Stand

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.

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106 Responses to Michael Behe on the Witness Stand

  1. The judge and plaintiffs lawyers equivocated evolution with blind watchmaker evolution.

    It was very telling that the pro-ID lawyers did NOT object when this stunt was pulled- and that tells me theye didn’t know what ID is arguing against.

  2. Re:

    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.

    A rhetorical/propaganda stunt that should have been ruled out of order by the judge.

    KF

  3. as to:

    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.

    Yet,,, In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparitive Immunology, where he realized that the papers being published were comparative studies that had nothing to do with the actual evolution of the immune system at all (i.e. begging the question).

    What Does Evolution Have to Do With Immunology? Not Much – April 2011
    http://intelligentdesign.podom.....9_03-07_00

    Earlier Dr. Ewert related how the ‘literature dump’ on immunology at Dover was in fact a deceptive tactic on the Darwinists part

    “A Masterful Feat of Courtroom Deception”: Immunologist Donald Ewert on Dover Trial – audio
    http://intelligentdesign.podom.....1_03-08_00

    The immune system is now found to be far more complex than at first realized,,, Irreducible complexity meets multifunctionality:

    Immune system molecule with hidden talents – January 22, 2013
    Excerpt: The human immune system is made up of some half a dozen different cell types that are all working in tandem. Team work is key since each cell type has a single unique job to perform, which is central to its ability to help defend the body against invaders and ward off disease. If one of these players is taken out of commission, the entire system is thrown out of whack.,,,
    “We had no idea that B cells and dendritic cells use immunoglobulins to communicate with each other. It just goes to show you how complex the immune system really is and how we are a long way from truly grasping the full scope of its complexity,”
    http://medicalxpress.com/news/.....lents.html

    Of related note: Immunity bacteria are shown to be species specific (Regardless of the surprising result, Darwinists still insist evolution did it.)

    Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone – ScienceDaily (June 21, 2012)
    Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. “I was very surprised to see that,” Chung said. “Naturally, I would have expected more of a half-way response.”
    http://www.sciencedaily.com/re.....130643.htm

    As well, the deception (literature dump/bluff), from Darwinists at Dover did not stop with immunology (nor with the plagiarism of Judge Jones opinion from the ACLU’s legal brief);

    The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information – Casey Luskin – March 2010
    http://www.discovery.org/a/14251

  4. I was banned here once for criticizing Bill Dembski’s reply to a student who challenged him at a presentation at some college. She challenged Dembski by saying Darwin showed this and that in his research and what he showed was obvious. Dembski did not address her specific questions by given Darwin his due but tried to just defend the ID hypothesis. He instead should have responded to her by saying that she was missing the point. Darwin’s ideas while very insightful were very limited. Darwin’s failure was not that he discovered a bogus process but that he oversold the process.

    In other words the ID community has failed to address the actual problem in some very visual forums. The Dover trial was a case in point. 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. If it becomes part of the ID genetic make-up, they will have the upper hand. But instead they end up defending what are often vague positions.

    It flows from an almost pathological resistance to the issue by some which says I will not give Darwin or any evolutionary processes any credence. It is one of the things I found on this forum when I first started commenting here 7 years ago. It ends up making those who take this tact look anti science and misguided or just plain stupid. And who wants to listen to such people.

  5. 5

    I recommend you try these arguments in the next court case. Waving one’s hand to dismiss scientific literature on exactly the question at hand with excuses, attempts to change the subject, and mischaracterizations of the literature will certainly work for sure next time!

    And, the evolutionary origin of the vertebrate immune system, which was brought up by Behe himself, for goodness’s sake! You can’t just go say ID is not about the immune system, but instead about the origin of life and the Cambrian explosion.

  6. I wonder how this news would have been recieved. Surely it flies in the face of what ‘evolution’ is supposed to do?

    Yes … no?

    Excert:

    A diminutive species of human whose remains were found on the Indonesian island of Flores could have shrunk as a result of island dwarfism as it adapted to its environment.

    A study of the remains of the creature, nicknamed the “hobbit”, shows that it is possible for it to have been a dwarf version of an early human species.

    For more see link below :)

    http://www.bbc.co.uk/news/scie.....t-22166736

  7. DennisJones:

    “. . . the collective whole of the papers published gives us a picture of how the immune system evolved.”

    Really? Or do they instead give us comparative genomics, handwaving stories, guesses, and suppositions?

    —–

    jerry:

    I disagree. 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.

    —–

    Nick,

    You know that the courtroom theatrics and arguments — in which you were likely involved — were just that. Stacking up a bunch of books and papers does not constitute a refutation of anything Behe said; it doesn’t matter who brought up the topic. You are famous here for your literature bluffs. The courtroom theatrics were just another literature bluff.

