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Stephen Meyer’s Book Ranked #1 in Science/Physics/Cosmology at Amazon

Over at Amazon in the Physics/Cosmology section, Dr. Meyer’s book got the surprise ranking ahead of Stephen Hawking’s book, A Brief History in Time.

There is a section on cosmology and the origin of life in Signature in the Cell.

Here are the Amazon Stats:

Signature in the Cell: DNA and the Evidence for Intelligent Design
Hardcover: 624 pages
Publisher: HarperOne (June 23, 2009)

Amazon.com Sales Rank: #799 in Books (See Bestsellers in Books)

Popular in these categories:

#1 in Books > Science > Astronomy > Cosmology
#1 in Books > Religion & Spirituality > Christianity > Theology > Creationism
#1 in Books > Science > Physics > Cosmology

Congratulations Dr. Meyer!

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246 Responses to Stephen Meyer’s Book Ranked #1 in Science/Physics/Cosmology at Amazon

  1. Congratulations Dr. Meyer!

  2. After great works from Behe, Dembski and now Meyer, I think it is a good time for nay-sayers to put away their hyper-skepticism. It’s a waste of precious time. It’ll only get in the way of them understanding what the physical realm is all about.

    If you deny design, then you cannot understand nor accept the intuition that humanity (as a designed and intelligent organism) has the wherewithall RIGHT NOW to understand what its about. They will tell us that ‘we will figure it out one day in the distant future’.

    The fact is when accept design and the existence of a designer, you short-circuit that long wait and can begin to understand it that much faster.

    It is a wonder skeptics don’t understand this simple intuition. The great scientists of the past few centuries understood this point well. Skepticism is just a drag on understanding.

    …Silence is the energy of understanding and humility its engine.

  3. Mr Cordova,

    I admire your honesty in showing that the book also ranks #1 in Creationism. Ah, the wisdom of crowds…

  4. Nakashima,

    Indeed, the wisdom of scientific crowds said

    1) 200 years Dino-Bird theory is correct
    2) Darwin’s TOL is correct
    3) Gradualism is correct
    4) JunkDNA is correct

    Yet this house of cards of scientific consensus thinking is falling and flailing.

    Smiles, how many transitional fossils are there these days Mr. Nakashima?

  5. DATCG,

    1) 200 years Dino-Bird theory is correct

    what is your evidence that this theory has been falsified?

  6. Kudos to Dr. Meyers. Perseverance in spite of the hatred, vitriol, bigotry and small-minded scientific “crowds” that acted like fascist towards him and Dr. Sternberg in the past.

    But I guess that is OK for some people in science who would rather a dogmatic orthodoxy reign supreme instead of genuine and open debate.

  7. Khan,

    There isn’t any genetic evidence to support the transformation- dino to bird.

    Does anyone even know what it takes to get the femur to remain fixed

    Birds have a fixed femur that allows them to breathe.

    Dinos didn’t have that.

  8. Congrats to Dr Meyer!!!

    Even though I disagree with the premise that the genetic information is the sequence his work may help others make the connection to at least the possibility that the real information resides on/ in the structures inside the cell and the sequence specificity is only required to carry out the instructions.

    IOW just as the information on a computer disc is not reducible to the molecules which make it up, neither is the information in living organisms reducible to any molecular sequence.

  9. Khan,

    What is your evidence that such a transition ever was correct, besides massive speculation and large fanfare media annoucements like that of Ida?

    National Geographic? Discovery Channel? These are largely propaganda mouthpieces for Darwinian zealots.

    Unfortunately after the hoopla is over, real scientist study the evidence and find that the claims made by the Darwinian zealots are much ado about darwinian orthodoxy and not about science.

    I’ll start with the most recent study from a secular institution: Oregon State. Dr. Ruben poured light onto the different anatomy of dino and birds recently in published work in Journal of Morphology.

    Science Daily Doubts on Dino-Bird theory

    This issues he raises have been serious problems since the beginning. There is nothing intuitive about dinosaurs sprouting wings and “sailing into the sunset”

    Fairy tales on TV never made it so, yet it was promoted as truth and fact on TV, in museums and in textbooks.

    “Frankly, there’s a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions.” Ruben said.

    more from the link:

    “This is fundamental to bird physiology,” said Devon Quick, an OSU instructor of zoology who completed this work as part of her doctoral studies. “It’s really strange that no one realized this before. The position of the thigh bone and muscles in birds is critical to their lung function, which in turn is what gives them enough lung capacity for flight.”

    However, every other animal that has walked on land, the scientists said, has a moveable thigh bone that is involved in their motion – including humans, elephants, dogs, lizards and – in the ancient past – dinosaurs.

    The implication, the researchers said, is that birds almost certainly did not descend from theropod dinosaurs, such as tyrannosaurus or allosaurus. The findings add to a growing body of evidence in the past two decades that challenge some of the most widely-held beliefs about animal evolution.

    Fraudian slip? “Beliefs” So is it “science” to “believe” in Dino-Bird theory?

    “For one thing, birds are found earlier in the fossil record than the dinosaurs they are supposed to have descended from,” Ruben said. “That’s a pretty serious problem, and there are other inconsistencies with the bird-from-dinosaur theories.

    I’ve read where Creationist challenged this data as well, yet are still mocked by others. It appears all the mockers and scoffers have egg on their face.

    “But one of the primary reasons many scientists kept pointing to birds as having descended from dinosaurs was similarities in their lungs,” Ruben said. “However, theropod dinosaurs had a moving femur and therefore could not have had a lung that worked like that in birds. Their abdominal air sac, if they had one, would have collapsed. That undercuts a critical piece of supporting evidence for the dinosaur-bird link.

    Indeed, yet how long was this “intuitive believe” taught to the general public as “fact”?

  10. Joseph,

    Sorry we don’t have every last detail worked out. what’s your interpretation of this:

    http://machineslikeus.com/news.....-confirmed

  11. DATCG,

    i figured it was that one study. unfortunately (despite RUben’s claims), almost nobody was arguing that theropods had air sacs that functioned like birds. read this article:
    http://www.plosone.org/article.....ne.0003303

    so they are really tearing down a straw man. the protofeathers, feathers, furcula, hollow bones, incubation behavior etc of theropods, as well as genetic evidence (see above in response to Joseph) all point to theropods being ancestors of birds.

    as far as theropods appearing after birds, that’s false as well. theropods first show up in the fossil record in the triassic, birds in the jurassic.

    any other evidence you want to put forward?

  12. Khan,

    Here is more secular scientist fighting against Darwinian zealotry. A letter from Storrs L. Olson, Curator of Birds, Smithsonian, 1999 to National Museum of Natural History:

    With the publication of “Feathers for T. rex?” by Christopher P. Sloan in its November issue, National Geographic has reached an all-time low for engaging in sensationalistic, unsubstantiated, tabloid journalism.

    Surprise, surprise that Darwinian zealot media leaders would be involved in “sensationalistic, unsubstantiated, tabloid journalism” yet again and again.

    Question: Is National Geographis interested in skeptical commentary and presenting both sides?

    Prior to the publication of the article “Dinosaurs Take Wing” in the July 1998 National Geographic, Lou Mazzatenta, the photographer for Sloan’s article, invited me to the National Geographic Society to review his photographs of Chinese fossils and to comment on the slant being given to the story. At that time, I tried to interject the fact that strongly supported alternative viewpoints existed to what National Geographic intended to present, but it eventually became clear to me that National Geographic was not interested in anything other than the prevailing dogma that birds evolved from dinosaurs.

    Answer: NO!

    They could care less about the truth, only spearheading a dogmatic propaganda piece for their worldview. They refused to look at objective dissent. As a result, zealots at National Geographic have now been tar and feathered as zealots for a cause, not as an objective publication.

    Mr. Olson continues to shred the Dino-Bird theory, “feathered dinos” and zealotry of different “professional science” publications. Who are these great scientific journals of record?

    Lets see…

    The hype about feathered dinosaurs in the exhibit currently on display at the National Geographic Society is even worse, and makes the spurious claim that there is strong evidence that a wide variety of carnivorous dinosaurs had feathers. A model of the undisputed dinosaur Deinonychus and illustrations of baby tyrannosaurs are shown clad in feathers, all of which is simply imaginary and has no place outside of science fiction.

    The idea of feathered dinosaurs and the theropod origin of birds is being actively promulgated by a cadre of zealous scientists acting in concert with certain editors at Nature and National Geographic who themselves have become outspoken and highly biased proselytizers of the faith.

    Whoooa! “Proselytizers?” “…of the faiths?” Hahaha… is this “hyperbole” or the truth? I’d say Mr. Olson is onto the dirty truth that is false propaganda from supposedly untouchable scientific journals.

    He continues…

    Truth and careful scientific weighing of evidence have been among the first casualties in their program, which is now fast becoming one of the grander scientific hoaxes of our age—the paleontological equivalent of cold fusion.

    Indeed, truth fell long ago in science to an orthodox religion of Darwinism, where zealots rule and the public is not informed of the truth and facts because the zealots own the media that act as gatekeepers. Gatekeepers that withhold information and push out the false information of the faithful.

    If anyone should have books in “Creationism” today, its Darwinist like this. Science-Fiction Creationism of Darwinian Orthodoxy.

  13. Khan (con),
    It seems actually proving the generation of functional information in molecular biology doesn’t interest you,, it seems all that matters to you is to create enough obfuscation to keep your materialistic delusion semi-viable in your misguided mind!

    Dinosaur Feathers and Pink Unicorns
    http://www.tangle.com/view_vid.....37e698c6f2

    Another Strange Chinese Fossil Found: Dinosaur or Bird?
    Oct 22, 2008 ‘Feathers and wings are among the most distinguishing characteristics of birds. ‘Integumenary features’ have been found on some dinosaur fossils, and true feathers have been found on some strange-looking extinct birds. The news media often try to marry the two into a committed relationship using exaggerated artwork. They have been found imagining feathers on fossils where the data are dubious or even missing (09/29/2008, 06/13/2007). What makes a structure a true feather? When does it support linking an unknown species into an evolutionary relationship to birds?
    The latest case involves a strange fossil from China reported in Nature.1 Dated Middle to Late Jurassic in age, it is one of the earliest species to sport integumentary structures (see 10/06/2004, 10/12/2005), but it was nearly contemporary with early birds having true feathers. The media reports typically announce a ‘feathered dinosaur’ has been found (e.g., BBC News ‘New feathered dinosaur discovered’ and National Geographic ‘First Dinosaur Feathers for Show, Not for Flight?’) though some titles leave other interpretations open (e.g., Live Science, ‘Bird-Like Dinosaur Sported Bizarre Tail Feathers).
    Instead of allowing for the possibility that unrelated species had similarities, the articles often state matter-of-factly that birds evolved from dinosaurs. The BBC article was the most blatant in this regard, referring to the ‘critical transition from dinosaurs to birds’ and quoting a paleontologist at London’s Natural History Museum stating, ‘It provides fascinating evidence of evolutionary experiments with feathers that were going on before small dinosaurs finally took to the air and became birds.’
    The original paper did use the word feathers for the structures in the fossil of the new pigeon-sized creature from the Middle or Late Jurassic they named Epidexipteryx, but a closer look shows some findings that may not help the evolutionary scenario.
    1. None of the structures were pennate feathers, that is, with barbs and barbules from a central vane. The integumentary structures fell into two categories:
    1. ‘Shafted feathers’ Connected to the last ten tail vertebra were found two ‘membranous structures’ consisting of parallel shafts that each branch once. Each shaft has a thin unbranched vane of material, like a coating, along a central rachis. The result appears as four long nearly-parallel rods that join at the base. Collectively they are nearly as long as the skeleton of the creature. Mark Norell (American Museum of Natural History) commented, ‘These seem to lack that main shaft down the middle and are just a really long collection of very long, filamentous-like structures.’
    2. ‘Non-shafted feathers’ – These are rows of integument found outside the outline of skeleton, presumably from the skin. They all end in parallel rows of barbs, nothing like the cross-cutting structure of bird feathers; the BBC article calls it a ‘fluffy, down-like covering.’ The authors stated, ‘the free distal barbs of Epidexipteryx arise from the edge of a membranous structure (Fig. 2b, c, d, d’), an arrangement that has never previously been reported.’
    2. Some of the structures bear similarities to those on Jeholornis, a creature interpreted as being capable of powered flight (see 07/24/2002).
    3. The authors allowed for the possibility that this creature was ‘secondarily flightless’ i.e., that it once had feathers like a bird, but lost them; if so, it was not evolving from a dinosaur into a bird.
    4. The authors suggested that the feathers on Epidexipteryx were used for display, not for flight, but the LiveScience article hypothesized they ‘likely helped the creature balance on tree branches.
    5. The animal had a curious mosaic of traits. National Geographic remarked, Epidexipteryx’s anatomy seems to be a hodgepodge of features taken from a variety of animals.’ It seems to have been the ‘platypus’ of the Jurassic ‘ an improbable mixture of traits from different groups.
    6. Since the creature had a ‘surprising combination of physical features’ (BBC News), it should not be envisioned as a transitional form from one lineage to another. The BBC News article complicated the evolutionary story by stating, ‘The discovery adds yet more complexity to the early history of the era when small meat-eating bipedal dinosaurs evolved into birds.’ The evidence, therefore, makes the explanation more complex, not simpler, in contradiction to Occam’s Razor.
    7. The evolutionary date is too late to represent a pre-bird. The BBC article said, ‘whereas other feathered dinosaurs [sic] date from after the appearance of the first known bird, this fossil appears to be much closer in age, so it opens a new window on the evolutionary events at the critical transition from dinosaurs to birds.’ Live Science says that the dates are uncertain; at best it was ‘slightly older’ than Archaeopteryx. If it was nearly contemporaneous with a fully-feathered bird that was most likely capable of powered flight, it could not be a pre-bird, bird ancestor or missing link.
    8. The evolutionary link to birds is only inferential. Live Science quoted one of the authors saying, ‘Although this dinosaur cannot be the direct ancestor for birds, it is one of the dinosaurs that have the closest phylogenetic relationship to birds.’
    9. Mark Norell hinted that this fossil has more to say about diversity, not evolution. ‘Things more primitive than this have fully formed feathers’ he said. ‘This is just some weirdo kind of thing this animal has.

    The Live Science article elaborated on Mark Norell’s comments about diversity within groups:

    As scientists and others discover more and more dinosaur fossils with bird-like features, the picture of such creatures is becoming more complex, said Norell, who was not involved in the current study.
    ‘Just like the bird diversity we have living today goes all the way from hummingbirds to ostriches to toucans, it’s incredibly diverse,’ Norell said during a telephone interview. ‘Now we’re starting to see that sort of diversity extends not only in birds but also in the close bird relatives [which] were just as physically diverse as modern birds are.’

    To infer evolutionary relationships, scientists conduct two kinds of studies. One is the cladistic study, that measures the number of specific characteristics in a fossil or creature, like the angle of its pelvic bone or ratio of skull length to skull width, and scores it in relation to other similar creatures. The other, when possible, is the genetic study of DNA similarities and differences. Assuming that common descent is true, they produce phylogenetic diagrams of ancestral relationships based on degree of similarity. Norell’s comments suggest that among a highly diverse set of organisms, the possibility of subjective inferences to ancestry is high ‘ meaning that other inferences are legitimate, depending on which similarities are measured, and the relative weights assigned them by human minds. 1. Zhang et al, ‘ bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers,’ Nature 455, 1105-1108 (23 October 2008) | doi:10.1038/nature07447.

    The artists’ renditions go far beyond the evidence: they’ve put vibrant colors on the alleged feathers and given the creature a whole life and personality. The structures cannot be called feathers except by stretching the definition of the term. The tail structures look like long rods. The ‘down-like coating’ could be flayed skin, given that the creature was exceptionally well preserved. It may represent a mutant dodo-line of ancient birds that went extinct, or a member of a subclass of dinosaurs that shared the most similarities with birds without being related to them.
    Scientists should be very careful about making inferences about any complex set of data. The bones do not jump up and announce that they were evolving into birds. The supplementary data in the paper show nearly 300 traits that had to be compared to make a cladistic analysis. The significance of any one of them requires a human judgment. Which traits are you going to focus on? Humans share traits with this fossil, too: vertebrae, teeth, radius and ulna, and many organs not visible from the bones. It is conceivable that the scientists in another civilization might consider size, habitat, lifestyle or some other characteristic to be the overriding concern in their way of classifying things. What kind of inferences would they draw? Complexity, diversity and ‘mosaics’ of traits throw simplistic schemes into disarray. How would you rearrange your Evolutionary Tree of Tools if somebody handed you a Leatherman tool with a knife, screwdriver, pliers and scissors in a leather pouch?
    Even granting, for the sake of argument, the most generous leeway to the evolutionists and calling the structures on this thing feathers does not help their story. Other feathered birds were nearly contemporaries. If this was an ‘evolutionary dead end,’ where is the highway? A collection of dead ends may keep you busy, but is not going to get you anywhere.

  14. DATCG,
    thanks for the 10 year old letter to the editor. to return the favor, here are 4 peer-reviewed papers with empirical evidence for the bird-theropod link:

    http://findarticles.com/p/arti....._n9042561/

    http://www.sciencemag.org/cgi/...../5845/1721

    http://www.nature.com/nature/j.....02855.html

    http://www.sciencemag.org/cgi/.....6/5822/280

  15. BA^77
    I’ve already shown that you can generate functional proteins just by randomly stringing amino acids together. or are you moving the goalposts again?

  16. Khan,

    Thank you for 2008 Plos one paper that is unproven and still speculation.

    My first account was a 2009 paper in Journal of Morphology.

    I posted the other account to show you the history of propaganda and of hiding dissent.

    You would think such issues of hiding dissent would be important to you, but evidently not. Thanks for proving my point. You disregard one study in 2009 and you disregard dissent that is purposely not allowed in NG or Nature.

    Ignore this problem in science all you like.

    I showed you how the Darwinian zealotry and orthodox machine works. Disregard at your hearts content. Afterall, that letter was from a Curator at Smithsonian.

    Is this not important news to you?

  17. Mr DATCG,

    in re the 200 year old Dino-Bird theory, please lend me your time machine at your earliest opportunity! I assume you are commenting from the year 2061, the 200th anniversary of the discovery of the first Archeopteryx fossil.

  18. Mr Cordova,

    I admire your honesty in showing that the book also ranks #1 in Creationism. Ah, the wisdom of crowds…

    To put it more correctly, the creationist crowds are wising up. They are buying better literature!

    Creationism needs ID, creationists need to read more ID books.

    ID books need to be filling the shelves of creationists.

    I feel one of my immediate missions is to teach creationists about ID.

    One very very influential creationist left Darwinism because of an ID book by Michael Behe.

    I tell my fellow creationists, “buy ID books”.

    Most of my bookshelf is full of ID literature, only a fraction would be classified as creationist such as:

    1. “In the Beginning” by Walter Brown

    2. Evolution Possible or Impossible by James Coppedge

    I have Sarfati’s book only because someone gave them to me, and I haven’t read it (I find his style too polemic and pontificating).

    I think I have a book by Henry Morris about the Bible that I’ve not really read. Oh, yes, I have the Quote Mine Encyclopedia by Morris known as “That words may be used against them.” :-)

    One of the most influential creationist books was partly the result of Michael Behe’s book. This book could be properly classified as an ID and and creationist book, John Sanford’s Genetic Entropy.

    The ID staples (some of which can also be considered creationist, and which I note as such):

    1. Evolution a Theory in Crisis by Michael Denton

    2. Mystery of Life’s Origin by Thaxton, Bradley, Olsen

    3. Darwin’s Black Box by Behe

    4. Design Inference by Dembski

    5. Genetic Entropy by John Sanford [ID and creationist]

    6. Biotic Message by Walter ReMine [ID and creationist]

    7. Signature in the Cell by Meyer

    8. Politically Incorrect Guide by Jonathan Wells

    9. Icons of Evolution by Jonathan Wells

    10. Privileged Planet by Gonzalez and Richards

    11. The Anthropic Cosmological Prinicple by John Barrow and Frank Tipler

    12. The Mind of God by Paul Davies

    13. Information Theory and Molecular Biology by Hubert Yockey

    14. Nature’s Destiny by Michael Denton

    15. No Free Lunch by Dembski

    16. Cybernetic Approach to Evolution by A.E. Wilder-Smity [ID and creationist]

    17. The Science of God by Gerald Schoeder

    18. Not by Chance by Lee Spetner

    There are more titles, but that should give an idea…..

    I hope creationsts buy ID books.

  19. Khan,
    I did not ask for functional proteins buddy, I asked for a demonstration of the generation of ANY functional information that would violate the principle of genetic entropy and would explain the staggering levels of functional information we find in life:

    “The manuals needed for building the entire space shuttle and all its components and all its support systems would be truly enormous! Yet the specified complexity (information) of even the simplest form of life – a bacterium – is arguably as great as that of the space shuttle.”
    J.C. Sanford – Geneticist

    “In my opinion, there is no basis in known chemistry for the belief that long sequences of reactions can organize spontaneously — and every reason to believe that they cannot. The problem of achieving sufficient specificity, whether in consisting of or occurring within a water-based system, aqueous solution, or on the surface of a mineral, is so severe that the chance of closing a cycle of reactions as complex as the reverse citric acid cycle, for example, is negligible.” Leslie Orgel, 1998

    Here is the test buddy:

    For a broad outline of the “Fitness test”, required to be passed to show a violation of the principle of Genetic Entropy, please see this following video and article:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.youtube.com/watch?v=_BwWpRSYgOE

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    This “fitness test” fairly conclusively demonstrates “optimal information” is encoded onto a “parent” bacteria by God, and has not been added to by any “teleological” methods in the beneficial adaptations of the sub-species of bacteria. Thus the inference to Genetic Entropy, i.e. that God has not specifically moved within nature in a teleological manner to increase the functional information of a genome once He has created the parent species genome, still holds as true for the principle of Genetic Entropy.

    Though I am surely no expert on the math of LCI, and may be in error as to how strict the limit for conserved information now is, it seems readily apparent to me, even with Dembski’s and Mark’s strict definition of LCI in place, to conclusively demonstrate God has moved within nature, in a teleological manner to provide the sub-species with additional functional information over the “optimal” genome of the parent species, the “fitness test” must still be passed by the sub-species against the parent species. If the fitness test is shown to be passed, then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it gained in the beneficial adaptation, and then be found to be greater than 140 Fits of functional information. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by totally natural processes over the entire age of the universe. This fitness test, and calculation, must be done to rigorously establish materialistic processes did not generate the functional information (Fits), and to rigorously establish teleological processes were indeed involved in the increase of Functional Complexity of the beneficially adapted sub-species.

    Can you see my curiosity of the matter Khan (con) , I mean look at the staggering levels of functional machine like complexity in the cell…yet when we test for increased functional complexity against a parent bacteria we never find it…Help me out with this Khan as I am sure you can see this is foundational for evolution to even be considered true in the first place!

  20. What this all points to in my opinion is Dr Meyers book deserves a substantial hearing and not mockery or derision.

    Dissenting opinions are important. Fossil records can be manipulated, indeed falsified. But operational science in molecular biology today, in cellular research leads to a Design Centric future Paradigm.

    Meyers book should be treated as scientific dissent and opposition opinion.

    Congratulations again Dr. Meyer, well done, well done.

  21. Mr Joseph,

    Birds have a fixed femur that allows them to breathe.

    Dinos didn’t have that.

    I think you are overstating what Quick and Ruben were saying. Quick was saying that a fixed femur allowed a bird to breathe more efficiently. That is exactly the differential increment that drives evolution!

  22. Scordova,

    That little list is so frightening to Darwinian Zealots. You’d think their whole world is falling apart.

    I agree that Creationist should buy and utilize these books, as well as help ID fund research at Biologic Institute.

  23. DATCG,

    I used the PLoS paper to you why the Journal of Morpohology paper was interesting, but not really important. if you read the PLoS paper, you would see that they never claim that air sacs functioned in exactly the same way in theropods as they do in birds. they just show evidence that they were present.

    posted the other account to show you the history of propaganda and of hiding dissent.

    hiding dissent? anti-theropod people have published in prestigious places like Proceedings of the Royal Society of London B. they just have very weak arguments and evidence.

    Afterall, that letter was from a Curator at Smithsonian.

    who hasn’t published a single paper to support his views.

  24. BA^77
    how about duplication of an entire genome, twice. does that violate genetic entropy?

    http://www.plosbiology.org/art.....io.0030314

  25. how about duplication of an entire genome, twice. does that violate genetic entropy?

    If there is duplication, it would appear not to be random noise.

    I was visiting with Dr. Sanford two weeks ago, and he opened my eyes to a major understatment by the ENCODE project. They said there are large “non-random patterns” across genomes.

