Saturday, June 23, 2012

You Won’t Believe This One: Gene Splicing Stuns and Bewilders Evolutionists

Proteins perform a wide variety of tasks in the cell and when a particular job needs to be done the right protein is quickly synthesized by unwinding the right DNA gene, making a copy, editing the transcript, and translating the transcript, according to the DNA code, into a sequence of amino acids. Evolutionists had no explanation for this incredible and profound molecular manufacturing system (which still out performs anything scientists can come up with), but they remained steadfast. Indeed they argued all of this provided yet more proofs for evolution. Why? Because the DNA code was essentially universal. As one evolutionist explained, while the genetic code is preserved across species, it would not be if the species had been created independently. [1] If that’s true then the genetic code must have somehow evolved. Is that true? It’s difficult to say because that is, as usual, a non scientific claim. But aside from the metaphysics and the unexplained molecular manufacturing system, there is another problem with this story. It has now turned out to demolish evolutionary theory and has left evolutionists staring into the headlights.

Years after the universal DNA code was discovered, several other codes were also discovered which were not only astonishingly complex, but they were not universal. One such code is the so-called splicing code.

In higher organisms many of the genes are broken up into expressed regions, or exons, which are separated by intervening regions, or introns. After the gene is copied the transcript is edited, splicing out the introns and glueing together the exons. Not only is it a fantastically complex process, it also adds tremendous versatility to how genes are used. A given gene may be spliced into alternate sets of exons, resulting in different protein machines. There are three genes, for example, that generate over 3,000 different spliced products to help control the neuron designs of the brain.

And how does the splicing machinery know where to cut and paste? There is an elaborate code that the splicing machinery uses to decide how to do its splicing. This splicing code is extremely complicated, using not only sequence patterns in the DNA transcript, but also the shape of transcript, as well as other factors.

What is also complex about the new code is that it is context-dependent. In fact it even varies in different tissue types within a species. And studies of RNA binding proteins show even more complexity. These proteins are part of the molecular splicing machinery and they often regulate each other leading to an “unprecedented degree of complexity and compensatory relationships.” As one researcher explained:

We identified thousands of binding sites and altered splicing events for these hnRNP proteins and discovered that, surprisingly these proteins bind and regulate each other and a whole network of other RNA binding proteins.

Regulate each other and a whole network of other RNA binding proteins? Needless to say there is no scientific explanation for how this marvel could have evolved. And since this code is not universal but, quite the opposite, highly varying even between tissues, we can safely conclude the “universal code” prediction of evolution is falsified.

If evolution is true then we expect codes to be universal. Here we have an obvious example of a code that most definitely is not universal, so the prediction is false. And if a prediction is false, then either the theory is false, or it must be modified. But with so many falsifications, and so many modifications that make no sense on evolution, it is obvious that something is very wrong with the theory. In this case we would have to say that random mutations just happened to create many different splicing codes, over and over, of unimaginable complexity.

1. Mark Ridley, Evolution. (Boston: Blackwell Scientific Publications, 1993) 49.

124 comments:

  1. Move along nothing to see here:
    http://www.youtube.com/watch?v=rSjK2Oqrgic

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    1. In case some did not see this at the end of the comments in the last publication from Cornelius:

      BA77 (aka "batspit"), Your interchanges with the evolutionist proponents on this site provokes within me thoughts of a rather humorous allegorical type of comparison coming from the film industry. It is a scene from the Monty Python film, In Search of the Holy Grail. It is a scene where King Arthur is confronted by the Black Knight. You can see it at:

      http://www.youtube.com/watch?v=2eMkth8FWno

      No doubt your arguments are perceived by the evolutionists as: "tis but a scratch" "only a flesh wound", "I have had worse" and the response is "I am invincible", "the black knight always triumphs", "come back here, I'll bite your legs off".

      Watch it through a couple of times. It gets funnier each time.

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    2. This comment has been removed by the author.

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    3. You're not the first to compare batspit77's hopeless flailing to that of the Black Knight. Although the Black Knight could at least form coherent sentences.