    Unfortunately, the trial was presided over by someone who didn’t know what he was doing and who, unfortunately, swallowed hook, line and sinker your (the NCSE’s) flawed memo and reasoning to put together his opinion. Which, ironically, which was discovered using intelligent design principles. :)

  8. “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.”

    I’ve read both of Behe’s books and a book by Broom and listened to several of Berlinski’s talks on video. Where did you EVER get the idea that Intelligent Design is ONLY about “the outset of life” or “the Cambrian Explosion”??

    Specifically, in “Edge of Evolution”, Behe argues that there must have been AT LEAST 4 SEPARATE interventions into life on Earth because random mutation is incapable of producing the huge leaps of complexity that appear between single celled and multi-celled life or between birds and mammals.

    So the Designer didn’t simply employ some panspermian seeding to get life STARTED on Earth. The Designer has contnued tinkering with life on Earth over a period of several hundred million years. And the fact of that continued tinkering is an important and intriguing as the fact that Neo-Darwinism cannot explain the original rise of life from mere chemicals.

  9. Eric,

    I am going to have to disagree with you. I have not seen any places where the approach I recommend has been taken by the ID community and when it does it is subtle not straightforward. Certainly not here though I have not been around much in recent years or followed the ID discussion very much recently but reading a few comments recently it seems that nothing has changed.

    I have no idea how much change that selection or other naturalistic approach can explain in the biological world but it definitely explains some if not a fair amount. That should be a given in any discussion involving ID just to get it out of the way.

    If ID is not going to address the incredible bio-diversity on the planet then its message will get lost except amongst the few who examine it in detail. ID lost a chance to educate the judge and the public at Dover. As far as I can see ID is still doing that.

    Look at Matzke’s response. It is a childish one which indicates he does not really have anything worthwhile to defend his position but he somehow thinks it will work, not here but in the world. Because out in the real world this tactic works and ID let’s it work.

  10. jerry #4: In other words the ID community has failed to address the actual problem in some very visual forums. The Dover trial was a case in point. 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.

    What exactly are you proposing above as to how the present lifeforms came to be?

    Take a female elephant and trace back to her mother, to her mother’s mother,… Are you saying that there was some farthest ‘mother’, which was similar to elephant, within the presumed limits of ‘micro-evolutionary process’ (whatever exactly that means to you)? But then what did that farthest mother ‘elephant’ come from? Did she just materialize out of nothing as ‘approximate elephant’ (whatever that means in terms of your ‘limits of micro-evolution’)? Or did something shape it out of dust or mud? Or was she born of some other mother?… Or how exactly did that farthest mother elephant come into being according to your ‘scientific theory’ proposal?

    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.

    Such ‘part time ID’ position is as untenable as would be taking a copy of the paper map of Florida that has a pencil hole and declaring that there this means there is a sinkhole in Florida at the corresponding location.

  11. Unfortunately, in the real world, sound arguments and logic have little to no significant effect. Rhetoric and intimidation is generally what wins the day.

  12. Nick Matzke:

    I recommend you try these arguments in the next court case.

    Seeing that the next case will most likely include the fact that ID is NOT anti-evolution, I will be using those arguments in the next court case.

    Waving one’s hand to dismiss scientific literature on exactly the question at hand with excuses, attempts to change the subject, and mischaracterizations of the literature will certainly work for sure next time!

    Except that diatribe isn’t scientific by any definition of the word. Science requires testing and right now there isn’t any way to test unguided/ blind watchmaker evolution.

    And, the evolutionary origin of the vertebrate immune system, which was brought up by Behe himself, for goodness’s sake!

    No Nick. Behe brought up the DARWINIAN origin of the vertebrate immune system- meaning what bluind and undirected chemical processes produced it. And the literature doesn’t cover that.

    You can’t just go say ID is not about the immune system, but instead about the origin of life and the Cambrian explosion.

    Sure we can, Nick. Ya see HOW life originated directly impacts HOW it evolved. OoL = design then evolution occurred by design, as in organisms were designed to evolve and evolved by design. No room for the blind watchmaker except when it comes to breaking and deteriorating.

    Ya see Nick, YOUR position cannot handle the truth.

    Can’t wait to see you in court cupcake…

  13. I think another thing to keep in mind is that Design theory is not perfect. Like all scientific theories, they all have their problems. And even if Behe was wrong, and the articles presented about immune system evolution were good science, then maybe the predication was incorrect. Just like evolution, where predictions are incorrect all the time, we still see that to be labeled “good science”. I see the word “surprise” a lot more in evolutionary literature than I see it in ID literature. It seems that ID, though it does have holes here and there, seems less surprised by life than Darwinism.