    This is like saying computer chips with their Manhattan VLSI architecture exhibit highly non-random patterns, or a New York skyscraper exhibits highly non-random patterns.

    The biological community will eventually have to come to terms with highly ordered pattern in the genome. The ENCODE project did, so will the rest of science if they are willing to open their eyes.

    The Darwinian story that the genome is cobbled mess of DNA is becoming less and less defensible every day.

    By the way, Edward Max of TalkOrigins in 2003:

    scientists generally accept the notion that most of this DNA is junk.

    ….
    the arguments I just presented based on presently available evidence suggest that most DNA sequences that appear to be functionless are just that.

  26. Sal,
    whole genome duplication happens pretty regularly in plants. is this random noise, or not?

  27. Well Khan,,
    Let’s be fair with the evidence,,,
    The evidence they present is a vast hypothetical conjecture based on their biased take of evolutionary history…The burning question is why is the “fitness test” I outlined not been violated? Would not you have to show a increase of information at this most basic level in the laboratory before you extrapolated to such grand sweeping claims for evolution in general? You can see my curiosity here can you not Khan (con)?
    Please Explain in detail Why evolution should be given free pass on this fitness test since it is so foundational to there claims.

  28. Mr Cordova, I admire your honesty in showing that the book also ranks #1 in Creationism. Ah, the wisdom of crowds…

    Does Amazon even have an ID category for books, or do they just automatically classify ID books in the creationist category?

  29. BA^77
    for the sake of argument let’s say the researchers are correct. does this violate genetic entropy or not?

  30. Well Khan seeing as John Sanford made his “without peer” mark in the world of plant genetics, I would have to say you are barking up the wrong tree again:

    Genetic Entropy & the Mystery of the Genome
    http://www.amazon.com/Genetic-.....1599190028

    Of note:
    Summary of attempts to accelerate evolution artificially, using real organisms (including polyploid plants): “an enormous failure.” The author speaks from experience on this.

  31. Khan, good question!
    What would indicate if it violated genetic entropy is if the sub-species had a greater ability to survive in the parents native environment…The Fitness Test…
    The fitness test is the only viable test i know of to differentiate, on the first order of investigation, if a increase of functional complexity has occurred in the sub-speciation. Is not Darwinism claiming that it is “more fit”,,,if this is so then the fitness should not be limited to “new environments” in all adaptations,,,as what we are witnessing in bacteria,,,but should be “across the board” and show increase fitness over parent species in native environment…Follow?

  32. Sal,
    whole genome duplication happens pretty regularly in plants. is this random noise, or not?

    The problem in making this characterization is that sometimes it is presumed a duplication happened when in fact identity may have been there to begin with.

    Yes, there are duplications we observe in operation today, just as we observe HGT. But we actually don’t know for sure the cause for some identical sequences.

    It is to premature to say. But one thing I will say, as a matter of policy, if the Darwinists have said it was an accident and cobbled mess, the chances are they are being hasty in their inferences.

    What about all those identical sequences that were attributed to common ancestry. It seems the most prestigious scientific journal in the world is casting doubt on the hypothesis that the identical sequences are the “proof” of common ancestry:

    Collectivist revolution in evolution Mark Buchanan Nature Physics 5, 531 (2009) doi:10.1038/nphys1352 excerpts

    “A coming revolution in biology, may go so far as to unseat Darwinian evolution as the key explanatory process in biology.

    HT idnet.au

    It has been a disturbing practice to see biolgists witness an indel or error that results in duplication, and then whenever they see an identical sequence somewhere else in the genome they presume the cause was an error.

    This is as bad as saying that you once witnessed someone make a cut and paste error that resulted in a wasteful duplication, and then when you see larger server farms whose role is to provide backup copies that therefore the server farm was a major error! Or that when you see a skyscraper with its repeated patterns that the product of a duplication error! The ENCODE project was a major breakthrough in crushing the misperceptions of “bad design” and “junk DNA” promoted by Darwinism.

  33. well put bornagine777. You dealt with relative fitness issue quite well. by the way what happen to your youtube channel?

  34. GilDodgen (#28) asked: “Does Amazon even have an ID category for books, or do they just automatically classify ID books in the creationist category?

    Because “Signature In The Cell” was published by the religious book publisher HarperOne, Amazon correctly placed it in the “Books > Religion & Spirituality > Christianity > Theology > Creationism” category. I can’t imagine how it got ranked in the Astronomy, Physics or Cosmology sections, although Amazon’s system has been gamed before.

    What is also extremely revealing is the books that Amazon lists as having been bought with “Signature”:

    “Glenn Beck’s Common Sense: The Case Against an Out-of-Control Government”

    “Liberty and Tyranny: A Conservative Manifesto”

    “The Darwin Myth: The Life and Lies of Charles Darwin”

    “Answering the New Atheism: Dismantling Dawkins…”

    “The End of Christianity: Finding a Good God in…”

    Not one science book in the group…

  35. BA77, you’ve mentioned FSCI so often recently that I am not sure that you aren’t sock puppeting KF. On the other hand I had the impression that Jerry and Joseph did the same. So either FSCI gains momentum at UD or are the four of you one and the same? BTW, Dr. Dembski seems to be reluctant about FSCI or did he mention it lately?.

  36. Spark,
    I’m quite sure it (Genetic Entropy) can be put a lot better,,but I am happy it was good enough that you were able to follow what I was trying to get across,,,

    I have a new channel:

    Evolution vs Genetic Entropy
    http://www.youtube.com/watch?v=mmbRbyv2PA0

  37. Those people observing this thread should know that not all of those who support ID believe that genetic entropy is a valid concept or that we agree on just what it is. Sanford is a YEC and the book was written to support YEC so many of us who support ID are very wary of its conclusions. Sanford is a geneticists and so his ideas are supposedly in sync with genetic theory.

    Sanford is a legitimate scientist who invented a very useful instrument called the Gene Gun and has made some money off of it. He still has an office at Cornell though I am not sure if he teaches or does any research anymore. Apparently Sal will know since he talked with him recently.

    It has been awhile since I read the book but some of its conclusions are so counter intuitive that one has to ask how did Sanford come to these conclusions. One of the basic conclusions of the book is that every species is so deteriorated genetically that it is a wonder that anything is functioning out there in the world. Each generation brings with it more deterioration but since we only started 6,000 years ago we have not yet reached the point of of complete breakdown.

    I personally believe for ID to hang their hat on what Sanford believes is asking for the same trouble that it gets when it gets too close to any of the YEC science. I also know that a lot of pro ID people will be very upset at the questioning of Sanford but I believe it is best to distance themselves from him until his ideas can be evaluated better.

  38. What is also extremely revealing is the books that Amazon lists as having been bought with “Signature”:

    “Glenn Beck’s Common Sense: The Case Against an Out-of-Control Government”

    “Liberty and Tyranny: A Conservative Manifesto”

    “The Darwin Myth: The Life and Lies of Charles Darwin”

    “Answering the New Atheism: Dismantling Dawkins…”

    “The End of Christianity: Finding a Good God in…”

    If ID advances, it will change culture. That is revealing.

    Not one science book in the group…

    But the other way to look at it is that people who were not interested in science are now buying science books! Your prejudices may be coloring your perceptions.

    I’m finding that people who were very interested in politics but never gave much thought to ID in the prior decade are now taking the subject of ID more seriously today.

    ID wasn’t even on the map 15 years ago. That is changing, and it is slowing becoming the fuel which helps people believe there is purpose in the universe. This will naturally be important to political and cultural issues.

    I would welcome that when people buy religious or political books, they will also pick up science books like Stephen Meyer’s book.

    For too long, the issue of Darwinism vs. ID has been taking a back seat in culture and even religion. That is changing. ID will hopefully become influential to theologians, pastors, and priests, and everyone else.

    I can tell you from experience, that ID is not very much studied in Christian circles, seminaries, and churches. That may be slowly changing.

  39. Sanford dedicated a few pages to polyploidy in the case of both plants and animals in his book. A full genome duplication (polyploidy) in humans always results in prenatal death, whereas aneuplody results in severe defects such as down syndrome.

    It’s important to note that a large portion of Sanford’s PHD dissertation was on exactly that- polyploidy in plants, as that was one of his special areas of interest. The following links might be helpful as they are words directly from Sanford:

    Page 1
    Page 2

  40. One of the basic conclusions of the book is that every species is so deteriorated genetically that it is a wonder that anything is functioning out there in the world.

    That is not completely accurate.

    First of all Sanford was a Theistic Darwinist up until 2000 or so. But that slowly began to change when he read Behe’s book……

    He then began to explore the question of genetic deterioration. It accords well with the possibility HUMANS are a recent phenomenon. Whether the rest of the world is young is a separate question….

    Bacterial species are not so genetically deteriorated becasue purifying selection works very well given their extreme reproductive excess.

    The same is not true of creatures like humans who do not have the same reproductive excess.

    Sanford is not alone in his views of genomic deterioration. Bryan Sykes at Oxford (where Dawkins was based) argues also for genomic deterioration in humans. See his book Adam’s Curse.

    Geneticist John Joe McFadden argues for the deterioration of the genome. A large segment of the pro-Darwin, pro-Eugenics movement argues this.

    Not that I agree with the policies of Eugenics, but isn’t it strange that such divergent interests seem to agree that we should be concerned?

    I’d say Sanford is hardly archaic or obscure in his concerns about genomic deterioration in humans.

    In any case, with the emergence of Solexa and Illumina cheap sequencing technologies, it may become brutally apparent that Oxford Geneticist Sykes and Cornell Geneticist Sanford are correct.

  41. Well,
    Not to digress to much on a thread devoted to “Signature”, but I would like to clearly state I am not a YEC and that Genetic Entropy extrapolates extremely well to OEC views. as well as to foundational principles of science (The Second Law and LCI),,,is backed up by the fossil record (Trilobites: Webster) and what we can observe for adaptations (Behe: Sanford…i.e. Genetic Entropy is extremely robust in its explanatory power for biology!

  42. I’m more interested in the progress of Dr. Sanford’s work on Mendel’s Accountant than Genetic Entropy, the book. Genetic Entropy posited an idea, he’s trying to back it up rigorously with MA.

  43. 43

    I am about two thirds through Signature in the Cell right now. I have not been reading it with the same excitement as I read Behe’s books, probably because I’ve heard all these arguments before. It’s really a very simple argument, but Meyer supports it very well and completely from the history of science and the scientific literature, which is the most helpful aspect of this book. He’s a bit redundant at times, but very compelling and readable to a large audience. Those Amazon rankings say they count the entire history of a book’s sales, so it’s quite surprising that Meyer’s book would outsell Hawking’s, which is over ten years old. Perhaps because Amazon is the only place you can buy Meyer’s book?

    scordova @25:

    I was visiting with Dr. Sanford two weeks ago, and he opened my eyes to a major understatment by the ENCODE project. They said there are large “non-random patterns” across genomes.

    From Signature, pg 239:

    Which sequence of characters is used to convey a message is not determined by physical law, but by the choice of the users of the communications system in accord with the established conventions of vocabulary and grammar – just as engineers determine the arrangement of the parts of machines in accord with the principles of engineering.

    Meyer did tell me something that I didn’t know before, and as I read the end of the book I expect more of that. He says that different genetic codes have been discovered in different organisms, besides the one we have all been taught. I suspect that the same will be true of the grammar and vocabulary of the cannon genetic code. All the genetic code really does is translate one set of letters to another set. We don’t really know much about the grammar and vocabulary yet. I suspect there are linguistic rules in the one dimensional sequence which contain three dimensional structural information. I also suspect that these rules will be found to be completely different in different organisms, even organisms with the same genetic code. Polish and all the Romance languages use basically the same alphabet as English, but are entirely different systems. This means that secondary and tertiary structure of proteins would not be dependent merely on how they would naturally fold according to their chemical properties (which is a point Meyer makes about the DNA sequence itself) but dependent on the chaperone system, which would serve as the translator from one dimension to three. It also means that genes which work in one organism would not work in another unless you also transform the genes for the correct chaperone system and put the right promoters on everything. It may even be more interconnected than that, requiring the right regulatory system as well. If so, we could be on the verge of an entirely new classification system based on genetic linguistics, one that won’t be tied to either to the Linnaean system or any sort of evolutionary tree. Although it would appear there is already evidence against this. For instance that crazy Korean guy has transformed fluorescent proteins from jellyfish into cloned dogs and it works just fine. I wonder though if he had to use any other genes besides just the fluorescent protein?

    I also found what might be a small error in one of Meyer’s analogies and I’m wondering if anyone could clear this up for me. On page 190 he says that the chance of a ball landing on the same spot of a roulette wheel twice in a row is 38*38, or 1/1,444. Then he says that if the croupier spins the wheel 1,444 times “he will quite likely witness this otherwise unlikely event”. Since each trial consists of two spins of the wheel, I would think that depending on how the croupier counts his sequence of two the total number of trials would be different. If he is not picky, then every spin could be the start of a two-spin trial, and to complete 1,444 trials he would need to spin the wheel 1,445 times. Or if he starts each trial at each even numbered spin, it would take 2,888 spins. Is this correct?

  44. 44

    Joseph @8:

    Even though I disagree with the premise that the genetic information is the sequence his work may help others make the connection to at least the possibility that the real information resides on/ in the structures inside the cell and the sequence specificity is only required to carry out the instructions.

    Meyer argues that it is the other way around, but either way it is a chicken and the egg problem. They are dependent on each other, that much is certain. I think it makes much more sense to say that the genes carry the information/instructions and proteins are required to carry them out. Why do you think differently?

  45. I’m more interested in the progress of Dr. Sanford’s work on Mendel’s Accountant than Genetic Entropy, the book. Genetic Entropy posited an idea, he’s trying to back it up rigorously with MA.

    It will be forthcoming. I don’t know the time frame, but things are in the works.

    In the mean time, what can be done is to look up Jody Hay’s simulation at Rutgers.

    It is not as user friendly as MA, but it can generate comparable results with some caveats which perhaps Walter ReMine and I will post on here at UD.

    I hope to see Walter this month and we can talk more about Nuny’s simulation and Jody Hay’s simulation at Rutgers.

    By the way, Nakashima-san, do you have any background in population biology.

    I would welcome your cross check of some of my calculations.

    Incidentally, when Meyer presented Signature in the Cell at McLean Bible, Meyer said that for the sake of argument one can assume that Darwin was right about life after the first cell (and that is only for the sake of argument since Meyer thinks Darwin was wrong).

    Meyer argues about the difficulty of creating the first cell. He articulates the case so clearly and lucidly.

  46. I suggest that people interested in this discussion get Sanford’s book and read it and see what they take away from it. I took away from it something so at odds with the world I look at each day that it made me think what is wrong with this reasoning to come to these conclusions. Sanford is a trained geneticist of world wide fame for his inventions. But I disagree with the robustness of Sanford’s conclusions. He predicts genetic deterioration and it is rapid and all I know is that the animals in my world are doing just fine.

    Why humans and not other organisms? That does not seem to make sense. Bringing up bacteria is a non relevancy. That’s not the issue.

  47. I wrote:

    This is as bad as saying that you once witnessed someone make a cut and paste error that resulted in a wasteful duplication, and then when you see larger server farms whose role is to provide backup copies that therefore the server farm was a major error! Or that when you see a skyscraper with its repeated patterns that the product of a duplication error! The ENCODE project was a major breakthrough in crushing the misperceptions of “bad design” and “junk DNA” promoted by Darwinism.

    Richard Sternberg gives insights:

    ITSs…interstitial telomeric sequences…the chromosome scars, the pieces of junk DNA he was lecturing me about earlier. As you know, telomeres are the ends of chromosomes. In many species, including chimps and humans, the DNA sequences that are found at these genomic tips are tandem repetitions of TTAGGG. That’s right…TTAGGGTTAGGGTTAGGG…over and over and over again. A notable exception to this rule is the fruit fly, an organism that in this regard has provided the junk DNA notion no succor, since its telomeres have complex combinations of three different retrotransposons instead of those six-basepair units. What is important to note, though, is that telomeric sequences are essential to the cell, and it seems that hardly a week does not pass without some new role being discovered for these elements.

    How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique “suborganelle” — for the lack of better term — at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations.

    I try to outline all the functions of telomeric repeats, but my friend tells me that I am getting off the subject.

    He wants to me to focus on the ITSs, the tracks of the hexamer TTAGGG that reside within chromosome arms or around the centromere, not at the ends. I tell him that I was just coming to that topic. The story, you see, is that in the lineage leading up (or down, I forget which) to chimps and humans, a fusion of chromosome ends occurred — two telomeres became stuck together, the DNA was stitched together, and now we find the remnants of this event on the inside of chromosomes. And to be fair, I concede at this point that the 2q13 ITS site shared by chimps and humans can be considered a synapomorphy, a five-dollar cladistic term meaning a genetic marker that the two species share. As this is said, it is apparent that the countenance of my acquaintance lightens a bit only to darken a second later. For I follow up by saying that of all the known ITSs, and there are many in the genomes of chimps and humans, as well as mice and rats and cows…, the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates (Farré M, Ponsà M, Bosch M. 2009. “Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates,” Cytogenetic and Genome Research 124(2): 128-131.). In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed.

    Richard Sternberg

  48. Why humans and not other organisms? That does not seem to make sense. Bringing up bacteria is a non relevancy. That’s not the issue.

    I posed your question to Dr. Sanford two weeks ago. He gave a very good response, and the bacteria are an issues since they are on the other end of a wide spectrum of species. Much has to do with the number of generations between germline cells and reproductive excess.

    In any case, your reservations are valued.

    The experimental and obvservational evidence will settle the issue in the fine traditions of science.

    I suggested another way to indirectly affirm the presence of genetic entropy is to use Solexa and Illumina technology to detect the spread of Single Nucleotid Polymorphisms in large conserved sequences. It will demonstrate unequivocally that Natural Selection cannot possibly effect purifying selection to maintain these large conserved regions.

    This will indirectly confirm that the genomes are changing at a rate that is inconsistent with mainstream suppositions.

    There will not have to be decisions about whether we are deteriorating (as in becoming sicker) or not. It will merely demonstrate selection cannot possibly operate on large genomes given the limited reproductive excess afforded humans and other species. One will not necessarily have to affirm the full implications of genetic entropy in order to demonstrate the overwhelming majority of the genome is outside the reach of natural selection because natural selection cannot simultaneously select for or against every nucleotide or even the majority of nucleotides in the genome.

    Science values experiment and obvservation and data gathering. I welcome settling of the issues via the scientific method. We will, God willing, know the answer more clearly and it will be confirmed by many independent laboratories.

  49. 49

    I have extremely poor eyesight, a back defect I got from my mother (who had to have major surgery on it), and a heart murmur. A Darwinist would say that this is evidence against a designer, or at least against a good one. I say genetic entropy. What say you, jerry?

  50. 50

    Perhaps my descendants will finally exhibit the finished design once the frontloading program has finished running, and will no longer have these problems.

  51. OT – my apologies.
    When my aunt died all her house plants bloomed. If man had been keeping the same kinds of houseplants for millions of years, then it could be said that evolution favored the survival of plants that mimicked empathy, therefore humans would be duped to continue to care for the plants. I don’t think there was enough time for this, though. So maybe this was a one in a million coincidence, or the Creator endowed plants with awareness. On a similar note, I was seriously thinking of chopping down a cherry tree that was producing very little, and the next spring it produced a bazillion blossoms. I’ve read of this happening with someone else concerning a different kind of plant.

  52. Khan,

    My point of posting Olson was that dissent is not allowed or rarely allowed and that propaganda much like Ida is part of the problem in science today. It happend 10yrs ago and it happened in NYC with Mayor Bloomberg recently part of a sham event bamboozling the public.

    Do I need to remind you of hoaxes once considered Dino-Birds?

    Or as usual, if you dissent you are seen as 1)radical, 2)on the fringe, 3) anti-science.

    Lets look at another evolutionist, but dissenter, Alan Feduccia Q&A:

    Question: So far, only one feathered dinosaur, Archaeoraptor, has been publicly acknowledged as a forgery. You think there are others?

    Answer:
    Archaeoraptor is just the tip of the iceberg. There are scores of fake fossils out there, and they have cast a dark shadow over the whole field. When you go to these fossil shows, it’s difficult to tell which ones are faked and which ones are not. I have heard that there is a fake-fossil factory in northeastern China, in Liaoning Province, near the deposits where many of these recent alleged feathered dinosaurs were found.

    This is a well qualified research evolutionist stating these truths about fraud. Remember when Acheaoraptor was truth? Now a forgery. How many more?

    But look what Feduccia states next about Nature, the Premier scientific journal:

    Journals like Nature don’t require specimens to be authenticated, and the specimens immediately end up back in China, so nobody can examine them. They may be miraculous discoveries, they may be missing links as they are claimed, but there is no way to authenticate any of this stuff.

    Is that good science? Is that how science works?

    Question:
    Why would anyone fake a fossil?
    Answer:
    Money. The Chinese fossil trade has become a big business. These fossil forgeries have been sold on the black market for years now, for huge sums of money. Anyone who can produce a good fake stands to profit.

    The largely untold story to the public is frauds are sold and sometimes unskeptical scientist buy into the mixture of bones as authentic.

    Question”
    If there are good reasons to be skeptical, why are you perceived as being on the scientific fringe?

    Bingo, don’t dare cross the faithful zealots of Darwinian theory.

    Answer:
    The idea of being able to watch living dinosaurs by looking out at the birds in your backyard bird feeder is very appealing. The popular press naturally jumped all over it. It’s also a money game. Many museums have promoted the idea of birds being living dinosaurs, and they have spent huge amounts of money on exhibits about that link. Plus, some paleontologists have spent three decades saying that birds evolved from dinosaurs, so there are careers at stake.

    Motive? Oh yes, Money spent, money made, Fame, Careers on the line. So perpetuate the myth despite the ability to ascertain the truth.

    Fictional stories – yes. Undisputable evidence? No. Frauds? Yes.

    Feduccia is author of more than 125 scientific publications.

  53. PaulBurnett,

    Do you think he had much of a choice where to publish?

    Do you remember what happened when he published a scientific paper in the past and how Smithsonian “scientist” behaved toward their fellow scientist?

    Remember how the scientific community at Smithsonian along with NCSE acted like a bunch of fascist cutting off Editor Richard Sternberg?

    Lovely is it not? Stifling dissent, then refusing to acknowledge it happens?

    But you keep on defending those double standards.

  54. Scordova,
    I would like to point out one more key piece of evidence for Genetic Entropy:

    Ancient bacteria that have been revived!

    There are many ancient bacterium recovered and “revived” from salt crystals and amber crystals which have been compared to their living descendants of today. Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence.

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
    Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart, (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

    ——–

    I had asked both Vreeland and Cano about a fitness test. Cano was graciously forthcoming with the test he had performed, but Vreeland mocked severely me as one of those “creationists” and would not divulge if the descendants of the 250 million year old bacteria had lost molecular functionality… (It was not a pleasant day for me)

    Hopefully one of you guys can see the need for this test and can do something about obtaining the results, or having the proper test conducted…

    Though this would not be “conclusive”, I feel the the “prediction” for finding deterioration of molecular functionality in the descendants of the 250 million year old bacteria would be a major feather in the cap for the Genetic Entropy model. It sure would add weight to Behe’s line of evidence as well.

  55. 55

    Scordova, I enjoyed Meyer’s book and look forward to watching it deliver.

    By the way, your bookshelf looks alot like mine. I skipped The Biotic Message…but added Berlinski’s The Devil’s Delusion.

  56. I posted this at TT and will augment it a bit here:

    An issue that comes up with OOL is the idea of equilibrium.

    In statistical mechanics we can characterize systems that are not yet at equilibrium or are far from equilibrium.

    For example, if we had a thousand dice and they were all showing the number 5, and these dice were in some sort of shaking mechanism, that configuration would not last long, as it is far from equilibrium.

    Trying to characterize what “equilibrium” actually means with respect to the OOL issue is a little more subtle. But if we loosely define “equilibrium” as the non-living state for the sake of argument. This is not to be confused with the formal definitions of equilibrium from the notions in physics, but I am borrowing the idea somewhat from physics. The idea of “configurational entropy” and hence configurational equilibrium is taken from Thaxon, Bradley, and Olsen’s book, Mystery of Life’s Origin.

    A house of cards can be said to be far from the most likely equilibrium condition, or at least it is and extremely unstable configuration that is in quasi equilibrium and is unstable. It is very easy to conceive of the house of cards collapsing under various conditions (like a slight breeze, whatever). It is hard to conceive of its construction under any normal circumstance aside from intelligence.

    The emergence of life poses the same problem. If life were as inevitable as the equilibrium conditions that other physical systems tend toward, the design inference would be dead in the water. If the physical universe made life inevitable, life would be as normal as ice melting in the presence of heat, but we know that life does not seem inevitable given what we know about typical conditions in non-living matter.