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    4. Thorton,
      Nice try to distort the message that was actually being presented. But alas, what else to expect from you my friend.

      Delete
  2. Hunter: If evolution is true then we expect codes to be universal. Here we have an obvious example of a code that most definitely is not universal, so the prediction is false. And if a prediction is false, then either the theory is false, or it must be modified. But with so many falsifications, and so many modifications that make no sense on evolution, it is obvious that something is very wrong with the theory.

    It's an interesting take on science in general. Let's apply it to some other branch of scientific knowledge: optics.

    Geometrical (ray) optics, which was the only game in town until the 19th century, pictured light as a stream of particles. It was falsified by a famous observation of Poisson's spot, which revealed the diffraction of light, thus proving it to be a wave phenomenon.

    Although Fresnel's wave theory of light predicted Poisson's spot and thus triumphed over the old Newtonian picture, it was not without its own set of problems. Because the theory worked with a scalar field, it failed to explain polarization of light. A proper vector theory had to wait until Maxwell's equations.

    Then wave optics ran into a conflict with statistical mechanics. The ultraviolet catastrophe indicated that light waves inside a warm oven possessed infinite energy at any finite temperature and thus would suck out all the energy in the world. Fixing that little problem required the introduction of the quantum of energy and light became a stream of particles (photons). Light was now a wave and a particle! That's truly preposterous!

    So, despite all these makeovers (well, in fact, because of them), optics somehow survived and is now regarded as a mature science. And moreover, the good old geometrical optics remains with us even though it was falsified by Arago's observation of Poisson's spot two hundred years ago! The shape of lenses in your glasses is calculated on the basis of geometrical optics. That which has been discredited in the 19th century!

    Of course geometrical optics wasn't discredited. Physicists found that it had limitations. But within its boundaries of applicability geometrical optics remains alive and well.

    Cornelius paints a naive picture of science. New discoveries do not necessarily relegate the old theory to the dustbin of history. Einstein's relativity peacefully coexists with Newtonian mechanics. Wave theory of light agrees with geometrical optics in the appropriate limit, where both apply.

    Likewise, Darwin's original theory was just the beginning. It merged with Mendelian genetics and was refined to include neutral evolution alongside natura selection. Evolutionary biology will continue to evolve (no pun intended), but it will not die as Cornelius naively hopes.

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    1. Oleg:

      Nice story, but this is "apples" to evolution's "oranges."

      As you state:
      Einstein's relativity peacefully coexists with Newtonian mechanics. Wave theory of light agrees with geometrical optics in the appropriate limit, where both apply.

      In the "limit" they are equivalent. And both Newtonian gravity, and Einstein-ian gravity, bring about correct results. You use one, or the other, given your needs. (Didn't Feynman calculate that the difference between the gravitational potential on the surface of the Sun using GR was different from Newtonian calculations by a factor of something like 1 in 10^12?)

      The situation with NS is very different. It's predictions are almost nil; and most of Darwin's predictions have turned out to be wrong. Darwinism HAD to be joined to Mendelian genetics, and it was done only in a vague sort of way [R.A. Fisher, the Godfather of neo-Darwinism, used a formula (the genetical theory of evolution) which is used in statistical mechanics---so vague is it.]. And the Neutral Theory originated because of the complete failure of neo-Darwinism to explain the extremely high levels of polymorphism found in living beings (another "prediction"---this time of "neo"-Darwinism---that was wrong).

      And, per the originator of Neutral Theory, Kimura, there are severe limitations to what Neutral Theory can do.

      So, where does that leave us? Well, at the The Edge of Evolution! That is, NS does indeed have some applicability (Here's a prediction: in fifteen years, even the little that NS is supposed to be able to do will be shown to rely on other in vivo processes); but, it is indeed only at the 'edges', and very limited indeed.

      When this limited mechanism encounters the type of problem-to-be-solved that CH is describing, no amount of NS/Neutral Theory, or whatever nonsense you want to throw at the problem, is going to even come remotely close to explaining its origins.