  14. What exactly are you proposing above as to how the present lifeforms came to be?

    They were intelligently designed.

    But then what did that farthest mother ‘elephant’ come from?

    From intelligence.

    Now if you want to know how intelligence created it, or when, or why, then I can explain that to you, but it would have to be on another blog or something, because those are not scientific questions, and we only talk about science here.

  15. NickMatzke_UD #5: You can’t just go say ID is not about the immune system, but instead about the origin of life and the Cambrian explosion.

    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).

    For example, say you offer a theory NM_UD that declares among others:

    … x*x > 10 for all integers x.

    To invalidate NM_UD, it suffices to show an integer x, such as x=3, for which this NM_UD statement is false. That’s a falsification by counterexample. Whether there are some integers x for which x*x>10 holds, or whether NM_UD has some other statements which are valid, is irrelevant regarding the established fact that NM_UD is a falsified theory.

    There is also no logical or scientific requirement that a falsification by counterexample must also provide an alternative theory that explains the phenomena that NM_UD sought to explain in order to declare NM_UD a falsified theory.

  16. #14 lastyearon: From intelligence.

    Now if you want to know how intelligence created it, or when, or why, then I can explain that to you, but it would have to be on another blog or something, because those are not scientific questions, and we only talk about science here.

    But “jerry” was claiming that his proposal was supposed to be a scientific proposal that could have been defended in court as such. My objection, which your statement obviously agrees with, is that his proposal is not tenable as a scientific position.

    Whether that position makes sense or not outside of that context is another subject, as you also seem to agree.

  17. 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.

  18. 18

    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.

  19. 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.

  20. 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/2.....44801.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/1067.....-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/2.....66921.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/2.....71121.html

  21. 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.

  22. 22

    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.

  23. 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.

  24. 24

    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.

  25. 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.

  26. 26

    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.

  27. 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. Thanks

  28. 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.

  29. 29

    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.

  30. 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.

  31. 31

    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. :)

  32. 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.

  33. 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/2.....n_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/.....O-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/.....O-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.
    http://www.uncommondescent.com.....rwin-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.or.....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/.....enome.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/re.....161406.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/w.....n_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.

  34. 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.

  35. 35

    BA77 @33, no problem. Thanks for another post rich in material to distract, fascinate and educate. :D

  36. 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?

  37. 37

    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.

  38. 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.

  39. 39

    @38, seconded. 8)

  40. 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.

  41. #40
    Some people miss the point entirely.

  42. 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?

  43. 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.

  44. 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!

    Andre

  45. 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!

  46. 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/re.....131725.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.....P020081118

    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.....m-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/.....93984.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/j.....11233.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/phy.....on-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.

  47. bornagain77:

    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.

    That has all changed thanks to evo-devo. Now it isn’t so much changing genotypes but the way the genotypes are used, especially during development. Same genes used in different ways is now the mechanism for macroevolutionary change – see Shubin “Your Inner Fish”.

  48. Eric,

    You are coming around to the position I was arguing here 6 years ago:

    http://www.uncommondescent.com.....ment-64266

    And continued to argue over the years. The evolution argument has always been about alleles and their origin. By pointing out that Darwinian processes (code word for naturalistic processes) are limited, you put the anti ID people in a box. The key is separating the two and clearly doing it.

  49. as to:

    That has all changed thanks to evo-devo.

    And yet:

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth – No Evidence For Body Plan Morphogenesis From Embryonic Mutations (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    http://www.evolutionnews.org/2.....45581.html

    Moreover:

    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/?.....plicing%2F

    The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    Humans, Chimpanzees and Monkeys Share DNA but Not Gene Regulatory Mechanisms – (Nov. 6, 2012)
    Excerpt: Dr. Gilad reported that up to 40% of the differences in the expression or activity patterns of genes between humans, chimpanzees and rhesus monkeys can be explained by regulatory mechanisms that determine whether and how a gene’s recipe for a protein is transcribed to the RNA molecule that carries the recipe instructions to the sites in cells where proteins are manufactured.,,,
    Dr. Gilad also determined that the epigenetics process known as histone modification also differs in the three species. The presence of histone marks during gene transcription indicates that the process is being prevented or modified. “These data allowed us to identify both conserved and species-specific enhancer and repressor regulatory elements, as well as characterize similarities and differences across species in transcription factor binding to these regulatory elements,” Dr. Gilad said.
    http://www.sciencedaily.com/re.....201124.htm

  50. Of note: More on “Complexity by Subtraction”: You Think They’re Kidding? They’re Not – April 18, 2013
    Bottom Line: Advocates of intelligent design can take heart at this paper. That scientists at the NSF-funded National Center for Evolutionary Synthesis would seriously entertain this absurd hypothesis is a sign of general desperation. Darwinists know what they’re up against, they recognize the power of the challenge posed by ID, and they have no rigorous answers.
    http://www.evolutionnews.org/2.....71241.html

  51. jerry @48:

    Except that “evolution” is in fact used to mean a great many things, including things that go far beyond change in allele frequency. Indeed, the primary rhetorical trick of the larger evolutionary storyline is to define evolution as “change over time” or “change in allele frequency” — which no-one disagrees with — and then piggyback on the evidence for those minor microevolutionary changes in an attempt to prove the larger materialist creation storyline, for which there isn’t good evidence.