    The problem is that life is inherently unstable, like a house of cards. Death or non-life seems to be a highly stable configuration from the standpoint of physics and chemistry, just like card lying flat on a table versus them being assembled into a house of cards.

    It seems the equilibrium conditions (and I use the term informally) and the equilibrium tendency is toward non-life, not life. This is the problem for OOL. They are trying to show that the emegence of life is not really that problematic, that the emergence of life is not that improbable after all.

    But, qualitatively, it seems that life is very far from maximum equilibrium where the maximal equilibrium state is non-life.

    Why should life exist in the first place given that what we know about non-living matter suggest that life would not spontaneously emerge anymore than we would expect a breeze to assemble a house of cards.

    I think, scientifically speaking, life was created by a mechnism that we no longer see in operation today. The mechanism that made the first life was truly unique. That is a falsifiable, scientific claim in my humble opinion.

    Whether creation or ID is involved is another story, but I think this less ambitious claim that life proceeded from exceedingly rare and now, non-existent mechanism, is a scientifically falsifiable claim

    It seems that the physical universe is oriented toward “configurational entropy” or the destruction of specified complexity.

    The physical universe has a natural tendency to destroy specified complexity and life, not create it. This seems empirically and theoretically correct.

    If so, then Meyer is correct that the Signature in the Cell is suggestive of design. To a lesser extent, eventual exitinction seems inevitable, not unlimited progress (as Darwin’s Bulldog Huxley and Haeckel envisioned). The question is how fast will “configurational entropy” overtake living matter.

    The decoupling of “thermal entropy” and “configurational entropy” was ontlined in the ID Classic Mystery of Life’s Origin.

    For the reader’s benefit, this entire ID classic is available online here:

    http://themysteryoflifesorigin.org

  57. bornagain,

    Thanks!!!!! Actually Dr. Sanford is visiting lots of salt mines and looking for ancient bacteria.

    Thanks for reminding me of this important area of research.

    Sal

  58. Cool, please do keep us posted on Sanford’s results.

  59. Nakashima,

    What is the genetic evidence that demonstrates a fixed femur can evolve from a moving femur?

  60. Khan,

    1- If they found DNA in a dinosaur then it is safe to say said dino is not millions of years old.

    2- Genetic similarities can be accounted for by common design and convergence

    3- there isn’t any data which demonstrates organisms are the sum of its genome.

    4- We do not know what makes a bird a bird other than the fact a bird is born when two other birds succesfully mate.

  61. To help set the record straight one can compare an

    ID bookstore

    to a

    creationist bookstore

    There is some overlap, but it should be clear to those who want to render a fair assessment, that the two camps are distinct.

    If ID books were in every creationist household (say about 50 million in the USA), I would personally be very happy!

    I would argue that creationists are a large untapped market which ID proponents would do well to market to.

    May Stephen Meyer’s book reach all markets and libraries and bookshelves.

  62. tragic mishap,

    My premise is that the genetic information, like a compuetr’s information, is not the hardware.

    DNA, RNA and proteins are hardware.

    That said I say that genetic information rides on/ in the organisms’ hardware.

    It is that information which tells the hardware what to do, and when to do it.

  63. Re: book categories.

    I found Dr. Behe’s Edge of Evolution in the Science category of a local library.

    Yet, Amazon had a category listing of his book under religion as well.
    So what?

    Bias exist in many places. Just look at some of the tags by Behe’s critics. Some tag it as “delusional” and “religious fiction”

    It appears the Darwinian zealots are angry like monkeys in a cage. When they discover intelligent beings looking in, they fling up anything near them through the cage at the onlookers. The intelligent passers by, laugh at the temper tantrums and move forward to enjoy other animals on display.

  64. DATCG,

    Fedducia’s words are disgraceful and a sign of real desperation. accusing other scientists of making up data for monetary gain and to save their reputations, with no evidence to back it up, is as low as you can go.

    in any event, the point that he has 125 papers (many of them anti-theropod) kind of argues against your point that dissenters are squelched, doesn’t it?

    you should really read this paper to see how incorrect his views are, and how little he and RUben, etc. have to support them:

    http://findarticles.com/p/arti....._n9166691/

  65. Joseph,
    I take it from your response that you reject all morphological and molecular phylogenies as evidence for common ancestry?

  66. Khan,
    Don’t you think you are being hypocritical in that question?

    When we point out that the fossil record is severely in conflict with Darwinism, especially at the Cambrian Explosion,,,you reject this… When we point out that molecular evidence is “all over the board” you reject that as well..Why should only your philosophical bias of materialism count when looking at the evidence,,, especially since materialism does not even have a coherent foundation in modern science? Clearly you are severely misguided in what it means to be fair with the evidence and to lay preconceptions to the side:

    “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009)
    Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,”,,,“despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” ,,,,Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”,,,“We’ve just annihilated the (Darwin’s) tree of life.”
    http://www.evolutionnews.org/2......html#more

  67. Khan,

    Without the genetic data that demonstrates that the transformations required are even possible, common ancestry is nothing more than a speculation based on the assumption.

    As I said molecular and morphological similarities can be explained by common design and convergence.

    So without that genetic data all of those scenarios should be taught in a science classroom.

    BTW there is a peer-reviewed paper that demonstrates non-telic processes just don’t have enough time to do what you are claiming they did.

    You know that paper that tried to refute Behe’s “Edge of Evolution” but ended up confirming it.

  68. Mr Joseph,

    What is the genetic evidence that demonstrates a fixed femur can evolve from a moving femur?

    I’ve been looking into this, and I’m actually having doubts about the description of the bird femur as ‘fixed’. I Googled “bird femur” and there is an interesting hit from “Principles of Paleontology”. Page 130 et seq. discusses bird femurs, and shows a range of motion of perhaps 35-45 degrees. Should that be called fixed?

    The example was for a terrestial bird, the chicken. Quick and Ruben may have been making a point very specifically about flight, or the position of the femur during flight. I haven’t tried to access Quick’s PhD thesis to see.

    But in general, the formation of the bones, muscles etc are controlled by BMP and other developmental hormones, which are accessible to genetic change.

  69. Joseph,
    i’ve already linked to good molecular evidence for the mechanism of evolution of feathers. it shows that such changes are indeed possible and just requires the interaction of two previously existing genes (Shh and Bmp2).

    http://www.pnas.org/content/102/33/11734.abstract

    the durrer paper doesn’t help you because, as you know from your love of convergence, the same thing can happen in many different ways and is not “prespecified.”

  70. Fraudian slip?”

    That is the funniest typo I’ve seen all day.

  71. Khan,

    It appears you like it both ways.

    Is it OK what Richard Dawkins does? PZ Meyers? Pandas Thumb? And many of the other atheist? Darwinian Zealots? The day you put these zealot psuedo-intellectual thugs in perspective and in place, then you’ll have more respect.

    Dr. Feduccia’s claims are hardly new, look what happened to Ida? What about Tiktaalik? The announcement was made before any critical skeptics could examine evidence.

    This is the norm for Punk Darwnian “science.”

    Dissent was limited and in many cases not allowed or not subjected to critical scientist. Sorry you do not like the facts or consequences of shining the light on them.

    But the truth is you cannot disparage and deride every dissenter. Especially since these are not tied to ID or Creationist.

    I’ve delivered enough evidence to the contrary and cited dissenters. Your assertions do not knock them down.

    I’ll check out the paper you cited later tonight or tomorrow morning. I have a scheduled meeting tonight.

  72. 72

    Joseph @62

    Well it doesn’t sound like you are disagreeing with Meyer then. Sounds like you are saying exactly the same thing.

  73. “I have extremely poor eyesight, a back defect I got from my mother (who had to have major surgery on it), and a heart murmur. A Darwinist would say that this is evidence against a designer, or at least against a good one. I say genetic entropy. What say you, jerry?”

    I say neither. Mutations happen. No one denies that and some are debilitating because nearly all are negative. Many pregnancies end in miscarriages ane are most likely due to some genetic mishap. And in every one of us there are some problems. I had bad eyesight since I was 13 and I know of families in which depression has run for several generation and one or two of each generation seem to have it while others were perfectly normal. For it to be genetic entropy it would mean that it is present in all genomes and getting worse with each generation.

    This part of Darwin’s ideas seem to make sense and in the wild the organisms with these defects would be less likely to survive. As humans we can affect the outcome of our species more than any other and these defects are less of a hazard to survival as in the wild. I can tell you that a mother will love a child with a defect just as much as one without it. I have a friend who had a spina bifida baby and was told that baby would probably not reach past 10 years old. This was 25 years ago and that child is now a fully functioning adult mainly due to her mother’s love.

    There has been a whole series of threads by Cornelius Hunter in the last couple months on the religious nature of Darwinism. The Darwinist who makes the comment that this is a bad designer is making a religious argument. ID does not claim that the designer is God or even god like. The purpose in life is unknown to us through science though many here will have their own ideas from somewhere else. But one thing seems to be evident, the designer implemented a system that allows for adjustment over time and this system of adjustment has its hazards. Consequently you have bad eyesight and a back defect, my friends have the possibility of depression in their children and many others have different problems.

    Philosophically, if you or your mother had none of the things you listed or others did not have any similar problems, there would be new problems that would occupy our concerns. The family which had depression running in it, the great grand mother died at 70, the grand father at 86 and the three children are all functioning well and so are their children so far. His sister has several grand children and one seems to have it.

    I see tons of young functioning children around my town and the kids in the schools are doing things I never dreamed we could do when I was in grade school. New records are being broken athletically each year. I do not see genetic entropy as trend in the world. I think it is mainly nonsense.

  74. Jerry,

    You should read Sandford’s book if you don’t believe in genetic entropy.

    BTW. The Bible says that God created life and saw that it was good but then the creation was subjected to frustration. So, at least from a Judeo-Christian perspective, these types of problems are very consistent with what we expect to see.

  75. “You should read Sandford’s book if you don’t believe in genetic entropy.”

    What makes you think I haven’t read Sanford’s book. My opinions on this came about after reading it. We had a very long discussion on this just over a year ago.

    http://www.uncommondescent.com.....-theories/

  76. Mr Cordova,

    With two adopted children, I would have to admit that my knowledge of population biology is purely theoretical! :) But I encourage you to share your calculations. My background is computer science – compiler theory, databases, evolutionary computation, computer graphics, and XBRL.

    You are probably aware of the discussions of Mendel’s Accountant over at Theology Web and the Evolutionary Computation thread of AtBC. Excellent examples of ‘come let us reason together’!

  77. Khan,

    I’ve read several pages of the rebuttal by Richard Prum to Feduccia.

    So, you provided a lengthy opinion against Feduccia.

    Please cite the actual research papers with feathered dinosaurs.

    Right now, what you have are two differing opinions, both experts in the field.

    Bluffs like this do not work. Please give a specific published paper – that hopefully – includes pictures of “feathered dinosaurs” prior to birds.

  78. DATCG,

    um, try the numerous references at the end of the Prum paper?

    or any of the other 3 papers I provided way back at 14?

  79. 79

    jerry, so you don’t believe that mistakes can accumulate over time? I haven’t read Sanford’s book so I don’t know exactly what he means by “genetic entropy”, but if mistakes happen and at least sometimes are passed on to the next generation, that means mistakes will accumulate over time. It seems self-evident to me.

    You chide Sanford for singling out humans, yet you do so yourself.

    “As humans we can affect the outcome of our species more than any other and these defects are less of a hazard to survival as in the wild.”

    In other words, it’s more likely that humans will pass on genetic defects. So doesn’t it follow from this premise that humans will accumulate more defects than other species? I don’t think any of my defects will affect my reproductive success, as long as I wear contacts or get LASIK. :D

  80. Khan,

    I’m not here to search piles of publications. You keep making assertions without specifics.

    Point me to a specific paper for dino-bird or dino-feathers that is conclusive and studied by more than just the claimants assertions.

    Either cite specifics or stop making assertions.

    The rebuttal you linked is dated 2002 which means all papers are 2002 or prior years. Is is not up to me to read through every single paper cited, many of which can be outdated and overturned by new evidence.

    This is known as intellectual bluffing.

    Again, please cite specifics of dinosaur feathers that overturn latest findings.

    A more recent paper than the one you cite reports that so-called “proto-feathers” were nothing but skin, collagen. And it puts into perspective the China scam that Feduccia mentions. So, he is not behaving badly, he is being honest and open about the problems with fraudulent fossils and a rush to claims.

    Dated 2005…

    Bald truth about dinosaur feathers

    Quotes from Prof Lingham-Soliar about his research which overturns so-called dino-feather fossils out of China…

    “I am convinced from the nonsense spouted by many of the people who denounce collagen in favour of protofeathers that they have never actually seen collagen in its natural or decomposing state.”

    “He adds that, thanks to a quirk of preservation, the fossil provides a “remarkable, unprecedented” insight into the structure of dinosaur skin.”

    “What is highly significant in the present study are the masses of collagen fibres found – over 40 dermal layers seen for the first time in a fossil animal, which shows how vitally important collagen was in providing support and protection of the enclosed body mass of dinosaurs per se.”

    “It is hardly surprising that the Chinese dinosaurs, as they decomposed, exposed quantities of these structures.”

    “Earlier this year he cast doubt on the relevance to modern birds of turkey-sized Sinosauropteryx, a fossil found in 1994 by a farmer in Liaoning province, northeastern China, where red-grey mudstone has provided a trove of remains from the Early Cretaceous period some 130 million years ago.”

    “The long-tailed meat-eater was preserved fibre-like structures that, its Chinese researchers claimed, were primitive feathers. But subsequent work by the South African professor concluded they were actually the remains of collagen fibres that reinforced a frill that ran down the dinosaur’s back from head to tail, as well as the skin.

    This is a pattern of fraud and false claims being exposed.

    Provide a recent paper that shows actual evidence for dino feathers. I’ll then see if 1) there are pictures, diagrams, etc., for public perusal, and 2) if the findings and fossils have been open to other critical commentary and research.

    Usually, these fraudulent announcements and claims are made with a big splash and cannot be easily examined for years. In this case it took 7-9yrs before qualified people could get a look at the discovery and reject the false claims.

    As a result of such fraud and splashy claims I am always skeptical. You have not provided any new information, only old information.

  81. “jerry, so you don’t believe that mistakes can accumulate over time? I haven’t read Sanford’s book so I don’t know exactly what he means by “genetic entropy”, but if mistakes happen and at least sometimes are passed on to the next generation, that means mistakes will accumulate over time. It seems self-evident to me.”

    I didn’t say that mistakes cannot be passed on. Whether they accumulate is another issue. A mistake in one person does not enter the genes of all the rest of the population. The gene pool for humans is over 6 billion and you can bet a lot of problems are in the gene pool somewhere but that does not mean every individual has these problem or that the species as a whole will have all the problems or even a few of them. So the relatively problem free organisms are also passing on their genes too.

    Sanford predicts doom and gloom right now. I don’t see it. His book is a justification for YEC. His ideas should affect every species on the planet but I see no evidence of this happening anywhere. So I have to question his ideas. Just as I question Darwin’s ideas for macro evolution. I don’t see it.

  82. Khan,

    Just because genes can influence the development of feathers doesn’t mean they determine that development.

  83. tragic mishap,

    I am under the impression that Dr Meyer equates the genetic information to the sequence specificity.

    I am saying that the real information cannot be seen by a microscope- just as the info on a disc or in a PROM cannot be seen visually.

    The info on the disc is not reducible to its molecular sequences.

  84. DATCG,
    I already linked you to three (all post-2005) in comment #14. do I have to hold your hand and click on the mouse button for you?

  85. DATCG,
    my mistake, one of them was from 2004. here’s another one from 2009
    that specifically addresses (and refutes) the hypothesis that they could be collagen fibers

    http://www.nature.com/nature/j.....07856.html
    and for good measure another one:

    http://www.pnas.org/content/106/3/832

  86. You in love with that feather thing Khan?
    And even if you could find a fully plausible sequence within historical methodology for the feather, which I believe you are far from doing, how do you propose to establish it was not a teleological processes that did it? It is a historical science for crying out loud! And Especially when all current fully elucidated mutational studies show overwhelmingly negative mutation rate for molecular biology… Do you not find it funny that you would have to “hide in the shadows” of historical science, in order to try to make your case for evolution, a bit suspicious? Why do you not demand more integrity from yourself as far as empirics is concerned? Why are you so ready to accept very questionable evidence but ignore more rigorous evidence?

  87. BA^77,
    Functional proteins are rare
    beneficial mutations are rare
    what is your point? we teach this in Evolution 101

  88. Khan,
    Did not any of you poor evolutionary 101 students think to raise your hand and ask, “If all these mutations are bad how did life evolve?’ or did you faithfully become the “Darwinbots” you now are, without ever questioning your brainwashing, and without utilizing any of your critical thinking skills…just mindlessly repeating the same “imprinted” falsehoods over and over?

  89. Khan,
    Do you even want to wake up?

    Matrix – The pill
    http://www.youtube.com/watch?v=te6qG4yn-Ps

  90. BA^77
    where did you get “all these mutations are bad” from “beneficial mutations are rare”?

  91. Khan,
    All so called beneficial mutations turn out to come at a cost of molecular functionality,,,Yet, as with all other evidence, evolutionists ignore the detrimental affect to the molecular function and only count the “burning of the bridge” which gave a greater survival advantage…Shoddy science once again promoted as proof!

    The following sources reveal the overwhelmingly negative mutation rate which has been found:

    “I have seen estimates of the incidence of the ratio of deleterious-to-beneficial mutations which range from one in one thousand up to one in one million. The best estimates seem to be one in one million (Gerrish and Lenski, 1998). The actual rate of beneficial mutations is so extremely low as to thwart any actual measurement (Bataillon, 2000, Elena et al, 1998). Therefore, I cannot …accurately represent how rare such beneficial mutations really are.” (J.C. Sanford; Genetic Entropy page 24) – 2005

    Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? (Thomas Bataillon)
    Abstract……It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
    http://www.nature.com/hdy/jour.....7270a.html

    Distribution of fitness effects caused by random insertion mutations in Escherichia coli
    Excerpt: At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect. http://www.springerlink.com/co.....q5l0q3832/

    High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley)
    “In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load…the presence of a large class of mildly deleterious mutations can never be ruled out. ”
    http://www.sciencemag.org/cgi/...../5434/1748

    “But in all the reading I’ve done in the life-sciences literature, I’ve never found a mutation that added information… All point mutations that have been studied on the molecular level turn out to reduce the genetic information and not increase it.”
    Lee Spetner – Ph.D. Physics – MIT – (Not By Chance: Shattering the Modern Theory of Evolution)

    “Bergman (2004) has studied the topic of beneficial mutations. Among other things, he did a simple literature search via Biological Abstracts and Medline. He found 453,732 “mutation” hits, but among these only 186 mentioned the word “beneficial” (about 4 in 10,000). When those 186 references were reviewed, almost all the presumed “beneficial mutations” were only beneficial in a very narrow sense- but each mutation consistently involved loss of function changes-hence loss of information.” Sanford: Genetic Entropy

    “Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity change shows unambiguous evidence that random mutation itself, even with geographical isolation of populations leads to speciation.”
    Lynn Margulis – Acquiring Genomes [2003], p. 29.

    “But there is no evidence that DNA mutations can provide the sorts of variation needed for evolution… There is no evidence for beneficial mutations at the level of macroevolution, but there is also no evidence at the level of what is commonly regarded as microevolution.”
    Jonathan Wells (PhD. – Molecular Biology)

    “Of carefully studied mutations, most have been found to be harmful to organisms, and most of the remainder seem to have neither positive nor negative effect. Mutations that are actually beneficial are extraordinarily rare and involve insignificant changes. Mutations seem to be much more degenerative than constructive…” Kurt Wise, paleontologist (2002, p.163)

    “The neo-Darwinians would like us to believe that large evolutionary changes can result from a series of small events if there are enough of them. But if these events all lose information they can’t be the steps in the kind of evolution the neo-Darwin theory is supposed to explain, no matter how many mutations there are. Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume.” Lee Spetner (Ph.D. Physics – MIT – Not By Chance)

    “It is entirely in line with the accidental nature of naturally occurring mutations that extensive tests have agreed in showing the vast majority of them to be detrimental to the organisms in its job of surviving and reproducing, just as changes accidentally introduced into any artificial mechanism are predominantly harmful to its useful operation”
    H.J. Muller (Received a Nobel Prize for his work on mutations to DNA)

    “The opportune appearance of mutations permitting animals and plants to meet their needs seems hard to believe. Yet the Darwinian theory is even more demanding: a single plant, a single animal would require thousands and thousands of lucky, appropriate events. Thus, miracles would become the rule: events with an infinitesimal probability could not fail to occur …. There is no law against day dreaming, but science must not indulge in it.” Pierre P. Grasse – past President of the French Academie des Sciences

    Evolution Cartoon – Waiting For That Beneficial Mutation – video
    http://www.youtube.com/watch?v=71-QYtxi8Bw

    “Most biological reactions are chain reactions. To interact in a chain, these precisely built molecules must fit together most precisely, as the cog wheels of a Swiss watch do.,,,, Saying it can be improved by random mutation of one link, is like saying you could improve a Swiss watch by dropping it and thus bending one of its wheels or axis. To get a better watch, all the wheels must be changed simultaneously to make a good fit again.” Albert Szent-Györgyi von Nagyrapolt (Nobel prize for Medicine).

    Genetic Mutations and Molecular Information – Genetic Entropy – video
    http://www.youtube.com/watch?v=GifFN26au04

    “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter” Dr. Werner Gitt, former director and Professor of Information Systems at the prestigious German Federal Institute of Physics and Technology

    This following article refutes Lenski’s supposed evolution of the citrate ability for E-Coli:

    Multiple Mutations Needed for E. Coli – Michael Behe
    http://www.amazon.com/gp/blog/.....96N278Z93O

    In fact, trying to narrow down an actual hard number for the “truly” beneficial mutation rate is what Dr. Behe did in this following book:

    “The Edge of Evolution: The Search for the Limits of Darwinism”

    Dr. Behe states in Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation. Thus, the actual rate for “truly” beneficial mutations, which would account for the staggering machine-like complexity we see in life, is far in excess of one-hundred-billion-billion mutational events. So this one in ten-thousand, to one in a million, number for “truly” beneficial mutations is actually far, far, too generous. In fact, from consistent findings such as these, it is increasingly apparent the principle of Genetic Entropy is the overriding foundational rule for all of biology, with no exceptions at all, and belief in “truly” beneficial mutations is nothing more than wishful speculation on the materialist part which has no foundation in empirical science whatsoever.

    Evolution vs. Genetic Entropy – video
    http://www.youtube.com/watch?v=mmbRbyv2PA0

    The foundational rule of Genetic Entropy for biology, which can draw its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks), can be stated something like this:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment,
    will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

    Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to the DNA of humans which would violate the principle of genetic entropy. Although a materialist may try to claim the lactase persistence mutation as a lonely example of a “truly” beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate Genetic Entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is overwhelming for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

    “Mutations” by Dr. Gary Parker
    Excerpt: human beings are now subject to over 3500 mutational disorders.

  92. thanks for the literature. yep, beneficial mutations are rare. but here are some that confer fitness advantages both in the new environment(with antibiotic) and in the original environment (without antibiotic). does that pass the Fitnes Test?

    Kassen, R. and Bataillon, T. 2006. “Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria.” Nature Genetics 38: 484-488

    http://www.nature.com/ng/journ.....g1751.html

  93. Sanford predicts doom and gloom right now. I don’t see it. His book is a justification for YEC. His ideas should affect every species on the planet but I see no evidence of this happening anywhere. So I have to question his ideas. Just as I question Darwin’s ideas for macro evolution. I don’t see it.

    See: The Mutational Meltdown in Asexual Populations

    Sanford told me the principle author of the above paper, Micahel Lynch was influential in his thinking.

    I don’t see that Sanford is far away from the mainstream, he’s just willing to take the implications to their logical but often uncomfortable conclusions.

    The notion of genetic entropy is indirectly relevant to Meyer’s work. If the non-living state is the state of maximum configurational equilibrium, then it would appear a unique event was the cause of life.

    The mechanism which created the first life appears not to be in operation today.

  94. Khan asks?
    “does that pass the fitness test?”

    Well considering they did not actually pass a fitness test but only assayed “the limitations of current population genetic theory for predicting adaptation to severe sources of stress,” I would have to say the answer to your question is a big fat NO!!!!

    Excerpt: These results demonstrate the limitations of current population genetic theory for predicting adaptation to severe sources of stress, such as antibiotics, and they highlight the utility of integrating statistical and biophysical approaches to adaptation.”
    http://www.plosgenetics.org/ar.....en.1000406

    Thanks for the paper Scordova!