      As CH points out, it's time to leave Darwinism on the dustbin of history, and to move on to something that makes sense: intelligent design.

      BTW, Dr. Cornelius, here's a rejoinder to the argument made about the "universal" code: there are all kinds of computers, with all kind of different capabilities, running all sorts of different and very complex software programs, and they all are built on the x86 architecture. Does this prove that they evolved from one another? IOW, what limits a Designer from using the same design over and over, while building more powerful machines and software programs.

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    2. Oleq , you mention many branches of science that have been modified as new evidence has come along. The trouble with your analogy is that at least those nascent theories had a mathematical foundation that comported somewhat roughly to reality to start off with. Darwinism never has had any such mathematical foundation;

      Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism - Casey Luskin - February 27, 2012
      Excerpt: "In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) -
      http://www.evolutionnews.org/2012/02/nobel_prize-win056771.html

      Murray Eden, as reported in “Heresy in the Halls of Biology: Mathematicians Question Darwinism,” Scientific Research, November 1967, p. 64.
      “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.
      http://www.creationscience.com/onlinebook/ReferencesandNotes32.html

      Michael Behe on the theory of constructive neutral evolution - February 2012
      Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. - Michael Behe
      http://www.uncommondescent.com/evolution/michael-behe-on-the-theory-of-constructive-neutral-evolution/

      Oxford University Admits Darwinism's Shaky Math Foundation - May 2011
      Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.
      http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html

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    3. bornagain77: "However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind."

      Thanks! Excellent example of a quote-mine. It's a second-hand quote. It's a syllabus, not a scientific paper. And you show no understanding of — or even a desire to understand — what the the quote actually means.

      There is a disparity between what biologists mean by fitness, and what mathematicians mean by fitness. Mathematicians take fitness to mean movement through an abstract genotype space. Biologists are usually concerned with specific phenotypic traits. Notably, the syllabus concerned working with Alan Grafen who has written several papers helping resolve this discrepancy. In other words, according to your own source, the problem was with limitations of the mathematical models, not with biological understanding.

      Grafen, Formalizing Darwinism and inclusive fitness theory, Philosophical Transactions of the Royal Society Biological Sciences 2009.

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    4. bornagain77: Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism

      Because we always look to quantum physicists for biological insights. In any case, since Pauli's time, biologists have been able to observe and measure rates of natural selection and have shown that observed rates are much faster than necessary to explain historical transitions.

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    5. bornagain (quoting Behe): "I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. "

      Heh. That's funny.

      The authors provide a schematic view of their hypothesis. Despite Behe's well-disregarded papers on the subject, there is nothing implausible about the addition of elements to existing complexes.

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    6. Zach, perhaps you should apply for the job at Oxford and straighten all those population geneticists out:

      DNA Degeneration: Top Population Geneticists agree neo-Darwinism is not supported by the data – John Sanford
      http://www.youtube.com/watch?v=tYEkqwOXE5U

      Genetic Entropy - Dr. John Sanford - Evolution vs. Reality - video (Notes in description)
      http://vimeo.com/35088933

      There is a graph on this video that clearly shows what the main problem is for Darwinism from population genetics:

      Evolution Vs Genetic Entropy - Andy McIntosh - video
      http://www.metacafe.com/watch/4028086

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    7. bornagain77: perhaps you should apply for the job at Oxford and straighten all those population geneticists out:

      We pointed out that your quote from the particulars for a research project with Alan Grafen was taken out of context, and provided you that context. In reply, you continued to ignore that context.

      Grafen, Formalizing Darwinism and inclusive fitness theory, Philosophical Transactions of the Royal Society Biological Sciences 2009.

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  3. Can anyone shed light on how this affects studies such as http://www.worldscinet.com/jbs/18/1802/S0218339010003408.html, where it's assumed lateral transfers created large parts of organisms?

    Or http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html?, where: "Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. 'Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,'"

    It seems that (even ignoring the difficulty in maintaining functional gene networks) incompatible splicing would make such assemblies through lateral transfer nearly impossible. But I would appreciate a Darwinist perspective on this.