    The better approach, rather than trying to go along with this definition of evolution is to point out that evolution has numerous meanings, ranging from the obvious and the well-supported to the outrageous and the wildly-speculative. And that, further, the whole enterprise is assumed to operate without any plan, purpose, or direction.

    The right answer when someone asks whether I believe in evolution is not “yes” or “no,” hoping that we are using the same definition. Rather, the correct response is: “Depends. What do you mean by evolution?”

  52. 52

    BA77 @50, I read that article this morning — amazing. The last paragraph hits the nail on the head.

  53. Hey Andre- Lizzie Liddle sez that if you use Google Scholar you will find the answers to your questions. And she really believes that, which I think is sad because she obviously hasn’t read any of the sources she sights. If she had she would see the questions are not answered.

    Heck one book she cites can’t even demonstrate bacteria can evolve into something other than bacteria. Yet it says something about the evolution of the heart from bacteria to man.

    So if you like a literature bluff, use google scholar but don’t read the references. For example the first two links in her lung link is about comparitve anatomy- not genetics nor even evo-devo. IOW not one word about mutations to what genes producing what result.

    Seriously laughable…

  54. footnote to post 49 ‘evolution by splicing’ link:

    ,,,Alternative splicing,,, may contribute to species differences – December 21, 2012
    Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,,
    The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. “Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus,” Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,,
    Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified;
    http://phys.org/news/2012-12-e.....wires.html

    Finding widely different ‘alternative splicing codes’ regulating ‘alternative splicing events’ of different species is devastating to neo-Darwinism because of neo-Darwinism’s inability to account for any changes of any fundamental code once it is in place. The reason why drastically different alternative splicing codes between different species is devastating to neo-Darwinian evolution is partly seen by understanding ‘Shannon Channel Capacity’:

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

    But the reason why this is so devastating to neo-Darwinian evolution is perhaps best understood by taking a look at what Richard Dawkins said about what would happen if one were to ‘randomly’ change the genetic code once it is in place:

    Venter vs. Dawkins on the Tree of Life – and Another Dawkins Whopper – March 2011
    Excerpt:,,, But first, let’s look at the reason Dawkins gives for why the code must be universal:
    “The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.” (2009, p. 409-10)
    OK. Keep Dawkins’ claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does “one or two” equal 23? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2.....44681.html

    Bottom line is that if any regulatory code, such as the alternative splicing code, is ‘randomly changed’ in part, it throws the entire code out of whack and will be ‘instantly catastrophic’, to use Richard Dawkins most appropriate words, thus rendering gradual change impossible. The entire code must be implemented ‘top down’ when the species is created:

    It is also interesting to remember how hard it was to crack the alternative splicing code for humans:

    Breakthrough: Second Genetic Code Revealed – May 2010
    Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,,,
    http://crev.info/content/break.....e_revealed

    Also of note

    “In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10].
    Donald E. Johnson – Programming of Life – pg.51 – 2010

    “Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source — from a mind or personal agent.” (Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).)

    “A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter. Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
    (The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

    Verse and music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.

    Kutless: Promise of a Lifetime – Live
    http://www.youtube.com/watch?v=2wgA93WQWKE

  55. 55

    BA77 @46, I’m finding lifepsy’s videos very helpful, and worth paying careful attention to, specifically the Research & Reflection on Evolution playlist. They generally warrant more than one viewing to absorb the material. I hope he continues to produce them.

  56. Yes Chance, I thought lifepsy did an excellent job on the videos. I asked kf to post one, or perhaps a few of them, to bring more attention to them but nothing ever came of it. They are gems in my book though!

  57. Andre @44

    Andre could you please give me a step by step account of your ancestry starting from 500 generations ago to the present day. If you can’t do that, should I doubt that you exist?