  95. Mr Cordova,

    A very relevant paper to obligately asexual populations of less than 10,000 individuals. What about the rest of us? Where is the paper that shows this applies to sexual populations, ie almost every plant and animal? Unless Dr Sanford has that in hand, he is vastly overgeneralizing.

  96. “But in all the reading I’ve done in the life-sciences literature, I’ve never found a mutation that added information… All point mutations that have been studied on the molecular level turn out to reduce the genetic information and not increase it.”
    Lee Spetner – Ph.D. Physics – MIT – (Not By Chance: Shattering the Modern Theory of Evolution)

    Does Dr Spetner think tricolor vision is a loss of information?

  97. Nak(awaiting moderation)ashima,

    The effects for large populations are revealed in a variety of ways”

    the accumulation of slightly detrimental mutations in humans is revealed by this following fact:

    “When first cousins marry, their children have a reduction of life expectancy of nearly 10 years. Why is this? It is because inbreeding exposes the genetic mistakes within the genome (slightly detrimental recessive mutations) that have not yet had time to “come to the surface”. Inbreeding is like a sneak preview, or foreshadowing, of where we are going to be genetically as a whole as a species in the future. The reduced life expectancy of inbred children reflects the overall aging of the genome that has accumulated thus far, and reveals the hidden reservoir of genetic damage that have been accumulating in our genomes.”
    Sanford; Genetic Entropy; page 147

    The effects in the fossil record are revealed by this:

    The following article is important in that it shows the principle of Genetic Entropy being obeyed in the fossil record by Trilobites, over the 270 million year history of their life on earth (Note: Trilobites are one of the most prolific “kinds” found in the fossil record with an extensive worldwide distribution. They appeared abruptly at the base of the Cambrian explosion with no evidence of transmutation from the “simple” creatures that preceded them, nor is there any evidence they ever produced anything else besides other trilobites during the entire time they were in the fossil record).

    Excerpt from article:”From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; commenting on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    Evolution vs. Trilobites – Prof. Andy McIntosh – video
    http://www.youtube.com/watch?v=9P-gHO2Vl5g

    At one of the few petrified forests that sports ginkgo wood, I was told by the naturalist that ginkgos are old in the fossil record—they date from the Permian back when trees were first “invented”. She said that there are many species of fossilized Ginkgoaceae, but Ginkgo biloba, is the only living species left. – Rude – Uncommon Descent

    “As Niles Eldredge and Stephen Jay Gould pointed out almost three decades ago, the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time.” Allen MacNeill PhD.; 2007 (Evolutionist) Teaches introductory biology and evolution at Cornell University in Ithaca, NY. — Quoted right here on UD

    Thus the evidence is extremely robust

  98. Nak(he’s talking to me again)ashima;

    “Does Dr Spetner think tricolor vision is a loss of information?”

    You got evidence for bacteria getting tri-color vision?

    Now that would be proof I could accept!!!!,I would head right over to PZ’s blog and kiss his b**t, and start talking about all the morons over here at UD.

  99. Where is the paper that shows this applies to sexual populations, ie almost every plant and animal?

    The population genetics of linkage blocks in sexually reproducing creatures is correctly approximated by Mueller’s ratchets. Same for the Y-chromosome or similar type chromosomes. Recombination is less if not non-existent factor. This was not lost upon Bryan Sykes. See:

    Adam’s Curse a Future without Men.

  100. Mr BA^77,

    The evidence of what is robust? That your species can last for hundreds of millions of years until you all start marrying your first cousins? How are trilobites, ginkos, and “gradual decline over relatively long periods of time” evidence of mutational meltdown? If mutational meltdown means lasting from the Permian until now, I’ll take the giant economy size, please.

  101. Mr Cordova,

    The population genetics of linkage blocks in sexually reproducing creatures is correctly approximated by Mueller’s ratchets.

    I’d like to see a citation on that, of course, but in the meantime I’ll take your word for it. Now convince me that linkage block issues dominate the population genetics of sexual populations, and you still need something to extend the results to populations larger than 10,000 or so. Gambatte!

  102. Mr BA^77,

    You got evidence for bacteria getting tri-color vision?

    Strange, I had not noticed Dr Spetner’s reading in the life sciences was restricted to bacteria.

    BTW, I’m happy to discuss science and its variations with you. I thought that was clear.

  103. and you still need something to extend the results to populations larger than 10,000 or so. Gambatte!

    Nachman’s U-Paradox.

    We can in principle, with the Solexa and Illumina technology emprically validate ReMine and Sandford’s interpretation of Nachman’s U-Paradox.

    Nachman argues a mechanism (like synergistic epistasis) must be in place to thwart the paradox since Darwinian evolution is obviously true, but this line of reasoning is some what circular (just like Lynch saying that “cloroplasts have existed for 10^9 years, so something must be preventing mutational meltdown”). So Nachman has his interpretation for Nachman’s Paradox, and Sanford has his interpretation of Nachman’s Paradox.

    Empirical discovery will settle the issue, just like it did over erroneous claims of Junk DNA and the Urey-Miller experiments.

  104. BA^77 (94)
    it would probably help if you read the correct paper:

    Kassen, R. and Bataillon, T. 2006. “Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria.” Nature Genetics 38: 484-488

    see the yellow below here? that means when you click it it takes you to the paper

    http://www.nature.com/ng/journ…..g1751.html

  105. and you still need something to extend the results to populations larger than 10,000 or so. Gambatte!

    But if the non-living state is equal to a state of configurational equilibrium (as oulined by Thaxton and whose writings Meyer cites), then as a general principle, living systems will tend to maximize configurational entropy as they reach configurational equilibrium.

    If this is so, and this is a reasonable hypothesis, preservation of living population is an unstable state. Non-life is the more stable state and therefore living entitities will, as a matter of principle, tend toward non-life.

    Darwin and statistical mechanics don’t mix.

  106. But if the non-living state is equal to a state of configurational equilibrium (as oulined by Thaxton and whose writings Meyer cites), then as a general principle, living systems will tend to maximize configurational entropy as they reach configurational equilibrium.

    I must admit difficulty parsing this. If you are saying that we expect that all things die, or that all species eventually go extinct, you’re not saying anything uncontroversial.

    Your last claim is quite amusing. Do you know any population geneticists who would agree with that sentiment?

  107. 107

    Khan,,,sorry about that, is this the correct paper you are so excited about?:,

    Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria.”

    Excerpt: “Here we test these predictions by assaying the fitness of 665 independently derived single-step mutations in the bacterium Pseudomonas fluorescens across a range of environments. We show that the distribution of fitness effects among beneficial mutations is indistinguishable from an exponential despite marked variation in the fitness rank of the wild type across environments. These results suggest that the initial step in adaptive evolution–the production of novel beneficial mutants from which selection sorts–is very general, being characterized by an approximately exponential distribution with many mutations of small effect and few of large effect.
    http://www.ncbi.nlm.nih.gov/pubmed/16550173

    special emphasis on this quote:
    “These results suggest that the initial step in adaptive evolution–the production of novel beneficial mutants from which selection sorts–is very general”

    Of first note in criticism: these are single beneficial mutations they are assaying,,,far from the 140 functional information bits (Fits; Durston) they would have to generate to violate Genetic Entropy:

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.youtube.com/watch?v=vUeCgTN7pOo

    And please consider this,,, once you up the ante to looking for JUST two beneficial mutations that would increase functional complexity, then you get into Behe’s home field, a home field where he has yet to lose a game, and run into huge problems as he clearly iterates here:

    Waiting Longer for Two Mutations, Part 5:
    “This is very strong support that the central contention of The Edge of Evolution is correct: that it is an extremely difficult evolutionary task for multiple required mutations to occur through Darwinian means, especially if one of the mutations is deleterious. And, as I argue in the book, reasonable application of this point to the protein machinery of the cell makes it very unlikely that life developed through a Darwinian mechanism.”
    http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2

    In fact his “Edge Of Evolution” was humorously confirmed by those who were seeking to show it was wrong!

    So even now when I am looking at the right paper,,,the answer, to if genetic entropy has been violated, is still a big fat NO!!!!

    In fact I will lay the standard out again for you:

    it seems readily apparent to me, even with Dembski’s and Mark’s strict definition of LCI in place, to conclusively demonstrate God has moved within nature, in a teleological manner to provide the sub-species with additional functional information over the “optimal” genome of the parent species, the “fitness test” must still be passed by the sub-species against the parent species. If the fitness test is shown to be passed, then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it gained in the beneficial adaptation, and then be found to be greater than 140 Fits of functional information. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by totally natural processes over the entire age of the universe. This fitness test, and calculation, must be done to rigorously establish materialistic processes did not generate the functional information (Fits), and to rigorously establish teleological processes were indeed involved in the increase of Functional Complexity of the beneficially adapted sub-species.

  108. I must admit difficulty parsing this. If you are saying that we expect that all things die, or that all species eventually go extinct, you’re not saying anything uncontroversial.

    Nakashima-san,

    Finally we agree on something. With that perhaps it is time for me to call it a day. Maybe tomorrow.

    Regarding Mendel’s Accountant, I have not visited Theology Web or ATBC in a loooong time.

    I expect there will be scholarly debates and exchanges forthcoming.

    ReMine has talked to Michael Lynch and also examined Jody Hays simulation at Rutgers. I hope to discuss these developments later.

    I have an audio interview with ReMine regarding Nuny’s simulation….

    Too much to do…

    These are important issues. They will not be settled any time soon. Such is science.

    I appreaciate your forebearance.

    regards,
    Sal

  109. 109

    Nakishima,
    You think your pretty smart in science? If so prove it to me and dig around and falsify the standard for genetic entropy i laid out for Khan…

    a broad outline of the “Fitness test”, required to be passed to show a violation of the principle of Genetic Entropy, please see this following video and article:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.youtube.com/watch?v=_BwWpRSYgOE

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    here’s the math you will need:

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

  110. 110

    Nak & Khan,
    Before you guys waste your time trying to falsify Genetic Entropy (not to discourage you from trying), I would like to point out that there are some pretty strong reasons to believe there are strict limits for what can be expected of Darwinism as far as generating functional information.

    Micro or Macro? Microbiologist Ralph Seelke on Evolution

    http://intelligentdesign.podom.....7_12-07_00

  111. 111

    The meat of the argument is around the 7:30 minute mark

  112. bornagain77:

    even with Dembski’s and Mark’s strict definition of LCI in place

    You refer the the LCI quite often, citing it as one of the twin pillars of Genetic Entropy. A lot of ideas that get thrown around in this debate are matters of expert opinion, but the LCI is purely mathematical, so the facts surrounding it are not subject to opinion. Here are the facts that you should know:

    - The “strict definition of LCI” in Marks’ and Dembski’s latest paper is easily shown to be false.

    - The three examples of it that they present, namely their three CoI theorems, all assume conservation of information in the form of P(A)=P(B). From that, they derive CoI in the form of P(A)<=P(B&C). The latter follows trivially from the former, regardless of the meanings of A, B, and C.

    - As such, the LCI tells us nothing about empirical reality, and tells us nothing substantial about mathematics. Unless you consider it substantial that P(A)<=P(B&C) follows from P(A)=P(B), which you shouldn’t.

  113. In the above post, P(A)<=P(B&C) should be P(A)>=P(B&C). Sorry.

  114. Sal,

    I am so happy to see his book is doing well. I have been reading it and it is excellent. Meyer does a top notch job writing about the argument from DNA to design. I would like to add for everyone on this site’s enjoyment- that I snet Meyer an email suggesting that he go on Coast to Coast am over a month ago- I also sent an email to the host of the show George Noorey suggesting he get Stephen to discuss his new book. Recently as UD covered the show took place. Maybe they used my email, maybe not but it was Steve’s first time on coast to coast.

    Better yet the awesome show can be listened to here

    http://www.youtube.com/watch?v.....re=related

    Steve knocks it out of the park and does the theory of ID significant justice in this great interview.

  115. As Steve likes to humorously put it; The period where it was said to be “over after Dover,” is over!

    And a book written this well should never get any one star ratings- so I would throw out all of the one star ratings and average the rest to get a real sense of his books average appeal and rating.

  116. Mr BA^77,

    Sorry if this takes a few posts. I’m having a hard time figuring out exactly what your challenge entails.

    As near as I can figure out, your fitness test says:

    If
    a sub-population has increased fitness compared to the wild type in some context
    and
    the sub-population has increased fitness in the normal context of the wild type
    and
    the number of additional Fits in the sub-population’s genome is greter than 140
    then
    God’s Finger has nudged the world in a new direction.

    The falsification of this test would occur if the three conditions could be shown associated with a clearly materialist explanation, since this would lead to a contradiction.

    Points arising from the preceding:

    1 – I can’t see that this has anything to do with genetic entropy.

    2 – Many would argue that God can use any material means to affect a change, so any particular counter-example, and all counter-examples in general do not succeed in falsifying anything.

    3 – I must therefore take it that you believe in a God Who has chosen to only use miraculous means to make changes of greater than 140 Fits to the Universe.

    4 – The verse stating this is missing from my Bible.

    Let’s say I have a salamander species, living in pond water, and it carries around a load of cyanobacteria on its back. The bacteria use chlorophyll to produce sugar for themselves, and the oxygen byproduct is easily absorbed by the salamander. Along comes an exceedingly materialist virus, clips the chlorophyll genes out of the bacteria and drops them into the salamander genome. Said package of genes is definitely worth 140 Fits, retail. The plate umpire rules that the infield fly rule is in effect.

    I say the BA^FT has been falsified. The super-salamander has increased fitness over wild type in both bacteria free and normal ponds. Chlorophyll production is worth 140 Fits, and the whole thing was done by a virus.

    Case 2: Same fact pattern as before, but this time the transfer takes place over 1,400,000 years one Fit at a time by 140 or more viral events, once every 10,000 years. BA^FT is still falsified. The batter is declared out and the runner does not advance. :)

  117. Sal @ 32:

    Sal,
    whole genome duplication happens pretty regularly in plants. is this random noise, or not?

    “The problem in making this characterization is that sometimes it is presumed a duplication happened when in fact identity may have been there to begin with.”

    The anti-gout medication colchicine can induce polyploidy in plants.

    http://users.rcn.com/jkimball......loidy.html

    Normal plant plus colchicine = polyploid plant. We can be certain that the “identity” was not there to begin with.

    Further along in 32:
    “But one thing I will say, as a matter of policy, if the Darwinists have said it was an accident and cobbled mess, the chances are they are being hasty in their inferences.”

    Who was too hasty to Google before hitting “Submit Comment”?

  118. 118

    I just finished watching the TVW video debate between Stephen Meyer and Peter Ward.

    I am truly embarrassed for the opposition.

  119. 119

    ROb,
    I am not seeking to verify LCI. In fact Dembski/Marks make it clear what LCI will do:
    “Though not denying Darwinian evolution or even limiting its role in the history of life, the Law of Conservation of Information shows that Darwinian evolution is inherently teleological. Moreover, it shows that this teleology can be measured in precise information-theoretic terms.”
    http://www.evoinfo.org/Publications/Life.html

    I am in fact laying out a rough outline of the ground rules for falsifying Genetic Entropy. As well, my reason for believing that information can’t be had on the cheap, by Darwinian processes, comes from many other corroborating sources:

    “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter” Dr. Werner Gitt, former director and Professor of Information Systems at the prestigious German Federal Institute of Physics and Technology

    as well:

    “… no operation performed by a computer can create new information.”

    – Douglas G. Robertson, “Algorithmic Information Theory, Free Will and the Turing Test,” Complexity, Vol.3, #3 Jan/Feb 1999, pp. 25-34.

    as well:

    It is also extremely interesting to note, the principle of Genetic Entropy lends itself very well to mathematical analysis by computer simulation:

    “No human investigation can be called true science without passing through mathematical tests.”
    Leonardo Da Vinci

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances. Using realistic estimates for the relevant biological parameters, we investigate the rate of mutation accumulation, the distribution of the fitness effects of the accumulating mutations, and the overall effect on mean genotypic fitness. Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    Whereas, evolution has no rigorous mathematical foundation with which we can rigorously analyze it in any computer simulation:

    Accounting for Variations – Dr. David Berlinski: – video
    http://www.youtube.com/watch?v=aW2GkDkimkE

    EV Ware: Dissection of a Digital Organism
    excerpt: Ev purports to show “how life gains information.” Specifically “that biological information… can rapidly appear in genetic control systems subjected to replication, mutation and selection.” (We show that) It is the active information introduced by the computer programmer and not the evolutionary program that reduced the difficulty of the problem to a manageable level.
    http://www.evoinfo.org/Resources/EvWare/index.html

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009

    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it:

    “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.”
    http://www.pubmedcentral.nih.g.....id=2662469

    etc…etc…

    Thus ROb if you want to argue the intricacies of the math of LCI, I suggest you befriend Demski and Marks and discuss it with them for I only use it as a benchmark to the principle of Genetic Entropy I seek to make a rough outline of.

  120. 120

    Sanford apparently missed this paper when writing his book, which shows how populations with very high genetic loads recover fitness quickly. This, of course, shouldn’t happen if Sanford is correct.

    Estes S and M Lynch (2003). Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans. Evolution 57(5) : 1022-1030.

    From the abstract:

    Deleterious mutation accumulation has been implicated in many biological phenomena and as a potentially significant threat to human health and the persistence of small populations. The vast majority of mutations with effects on fitness are known to be deleterious in a given environment, and their accumulation results in mean population fitness decline. However, whether populations are capable of recovering from negative effects of prolonged genetic bottlenecks via beneficial or compensatory mutation accumulation has not previously been tested. To address this question, long-term mutation-accumulation lines of the nematode Caenorhabditis elegans, previously propagated as single individuals each generation, were maintained in large population sizes under competitive conditions. Fitness assays of these lines and comparison to parallel mutation-accumulation lines and the ancestral control show that, while the process of fitness restoration was incomplete for some lines, full recovery of mean fitness was achieved in fewer than 80 generations. Several lines of evidence indicate that this fitness restoration was at least partially driven by compensatory mutation accumulation rather than a result of a generic form of laboratory adaptation.

  121. 121

    Nak states:

    “I can’t see that this has anything to do with genetic entropy.”

    Genetic Entropy holds that Darwinian processes of Random Variation and Natural Selection cannot increase functional Information above what is available to the probabilistic resources of the universe as a whole (140 Fits; most likely less).

    Then Nak states:

    2 – Many would argue that God can use any material means to affect a change, so any particular counter-example, and all counter-examples in general do not succeed in falsifying anything.

    Well God can use any means as He wants, as Dembski-Marks make clear in their abstract, but genetic entropy holds that God has limited the role in which He will act within nature to increase the functional information,,,If you want to argue whether it was natural processes or God that increased the information you would first have to falsify the tentative 140 Fit limit and then seek to prove either the Theistic or materialistic premise is correct for reality. i.e. you would have to disprove God and/or prove materialism…(Good Luck with that route,,, LOL)

    then Nak asks:

    3 – I must therefore take it that you believe in a God Who has chosen to only use miraculous means to make changes of greater than 140 Fits to the Universe.

    My overwhelming intuition, from all the evidence I’ve seen so far, and from Theology, is this; Once God creates a parent kind, the parent kind is encoded with “optimal information” for the specific purpose to which God has created the kind to exist, and God has chosen, in His infinite wisdom, to strictly limit the extent to which He will act within nature to “evolve” the sub-species of the parent kind to greater heights of functional complexity.

    4 – The verse stating this is missing from my Bible.

    Genesis 2:3
    Then God blessed the seventh day and sanctified it, because in it He rested from all His work which God had created and made.

    You seek to falsify genetic entropy by shuffling information for chlorophyll around, This all begs to question,,,Where did the bacteria get the chlorophyll genes in the first place? As well, if a chlorophyll adaption is indeed beneficial to the salamander in current, how do you propose to find the original “native environment” for the salamander so as to establish the salamander is indeed more fit? Does the salamander now conduct photosynthesis and you are saying it is more fit? Do you know for a fact the salamander did not have Chlorophyll before?… Me thinks I smell many weasels in your example!

    Then you try to be cute in your own eyes again with this:

    Case 2: Same fact pattern as before, but this time the transfer takes place over 1,400,000 years one Fit at a time by 140 or more viral events, once every 10,000 years. BA^FT is still falsified.

    Yet the only evidence we have tells us information is not being generated for bacteria, thus your “ultimate source” for stealing information with you virus (do you say the virus was not designed?), the bacteria falsifies your contention:

    The Paradox of the “Ancient” Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
    Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    and this:

    Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber
    Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart, (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution’s “genetic drift” theory requires.)
    http://www.sciencemag.org/cgi/...../5213/1060

    30-Million-Year Sleep: Germ Is Declared Alive
    http://query.nytimes.com/gst/f.....gewanted=2

    In reply to a personal e-mail from myself, Dr. Cano commented on the “Fitness Test” I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Umpire throws Nak out of the game for not even playing by the rules which were clearly laid out for him.

  122. 122

    Dave your paper does not falsify genetic entropy for the “recovery” of compensatory mutations never makes it back to the fitness that was had in the original parent species bacteria:

    Is Antibiotic Resistance evidence for evolution? – “The Fitness Test” – video
    http://www.youtube.com/watch?v=_BwWpRSYgOE

  123. What evolutionists don’t seem to understand is not only do they need beneficial mutations- beneficial being a reletive word because what is beneficial in one generation may not be in the next or other future generations- but they need them to accumulate in such a way as to give rise to new protein machinery and new body plans.

    And there isn’t any evidence that an accumulation of genetic accidents can do such a thing.

    IOW evolutionists cannot present positive evidence for their position.

  124. As for predictions- If scientific predictions are based on scientific observation and scientific testing, then what can be predicted based on the following…:

    Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state—scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type—the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.—geneticist Giuseppe Sermonti in “Why is a Fly Not a Horse?”

    …seeing that it is based on scientific observation and scientific testing?

  125. 125

    born,

    If Sanford is correct, Genetic Entropy should prevent populations that are heavily degraded with mutations from ever recovering fitness. At the very least, their fitness should have remained at the levels they were at the start of the experiment.
    They didn’t. Estes and Lynch empirically contradicted Sanford’s basic thesis.

  126. Mr BA^77,

    You see, I was right this would take several posts!

    From your response, can I take it that you agree with my restatement, and that the use of several small steps in case 2 was an acceptable part of an answer, even if you disallowed other parts?

    BTW, I don’t think you can object that the virus was designed. The action of the virus was entirely of a material nature. If you take refuge in this kind of “ultimate source” argument, then the whole game collapses again since you can always claim that the ultimate source of matter, energy, and the laws of the universe is God. That might be a comforting theological claim, but it makes for poor predictions in chemsitry and physics, as Newton found out.

    To the question of the ‘native environment’ it is not hard to find. It is the same pond they were in before the viral infection. That is where the wild-type salamanders live.

  127. 127

    Dave states:

    “If Sanford is correct, Genetic Entropy should prevent populations that are heavily degraded with mutations from ever recovering fitness. At the very least, their fitness should have remained at the levels they were at the start of the experiment.”:

    False! you/they start from a known degraded position and then try to rely on compensatory mutations to falsify Genetic Entropy,,,Whereas a strict rendering of the Genetic Entropy principle will hold that only the original un-degraded bacteria is optimal. My only gripe with them is that they claim “full” recovery from compensatory mutations, which is a dubious claim based on the sensitivity of the “Fitness test” they had used to ascertain fitness, I suggest they tweak the sensitivity of their fitness test:

    Testing the Biological Fitness of Antibiotic Resistant Bacteria
    by Dr. Alan L. Gillen and Sarah Anderson
    Excerpt:
    Initially, it was difficult to demonstrate differences between wild-type and clinical strains in a rich media (Nutrient or Typticase-soy agar). There were no differences in growth rate or colony size. However, after switching to minimal media and observing hourly, the differences were readily observed. In order to confirm and extend the differences in growth rates between the sensitive BS303S strain (isolated from pond water) and the resistant WFR strain, a fitness/competition assay was performed. This assay sought to simulate famine conditions in the natural environment by utilizing minimal media and to evaluate the wild-type against ampicillin resistant, clinical strains exhibiting loss of prodigiosin production. Once subjected to conditions that were “harsh,” differences were seen in their performance (growth rate and robustness of colonies).
    http://www.answersingenesis.or.....-drugstore

    Plus Dave from the only evidence available as of yet (Sanford is said to be in the salt mines looking for older samples right now, according to Sal) we find, that when extended to millions of years, the Genetic Entropy effect is very pronounced even in an un-tweaked fitness test:

    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus I would have to say, in being fair with the evidence, you have not falsified the principle of Genetic Entropy and have really just exposed a flaw in their assumption of believing the “compensated” bacteria had truly “fully” recovered.

  128. 128

    Nak,
    You cannot rule out theism in questions of origins since we are questioning the materialistic philosophy itself in these matters of origins!