  58. 5for, I know you are being petty because you consider the alternative to naturalism unthinkable, but actually, in regards to your question, there is actually fairly good evidence tracing the ancestry of man back pretty far:

    Tracing your Ancestors through History – Paul James-Griffiths – video
    http://edinburghcreationgroup.org/video/1

    Moreover, at around the 6:00 minute mark of the preceding video, one finds that the first ‘advanced’ human civilization, (with the oldest archeological evidence of metallurgy, agriculture, wine making, etc…), flourished near, or at, the Ankara area,,,(The Ankara area is called Anatolia in the video). Moreover, the Ankara area is the ‘center of the surface of the earth’:

    The Center of the Earth by Henry Morris, Ph.D.
    Excerpt: The problem is basically to determine that point on the earth’s surface, the average distance from which to all other points on the earth’s land surfaces is a minimum. This point is defined as the earth’s geographical center.

    (1) Divide all the earth’s land areas into small, equal, unit areas.

    (2) Select one of these unit areas as a possible location of the earth’s center.

    (3) Measure the distance along the earth’s surface from this reference area to each of the other unit areas, all over the earth.

    (4) Add up all these distances and divide the total by the number of individual distances measured. The result is the average distance from the reference area to all the other unit areas around the world.

    (5) Repeat the entire process in steps (1) through (4) above for each one of all the other unit areas around the world.

    (6) Compare the “average distances” so calculated for all the different unit areas. The one for which the average distance turns out to be the smallest is the earth’s geographical center.

    Actually, the calculation becomes feasible only if it can be programmed on a high speed computer. To accomplish the latter requires a knowledge of spherical trigonometry, geodesy, calculus, and computer science. In addition, there must be available accurate data on the earth’s land and water areas, arranged in a grid network tied to latitude and longitude. With these factors present, the computation then becomes quite feasible.

    RESULTS
    ,,, The exact center of the earth, insofar as Mr. Woods’ calculations could determine, was found to be near Ankara, the present capital of Turkey, at latitude 39° and longitude 34°, on the same latitude as Mount Ararat and essentially the same longitude as Jerusalem.,,,
    http://www.icr.org/article/50/

    And although, because of his Young Earth Biblical view, Paul James-Griffiths did not give the dating of the area, the dating of the first ‘advanced’ human civilization, around that area, is dated to around 12,000 years before the present:

    Stone Age Temple May Be Birthplace of Civilization
    Excerpt: The elaborate temple at Gobelki Tepe in southeastern Turkey, near the Syrian border, is staggeringly ancient: 11,500 years old, from a time just before humans learned to farm grains and domesticate animals. According to the German archaeologist in charge of excavations at the site, it might be the birthplace of agriculture, of organized religion — of civilization itself.
    http://www.freerepublic.com/tag/gobeklitepe/index

    Now this is very interesting!,,, That the first archeological evidence for a ‘advanced’ human civilization, with metallurgy, wine making, agriculture, would be very near, or even at, the ‘geographic center of the earth’ is a very ‘spooky’ thing for modern science to find! Pondering all the many places where the beginning of advanced human civilization ‘could have’ happened, instead of where it actually ‘did happen’, should make any reasonable person scratch their head in wonder!

    Moreover, besides the 12,000 years before present starting point for the beginning of ‘advanced’ human civilization, there is now mounting evidence for global catastrophic flooding, or ‘megafloods’, 13,000 years before the present:

    Humanpast.net
    Excerpt: Worldwide, we know that the period of 14,000 to 13,000 years ago, which coincides with the peak of abundant monsoonal rains over India, was marked by violent oceanic flooding – in fact, the first of the three great episodes of global superfloods that dominated the meltdown of the Ice Age. The flooding was fed not merely by rain but by the cataclysmic synchronous collapse of large ice-masses on several different continents and by gigantic inundations of meltwater pouring down river systems into the oceans. (124)
    What happened, at around 13,000 years ago, was that the long period of uninterrupted warming that the world had just passed through (and that had greatly intensified, according to some studies, between 15,000 years ago and 13,000 years ago) was instantly brought to a halt – all at once, everywhere – by a global cold event known to palaeo climatologists as the ‘Younger Dryas’ or ‘Dryas III’. In many ways mysterious and unexplained, this was an almost unbelievably fast climatic reversion – from conditions that are calculated to have been warmer and wetter than today’s 13,000 years ago, to conditions that were colder and drier than those at the Last Glacial Maximum, not much more than a thousand years later. From that moment, around 12,800 years ago, it was as though an enchantment of ice had gripped the earth. In many areas that had been approaching terminal meltdown full glacial conditions were restored with breathtaking rapidity and all the gains that had been made since the LGM were simply stripped away…(124)
    A great, sudden extinction took place on the planet, perhaps as recently as 11,500 years ago (usually attributed to the end of that last ice age), in which hundreds of mammal and plant species disappeared from the face of the earth, driven into deep caverns and charred muck piles the world over. Modern science, with all its powers and prejudices, has been unable to adequately explain this event. (83)
    http://humanpast.net/environme.....ent11k.htm

  59. wd400,

    Have you seen the price of textbooks lately!?

    Someone is making money.

  60. Hi Andre,

    We have it on good authority that what you are describing is not macro-evolution.

    Anything involving chemical/bio-chemical changes is clearly NOT macro-evolution.

  61. Perhaps a review is in order.

    Nick arrived in a huff one day whining that his “field” was being misunderstood, misrepresented and denigrated.

    His “field”? Macro-Evolutionary Theory.

    So I wanted to educate myself. I wanted Prof Tour to educate himself. I wanted everyone at UD to educate themselves.

    So I ask Nick for the leading textbook in his “field” of Macro-Evolutionary Theory. Silence.

    So I ask Nick for any textbook in his “field” of Macro-Evolutionary Theory. Silence.

    Must be nice to be able to manufacture a “field” and then complain at will about people misunderstanding or misrepresenting it. (Sort of like “the field” of “Intelligent Design” eh?)

    Since there are no established text in Nick’s “field,” who can show him to be wrong when he makes his declarations?

    Whatever Nick’s engaged in, it isn’t science.

  62. Publishers certainly make a lot of money in text books. Authors not so much.

    In any case. Macroevolution is a field of study, but I don’t know of any texts devoted to it specifically. There texts on phylogeny, phylogenetic comparative methods, speciation, genome evolution and paleontology, which are parts of macroevolution (the field, not the creationist version of the word).

  63. wd400 @62:

    . . . which are parts of macroevolution (the field, not the creationist version of the word).

    Can you succinctly share with us what the real word “macroevolution” means and contrast that with the creationist word “macroevolution”?

    Thanks.

  64. BA77 @50:

    Regarding the “Complexity by Subtraction” article:

    Didn’t we just get through discussing on another thread the “assume a can opener” fallacy? That is really what the authors are doing to try and “explain” the evolution of complex features. They start by saying “Assume a more complex structure . . .”

    In fairness, there are probably lots of examples in nature in which a complex structure got broken, fell out of use, etc. and ended up as a simpler structure. But in that case it would be “Simplicity by Subtraction” wouldn’t it? I’m struggling to understand how a complex structure can become more complex by removing parts . . .

  65. 65

    nightlight @32,

    “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.”

    I think I understand what you’re getting at, if the intelligent agency you’re referring to is the one presumed to have created life and the universe of law-like regularities.

    Contingency can be understood to be that which is logically neither impossible nor necessary. Discrete arrangements of matter qualify here, as long as the matter is inert with respect to its arrangement. Stephen Meyer uses magnetic letters as an example. They stick to a metal surface by necessity, but their ordering is contingent. In this regard contingency can be partitioned between random and specified. Random arrangements carry no definite meaning beyond the individual letters themselves, while specification conveys a message (all valid messages in a given language constitute a small subset of meaningful arrangements out of all the possible permutations). Randomness, with regard to uniform distribution, is destructive to specification, and specification destroys randomness. In this regard, the two are essentially mutually exclusive when fully expressed — imposing a random distribution of letters upon a message will destroy the message, and imposing a meaningful message atop a random distribution will destroy the random distribution.

    The nature of randomness is a bit enigmatic, but it’s rules are straightforward. I’ll use a discrete example. For a set of elements S with cardinality n, a uniformly random selection of N elements from the set will approach an even distribution of the elements s1, s2, …, sn as N gets very large. This is just another way of saying that, for example, if one rolls a fair die then after a very large number of trials the occurrence of ones will approach the same count as the occurrence of twos, and of threes, fours, and so on. The more trials, the more alike the counts will be in proportion to the total number of trials.

    With regard to the nature of randomness, we can consider both epistemological and ontological forms. Epistemological chance has to do with our ignorance of events, where a combination of deterministic factors influence the outcome of an event, but are too numerous or too unpredictable to account for. The outcome of a die roll is essentially an occurrence of epistemological chance. Physics can account for the outcome, so it’s basically deterministic, but it’s practically impossible to predict the result of a fair roll. Ontological chance — which only arguably exists — would be causal and nondeterministic, unaccountable to prior physical conditions. The location of an electron with regard to an atom could arguably be considered an example of ontological chance.

    But regardless of the nature of randomenss — epistemological or ontological — it has an important property, at least in the discrete case: the uniform distribution of all elements in a set. Even for most non-uniform distributions, the result will approach the expected value as the number of trials gets large.

    With all that in mind, it’s not logically impossible for intelligence to either: a) influence the outcomes of random events to some degree; or b) simulate random outcomes. For the latter, pseudo-random number generators are common and can even be cryptographically secure depending on how the seed is chosen. For the former, influencing random events toward a goal will destroy the random distribution. This is the crux of the problem with positing intelligent guidance through random events. While small and infrequent influences may not be measurable and hence not detectable, the attempt to arrive at specification through the influence of random events will, by necessity, make the result non-random.