    As well, materialism is horrendous in predictions for science! Need I break my list out again.

    As far as you salamander conjectures, please cite the study so as I can see what they found instead of only hear of what you think they found.

  129. 129

    born writes:

    {i]False! you/they start from a known degraded position and then try to rely on compensatory mutations to falsify Genetic Entropy,,,Whereas a strict rendering of the Genetic Entropy principle will hold that only the original un-degraded bacteria is optimal

    This is nonsense. Genetic Entropy should apply at any stage of a population’s lifetime. Fitness was measured in terms of producing progeny and those progeny surviving to maturity (Estes and Lynch used a eukaryotic, sexually-reproducing species rather than bacteria).

    If genetic entropy is operating, the fitness measurements should never improve significantly, and instead should decrease significantly if the mutational load is very high. Instead, what Estes and Lynch saw was increased fitness in some lines,

    That should never happen if Genetic Entropy is operating on those genomes, especially ones with such high genetic loads. .

  130. 130

    Dave states:
    “This is nonsense.”

    Why? You have not demonstrated an increase of fitness over the original bacteria? And in all fairness, if they tweak the fitness test, the compensatory mutations will be found to be slightly less fit,,thus they can not even claim “full recovery”…Whereas I am only holding that the original bacteria created by God is optimal! Why should you hold that Genetic Entropy is falsified when even modern computer programs have a slight capacity to recover data that has been lost (saving lots of heartache I might add),,,should not this ability argue even more forcefully for design? Especially since the original optimality is not trespassed? For you to blatantly ignore the fact that the original bacteria retains superior fitness, while only citing the ability to recover “near full” fitness is clearly biased on your part. If you were fair with the evidence you would also demand that the fitness test be violated by sufficient degree as to make the case for evolution unquestionable! But it seems evolution is allowed all sorts of free passes when it comes to hard science…Why is this Dave? Of what loss is it for you if evolution is found to be false? Why do you overlook such a clear requirement for evolution to pass?

  131. bornagain77:

    I am not seeking to verify LCI. In fact Dembski/Marks make it clear what LCI will do:
    “Though not denying Darwinian evolution or even limiting its role in the history of life, the Law of Conservation of Information shows that Darwinian evolution is inherently teleological. Moreover, it shows that this teleology can be measured in precise information-theoretic terms.”

    Yes, and what I’m saying is that their claim is, as a matter of easily verifiable fact, untrue. Including Marks’ and Dembski’s work in your arsenal of sources detracts from the otherwise stellar credibility of your arguments.

  132. 132

    ROb,
    Thanks for the information,,,I will have to look more closely on what has happened with LCI, and may have to use something else to balance against the second law….Although One thing for sure from the LCI abstract, that I had not ever realized before, is the teleological aspect of it all. i.e. Materialism is in no way to be allowed a free ride in these matters of origins.

  133. 133

    born writes:

    Dave states:
    “This is nonsense.”

    Why? You have not demonstrated an increase of fitness over the original bacteria?

    Um, yes they did. The populations recoved their fitness back to the fitness of the ancestral control population, i.e., before the mutational degradation. And they didn’t use prokaryotic, asexual bacteria. C.elegans is a eukaryotic, sexually reproducing species.

    And in all fairness, if they tweak the fitness test, the compensatory mutations will be found to be slightly less fit,,thus they can not even claim “full recovery”

    Fairness to whom? Sanford? They don’t need to tweak the fitness test. It is a simple, straightforward, comparative measure of reproductive success. If Sanford’s thesis works as he says it should, there should have been no fitness recovery to that of the ancestral control population.

    But there was.

  134. Dave states in response to if Genetic Entropy was violated:

    “Um, yes they did. The populations recoved their fitness back to the fitness of the ancestral control population”

    So the information content of the ancestral population is not exceeded by your own admission.

    Once again Dave, I am only holding that the ancestral parent lineage to be more fit (optimal) over its sub-species, I am in no way holding that God did not build in elaborate “compensatory” mechanisms. I am just holding that the “original” bacteria will never be exceeded in functional information by its sub-species.

    Why do you think their fitness test should not be tweaked for sensitivity? If you truly were concerned about the truth of the matter you would also demand a more sensitive fitness test, as I am suggesting, so in order to ascertain as clearly as possible if the ancestral population had been exceeded in fitness!

    Testing the Biological Fitness of Antibiotic Resistant Bacteria
    by Dr. Alan L. Gillen and Sarah Anderson
    Excerpt:
    Initially, it was difficult to demonstrate differences between wild-type and clinical strains in a rich media (Nutrient or Typticase-soy agar). There were no differences in growth rate or colony size. However, after switching to minimal media and observing hourly, the differences were readily observed. In order to confirm and extend the differences in growth rates between the sensitive BS303S strain (isolated from pond water) and the resistant WFR strain, a fitness/competition assay was performed. This assay sought to simulate famine conditions in the natural environment by utilizing minimal media and to evaluate the wild-type against ampicillin resistant, clinical strains exhibiting loss of prodigiosin production. Once subjected to conditions that were “harsh,” differences were seen in their performance (growth rate and robustness of colonies).

    I mean come on Dave,,, Do you not think evolution is up to the task of withstanding a little tweaking?
    Shoot you hold that evolution can accomplish far more complexity than what would be required for this one test, Do you not?

  135. 135

    @jerry 81:

    Well I might object to the doom and gloom alarmism as well. I usually do. But it still seems obvious that if errors occur and are not selected out in some way they will accumulate. I am a YEC as well, so I wouldn’t object to Sanford’s idea on theological grounds as you appear to be doing. It seems clear that genetic information will degrade over time. We know that happens. It’s why we forbid people to marry relatives. It also seems clear that errors which do not affect reproduction will not get selected out, so they will get passed on. The next generation will have more errors like this, and so on. Obviously fatal errors will result in miscarriages, so probably the alarmism is not really warranted. I might object so Sanford as well, but genetic entropy of some kind is an undeniable reality. I don’t see how it could be otherwise.

    Reading some of the other discussion, I doubt that all information loss affects fitness. In fact some information loss appears to affect fitness positively. I don’t think information loss can reliably be measured using fitness tests. The only way to measure it would be to determine functions versus non-functions and catalogue when function goes to non-function. The old, 19th century view of biology is not going to apply to new ideas.

  136. 136

    @Joseph 83:

    Well what is the information then? Dr. Meyer would not of course say we can see it with a microscope or with the naked eye. It’s too small.

  137. Tragic:

    The fitness test relates to both information and molecular functionality, thus is a accurate measure if molecular functionality/functional information (Fits) has been gained or lost:

    Three subsets of sequence complexity and their relevance to biopolymeric information – David L Abel and Jack T Trevors:
    Excerpt: Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction…No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization…It is only in researching the pre-RNA world that the problem of single-stranded metabolically functional sequencing of ribonucleotides (or their analogs) becomes acute. And of course highly-ordered templated sequencing of RNA strands on natural surfaces such as clay offers no explanation for biofunctional sequencing. The question is never answered, “From what source did the template derive its functional information?” In fact, no empirical evidence has been presented of a naturally occurring inorganic template that contains anything more than combinatorial uncertainty. No bridge has been established between combinatorial uncertainty and utility of any kind.
    http://www.pubmedcentral.nih.g.....id=1208958

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.youtube.com/watch?v=vUeCgTN7pOo

    In The Beginning Was Information – Werner Gitt – video
    http://video.google.com/videop.....6003871702

    etc… etc..

    In fact this is given even more weight since quantum teleportation has shown “information” is foundational to reality:

    Reflection on the quantum teleportation experiment:

    That a photon would actually be destroyed upon the teleportation of its “infinite” information to another photon is a direct controlled violation of the first law of thermodynamics. Thus, this is a direct empirical validation for the primary tenet of the Law of Conservation of Information (i.e. information cannot be created or destroyed). This conclusion is warranted because information exercises direct dominion of energy, which cannot be created or destroyed by any known material means, yet a photon of energy is destroyed by this transcendent means. Thus, this experiment provides a direct line of logic that transcendent information cannot be created or destroyed. Clearly anything that exercises dominion of the fundamental entity of this physical universe, energy, must of necessity possess the same, as well as greater, qualities. i.e. All information that can exist, for all past, present and future events of energy, already must exist. Another line of evidence, corroborating the primary tenet of the Law of Conservation of Information, is the required mathematical definition for infinite information needed to correctly specify the reality of a photon qubit (Armond Duwell).

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) — Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a qubit, an infinite amount of information must be transferred to teleport.

    As well many Quantum physicists hold that reality, at its base is information:

    Why the Quantum? It from Bit? A Participatory Universe?
    Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: “In the beginning was the Word.”
    Anton Zeilinger – a leading expert in quantum teleportation:

    This following experiment clearly shows information is not a “emergent property” of any solid material basis as is dogmatically asserted by some materialists:

    Converting Quantum Bits: Physicists Transfer Information Between Matter and Light
    Excerpt: A team of physicists at the Georgia Institute of Technology has taken a significant step toward the development of quantum communications systems by successfully transferring quantum information from two different groups of atoms onto a single photon.
    http://gtresearchnews.gatech.e.....mtrans.htm

  138. 138

    @scordova 93:

    “The mechanism which created the first life appears not to be in operation today.”

    I have heard even evolutionists agree with this. My biochem prof in college said he believes evolution is finished. I suppose he means that all possible paths have been traversed, not that random mutation and natural selection no longer operate.

  139. Re. #18:

    I get the message loud and clear: Scientist Salvador Cordova recommend creationists should read more ID literature.

    What’s wrong with science? Why should not creationists learn a little science; they most likely already know most of the arguments of creationism. Maybe a few doses of of argument from the horse’s mouth so to speak might give them a better understanding of what the debate is all about?

    Ought not an introduction to ID begin with Pandas and People, the Wedge Document before advancing to Darwin’s Black Box?

    But even before that, what about uncontroversial books like
    The Beak of the Finch, Weiner,
    The First Chimpanzee, Gribbin & Cherfas,
    Life As it Is, Loomis,
    Your Inner Fish, Shubin,
    Endless Forms Most Beautiful, Carroll.

    They are filled with facts…

    If someone abandons acceptance of evolution after reading a book by Behe is no more evidence for the validity of ID than the fact that a lot of rich and influential people trusted Bernie Madoff.

    BTW, Sal might enjoy a visit to AtBC; the new ID Timeline project looks like it may become an important ‘portal’ for newcomers to ID.

  140. 140

    bornagain:

    What I mean is it appears that what Dave Whisker’s cited paper refers to as “laboratory adaptation” entails organisms which lose information but gain fitness in controlled environments. Specifically, E. coli growing on glucose lose some of their ability to use other food sources. This appears to result in an increase in fitness since they no longer have to copy or translate genes they can’t use anyway. That’s all I meant.

    In a laboratory environment, it’s never clear whether increased fitness can be tied to information gain or information loss, until you have defined exactly what those are and controlled for them. That is the key statement of the Lynch paper, and the conclusions to draw from it would rest almost entirely on whether or not these “compensatory mutations” can be shown to independently increase fitness, without laboratory adaptations involved.

    Behe, after all, states that his CCC is probably one mutation that confers the benefit and one that compensates for the deleterious effects of the first. If the compensatory mutations in the Lynch paper are only “compensating” for information loss during the course of the experiment (laboratory adaptation) and not for information loss that occurred prior, then it’s not even interesting.

  141. Dave wrote:

    If genetic entropy is operating, the fitness measurements should never improve significantly, and instead should decrease significantly if the mutational load is very high.

    Part of the problem is that fitness is measured by reproductive success. We know natural selection is a powerful mechanim for infusing reproductive success at the cost of function (i.e. blind cave fish, anti-biotic resistance, sickle cell anemia, etc.)

    As Lewontin and Orr and Andreas Wagner point out, reproductive abundance is not necessarily the best barometer for increase in function, function that is, defined by the standards of engineers, not evolutionary biologists.

  142. Tragic,
    I am sorry for my misunderstanding, it seems you have a very good grasp on what is occurring.

    i.e. “If the compensatory mutations in the Lynch paper are only “compensating” for information loss during the course of the experiment (laboratory adaptation) and not for information loss that occurred prior, then it’s not even interesting.”

  143. Sanford apparently missed this paper when writing his book, which shows how populations with very high genetic loads recover fitness quickly. This, of course, shouldn’t happen if Sanford is correct.

    Estes S and M Lynch (2003). Rapid fitness recovery in mutationally degraded lines of Caenorhabditis elegans. Evolution 57(5) : 1022-1030.

    Dave,

    Thank you for participating. Much appreciated.

    And thank you for the citation, but my reading says that the deleterious mutations were not washed out (via purifying selection). Is that consitent with your reading?

    Sal

  144. Bornagain77,

    Dave states in response to if Genetic Entropy was violated:
    “Um, yes they did. The populations recoved their fitness back to the fitness of the ancestral control population”
    So the information content of the ancestral population is not exceeded by your own admission.

    Irrelevant to Sanford’s general thesis. The increase should never have happened.

    Once again Dave, I am only holding that the ancestral parent lineage to be more fit (optimal) over its sub-species, I am in no way holding that God did not build in elaborate “compensatory” mechanisms. I am just holding that the “original” bacteria will never be exceeded in functional information by its sub-species.

    That’s all well and good– I’m more interested in exploring Sanford’s general genetic entropy thesis. Your thesis is somewhet different, and Estes and Lynch’s experimental design is not relevant to that. I think it would require a different design to test what you seem to be talking about.

    Why do you think their fitness test should not be tweaked for sensitivity? If you truly were concerned about the truth of the matter you would also demand a more sensitive fitness test, as I am suggesting, so in order to ascertain as clearly as possible if the ancestral population had been exceeded in fitness!

    There is no need to tweak the test for ‘sensitivity’– the populations showed significant increases in fitness that were clearly measurable, and sensitive enough to contradict Sanford’s predictions. The only reason Gillen and Sanderson needed to tweak their fitness test was because they weren’t able to discern differences between the wild-type and the clinical strains. If differences are clearly discerned without tweaking, as Estes and Lynch saw, then their fitness assays need no modifications. As I mentioned above, what you are concerned with would involve a change in the basic experimental design (manipulating the environmental conditions) rather than tweaking the fitness assays.
    You seem to think the level of fitness in the ancestral population of C. elegans can never be exceeded. Estes and Lynch’s experiment was not concerned with that, and neither am I in this thread. What Estes and Lynch clearly showed, however, is that species can overcome mutational degradation on their own. Entropic degradation of their genomes is not inevitable, nor is decline in fitness. That is a problem for Sanford’s general thesis.

    I mean come on Dave,,, Do you not think evolution is up to the task of withstanding a little tweaking?

    I don’t believe in tweaking for tweaking’s sake. I certainly don’t believe in tweaking when the the actual modifications to test your contention (as opposed to Sanford’s general thesis) involve something other than the fitness assays!

  145. Cabal wrote:

    Ought not an introduction to ID begin with Pandas and People, the Wedge Document before advancing to Darwin’s Black Box?

    I can’t speak for others but after the reading the Wedge document, I thought to myself, “sign me up for the ID movement”. And then I sent a donation in.

  146. Hi Sal,

    Thanks for the greeting. I know about your concerns about measuring fitness from our ARN days, but in thius case that is not an issue. Sanford echoes Crow’s concern about declining fitness in the human population, and Crow’s definition of fitness has always been reproductive success, so unless Sanford specifically defines fitness differently (and I don’t recall him doing so in his book, but I could be wrong) Estes and Lynch’s fitness assay is applicable to evaluating the genetic entropy thesis.

  147. Dave you state:
    “You seem to think the level of fitness in the ancestral population of C. elegans can never be exceeded. Estes and Lynch’s experiment was not concerned with that, and neither am I in this thread.”

    Well I hold that they are flawed in their test for they have not used sufficient sensitivity in the fitness test and thus failed to show that the compensated bacteria are less fit than the original ancestral strain..Thus its strains incredulity to maintain that they have falsified Genetic Entropy…Clearly you are biased in what you will accept as evidence since it is clear a designer, God in this instance, would very likely build compensatory mechanisms in the original bacteria,,,as well if they were fair to the evidence they would have demanded more sensitivity on the fitness test to differentiate as clearly as possible that the compensated strain had achieved “perfect” equilibrium of fitness,,,I have shown what it takes to “up the sensitivity” of the test. And make the bold prediction that the ancestral strain will indeed be found to be more robust than the “compensated strain…

  148. Scordova,

    Careful buddy, your actions will be reported to [email protected] or maybe even [email protected].

    vWe have vwwaaays of dealing vwith people vlike vyou.

    The proletariot brothers and sisters have arisen in America, we know your evil plans and vweee vwwilll crusssh them! Because afterall, we beleive in Darwin and thus are at a higher level of reason than you.

    For all fellow brothers and sisters monitoring this site, ahmm, I mean, participating democratically and freely in open discussion on this site, please report any Darwinian Fishy tales to [email protected].

    Or report back to our komrades at Peoples Cube and press the Hammer and Sick…, uh the OnCare Button on the Far Left Side of our web site. It will take you immediately to our watchdog information specialist for formulation and twisting. They will either make more reports and filings with our Dear Leaders, or file a lawsuit against the UnConformers! Blashemy!

    The Peoples Cube – Down on Dissent, Conformity is Comfy

    Remember, anyone not aligned with our position, you can report your family, friends or just passers by you overhear at restuarants and any public place who may say something Fishy. You can report yourself should you feel guilty about your past and need to attend our Re-Education camps like DawkinDelight and PZ-Peewee Camp for reintro to a normal conformed transformatoin makeover.

    Report any fishy details from blogs against Darwin, or heck, just against atheist and leftist truth. Because there can only be one truth and the truth only points to Teh One – Darwin. If you do not have time to visit the Peoples Cube, you may go directly to our Komrades at ACLU.com.

    Thank you for your time brothers and sisters in arms, we marx, uh, we march arm in arm for justice so that everyone thinks like we do. Tear out the rats of non-confirmity and those who dare dissent today. Or like a disease their scurry rat virus will spread and soon, people will begin to think outside the Borg Collective and all salvation for the many will be lost.

    This is a message from your DisInformation office of the High Elite Council and Guardians of Teh One.

  149. Dave states:

    “so unless Sanford specifically defines fitness differently (and I don’t recall him doing so in his book, but I could be wrong) Estes and Lynch’s fitness assay is applicable to evaluating the genetic entropy thesis”

    Appealing to authority, as to what I clearly have shown has been brought into question, makes you no less wrong in what the truth of the matter is. Namely Genetic Entropy’s primary tenet of “zero gain” in functional complexity over ancestral strain, and more importantly a loss of functional complexity in the compensated bacteria’s robustness… til you prove otherwise your argument that GE is falsified is without true merit whether you admit it or not, and no amount of appealing to authority will change the truth of the matter!

  150. And thank you for the citation, but my reading says that the deleterious mutations were not washed out (via purifying selection). Is that consitent with your reading?>/i>

    Yes, as the pattern of fitness recovery (and its rapidity) indicated that compenmatory mutations were the most likely explanation in this case. But the experimental design should be kept in mind here. The large degraded population was brought about by bringing together multiple lines where the mutations were concentrated in each line via extreme periodic bottlenecks. So the genetic load was not only enormous but sudden as well.

  151. born,

    Well I hold that they are flawed in their test for they have not used sufficient sensitivity in the fitness test and thus failed to show that the compensated bacteria are less fit than the original ancestral strain..

    If the experimental population showed significant increases in reproductive success, then they are showing increases in fitness. A demand for more ‘sensitivity’ isn’t necessary, and is irrelevant.

  152. Hi Sal,

    Thanks for the greeting. I know about your concerns about measuring fitness from our ARN days, but in thius case that is not an issue. Sanford echoes Crow’s concern about declining fitness in the human population, and Crow’s definition of fitness has always been reproductive success, so unless Sanford specifically defines fitness differently (and I don’t recall him doing so in his book, but I could be wrong) Estes and Lynch’s fitness assay is applicable to evaluating the genetic entropy thesis.

    Hi Dave,

    Your observation has merit. When I was visiting with Dr. Sanford, I suggested a more accurate way to empirically measure the phenomenon would be through examining the spread of single nucleotide polymorphisms (or any mutation for that matter) in deeply “conserved” regions between humans and mice or even between humans.

    This could be done provided companies like Solexa and Illumina come through with their promised ultra cheap sequencing technologies whereby an entire mapping a person’s genome could be done for $3,000.

    The benefit of this approach is that classifying something in terms of fitness and function becomes irrelevant. It measures the inability of selection to police and purify large genomes. It could pontentially reinforce Kimuras thesis that most of molecular evolution is not subject to selection. This would then pose a problem for explaining the vast amount of function in “junk DNA”.

    Unfortunately, the idea came up at the end of an 8-hour conversation at his home, and we weren’t able to work out the details of a possible exploration and appropriate experiments and observations. Maybe next time. I hope to see Walter ReMine in a few weeks.

    In any case, Jody Hay’s simulation at Rutgers might have bearing on these issues. Hay’s simulation had some peculiar idiosyncracies that are disconcerting and they need to be addressed, but Hay’s simulation on balance seems in the right direction.

    Unfortunately, I don’t have strong background in population biology. Do you have expertise in this area. I would welcome critique of some of my ideas.

    regards,
    Sal

  153. Frost122585,

    I looked for you at Stephen Meyer’s presentation at McLean Bible Church June 25, 2009. Were you there?

    In any case, nice to see you again here at UD.

    Sal

  154. Sal,

    When I was visiting with Dr. Sanford, I suggested a more accurate way to empirically measure the phenomenon would be through examining the spread of single nucleotide polymorphisms (or any mutation for that matter) in deeply “conserved” regions between humans and mice or even between humans.

    What phenomenon? Fitness? What would looking at SNP’s in deeply conserved areas would tell you? Maybe I just don’t understand exactly what you are getting at. If you like, drop me a PM over on ARN. I work in molecular ecology, which combines molecular biology and population biology, so maybe I can understand where you’re coming from.

  155. 155

    As Sal and I have both stated, fitness is not a reliable measure of information loss/loss of function. The idea of fitness is an evolutionary idea. Design theory is likely to produce more stringent criteria. If Sanford’s GE depends on fitness as a measure, than it is likely flawed. That does not mean, however, that “genetic entropy” of some type does not occur. I think it does. Here’s an excerpt from Stephen Meyer’s interview on Coast to coast (thanks for the youtube link bornagain):

    SM: One of the parts of the research program of the intelligent design research community is to distinguish what we call the aboriginal design from subsequent decay. And we do see in life things that are not functioning as they were originally intended. Mutations are a great example.

    Interviewer: How about disease?

    SM: Disease is another example. I have a colleague, Scott Minnich, a microbiologist at the University of Idaho, who works on virulence and all these different diseases that are produced, things like the plague for example. It’s an interesting discovery in this field that very often times these diseases that are so undesirable from a human point of view have been produced because of mutations in the aboriginal, the original genomic instructions, the degradation of the original genomic program. You can trace the mal-adaptive or outright nasty diseases to those changes which have taken place.

  156. Mr BA^77,

    With respect to the demand that a sub-population have better fitness than the ancestral population in the environment of the original population – why?

    Penguins don’t have to fly to be good swimmers, just the opposite. Whales don’t run very well. I don’t absorb oxygen through my gills as well as my fishy anscestor. None of those are examples of genetic entropy. A penguin with shorter wings and more fat has not lost information as it gained function in a new environment.

    Your Sermonti quote above assumes the wind stops blowing. That doesn’t admit that there are permanently different ecological niches, and that species can migrate in and out of them.

  157. tragic mishap,

    Dr Meyer thinks the information is the sequence.

    I say the sequence alone cannot direct the chemical reactions, the timing, the placement, the transcription and translation, the proof0reading, the error-correction, the assmebly, etc., etc.

    The is information embedded onto/ into the sequence.

    Are you familiar with how computers operate?

    Do you understand the difference between hardware and software?

  158. Design can counter genetic entropy.

  159. Dave,

    Thank you for the kind offer, I would like to take the matter up with you.

    First off:

    I just looked at ARN, there is no “Dave Wisker” in the membership list. You probably posted under a different handle there.

    I realize now who you might be.

    I am sensitive to privacy concerns so perhaps there is a way we can communicate via another channel.

    You provided an e-mail address you UD registration. I can contact you through that e-mail address and then we can arrange a way to communicate if you feel uncomfortable using the e-mail address.

    Also, this if you feel uncomfortable with UD having the e-mail address you provided, you might be able to change it.

    Let me know what works for you.

    regards,
    Sal

  160. Dave,

    The other thing.

    If you try to reach me at ARN, give me a few minutes to re-enable my PM box. I shut it off for the last two years.

    Sal

  161. Apparently fitness is not a good measure of information gain either. People who suffer down syndrome have more genetic material than those who do not.