    (Incidentally, necessity has a destructive relationship with contingency. The full expression of one is destructive to the other.)

    For an example of how a random outcome might be altered without upsetting the distributions, consider the game of craps. If one were to roll 7, 8, 6, and 8, the outcome is significantly different from 6, 8, 8 and 7. The first series of rolls wins twice, the second series loses; but the distribution remains undisturbed. A being with the requisite abilities could alter the order of outcomes in his favor without upsetting the distribution, as long as the influences were slight and relatively infrequent.

    So if you’re suggesting that certain types of random events are guided, that may well be the case; but with only minor exceptions — slight and infrequent influences — random events must actually be random or they no longer fit the definition. A thing cannot be both specified and random, unless it’s actually specified to be random, as in the case of pseudo-random number generators. For this reason it’s difficult to account for guidance through random factors for highly specified results, because specified results are entirely non-random.

    Perhaps you have something else in mind, but it should be noted that only discrete intervention, either up front or over time, seems to allow a designing agent to produce a specific result; neither necessity nor randomness can be used to build certain types of highly specified systems, because the sort of specificity that produces complex and integrated functional systems through digital codes processed by mechanical systems appears completely incompatible with chance and necessity.

  66. 66

    Chance @ 65: “consider the game of craps. If one were to roll 7, 8, 6, and 8, the outcome is significantly different from 6, 8, 8 and 7. The first series of rolls wins twice, the second series loses”

    Hmmm. In the first series the 7 comes first, which is win, and then the point is set at 8 on the next roll and hit on the 4th roll. Two wins. You are correct.

    In the second series the first 6 means nothing. The point is then set at 8 and hit on the next roll for a win. Then the 7 hits for another win. Two wins.

    Your larger point is obviously true. The same numbers rolled in craps can have radically different outcomes. Your example needs work.

  67. EA: “I’m struggling to understand how a complex structure can become more complex by removing parts . . .”

    Eric, don’t ya know, you just to accept that kind of stuff on faith and call anyone who doubts you anti-science :) That’s just how science is done nowadays!

  68. mung

    Since there are no established text in Nick’s “field,” who can show him to be wrong when he makes his declarations?

    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 (based on the citations provided for mung)?

  69. 69

    Barry @66, Thanks for the comment. I could be mistaken, but I think that in the second series the point is set at 6, then 8 and 8 do nothing, and 7 loses. It’s been a while since I played though. :)

  70. 70

    Eric @64, they’re doing SCIENCE man! Evolution can proceed by either starting simple and building to complexity, or starting very complex and then winnowing down to “streamlined”.

    Indeed, what is favored is streamlined simplicity. If functional structures are complex, it may be in part because they start that way, because initial complexity is easy.

    Since we all know that initial complexity is easy, and is bound to be at least minimally functional, then letting complexity run downhill from there is a given.

    “there is no reason to think that their initial state — characterized by high levels of differentiation — is more than minimally functional.”

    More on “Complexity by Subtraction”: You Think They’re Kidding? They’re Not

    Please note that this is science, not irreducible complexity.

    :P

  71. Can you succinctly share with us what the real word “macroevolution” means and contrast that with the creationist word “macroevolution”?

    The simplest meaning is the study of how evolution works among, and not within, genepools.

    Tools like classical population genetics are very good at telling us about, say, changing allele frequencies and the dynamics of mutations within populations. But when we want to study the results of those processes on broader (or deeper) scales we use other tools (phylogeny, statistical model etc etc). The distinction in “macroevolution” is really a methodological one.

  72. wd400 @71:

    Thanks. By gene pool, I presume you are referring to a population made up of those individuals that can freely inter-mate. Not 100% tight in terms of definition, but fair enough. This is also similar to many proposed definitions of species. So we can refer to gene pool or species and someone might quibble about which is the best definition/approach, but on the continuum of evolutionary change, in common vernacular we are somewhere near the species level.

    I haven’t done a scientific survey, but my impression is that change beyond the species level is in fact what most people are referring to when they use the word “macroevolution,” so I’m still a little unclear on what other creationist definition you think is being used. It seems that most people, regardless of persuasion, are referring to changes beyond the species level, although, again, we might quibble over how to pin that down.

    I’m wondering, though, if you are trying to draw a strict distinction between what happens within a gene pool and what happens outside, without reference to the magnitude of change.

    For example, if, within a single gene pool, a new phenotype arises that has, say, a functional eye where none was previously present, would you say this is an example of macroevolutionary change, or is it (by definition) microevolutionary change because it occurred within the same gene pool?

    Similar question on the other side of the coin. If only small changes happen among two different gene pools, say, just a change in beak size of two different birds that belong to two different gene pools, is that automatically macroevolution because it deals with a change outside of a single gene pool?

    It seems that “macroevolution” as typically used in the evolutionary literature (i) can refer to changes outside the species level, and (ii) it is generally thought that large morphological changes (eyes, lungs, wings, new body plans, etc.) constitute some of those kinds of changes that would be expected among different gene pools, rather than within a single gene pool. And the word is often used in either or both of those senses.

    Now we could, of course, take a strict approach to the word and confine it only to changes among gene pools without reference to the kinds of changes in question. But I don’t think the word has historically been that limited. And in any event, then we would just have to come up with a new word to describe the kinds of large phenotypic changes that we in fact see.

  73. 73

    RE: My #69, yes that seems correct. The series 6, 8, 8, 7 results in a loss. The first roll is 6, so that establishes the point. The two successive rolls of 8 do nothing, and then 7 ends the run in a loss. This assumes the bet is on the pass line, where an initial roll of 7 or 11 wins but 2, 3, or 12 loses. Any other number establishes the point, which must be rolled again before 7 comes up.

  74. It seems that most people, regardless of persuasion, are referring to changes beyond the species level, although, again, we might quibble over how to pin that dowm

    Macroevolution is about a lot more than that. The point I’m trying to make is that macroevolutoin is what happens when you have a lot of microevolution in separated gene pools(so changes in one don’t effect the other). It just happens that the best way to study, say, changes in extinction rate or the correlation between body size and brain-size, isn’t to use the tools used to study evolution at the finest grain (just like you don’t use quantum mechanics to build bridges).

    So macroevolution is a field of study, using many different techniques to study patterns and processes of evolution above the species level. As opossed to the creationist version, which, as far as I can tell is declaring “this thing is really complex so couldn’t evolve”.

  75. wd400:

    The point I’m trying to make is that macroevolutoin is what happens when you have a lot of microevolution in separated gene pools(so changes in one don’t effect the other).

    Yes, microevolution writ large . . .

    But that still doesn’t address any significant novelty in biology. How microevolution stacks up over time to get things like hearts, lungs, eyes, new genera, families, orders, body plans and so on, is very much a part of the question. Just vaguely referring to “microevolution in separated gene pools” doesn’t address any issues of biological novelty. And for the moment, whether there are alleged explanations for biological novelty somewhere out there in the literature is a separate issue. Right now we’re just trying to pin down a definition.

    You seem to be taking the position that macroevolution is neither a process nor a result, but a field of study. So are you suggesting that novel phenotypic structures are not examples of macroevolution?

    What, then, shall we call them?

    And is microevolution the same thing — a field of study?

    —–

    And, by the way, I am sure there are some people who haven’t thought a lot about the issues and reflexively say something like “this is really complex so it couldn’t evolve.” Certainly their intuition is leading them in the right direction. But presumably you also know that no prominent ID proponent, nor most of the people on this blog, take that position, so questions here about macroevolution are not based on any such definition.

  76. wd400:

    The point I’m trying to make is that macroevolutoin is what happens when you have a lot of microevolution in separated gene pools(so changes in one don’t effect the other).

    That’s the propaganda anyway. Do you have any real world examples? Finch beak variation = micro-evolution. How can that lead to macro? Anti-biotic resistance comes from a loss of function- how is that going to lead to macro?

  77. 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 here

  78. Alan, that is nice and vague and totally useless.

  79. 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…

  80. 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.

  81. 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?
    http://www.uncommondescent.com.....e-details/

  82. 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.

  83. 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.

  84. 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?

  85. 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)

  86. 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. KF

  87. 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.

  88. 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/educ.....ucation.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/c.....2-2-29.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/tec.....rs/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/2.....62961.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/2.....64781.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/j.....11875.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/.....mbnails.pl

    etc.. etc..

  89. 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?

  90. 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?

  91. 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/20.....n5887.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/20.....n5756.html

    Note in particular, the fossil record statements.

  92. 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.

  93. 93

    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.

  94. 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?

  95. 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?

  96. 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-co.....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/...../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/2009/1.....ple-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.....ne.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/?.....plicing%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/

  97. 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.

  98. 98

    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.

  99. 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.

  100. 100

    Stephen, that might be exactly what I’m looking for. Thanks.

  101. 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.

  102. 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.

  103. mung, you are correct. I did not supply any reference(s).

    Did Nick?

  104. mung: Did Nick?

    Why are you asking? Is Nick the only individual who can supply references that will be accepted by you?

  105. frankin on the witness stand:

    No thanks. I’d have to perjure myself.

  106. 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?

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