    But then again, you could always say that because people with down syndrome are less likely to pilot a motor vehicle, then they are consequently less susceptible to being involved in catastrophic car accidents as well- which is more than we can say for those without down syndrome.

    Point being you can put a subjectively positive spin on pretty much anything, which constitutes a lot of what Darwinists put forth when reporting evolutionary advancements regardless of what detrimental factors may add up, outweigh, or even negate the positive effects. And sometimes the positive effects themselves don’t even follow from proposed Darwinian mechanisms because of preprogrammed information and/or machinery having already been present when the change is observed.

  162. 162

    Dave,
    For you to ignore the fact that the bacteria did not exceed the “fitness” of the ancestral strain, reveals your philosophical bias. If increased functional complexity was “no big deal”, as evolutionists maintain and blindly repeat over and over like the good Darwinbots they are, then why in the world are you satisfied with this test? It seems as obvious as the noon day sun that “equilibrium” is a very suspect thing to have in this experiment and should at the very least immediately bring about questions as to evolutions claim for “creating” all the life on earth…. Yet, when I point to work which has increased sensitivity of the “fitness test”:

    Testing the Biological Fitness of Antibiotic Resistant Bacteria
    by Dr. Alan L. Gillen and Sarah Anderson
    Excerpt:
    Initially, it was difficult to demonstrate differences between wild-type and clinical strains in a rich media (Nutrient or Typticase-soy agar). There were no differences in growth rate or colony size. However, after switching to minimal media and observing hourly, the differences were readily observed.
    http://www.answersingenesis.or.....-drugstore

    You are not even interested in the least to find if “true equilibrium” was regained by the compensated bacteria!

    That you would claim to have integrity in methodology, and not even concede the anomaly of equilibrium, that would send up red flags with any other scientist worth his salt, clearly tells me you could care less about the actual truth of the matter and apparently only care to cast GE in a negative light.

    When I pointed out that ancient 30 million year old bacteria conformed exactly to what was predicted by GE, even in a “un-sensitized” fitness test, again this fell on deaf ears…. Of what possible advantage is it to you to practice science in such an overtly biased manner? Should you not rigorously question such anomalies as “perfect equilibrium” when evolution clearly predicts increased functional complexity?
    Luckily science will advance anyway in spite of biases such as the one you are currently displaying.

  163. PaulN,
    do people with Down’s syndrome reproduce more often than those without?

  164. tragic mishap,

    It’s an interesting discovery in this field that very often times these diseases that are so undesirable from a human point of view have been produced because of mutations in the aboriginal, the original genomic instructions, the degradation of the original genomic program.

    I think it’s fair to say this view would still be unthinkable if not for the groundbreaking article by Dr. Jerry Bergman in Creation Ex Nihilo Technical Journal (web version here).

    AFDave Hawkins has a good survey on his blog. Conclusion: Teh bugs were created good!!

  165. 165

    Sal,

    I have no problem with communicating via PM. As you probably have guessed, I’m “KC” over there. If you prefer email, I don’t care if you use my email on UD.

    Either way is cool with me.

  166. PaulN,
    never mind, i was confused about your point

  167. Khan,

    do people with Down’s syndrome reproduce more often than those without?

    No, but that’s beside the point I was making. The point behind that post was to illustrate a misleading tactic often used by Darwinists to substantiate their claims. Perhaps I could have chosen a better example, but I’m sure you understand the idea nonetheless.

  168. You can disregard that last post, I must have been typing it while you posted the withdrawal from your question, sorry!

  169. Mr PaulN,

    Point being you can put a subjectively positive spin on pretty much anything[.]

    Which is why people keep coming back to reproductive success to measure fitness.

  170. Mr Joseph,

    Design can counter genetic entropy.

    Can you elaborate on that thought? If genetic entropy is acting constantly, does that mean that design intervention is happening constantly also?

  171. 171

    born,

    Before you go lecturing anyone on doing science, I suggest you reread your cited paper. The author’s experiment basically demonstrated only one thing: that the genotypes of resistant bacteria show differing fitnesses compared to wild-type depending on environmental conditions. Under ampicillin treatment, the mutant genotype has superior fitness to wild-type. Under normal laboratory conditions, the mutant genotytpe is selectively neutral, that is, it has the same fitness as the wild-type. However, under starvation conditions, the wild-type has superior fitness over the mutant. In other words, the resistant genotype’s adaptive value varies depending on the enviroment in which it finds itself.

    This is an utterly trivial and uncontroversial finding. Off the top of my head I remember Dobzhansky talking about adaptive value of a genotype being environment dependent in his 1937 book Genetics and the Origin of Species. So your paper’s authors are simply confirming what evolutionary biologists have known for a very long time. That you seem unaware of this suggests to me that you could benefit by catching up on at the very least the last 72 years of evolutionary biology.

  172. Nakashima,

    Which is why people keep coming back to reproductive success to measure fitness.

    Yes but is that metric not so course as to allow for imminent entropy? Surely if natural selection is limited to reproductive success then will not the majority of bad mutations(specifically those that do not completely cut off reproductive capability, of which there are many) fly right under the radar and into the next generation?

  173. Mr PaulN,

    Yes but is that metric not so course as to allow for imminent entropy?

    The metric does not create the condition. If entropy is happening, it is happening whether it is measured well or badly.

  174. 174

    Dave,
    Are you trying to cover up your blatant bias by pretending you have refuted me with such trivial obfuscation as that?

    To bring the point home to your heart:

    YOU HAVE NOT VIOLATED GENETIC ENTROPY!!!!

    Let’s read the paper more closely,

    “When nutrients and proper temperature are maintained, both wild-type and resistant bacteria grow nicely in the Petri dish and in the body. But as conditions turn harsh, only the more fit bacteria (wild-type) grow well. Therefore, in order to simulate competition in the wild, bacteria must be grown on minimal media. Minimal media mimics better what bacteria experience in a natural environment over a period of time. This is the place where fitness can be accurately assessed. Given a rich media, they grow about the same”

    Yet, you maintain that evolution will increase functional complexity?

    Yet when we look for it it is always missing in parents native environment.

    How in the world are you trying to turn this around on me, when the ancestral strain is clearly vindicated in a “raw” environment and you have demonstrated ZERO increase in functional complexity?

    The paper clearly illustrate to what most people, with common sense, can perfectly understand is that when sensitivity is increased in the fitness test the “ancestral” ALWAYS performs better!

    In fact Your VERY OWN TEST, which you cited, did not surpass the fitness of ancestral strain and I merely pointed out that the sensitivity could be increased in the test so as to differentiate the “equilibrium” anomaly witnessed….

    For you then to try to fudge things around and obfuscate the point that I have clearly made several times, is a crying shame on your part and reveals you would rather advance your philosophical bias than practice true science!

    I maintain Genetic Entropy stands unscathed.

    You said some snide comment that I should catch up on 72 years worth of science…

    EXCUSE ME,,,If they have had 72 years to correct this, but are still teaching (brainwashing) this complete and utter garbage of evolution to our kids,,, then apparently the evolutionary biologists of the last 72 years have been complete jokes as scientists! That you would lean so heavily on them to try to defend your indefensible position, does nothing to bolster my opinion of you in this matter and I feel you would do well to distance yourself from their horrendous work!

  175. Mr Cordova,

    Since you’ve mentioned it a few times on this thread, here is a link to FPG, a Forward Population Genetic simulator, from the lab of Jody Hey of Rutgers.

    It should be interesting to compare results with Mendel’s Accountant and Gregor’s Bookkeeper programs. Of note is the warning on population size, that the program runs much more slowly as population sizes increase past 1,000. Since few populations are this small in the wild, using the program for realistic studies might take some patience!

  176. 176

    born,

    Are you trying to cover up your blatant bias by pretending you have refuted me with such trivial obfuscation as that?

    I’m not pretending, just revealing the utterly trivial ‘results’ of your favorite ‘paper’ for what they are– inconsequential fluff.

  177. 177

    Dave,
    And yet the fitness test, even by your own admission, was not violated. Thus your claim for falsification of the overriding principle of GE is without any true merit. As well, of what should be of primary importance to you, but you blatantly ignore, Evolution has failed to be vindicated at even this most basic level of experimentation. Grumble all you want, disparage my education, and even drag my name through the mud, but no amount of obfuscation on your part is going to change the truth of these facts.

  178. Mr BA^77,

    Yes, lets read that paper closely.

    Initially, it was difficult to demonstrate differences between wild-type and clinical strains in a rich media (Nutrient or Typticase-soy agar). There were no differences in growth rate or colony size.

    So when we return the antibiotic resistant strain to the normal environment of the ancestral strain, there was no perceptible difference. Genetic entropy is falsified.

    But the researchers don’t like that result, so they decide to ‘tweak’ their fitness test to get the result they know they want. They decide to run a comparison under stressed conditions.

    At the end of 10 hours post inoculation, there was only a 4% difference between BS303S and WFR.

    The final result is a 4% difference. Is 4% statitically significant? They don’t tell you for two reasons:

    1 – this is not peer reviewed science, this is street theater on a YEC website.

    2 – the authors want you to ignore the 4% result and focus on the intermediate results.

    Our experience with competition studies reveals that demonstrating fitness costs in the laboratory is tricky and creation biologists should be careful about making dogmatic statements like, “Wild-type bacteria always outcompete antibiotic resistant mutants in nature.”

    Mr BA^77, they seem to be addressing you directly in this sentence.

  179. Nakashima,

    The metric does not create the condition. If entropy is happening, it is happening whether it is measured well or badly.

    Well I just happen to agree with that. =P

  180. 180

    Mr Nakashima,

    Thank you for bringing up teh “statistically significant” question. I saw that they said the resulst weer ‘significant”, but failed to notice they didn’t–as real scientists do– give the statistical analysis supporting that.

    Nice catch.

  181. 181

    Nak,

    you state “Genetic entropy is falsified.”

    But even you admit the mutated strain compete “equally” with wild,,, should not even you, as a dogmatic evolutionists, find the consistent lack of “improved” molecular functionality anomalous?
    Don’t you truly believe that bacteria turned into trees and cows and pigs and cute little bunny rabbits with absolutely no help from Almighty God? Of course you do! Then why do you not demand a modicum of proof for such grand claims?
    That the fitness would be so marginally successful (4%)for the wild does not detract from the fact that it is still a loss of fitness for the mutated,,,that they would fail to connect it to Genetic Entropy does not surprise me,,, tell you what Nak show me a test where the mutated had ANY % increase of fitness over the ancestral! How about that,,,then when and if you finally do that calculate to see if you have generated the 140 functional bits needed to falsify genetic entropy,,,until then the rigors of science are not being respected by you or Dave.

  182. Mr BA^77,

    But even you admit the mutated strain compete “equally” with wild,,, should not even you, as a dogmatic evolutionists, find the consistent lack of “improved” molecular functionality anomalous?

    What lack? The mutated strain is antibiotic resistant and makes its home in hospitals and nursing homes where the wild type can’t survive.

    Then why do you not demand a modicum of proof for such grand claims?

    Indeed, without the fossil record, biogeography, molecular phylogenies, genetics, the discovery of DNA, etc. etc. etc. the theory of evolution would have no basis at all, except for common sense.

    tell you what Nak show me a test where the mutated had ANY % increase of fitness over the ancestral! How about that,,,then when and if you finally do that calculate to see if you have generated the 140 functional bits needed to falsify genetic entropy,,,until then the rigors of science are not being respected by you or Dave.

    I don’t think the BA^FT is really about the rigors of science. We can talk more later about falsifying the Finger of God.

  183. 183

    Nak,
    You neglect to remember, At a cost of 4% functionality,,,albeit small, but still a indication it came at a cost of functional information… thus you reveal a bias,,,I am surprised you would cling to such a thing, just so you could deny what you disparagingly call “the finger of God”.

    You cite:
    the fossil record Yet,
    the Cambrian explosion destroys your foundation rationale to claim this as proof!

    molecular phylogenies:

    this is false also:

    “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009)
    Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,”,,,“despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” ,,,,Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”,,,“We’ve just annihilated the (Darwin’s) tree of life.”
    http://www.evolutionnews.org/2......html#more

    On top of that your supposed strongest proof for genetic similarity now lies in tatters:

    For prime example of the flimsy “similarity evidence” used by materialists to try to make their case for evolution, most materialists are adamant Darwinian evolution is proven true when we look at the supposed 98.8% genetic similarity between chimps and man. Though suggestive, the gene similarity, even if true, is not nearly good enough to be considered conclusive scientific proof. Primarily this “lack of conclusiveness” is due to concerns with the second law of thermodynamics and with the Law of Conservation of Information. But of more pressing concern, body plans are not even encoded in the DNA code in the first place. This inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance.

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    Part 1 http://www.youtube.com/watch?v=5JzQ8ingdNY
    Part 2 http://www.youtube.com/watch?v=o1bAX93zQ5o

    This inability for the DNA code to account for body plans is also clearly shown by extensive mutation studies to the DNA of different organisms which show “exceedingly rare” major morphological effects from mutations to the DNA code.

    Hopeful monsters,’ transposons, and the Metazoan radiation:
    Excerpt: Viable mutations with major morphological or physiological effects are exceedingly rare and usually infertile; the chance of two identical rare mutant individuals arising in sufficient propinquity to produce offspring seems too small to consider as a significant evolutionary event. These problems of viable “hopeful monsters” render these explanations untenable.
    Paleobiologists Douglas Erwin and James Valentine

    This includes the highly touted four-winged fruit fly mutations.

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    If all that wasn’t enough, the Human Genome Project really put the last nail in the coffin for “Genetic Reductionism”:

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”

    Thus the 98.8% similarity derived from the DNA code, to the body plans of chimps and man, is purely imaginary, since it is clearly shown that the overriding “architectural plan” of the body is not even encoded in the DNA in the first place. Of more clarity though, this “98.8% similarity evidence” is derived by materialists from a very biased methodology of presuming that the 1.5% of the genome, which directly codes for proteins, has complete precedence of consideration over the other remaining 98.5% of the genome which does not directly code for proteins. Yet even when considering just this 1.5% of the genome that codes for proteins, we find that the proteins, which are directly coded by that 1.5% of the genome, are shown to differ by a huge 80% difference between chimps and man.

    Chimps are not like humans – May 2004
    Excerpt: the International Chimpanzee Chromosome 22 Consortium reports that 83% of chimpanzee chromosome 22 proteins are different from their human counterparts,,, The results reported this week showed that “83% of the genes have changed between the human and the chimpanzee—only 17% are identical—so that means that the impression that comes from the 1.2% [sequence] difference is [misleading]. In the case of protein structures, it has a big effect,” Sakaki said.

    Eighty percent of proteins are different between humans and chimpanzees; Gene; Volume 346, 14 February 2005:
    http://www.ncbi.nlm.nih.gov/pubmed/15716009

    On top of that huge 80% difference in proteins, the oft quoted 98.8% DNA similarity is not even rigorously true in the first place. Just considering this 1.5% of the genome, other recent comparisons of the protein coding genes, between chimps and man, have yielded a similarity of only 96%. Whereas, the December 2006 issue of PLoS ONE reported that human and chimpanzee gene copy numbers differ by 6.4%, which gives a similarity of only 93.6% (Hahn). Even more realistically, to how we actually should be looking at the genomes from a investigative starting point, Dr. Hugh Ross states the similarity is closer to 85% to 90% when taking into account the chimp genome is about 12% larger than the human genome. A recent, more accurate, human/chimp genome comparison study, by Richard Buggs in 2008, has found when he rigorously compared the recently completed sequences in the genomes of chimpanzees to the genomes of humans side by side, the true genome similarity between chimps and man fell to slightly below 70%! Why is this study ignored since the ENCODE study has now implicated 100% high level functionality across the entire human genome? Finding compelling evidence that implicates 100% high level functionality across the entire genome clearly shows the similarity is not to be limited to the very biased “only 1.5% of the genome” studies of materialists.

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.

    If you noticed, the chimpanzee is found to have a 12% larger genome than humans. Thus, at first glance it would seem the chimpanzee is more evolved than us, but this discrepancy is no anomaly of just chimps/humans. This disparity of genome sizes is found throughout life. There is no logical “evolutionary” progression to be found for the amount of DNA in less complex animals to the DNA found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species and this mystery is known as the c-value enigma:

    C-value enigma
    Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;

    This following paper reiterates the biased methodology of establishing 98.8% similarity, between chimps and man, used by materialists:

    The Unbearable Lightness of Chimp-Human Genome Similarity
    excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. “Relative differences: The myth of 1%,” Science 316: 1836.). Part of the reason for this is if one decides to take into account the plethora of species-specific DNA insertions and deletions (“indels”) that are present along any segment compared between chimp and human, the percentage of identity drops. Another reason is that duplications, inversions, translocations, and transpositions at all scales uniquely characterize the two genome sequences — these have to be untangled before aligning the sequences in order to measure their similarity. Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes. Many mammalian protein-coding regions are highly conserved, however. We also have to consider that a detailed comparison of certain “heterochromatic” chromosome regions between chimps and humans has yet to be made. In short, the figure of identity that one wants to use is dependent on various methodological factors.
    you cite:

  184. 184

    Lets go back to the fossil record oh open minded Nak,

    This following quote, by a leading evolutionist in the field, is candid in its admission of the gaps for “human evolution” fossil evidence.

    A 2004 book by leading evolutionary biologist Ernst Mayr stated that “The earliest fossils of Homo, Homo rudolfensis and Homo erectus, are separated from Australopithecus (Lucy) by a large, unbridged gap. How can we explain this seeming saltation? Not having any fossils that can serve as missing links, we have to fall back on the time-honored method of historical science, the construction of a historical narrative.”
    Misrepresentations of the Evidence for Human Evolutionary Origins:
    http://www.evolutionnews.org/2......html#more

    Even though the preceding comment from a leading evolutionist in the field is crushing, to the smooth transition needed for the materialist to make his case for human evolution, you would think a materialist would at least have some sort of evidence he could cling to with Homo erectus and rudolfensis fossils Mayr cited. Yet when we look at the evidence, presented by the materialists themselves for the proposed evolution of Homo erectus, the evidence is anything but straight forward and appears to be, once again, “shoehorned” to fit their preconceived philosophical bias:

    Hominids, Homonyms, and Homo sapiens – 05/27/2009 – Creation Safaris:
    Excerpt: Homo erectus is particularly controversial, because it is such a broad classification. Tattersall and Schwartz find no clear connection between the Asian, European and African specimens lumped into this class. “In his 1950 review, Ernst Mayr placed all of these forms firmly within the species Homo erectus,” they explained. “Subsequently, Homo erectus became the standard-issue ‘hominid in the middle,’ expanding to include not only the fossils just mentioned, but others of the same general period….”. They discussed the arbitrariness of this classification: “Put together, all these fossils (which span almost 2 myr) make a very heterogeneous assortment indeed; and placing them all together in the same species only makes any conceivable sense in the context of the ecumenical view of Homo erectus as the middle stage of the single hypervariable hominid lineage envisioned by Mayr (on the basis of a much slenderer record). Viewed from the morphological angle, however, the practice of cramming all of this material into a single Old World-wide species is highly questionable. Indeed, the stuffing process has only been rendered possible by a sort of ratchet effect, in which fossils allocated to Homo erectus almost regardless of their morphology have subsequently been cited as proof of just how variable the species can be.” By “ratchet effect,” they appear to mean something like a self-fulfilling prophecy: i.e., “Let’s put everything from this 2-million-year period into one class that we will call Homo erectus.” Someone complains, “But this fossil from Singapore is very different from the others.” The first responds, “That just shows how variable the species Homo erectus can be.”
    http://creationsafaris.com/crev200905.htm

    This following quote sums up what materialists appear to be doing with this Homo erectus and rudolfensis, “hominid in the middle”, evidence:

    “But what is the basis for the human evolution thesis put forward by evolutionists? It is the existence of plenty of fossils on which evolutionists are able to build imaginary interpretations. Throughout history, more than 6,000 species of ape have lived, and most of them have become extinct. Today, only 120 species live on the earth. These 6,000 or so species of ape, most of which are extinct, constitute a rich resource for the evolutionists to build imaginary interpretations with.”
    http://www.darwinismrefuted.com/origin_of_man.html

    The first line of the “Evolution of the Genus Homo” paper illustrates the poverty of the fossil record in establishing human evolution:

    Evolution of the Genus Homo – Annual Review of Earth and Planetary Sciences – Tattersall, Schwartz, May 2009
    Excerpt: “Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis.”
    http://arjournals.annualreview.....208.100202

  185. 185

    Homo Rudolfensis was unseated recently as a “missing link”:

    “Dr. Leakey produced a biased reconstruction (of 1470/ Homo Rudolfensis) based on erroneous preconceived expectations of early human appearance that violated principles of craniofacial development,”
    Dr. Timothy Bromage – http://www.nyu.edu/public.affa.....R_1470.pdf

  186. 186

    I love this quote by a leading expert in the field:

    Man is indeed as unique, as different from all other animals, as had been traditionally claimed by theologians and philosophers.
    Evolutionist Ernst Mayr http://www.y-origins.com/index.php?p=home_more4

  187. 187

    On page 112, Sanford displays a figure plotting mutation accumulation in the human population over time. It never levels off. On page 113 takes that data and extrapolates fitness over time. It shows fitness declining to zero.

    On page 143:

    I do not believe the downward trend will ever level off. But even if we do not correct Crow’s model, it still shows genetic decay and declining fitness, rather than evolutionary progress.

    Leaving aside the wrongheaded idea of “evolutionary progress”, it should be clear that Sanford’s thesis is increased mutation accumulation leads to mutational meltdown and permanent loss of fitness.

    Now compare Sanford’s extrapolation to the hard data laid out by Estes and Lynch. They clearly show populations under very heavy mutational loads actually recovering fitness over time, rather than going extinct as predicted by Sanford’s extrapolation.

    Something is clearly wrong with the predictions emanating from Sanford’s extrapolation model.

  188. 188

    Nak you state this as “proof” for evolution

    “the discovery of DNA”

    Do you mind explaining to me how finding coded information in cells, coded information that is far far more complex than anything we have ever programmed,,in spite of tremendously negative mutation rates ,,, serves to bolster your confidence in “God -free” evolution?

    But of course this has been repeatidly pointed out to you here on UD,,, but you ignore and whistle in the dark and pretend it doesn’t matter,,,which makes me realize,,,
    you really don’t care one iota about the evidence Nak? Do you? You just love the fact that evolution has got that whole “God-free” thing to it? I don’t know what “strict religion” you are “recovering” from but is it worth living in such obvious deception as you are now doing?

  189. 189

    Dave, I totally agree with you that Sanford’s extrapolations to a YEC scenario are wrong,,,yet the ancient bacteria I cited, but you seemingly ignored,,,points to the fact that overall,,,even taking in the DNA repair mechanisms,,,the principle holds for life,,,As Well Webster’s comprehensive trilobite study adds even more impressive weight to loss of functional information,,hence GE,,, need I mention that it draws in accordance with the second law extremely well? thus does not require a gross violation of physics as evolution does?

  190. Dave,

    So there’s no such thing as extinction of different species?

    I’m confused, how many species have gone extinct and are currently going extinct under extreme pressures today?

    Saying that species can recover is a very good argument for design. A flexible design that allows for stress and recovers.

    In fact, that is what we see among many different species and ecosystems when variations due to extreme environmental ecozones move back into other or former zones.

    Please explain dog breeding?

    BTW, 72yrs is a drop in the bucket compared to at least 4000yrs of known breeding habits in history. Artificial breeding was around long before Darwin. He knew the limitations that where observed at the time.

    His theory was gradualism, which has failed and is certainly not “common sense” with todays information.

    Everyone understands variation, not everyone agrees it is an argument for unguided macro evolution.

  191. Mr BA^77,

    Your comment is awaiting moderation.

  192. 192

    NaK,
    Seems to me You never really defend your position,,you just try to cling to whatever little morsel of deception you can get away with and then claim you have made a comprehensive rebuttal…. I don’t know why you say you want to talk about science since all you really want to do is maintain your dogmatic atheism no matter what deception you have to say or solid evidence you have to ignore or obfuscation of smoke you have to blow,,, as I said before why should I even waste my time with you when you can’t even be honest with yourself? Maybe one day this will all change,,, and I hope for your sake it does but for now you are fooling nobody except yourself here on UD.

  193. Now compare Sanford’s extrapolation to the hard data laid out by Estes and Lynch. They clearly show populations under very heavy mutational loads actually recovering fitness over time, rather than going extinct as predicted by Sanford’s extrapolation.

    Something is clearly wrong with the predictions emanating from Sanford’s extrapolation model.

    Estes and Lynch highlighed situations where “fitness” was successfully restored, but this should not be extrapolated as a general principle. It was astonishing probably because it was not consistent with behavior of other populations (as noted in the paper).

    This sort of cherry picking of experiments can be likened to the poisoning a population, and then highlighting only the individuals that survived in order to make the case that this poison doesn’t affect individuals.

    Even in the papers, lynch and estes point to the difficulty in restoring lost function.

    Some degree of skepticims needs to be in play regarding compensatory mutations: this is like looking at blind cave fish and saying, “wow they developed beneficial compensatory mutations which made them blind but more reproductively successful. Evolution is more capable than we thought in increasing fitness.”

    Or this is like saying in Africa, look at how the sickle cell anemia trait increases fitness! One may not really know what the compensatory mutations may have done in order to succeed at reproductive success.

    One thing we know is that under the conditions which were used, these creatures were optimized for a particular laboratory environment. Things could be quite different in the wild.

    What these compensatory mutations may have affected is unknown.

    That is why I have suggested, once the bioinformatics and DNA sequencing industry come through with their promised products, we may actually be able to see the picture of what is happening more clearly.

    For now, we see through a glass darkly.

  194. 194

    Sal,

    Some of the lines did not show increases in fitness, but considering the random nature of mutations that should be expected. The point is, populations can come up with different ways to counteract lowered fitness due to mutational load– genetic entropy is not an inevitable cause of mutaional meltdown. You’ll remember the Reed and Aquadro paper I mentioned over at ARN which looked further at the human population, pointing out that the human population is increasing both in size and in level of panmixia– which, as you know, increases the efficiency of natural selection at removing even mildly deleterious mutations. They also point out the role of gametic selection in purging deleterious mutations from populations, and which Sanford doesn’t even begin to address. The Estes and Lynch paper is only part of the evidence which contradicts his general thesis.

  195. 195

    DATCG,

    So there’s no such thing as extinction of different species?

    Of course not– extinction can occur for many other reasons not germane to Sanford’s general thesis.

    I’m confused, how many species have gone extinct and are currently going extinct under extreme pressures today?

    The question is, how much of a mutational load can populations carry and not become extinct due to eroded fitness. Sanford’s thesis is that erosion is inevitable due to genetic entropy and that it is irreversible– he believes there is no “effective selection strategy to stop mutation accumulation”. His chart on page 113 shows inevitable fitness decline to zero (i.e., extinction) as mutations build. But–the evidence clearly shows that, even with a high accumulation of mildly deleterious mutations, fitness need not be inevitably eroded: populations have means of eliminating those mutations and/or compensating for them over time. Of course, evolution being a statistical property of populations, there will be examples that fall outside one standard deviation below the mean and extinction results. But, as I pointed out above, extinction can occur for a myriad of reasons apart from the accumulation of mutations.

  196. “I am a YEC as well, so I wouldn’t object to Sanford’s idea on theological grounds as you appear to be doing”

    I have no theological reasons for rejecting anything. I reject it on common sense. There is no deterioration of genomes going on as far as I can see. The world seems quite healthy out there. As I have said the weeds and bugs are doing just fine in my area nor have I seen any animals deteriorating either. I believe Sanford’s thesis is nonsense. It does not reflect reality.

  197. Dave states:,

    “fitness need not be inevitably eroded: populations have means of eliminating those mutations and/or compensating for them over time.”

    Well Dave I have severe reservations with your optimism;;;
    Number 1 I feel the case has been made that fitness recovery was not complete in your paper,,,and though you must “assume” full recovery was made,,,I feel enough question has been raised to make you at least partially unsure that recovery was full equilibrium?

    Yet to really nail the evidence down a comprehensive study of ancient bacteria must be made (which I believe Sanford is doing),,,Once again you must presuppose that no functionality will be found to be lost, I hold that functionality will be found to be lost,,, From your quote it seems you want to be optimistic that all slightly detrimental mutations are being removed, but once again I appeal directly to the fossil record which shows that gradual deterioration is the norm we witness after the “sudden appearance of the form in the fossil record.

    “As Niles Eldredge and Stephen Jay Gould pointed out almost three decades ago, the general pattern for the evolution of diversity (as shown by the fossil record) follows precisely this pattern: a burst of rapid diversity following a major ecological change, and then a gradual decline in diversity over relatively long periods of time.” Allen MacNeill PhD.; 2007 (Evolutionist) Teaches introductory biology and evolution at Cornell University in Ithaca, NY. — Quoted right here on UD

    As well Dave there are many studies that call into question your assertion that natural selection has the delicate touch to reach each and every deleterious mutation:

    Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Kondrashov A.S.
    http://www.ingentaconnect.com/.....4/art00167

    The Frailty of the Darwinian Hypothesis
    “The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,”
    http://www.evolutionnews.org/2......html#more

    High genomic deleterious mutation rates in hominids
    Excerpt: Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically (unusually) low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.
    http://www.nature.com/nature/j.....344a0.html

    Thus dave I feel you are vainly trying against what I feel is consistent empirical evidence for GE, though I appreciate you bringing home the point that it is not nearly as rapid as Sanford first proposed, Yet I also feel once the ancient bacteria studies are completed (hopefully) this will bring the point home for you and you will realize the principle is solid.

  198. Dave,

    Slow down. First, I’m not saying Dr. Sanford’s extrapolations are correct. They are forward looking predictions that could happen if the right events take place which increase mutation rates for any number of critical life resources in a chain of life.

    I personally think from a designers perspective life is designed to counteract mutations, not encourage them. Least, if I’m trying to see through Designer eyes.

    Do you think the Ozone layer is important?

  199. Sal @ 153,

    I had a transportation issue. My car had a flat and the spare was damaged as well. I really wanted to attend though as Meyer is a cool guy to me and super articulate. I really admire his accuracy, intensity, and breadth when explaining and discussing ID- such as in his new book “Signature In The Cell” and his fabulous presentation on Coast To Coast am-

    http://www.youtube.com/watch?v=UFM5op8WU5o

  200. Sorry,

    the new ID Timeline project

    [at AtBC]

    should be UD timeline

  201. 201

    born,

    Estes and Lynch cite the papers you mention as examples of what basically led them to do the study in the first place. Lynch had also published on the subject before (as Sanford mentions).

  202. 202

    Dave,
    Then it remains for the ancient bacteria to clearly differentiate if the “compensation” was truly a full recovery of molecular functionality/information as you (and they) maintain.. A piece of advice Dave,,, I wouldn’t bet too much money on the ancient bacteria backing your position if I were you,,, But hey this is why I love science,,,instead of just always having heated debates we can usually find a experiment that will settle the matter and end the disagreement.

  203. 203

    Hi DATCG,

    personally think from a designers perspective life is designed to counteract mutations, not encourage them. Least, if I’m trying to see through Designer eyes.

    Interesting. You could also look at life as a means of locally reducing entropy (albeit temporarily) in the face of a Universe ultimately winding down.

    Do you think the Ozone layer is important?

    Yes.

  204. So what’s the data that demonstrates an accumulation of genetic accidents can lead to new protein machinery and new body plans?

    What’s the data that demonstrates non-telic processes can cobble together regulatory networks?

    The point being is the only “evidence” the anti-IDists have is the complete refusal to accept the design inference.

  205. Dave Wisker:

    The point is, populations can come up with different ways to counteract lowered fitness due to mutational load– genetic entropy is not an inevitable cause of mutaional meltdown.

    Yes due to “built-in responses to environmental cues.”

    I believe Sanford was referring to life in a non-telic scenario.

    But as we know design can counter entropy.

  206. 206

    Dave you stated:

    “You could also look at life as a means of locally reducing entropy”

    And to which basis of “reality” are you going to appeal to reduce informational entropy? Energy? A dead horse as Kariofocus can well testify. Exactly from what basis of “material reality”, or combination thereof, do you presuppose that optimal Functional Information has the ability to be restored (compensated) outside of functional information’s own resources for such “data recovery”? If you appeal to some self-organization principle of material reality, Please clarify in detail. i.e. Exactly what basis of “material” reality do you tie this “entropy reducing, information restoring” ability to since information is now shown to be foundational to reality and the only known entity that can exercise such precise “compensation”?
    It seems you have appealed to some phantom ability that does not exist for brute “material” forces.

    Scientific Evidence For God Creating The Universe
    http://www.youtube.com/watch?v=JQhO906v0VM

    further reference presented earlier.

  207. 207

    Born,

    Do not confuse thermodynamic entropy with informational entropy.

  208. 208

    Dave,
    I was just asking what entity outside of information has the ability to “recover” information?,,I felt I was rather straight forward in the question.

  209. Footnote on Information and thermodynamics:

    Re: DW at 207 . . .

    Before trotting out well-worn talking points, kindly note that from Szillard, Brillouin and Jaynes et al [and as one may read in Harry Robertson's Statistical Thermophysics in details], there is a school of thought in Physics that does in fact see a significant link form information to entropy in both the informational and thermodynamic senses. (I note, too, that the names just listed are not exactly lightweights in Physics.)

    A dismissive talking point is not good enough. (Cf my discussion of thermodynamics in App 1 the always linked, points 3 – 5]

    Excerpting Robertson:

    _____________

    >> . . . It has long been recognized that the assignment of probabilities to a set represents information, and that some probability sets represent more information than others . . . if one of the probabilities say p2 is unity and therefore the others are zero, then we know that the outcome of the experiment . . . will give [event] y2. Thus we have [key operative term -- we possess the information already, so that further transmission will not be a surprise] complete information . . . if we have no basis . . . for believing that event yi is more or less likely than any other [we] have the least possible information about the outcome of the experiment . . . .

    A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability should be seen as, in part, an index of ignorance] . . . .

    S({pi}) = – C [SUM over i] pi*ln pi,

    [where [SUM over i] pi = 1, and we can define also parameters alpha and beta such that: (1) pi = e^-[alpha + beta*yi]; (2) exp [alpha] = [SUM over i](exp – beta*yi) = Z [Z being in effect the partition function across microstates, the "Holy Grail" of statistical thermodynamics]. . . .[pp.3 - 6]

    S, called the information entropy, . . . correspond[s] to the thermodynamic entropy, with C = k, the Boltzmann constant, and yi an energy level, usually ei, while [BETA] becomes 1/kT, with T the thermodynamic temperature . . . A thermodynamic system is characterized by a microscopic structure that is not observed in detail . . . We attempt to develop a theoretical description of the macroscopic properties in terms of its underlying microscopic properties, which are not precisely known. We attempt to assign probabilities to the various microscopic states . . . based on a few . . . macroscopic observations that can be related to averages of microscopic parameters. Evidently the problem that we attempt to solve in statistical thermophysics is exactly the one just treated in terms of information theory. It should not be surprising, then, that the uncertainty of information theory becomes a thermodynamic variable when used in proper context [p. 7] . . . .

    Jayne’s [summary rebuttal to a typical objection] is “. . . The entropy of a thermodynamic system is a measure of the degree of ignorance of a person whose sole knowledge about its microstate consists of the values of the macroscopic quantities . . . which define its thermodynamic state. This is a perfectly ‘objective’ quantity . . . it is a function of [those variables] and does not depend on anybody’s personality. There is no reason why it cannot be measured in the laboratory.” . . . . [p. 36.] >>

    ______________

    Mr Wisker, you may disagree if you please on this view on statistical thermodynamics; but kindly provide substantiation for the disagreement, not rhetorically dismissive talking points.

    And then, explain how lucky noise plus blind mechanical necessity somehow spontaneously rearranged dilute racemic organic molecules in a plausible prebiotic soup into a homochiral, functional information storing and processing system. Including inventing along the way: digital information stored in codes [thus also, computer language -- which thus precedes speech, perhaps by 3.8 BY on the conventional timelines], algorithms, data structures, programs, and the executing machinery to implement the hard and software system.

    Talking points will not be good enough for that, too.

    GEM of TKI

  210. PS: As for reducing the imagined evolutionary materialistic origin of life process to a simple one of energy at work through chance and necessity in whatever still warm pond or undersea vent or icy comet etc one wishes to dream up, I think Shapiro has long since laid the dead horse to rest in his remarks on genes first OOL chemistry research (which also inadvertently extends to his own metabolism first model):

    __________

    >>The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck. >>
    ______________

    Next time someone pushes the latest scenario, ask about what specific empirical work backs it up, how far; and what he evidence is that the same could — or did — happen in the prebiotic world without Chem labs and Chemists to take us over many active information steps with boosts form Le Chetalier’s principle of pushing reactions in directions that relieve constraints imposed on a mix of reactants.

  211. 211

    born,

    Off the top of my head, I’d say recombination is one way (and not necesarrily the only way) “recovery” of information can occur.

    Consider an indvidual with two different detrimental mutations that reduce activity levels of the proteins they code for. In addition, they reside on different but homologous chromosomes (think of a female with one mutation on one X chromsome, and one on the other X chromosome). This individual’s genome has lost some functional information because neither X exists in a pre-mutational state. If nothing else happens, all of its offspring will carry a chromosome with one less-than-fully functional gene. . However, in meiosis, recombination can produce a chromosome that has neither detrimental mutation. In other words, recombination has recovered the pre-mutation state of one of the chromosomes. .

  212. 212

    kf,

    Informational and thermodynamic entropy are analogous, not identical, which was my point.

  213. KF-san,

    I agree that basic statistics can lead to pessimism about OOL. We must appeal to the reality of chemistry and physics to overcome that pessimism.

    An example I have referenced several times, though not quite to the Lewontonian degree, is Sayama-sensei’s Evoloops. In the Evoloops CA, the laws of physics and chemistry cause life to be created quite spontaneously. Is our universe in the same category? It is the diligent study, such as this research on ribose and dissolved minerals, that will help decide that. Lack of results such as these would confirm Shapiro’s pessimism.

  214. Dave,
    But what is telling the detrimental mutation(s) to “recover”?,,,Surely the brute force of the material at the molecular level (prior to selection I might add) is neither aware, nor concerned, with the state of the mutation. Only a precise measurement based in some type of complex information algorithm would have the wherewithal to calculate an appropriate response in any reasonable amount of time. As well the experiment you are relying on so heavily to make your case to falsify GE has not even conclusively demonstrated a gain in functional information that was not known to be present before. Which brings us to the exact same problem which is crushing to OOL research, (Meyer; Signature), You have yet to conclusively demonstrate that functional information can arise outside of intelligence(Trevors; Abel).

    As well, in my assertion that the ancestral bacteria is optimal in information content and cannot be surpassed, I appeal to the fact that physicists have found many machines and processes in the cell operate at the “near optimal” capacities allowed by the law of physics… Which clearly ties very strongly into the anthropic principle and argues very strongly against the evolutionary assumption of life being an “accident” of physics.i.e. we would expect a lot more “slop” if life were truly an accident.

    William Bialek – Professor Of Physics – Princeton University:
    Excerpt: “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.”
    http://www.princeton.edu/~wbialek/wbialek.html

  215. 215

    Joseph:

    Yes, I understand the difference between hardware and software. If you are implying that the software in computers would not function as it should without the correct hardware, then you are correct. But the cell is not like a computer in this regard because the cell reproduces itself. Computers do not. Each individual computer must be programed so that its hardware and software are compatible.

    Cells on the other hand must have all the information to go from a single cell all the way to an adult organism, and then do it again the next generation, all without intelligent input. Proteins degrade in situ and must be continually replaced. There are no permanent biological structures which are designed to last the entire lifetime of the software (DNA). Every molecule in your body, including DNA, has probably been replaced several times since you were born. There are estimates of this but I don’t remember what they are. That doesn’t happen with computer hardware, although it can happen for software, so I can see where the confusion is coming from. The cell must generate and regenerate, quite literally, everything. Therefore all the information must be in the DNA, because DNA is the only chemical that replicates itself. It needs proteins of course, but where do those proteins come from? Invariably, from the DNA.

    jerry:

    Well ok. You can continue to state your opposition to Sanford’s thesis and ignore the point I am making. I suppose that’s your right.

    You and Sanford are both using fitness as a measure of information loss or genetic entropy. I have said that is obviously not an accurate measure, as organisms which lose information can lose fitness, gain it, or remain neutral. My back defect is not going to affect my reproductive success, which is the definition of fitness, yet I know that same back defect is a loss of information. In my mother, it was so bad that it required information input from an intelligence, i.e. surgery, to correct it, yet at the time she had already had all the kids she was going to have.

    You oppose Sanford’s thesis, and you may be right to do so. But the fact of the matter is when ID takes charge of science as opposed to being continually locked in debate with recalcitrant Darwinists, there will be new standards by which we judge whether or not genetic entropy is occurring. The following paper suggests that even neofunctionalization can occur along with degenerative evolution and loosened structural constraints on proteins.

    http://www.ncbi.nlm.nih.gov/pu.....d_RVDocSum

    In short, the way we judge whether or not information loss has occurred is not, in the future, going to depend on fitness functions, nor even on whether new functions have arisen. Just because Notre Dame has the most fans and broke their own records for losing seasons doesn’t mean they are the best football team.

  216. Mr BA^77,

    Only a precise measurement based in some type of complex information algorithm would have the wherewithal to calculate an appropriate response in any reasonable amount of time.

    Incorrect. All you need is a large population size. If DNA miscopies every 10^-9 base, simple mutation will sample every possible choice in the genome eventually. For c. elegans, the genome is 10^8 bases. So you would expect every 10th one to have a mutation somewhere. Collect a billion and you would expect to have a mutation in every location in the genome. A billion c. elegans would weigh less than a pound.

    That is just considering mutation. Sexual recombination will sample the space even more quickly.

    Bottom line – there is no need for intelligence. Chance and large numbers are sufficient. GE is still falsified.

  217. As a corollary to my last comment, the history of cryptography is one of elegant ciphers falling to brute force attacks. The Enigma breaking ‘bombes’ of Alan Turing were checking every possible combination as fast as they could. Botnets can be used to crack keys as easily as launch denial of service attacks.

  218. PPS – An interesting example of this brute force problem solving might be happening in the AIG story that BA^77 referenced earlier. If you sequenced the genome of the wild type and/or antibiotic resistant bacteria, you might find that the bacteria after ten hours (20 generations?) had shifted the genome in response to the famine media. Might be a fun experiment! :)

  219. DaveW,

    First, to correct any possible misunderstanding from my previous post about looking through a Designers eye, “design to counteract mutations…” I should make it clear that I believe mutations are allowed to a certain extent for variation if that was not obvious. But for survival purposes under stress, etc., that the design must be flexible and recoverable, plus maintain a core for distribution and storage of blueprints and unfolding life under different ecozones. Discovering the error correction programs to edit, splice, copy, destroy, disband, etc., is evidence of design.

    Now, to your response:

    “Interesting. You could also look at life as a means of locally reducing entropy (albeit temporarily) in the face of a Universe ultimately winding down.”

    You could, but why? Please expand. Why would “life” do anything? From an unguided perspective? There’s always an unmentioned ghost in the machine of unguided evolutionary logic which seems illogical to me. Its like saying mother nature did it. But why? Without purpose, goals, or reason for being, why? Why does “life” provide local zones of temporary protection?

    I asked…
    “Do you think the Ozone layer is important?

    You said,
    “Yes”

    Because why Dave? What does the Ozone layer provide protection from
    regarding “life.” You stated above that “life” provides temporary security from entropy, but that is simply not true if you take the Ozone layer and atmospheric layers away. Whatever you consider “life” to be cannot survive as we know it today without protection.

    What do we need protection from that the Ozone layer provides?

  220. Nakashima,

    You never explain how such a system came about in the first place.

    So far, origins is still a mystery. After 200yrs, billions spent, the many different conjectures, ideas, imaginations have failed to produce any evidence of origins.

    You talk about sophiticated programs as they are today and state no intelligence is required, yet you cannot recreate these intelligent bio-programs yourself even though you have great experience in life. Yet you say – easy.

    But why can you not create such an easy bio program Mr. Nakashima? With all due respect to your background which I do recognize.

    I’m not as bold as you. I admit there is much we do not know, to much to rule out a guided evolution possibility.

    Even Richard Dawkins refused to rule out possible seedings from advanced civilizations as responsible for the Code of Life.

    Why Mr. Nakashima? Why didn’t he rule it out? Why did he leave that possibility open? And if anything is possible according to Darwinians, why not intelligence?

  221. 221

    Nak states:
    ,
    “If DNA miscopies every 10^-9 base, simple mutation will sample every possible choice in the genome eventually.”

    4^1000000000 possible combinations

    Nak,,, How long will it take to search all of those possible combinations? Even with a population of say 10^40 bacteria?

    As well, I think you are trying to say there is absolutely no complex algorithmic information in the genome whatsoever and that we should look totally to “non information causes” in this recovery of information,, at least that is what it seems like from your naive appealing to totally “brute material forces” to recover the information that was lost.

    Here is yet another study that I am afraid you will completely ignore:

    “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?” – David L. Abel and Jack T. Trevors, “Three Subsets of Sequence Complexity and Their Relevance to Biopolymeric Information,” Theoretical Biology & Medical Modelling, Vol. 2, 11 August 2005, page 8

    Mycoplasma Genitalium – The “Simplest” Life On Earth – video
    http://www.youtube.com/watch?v=eRoMxpZWR7c

    As well, Nak just because you have somewhat deluded yourself into thinking Genetic Entropy is falsified, on such piddling evidence of “equilibrium” in Dave’s paper,,,and proudly proclaim GE is falsified over and over,,,does not detract from the truth that GE is not rigorously falsified within the scientific method,,, and in fact once again shows your unscientific bias of being a uncritical Darwinian cheerleader… Until the matter is fully ironed out with further rigorous experimentation, that is the true state of how the GE falsification matter sits… In fact in all fairness to the current state of the evidence, I feel the evidence looks very Good for GE being further solidified as the main principle for biology.

  222. BA77 and maybe Scordova?

    What are the current thinkings by Dr. Sanford on GenE? Is he still tracking an eventual mutational meltdown over time? If so, how long? Has he changed the timeline?

    I’m very curious to hear what Scordova discovers in future discussions with Dr. Sanford.

    I’m also curious what future events and conversations with Dr. Meyer.

  223. Mr DATCG,

    Come now, you must be aware that I do discuss origins all the time on UD! I just linked to an interesting paper today…

    You are conflating OOL and c. Elegans reverting some deleterious mutation. I don’t think that is a good idea.

  224. 224

    DatCG,

    You ask why is life a means of local entropy reduction. I would answer because it converts energy from the sun into carbon structures. But I don’t think that’s what you really want as an answer. That’s because you are asking a philosophical rather than a scientific question. Science answers what and how types of questions. Ask a philosopher for the why, as well as the why the ozone layer is important. My answers are bound to be uninteresting to you.

  225. Mr BA^77,

    4^1000000000 possible combinations

    Nak,,, How long will it take to search all of those possible combinations? Even with a population of say 10^40 bacteria?

    What problem do you think that is relevant to? Nothing we have discussed recently.

    As well, I think you are trying to say there is absolutely no complex algorithmic information in the genome whatsoever and that we should look totally to “non information causes” in this recovery of information,, at least that is what it seems like from your naive appealing to totally “brute material forces” to recover the information that was lost.

    Yes, it was lost by a brute materialist force and can be recoverd by the same force. Is that surprising?

    As well, Nak just because you have somewhat deluded yourself into thinking Genetic Entropy is falsified, on such piddling evidence of “equilibrium” in Dave’s paper,,,and proudly proclaim GE is falsified over and over,,,does not detract from the truth that GE is not rigorously falsified within the scientific method[...]

    Inasmuch as GE is formulated as necessarily true for all genomes, any single counter-example falsifies it. Any recovery in function is a falsification.

    At least it would be if GE were a scientific theory, published in a peer reviewed journal article. As a bunch of hand waving and opinion, it can squirm out of any uncomfortable situation. What is your definition of GE, now? “Genetic Entropy is a one way decline in function that is inevitable due to accumulating deleterious mutations, except when function is recovered, but not too much.” You might want to check with Dr Sanford on that.

    Here is yet another study that I am afraid you will completely ignore:

    I’m actually very interested in Abel’s three classes of sequence complexity. Abel doesn’t make any strong claims for the three classes, though you might be tempted to think he does by his writings.

    He doesn’t claim they are universal or that they are distinct. Is there possibly a fourth class? Abel doesn’t say yes or no. Do his three classes overlap? He doesn’t say yes or no. If they are universal and distinct, as he would like you to believe, is there a definite decision procedure that lets you distinguish which of the three classes a sequence belongs to? No, how could there be without resolving the first two issues?

    It is also interesting that Abel never references Wolfram and his classification system, even though that is the most relevant similar research. That bothered me, because it seemed to me that Abel was ducking some important questions about CAs with simple rules and simple inputs that generated quite complex sequences.

  226. Mr DATCG,

    Why Mr. Nakashima? Why didn’t he rule it out? Why did he leave that possibility open? And if anything is possible according to Darwinians, why not intelligence?

    I think he left it open out of intellectual honesty. The problem is detecting the signature of intelligence, subject of Dr Meyer’s book. The space aliens, like God, have done a good job of covering their tracks.

  227. 227

    DATCG,
    Well as I am not in contact with Dr. Sanford I cannot comment on his current work. I think Sal can help you there.
    As you may well already know, he has developed a computer program called Mendel’s accountant:

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances. Using realistic estimates for the relevant biological parameters, we investigate the rate of mutation accumulation, the distribution of the fitness effects of the accumulating mutations, and the overall effect on mean genotypic fitness. Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

    But as Dave has persistently pointed out on this thread, there is a compensation mechanism in operation that Dr. Sanford has apparently not taken full appraisal of yet (IMHO, the mechanism is far from being “the source” of functional information that evolutionists would need to falsify the principle of GE that Dave claims it is).
    Thus, in my very limited knowledge of the matter, I would have to say, from all the evidence I have been able to examine thus far, that if Dr. Sanford is able to solidify his baseline for GE, from improved, and rigorous, measurement of the loss of functional information/complexity/fitness in current “compensation” studies and extrapolate that baseline in a meaningful way to several sources of observed GE from ancient bacteria, he will have made the first move to meaningfully established GE as the principle for biology and will have provided a basis to elucidate it further mathematically in his MA program, that is to say he will have done so at least for the bacterial populations studied.

    I also know, from my nosebleed view of the entire spectrum of current evidence, that Dr. Sanford can take a fairly large amount of confidence in one of the prime predictions of GE, in that I firmly believe all ancient bacteria will be found to have more functional complexity than their current lineages (Sal told me Sanford is looking for ancient bacteria in salt mines).
    If the loss is somewhat consistent across all populations, from ancient to current, then it will give strong indication of a overriding law,,,and even if the loss is not consistent across the bacterial populations,,, it will at least be a very interesting area of investigation for Dr. Sanford and whomever is working with him.

    Other than that I really have no clue what Dr. Sanford is up to.

  228. 228

    Nak you stated:

    ,
    “If DNA miscopies every 10^-9 base, simple mutation will sample every possible choice in the genome eventually.”

    when I responded:

    4^1000000000 possible combinations

    Nak,,, How long will it take to search all of those possible combinations? Even with a population of say 10^40 bacteria?

    You then stated:

    What problem do you think that is relevant to? Nothing we have discussed recently.

    —-

    Nak why do you deny something you had made a direct claim to in the previous post?

    I believe they call the audacity of what you just did ,,,,DENIALISM,,,

    Denialism “is the refusal to accept an empirically verifiable reality.
    http://en.wikipedia.org/wiki/Denialism

    As they say in AA recovery programs Nak,,,Keep Comin Back”

  229. Mr BA^77,

    You are mistaken. 4^(10^9) is the number of genomes of length one gigabase. We were discussing how many c. elegans (not bacteria) it would take to cover a single base change in every one of the bases in their 100 megabase genome. Reverting mutations does not require searching all possible genomes. It requires looking at nearby genomes.

  230. tragic mishap,

    The DNA is the hardware that carries out the instructions of the software- the software written by the intelligent designer(s)- “the” genetic algorithm(s) if you will.

    I am saying there is software telling the DNA what to do and when to do it, etc.

    It is the software- unseeable- DNA can be seen- that runs the show.

    The sequence specificity is just to carry out the commands.

    When an RNA is formed software gets downloaded to it.

    When DNA replicates the software from the parent strands gets passed on- downloaded from parent to daughter.

    The ribosomes are programmed genetic compilers-

    BTW DNA does not replicate itself. It gets replicated as part of the cell when the cell replicates.

    And that is when the software from the parent cell gets downloaded in the daughter.

  231. Onlookers:

    Re Mr Wisker @ 212: Informational and thermodynamic entropy are analogous, not identical, which was my point.

    It is sadly clear that DW has not even seriously read much less interacted with even the brief excerpts in 210 above.

    Let us observe again, how the mathematics is drawn out from the context of the informational challenge of the macro- vs micro- state views of systems, by Jaynes et al.

    In particular, let us look at:

    _____________

    >> A remarkably simple and clear analysis by Shannon [1948] has provided us with a quantitative measure of the uncertainty, or missing pertinent information, inherent in a set of probabilities [NB: i.e. a probability should be seen as, in part, an index of ignorance] . . . .

    [Deriving . . . ] . . . .

    S({pi}) = – C [SUM over i] pi*ln pi,

    [where [SUM over i] pi = 1, and we can define also parameters alpha and beta such that: (1) pi = e^-[alpha + beta*yi]; (2) exp [alpha] = [SUM over i](exp – beta*yi) = Z [Z being in effect the partition function across microstates, the "Holy Grail" of statistical thermodynamics]. . . .[pp.3 - 6]

    S, called the information entropy, . . . correspond[s] to the thermodynamic entropy, with C = k, the Boltzmann constant, and yi an energy level, usually ei, while [BETA] becomes 1/kT, with T the thermodynamic temperature [this APPLICATION of a general analysis to a particular instance is what is being taken out of context to assert "analogy" without addressing the context that for instance is reflected in what follows] . . . A thermodynamic system is characterized by a microscopic structure [= microstates] that is not observed in detail [= uncertainty about the specific state] . . . We attempt to develop a theoretical description of the macroscopic properties in terms of its underlying microscopic properties, which are not precisely known. We attempt to assign probabilities to the various microscopic states [which represents information] . . . based on a few . . . macroscopic observations that can be related to averages of microscopic parameters. Evidently the problem that we attempt to solve in statistical thermophysics is exactly the one just treated in terms of information theory. [In short, we see not mere analogy but an analytical bridge] It should not be surprising, then, that the uncertainty of information theory becomes a thermodynamic variable when used in proper context [i.e we see an application of the analysis and associated theory] [p. 7] . . . . >>

    ________________

    That is what Mr Wisker needed to speak to cogently and it is what he has decided to duck with a dismissive claim about analogies.

    So, i draw Mr Wisker’s attention to the following from pp. Vii – viii of Robsertson:

    . . . the standard assertion that molecular chaos exists is nothing more than a poorly disguised admission of ignorance, or lack of detailed information about the dynamic state of a system . . . . If I am able to perceive order, I may be able to use it to extract work from the system, but if I am unaware of internal correlations, I cannot use them for macroscopic dynamical purposes. On this basis, I shall distinguish heat from work, and thermal energy from other forms . . .

    Now, of course there are debates in physics around such claims [and one needs not agree with the sort of reasoning above to arrive at a design theory conclusion], but they are not to be settled by mere dismissive rhetorical assertions about “analogies.”

    GEM of TKI

    PS: Nakashima-san: Mr Shapiro’s point was about the problem of the chemistry not just the statistics, save insofar as statistical thermodynamics issues are implied. And, I long since answered on evoloops [cf. 347 in the Eye into materialist assault thread], pointing out how they are ever so carefully constructed algorithmically to loop and to replicate; such entities in the real world simply would illustrate design at work; even as they express an intelligently designed and implemented algorithm in the simulated world that is presented. (I find it slightly annoying to see you resurrecting an answered matter as though it were not answered; when you did not respond on the merits when I pointed out what was wrong with the latest case being put up.]

  232. 232
  233. PPS: Sigh: Link seems messed up: try again for no 347 in the Eye thread of July 11, 2009.

    URL: http://www.uncommondescent.com.....ent-328014

  234. There are various kinds of entropy:

    1. thermal
    2. configurational
    3. informational

    ID is focused on the configurational entropy, “configurational entropy” was the term used in the founding book of the modern ID movement, Mystery of Life’s Origin, (link provided above).

    Informational entropy may refer in some cases to the compactness of information (the inability to compress a file for example may indicates high informational entropy). That is because from an informational standpoint, the lack of an algorithmically orderly structure is suggestive of maximum packing of information in every bit.

    If thermal entropy goes way up (like say bringing objects into a plasma state), then yes, configurational entorpy is maximized. They are tied at extreme points of the temperature scale.

    But there is a region where thermal and configurational entropy may not be in sync.

    For example, I can have a scrabble pattern that says, “me thinks like a weasel”. The cofigurational entropy won’t change much despite the fact the room temperature (and hence thermal entropy) may change…

    It is conceivable configurational entorpy can go up while thermal entropy goes down.

    A house of cards has low configurational entropy, it is in an ordered state with respect to what we consider designed patterns. When it collapses it is in a high state of configurational entropy and in it is also in configurational equilibrium.

    There is an analogous case for configurational entropy in OOL, and that case was made in Mystery, a book highly influential to Dr. Meyer.

  235. Dave Wisker

    Regarding the Lynch paper on C elegans, much of the recovery of the mutated lines had occurred in only 10 generations. In some of the lines it appears almost all of the recovery had occurred in that time. (i.e. they were almost as productive as the non-mutated original strain). The authors attribute recovery to “compensatory epistatic mutations” by dismissing other alternatives e.g. “beneficial mutations” and back mutations (because they were too improbable). The authors point out that compensatory epistatic mutations are not the same as “beneficial mutations” (even though they obviously benefit the organism). They postulate these mutations benefit the worst performing organisms the most. (It appears If the organism is mutated then the mutations are good and if the organism is not mutated, mutations are bad). They also state this, which I find revealing because it moves from supposition to fact in the space one sentence “… compensatory mutation appears to be the
    only viable explanation for the observed results. Given that
    the observed fitness restoration did in fact result from compensatory
    mutation accumulation, our findings suggest that
    a surprisingly high fraction of deleterious mutations can be
    compensated.”

    The title of their paper should have been: “Heavily Mutated Roundworms Rejuvenate in 10 Generations and We Don’t Know How.”

  236. Sal:

    Re: ID is focused on the configurational entropy, “configurational entropy” was the term used in the founding book of the modern ID movement, Mystery of Life’s Origin

    1 –> You are of course correct that the argument of Thaxton et al in ch 8 TMLO turns on splitting the TdS eqn into thermal and configurational parts, constituting entropy at micro level as requiring for the case of an informational polymer, [a]agglomeration of monomers from a scattered condition, then [b] the arrangement of the sequence of monomers in the resulting chain into a useful pattern.

    2 –> In turn, this rests on seeing that s = k ln w is based on the number of ways particles and energy may be arranged at micro-levels, consistent with prevailing macro-conditions.

    3 –> As Brillouin (who Thaxton et al are following explicitly) put it in analysing Maxwell’s Demon who is envisioned as using his [acquired . . .] information on the speed and direction of molecules moving between two connected containers to force their separation, driving the relevant temperatures into disequilibrium and apparently breaking the 2nd law of thermodynamics:

    Every physical system is incompletely defined. We only know the values of some macroscopic variables, and we are unable to specify the exact positions and velocities of all the molecules contained in a system. We have only scanty, partial information on the system, and most of the information on the detailed structure is missing. Entropy measures the lack of information; it gives us the total amount of missing information on the ultramicroscopic structure of the system.

    This point of view is defined as the negentropy principle of information . . . , and it leads directly to a generalization of the second principle of thermodynamics, since entropy and information must, be discussed together and cannot be treated separately . . . any observation or experiment made on a physical system automatically results in an increase of the entropy of the laboratory. It is then possible to compare the loss of negentropy (increase of entropy) with the amount of information obtained. The efficiency of an experiment can be defined as the ratio of information obtained to the associated increase in entropy. This efficiency is always smaller than unity, according to the generalized Carnot principle. [Sci and info theory, 2nd Edn; Cf point 3 and point 8, App 1 my always linked]

    4 –> Thus, Brillouin has opened an analytical door from thermal agitation and its randomised distribution to configurations, and highly informationally constrained configurations.

    5 –> Gary L Bertrand of U of Missouri-Rollo argues, similarly:

    The freedom [i.e. micro-level uncertainty] within a part of the universe may take two major forms: the freedom of the mass and the freedom of the energy. The amount of freedom is related to the number of different ways the mass or the energy in that part of the universe may be arranged while not gaining or losing any mass or energy. We will concentrate on a specific part of the universe, perhaps within a closed container. If the mass within the container is distributed into a lot of tiny little balls (atoms) flying blindly about, running into each other and anything else (like walls) that may be in their way, there is a huge number of different ways the atoms could be arranged at any one time. Each atom could at different times occupy any place within the container that was not already occupied by another atom, but on average the atoms will be uniformly distributed throughout the container. If we can mathematically estimate the number of different ways the atoms may be arranged, we can quantify the freedom of the mass. If somehow we increase the size of the container, each atom can move around in a greater amount of space, and the number of ways the mass may be arranged will increase . . . .

    The thermodynamic term for quantifying freedom is entropy, and it is given the symbol S. Like freedom, the entropy of a system increases with the temperature and with volume . . . the entropy of a system increases as the concentrations of the components decrease. The part of entropy which is determined by energetic freedom is called thermal entropy, and the part that is determined by concentration is called configurational entropy.”

    [ . . . ]

  237. 6 –> So, as I follow the Thaxton et al argument in my app 1, point 8:

    ______________

    >> degree of confinement in space constrains the degree of disorder/”freedom” that masses may have. And, of course, confinement to particular portions of a linear polymer is no less a case of volumetric confinement (relative to being free to take up any location at random along the chain of monomers) than is confinement of gas molecules to one part of an apparatus. And, degree of such confinement may appropriately be termed, degree of “concentration.”

    Diffusion is a similar case: infusing a drop of dye into a glass of water — the particles spread out across the volume and we see an increase of entropy there. (The micro-jets case of course is effectively diffusion in reverse, so we see the reduction in entropy on clumping and then also the further reduction in entropy on configuring to form a flyable microjet.)

    So, we are justified in reworking the Boltzmann expression to separate clumping/thermal and configurational components:

    S = k ln (Wclump*Wconfig) = k lnWth*Wc . . . [Eqn A.11, cf. TBO 8.2a]

    or, S = k ln Wth + k ln Wc = Sth + Sc . . . [Eqn A.11.1]

    We now focus on the configurational component, the clumping/thermal one being in effect the same for at-random or specifically configured DNA or polypeptide macromolecules of the same length and proportions of the relevant monomers, as it is essentially energy of the bonds in the chain, which are the same in number and type for the two cases . . . >>
    _______________

    7 –> In simpler terms, the fact of additivity of thermal and configurational entropy terms implies their common nature: you can only add apples, oranges and bananas together by finding a common nature as fruit.

    8 –> In this case, we see an increasing confinement of spatial location — hence my term “configuration space” for this cut-down version of phase space — which more and more sharply reduces the number of ways mass and emnergy at micro level may be arranged consistent with observable macro level constraints. (Thus, the example of the microjets in my point 6 the same appendix.]

    9 –> And so we have arrived at islands of configurations that yield a macro-observable function in a sea of initially possible configs.

    10 –> That is, we now see that we are at the issue of functionally specific complex information and the organising work that is required to get to it from a presumed initial at-random arrangement in a prebiotic soup, or less a clumped together but randomly sequenced polymer chain.

    11 –> And, of course, there is an informed sequence of constraints that must apply force to confine relevant components to a restricted zone then arrange them into a functional sequence to make one of the macromolecules of life.

    12 –> Then, to arrange the result5ing macromolecules into a functionally organised whole: including the info storage, reading and implementing systems required for the von Neuman self-replicator that is so central to cell based life.

    13 –> Such directed organised forces are physical work, and are further specified as to more or less macro-observable functional outcomes to be obtained.

    14 –> And so, we see how ther is indeed an analytical bridge between the energy and mass distribution issues of statistical thermodynamics, and the creation of functionally specific complex information lying at the heart of cell based life.

    GEM of TKI

  238. 238

    mad doc,

    Regarding the Lynch paper on C elegans, much of the recovery of the mutated lines had occurred in only 10 generations. In some of the lines it appears almost all of the recovery had occurred in that time. (i.e. they were almost as productive as the non-mutated original strain). The authors attribute recovery to “compensatory epistatic mutations” by dismissing other alternatives e.g. “beneficial mutations” and back mutations (because they were too improbable

    Actually, mad doc, the authors speculated on the cause, but only in the discussion section (where that kind of thing is common and perfectly appropriate). The actual scientific question they addressed in the experiments (and which is reflected in their design) was fitness recovery of populations that have been mutationally degraded.

    What we have then is a case of the authors keeping the speculation out of the main body of the paper (methods and results) and restricting any speculation to the discussion section where it belongs. So their choice of the title of the paper is fine as is.

  239. 239

    Mad doc,

    Another comment. Suzanne Estes’s lab has gone on to explore the genetics of adaptation, especially the role of compensatory mutations in C. elegans. In other words, she is taking the questions on the causes of the fitness recovery discussed in the original paper and developing a research program to explore them.

  240. KF-san,

    Mr Shapiro’s point was about the problem of the chemistry not just the statistics, save insofar as statistical thermodynamics issues are implied.

    Indeed. That was why my reference to Evoloops was apropos. Evoloops is a different chemistry that does support the creation of evolving life forms directly from random soups.

    I apologize for not following up your reply on that other thread when it was posted. I agree that Evoloops is intelligently designed. I said so twice on the other thread. That is not why I bring it up. It is an existence proof, nothing more. What it proves is that a Creator can walk away from Its creation after the “Big Bang” and life does form without subsequent assistance – in that chemistry.

    It might easily be objected that this particular chemistry is finely tuned to allow life to form. I agree again, and note that the fine tuning argument has been used for our chemistry also. An appropriate research question would be – are life supporting chemistries common? If 25% of chemistries support life, is it accurate to use the term fine tuned? (I chose 25% as a rough parallel to the number of universes that support stars.)

  241. Nakashima-san:

    Evoloops is an intelligently designed and controlled simulation in a computer, not chemistry.

    I note my remarks on how the analogy breaks down:

    ______________

    >> As genes circulate in the loop counterclockwise [note the non-random specificity], copies of them are made [Just how, kindly sir?] and sent [again, just how, and how will these copies just happen to program functional protein chains etc?] toward the tip of the arm. The arm grows through repetition of straight growth and left turning. [How is such "folding" initiated and controlled? Is not Right turning just as probable inherently, in a presumed prebioptic soup, and how are the "right" monomers going to be available in step by step sequence to carry out the info storage and onward metaboliic function etc?]. When the tip reaches its own root after three left turns, they bond together to form a new offspring loop. [an algorithm writes itself out of lucky noise -- or is that by an intelligent programmer's input] Then the connection between parent and offspring disappears [[ That is, we have termination here, a nontrivial issue in algorithm design]]. ( In such a way, the loop reproduces its offspring which has a structure identical to its parent’s in the right area, in 151 updates. >>
    ___________________

    In short,t he functionality of evoloops is crucially dependent on their specific design and coding.

    GEM of TKI

  242. KF-san,

    (I find it slightly annoying to see you resurrecting an answered matter as though it were not answered; when you did not respond on the merits when I pointed out what was wrong with the latest case being put up.]

    Are you referring to this?

    And then, explain how lucky noise plus blind mechanical necessity somehow spontaneously rearranged dilute racemic organic molecules in a plausible prebiotic soup into a homochiral, functional information storing and processing system. Including inventing along the way: digital information stored in codes [thus also, computer language -- which thus precedes speech, perhaps by 3.8 BY on the conventional timelines], algorithms, data structures, programs, and the executing machinery to implement the hard and software system.

    I do have a proof of materialistic OOL, but it is too long to fit in the margin! ;)

    Really if you take each of the adjectives in your description of the problem, you know that different researchers are working on that aspect of the problem. None of them is a showstopper. Dilute solutions can be concentrated, racemic mixtures sorted, organic molecules created, plausible atmoshperes calculated, and prebiotic environments tested. if you think one of these areas is a showstopper, point it out. If the last paper published in a field was done a few years ago, and it was a review of all the current work up until then which summarized why results had been negative, and the labs had closed and funding wasted away, and no PhD theses were being written in that area, I would certainly agree that the outlook was moribund and pessimistic, similar to Dr Shapiro. However, I don’t see that to be the case.

  243. PS: Cf Shapiro’s actual remarks:

    ______________

    RNA’s building blocks, nucleotides, are complex substances as organic molecules go. They each contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern. Many alternative ways exist for making those connections, yielding thousands of plausible nucleotides that could readily join in place of the standard ones but that are not represented in RNA. That number is itself dwarfed by the hundreds of thousands to millions of stable organic molecules of similar size that are not nucleotides . . . .

    The RNA nucleotides are familiar to chemists because of their abundance in life and their resulting commercial availability. In a form of molecular vitalism, some scientists have presumed that nature has an innate tendency to produce life’s building blocks preferentially, rather than the hordes of other molecules that can also be derived from the rules of organic chemistry. This idea drew inspiration from . . . Stanley Miller. He applied a spark discharge to a mixture of simple gases that were then thought to represent the atmosphere of the early Earth. ["My" NB: Subsequent research has sharply undercut this idea, a point that is unfortunately not accurately reflected in Sci Am's caption on a picture of the Miller-Urey apparatus, which in part misleadingly reads, over six years after Jonathan Wells' Icons of Evolution was published: The famous Miller-Urey experiment showed how inanimate nature could have produced amino acids in Earth's primordial atmosphere . . .] Two amino acids of the set of 20 used to construct proteins were formed in significant quantities, with others from that set present in small amounts . . . more than 80 different amino acids . . . have been identified as components of the Murchison meteorite, which fell in Australia in 1969 . . . By extrapolation of these results, some writers have presumed that all of life’s building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case.

    A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . I have observed a similar pattern in the results of many spark discharge experiments . . . . no nucleotides of any kind have been reported as products of spark discharge experiments or in studies of meteorites, nor have the smaller units (nucleosides) that contain a sugar and base but lack the phosphate.

    To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . .

    The analogy that comes to mind is that of a golfer, who having played a golf ball through an 18-hole course, then assumed that the ball could also play itself around the course in his absence. He had demonstrated the possibility of the event; it was only necessary to presume that some combination of natural forces (earthquakes, winds, tornadoes and floods, for example) could produce the same result, given enough time. No physical law need be broken for spontaneous RNA formation to happen, but the chances against it are so immense, that the suggestion implies that the non-living world had an innate desire to generate RNA. The majority of origin-of-life scientists who still support the RNA-first theory either accept this concept (implicitly, if not explicitly) or feel that the immensely unfavorable odds were simply overcome by good luck.

    ______________

    That’s not in the ballpark of 25% support. It’s in the context of lethal defects of speculative theories.

    And, of course, Orgel’s posthumous rebuttal was just as devastating to the metabolism-first model: >> It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . >>

    That’s why evolutionary materialist models and speculations on OOL are in crisis.

  244. “You oppose Sanford’s thesis, and you may be right to do so. But the fact of the matter is when ID takes charge of science as opposed to being continually locked in debate with recalcitrant Darwinists, there will be new standards by which we judge whether or not genetic entropy is occurring.”

    I am not sure what you are trying to say. I have no opposition to any type of research at all and am open to any supported conclusions. I just find Sanford’s conclusions not in sync with the world. If all our genomes are crap, I believe like a rusted out car is how Sanford described it, and we still function just fine, then that is a most interesting finding. But I see no indication that the organisms of this world are not functioning well when they have dysfunctional genomes. Some individual members may have problems or the occasional species but in general life is “peachy keen.”

  245. Dave Whisker

    “Actually, mad doc, the authors speculated on the cause, but only in the discussion section”

    I am aware of that and what I was trying to draw attention to was the illogicalities in their speculations: “The authors point out that compensatory epistatic mutations are not the same as “beneficial mutations” (even though they obviously benefit the organism). They postulate these mutations benefit the worst performing organisms the most. (It appears If the organism is mutated then the mutations are good and if the organism is not mutated, mutations are bad).”
    From their results, this is all supposed to have happened within 10 generations in several strains. This is a remarkable achievement for a random process and it puts Dawkin’s “weasel” program to shame.
    Basically I think random mutations are unable to do this in 10 generations. Either their experiment is flawed or there is another explaination. In any event their explaination in the discussion makes no sense for the reasons I have outlined before.
    I am glad that they are doing further investigations. About time too, as that paper is 6 years old. I would be interested to find out the results. I expect the answer will only be found when full genetic mapping of the mutated and non mutated strains can be done and I think you will find a highly efficient data recovery mechanism has been activated in the organism to recover the “lost” information.

  246. Kairosfocus:

    So, we are justified in reworking the Boltzmann expression to separate clumping/thermal and configurational components:

    S = k ln (Wclump*Wconfig) = k lnWth*Wc . . . [Eqn A.11, cf. TBO 8.2a]

    or, S = k ln Wth + k ln Wc = Sth + Sc . . . [Eqn A.11.1]

    Sth = thermal entropy
    Sc = configurational entropy
    S = total entropy

    Configurational entorpy is a deep subject, and so is amending the notion of “S” to include Sc (configurational entorpy).

    But this seems the most insightful because many creationist still invoke the second law without understanding the important distinctions between Sth( thermal entropy) and Sc (configurationl entropy).

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