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    1. I guess you have to call names to get a debate going around here. Forgive me, I'm new to this:

      "You Darwinists are all poopy-headed ninny munchers. Your women smell of garlic and your men are all swaddled in damp underwrappings."

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  4. I remember when they reverse engineered a good part of the splicing code (last year sometime wasn't it?) It would be really cool to see how the entire spliceosome moves and makes "decisions". The interesting thing is that this is a higher level code - ie. it's like C++ built upon the ASM code of DNA transcripts while the language suite itself is also built from ASM. What this means for evolution is that it somehow has to mutate the ASM level code which then has to be stable long enough to give the C++ code on top of it enough chance to evolve anything at all.

    At what point can it be considered intelligently programmed? Or as they said, "When Messiah comes, will he do more miracles than these?"

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    1. You might have something there, John, if you could develop it at bit further.

      Why waste your time posting here when you could be working on a publishable contribution to science?

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    2. Because I think at this point, the returns that interest me do so only because of their beauty and not really because they have some other type of life enhancing "contribution". If I had the time, resources, and specialized skills (method knowledge) to somehow crystallize and solve a spliceosome or editosome or some other large structure like that, I think I would go for it. But even then, I don't know if it would be worth the time to publish. I don't really know how much they pay for that type of information and the greater part of the reward for me would not be the money (unless maybe it was many millions :D)

      Sadly I knew almost nothing about protein biology while in college. If I could go back I might well choose differently.

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    3. John, I think of that passage quite often, whenever the detractors of ID play the black knight. These people would ascribe intelligence to a single rune scrawled on a cave wall, but when we discover algorithmically compressed machine code regulating sophisticated compound machinery at the root of biological life, they chalk that up to a cosmic fart. So my thought becomes “you say life is not designed, but if it had been designed, would it be even more algorithmic, fully integrated, optimized and fantastic than this?”

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    4. M. Holcumbrink

      These people would ascribe intelligence to a single rune scrawled on a cave wall,


      But we know the identity and can recognize the work of the designers of runes - humans - because we have an ample database of human techniques and capabilities. What is the identify, techniques, and capabilities of the Magic Designer?

      but when we discover algorithmically compressed machine code regulating sophisticated compound machinery at the root of biological life, they chalk that up to a cosmic fart.

      Except no one has ever discovered "algorithmically compressed machine code regulating sophisticated compound machinery" at the root of biological life. You clueless Creationsts really need to figure out that analogies are just that - analogies - and not reality.

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    5. But we know the identity and can recognize the work of the designers of runes - humans - because we have an ample database of human techniques and capabilities… Except no one has ever discovered "algorithmically compressed machine code regulating sophisticated compound machinery" at the root of biological life. You clueless Creationsts really need to figure out that analogies are just that - analogies - and not reality.

      An ample database of human techniques and capabilities? Just analogies and not reality? So are you suggesting that the codon triplet is not actually an optimized error correcting Hamming-style code? Or that RNA is not actually ratcheted through the ribosome and translated just like any other strand of machine code humans have developed at the macro scale (e.g. mylar tape)? And are you suggesting there are not really wheels, axles, levers and clutches at the molecular level in biological systems? Or do you not think that step-by-step procedures are necessary for consistently turning a single gene into thousands of different proteins (i.e. decompression)? Is semiotic convention not a human construct (e.g. runes)?

      Or maybe I should ask this: supposing there was actually algorithmically compressed machine code regulating sophisticated compound machinery at the root of biological life, would that give you pause, and cause you to say to yourself “you know, humans have devised techniques just like this in our modern world of computing, perhaps we were designed by someone of like mind”. Or would it be just another “ho-hum” if you were to suddenly realize this were the case? I guess we all know the answer to that one.

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    6. M. Holcumbrink

      An ample database of human techniques and capabilities? Just analogies and not reality? So are you suggesting that the codon triplet is not actually an optimized error correcting Hamming-style code? Or that RNA is not actually ratcheted through the ribosome and translated just like any other strand of machine code humans have developed at the macro scale (e.g. mylar tape)? And are you suggesting there are not really wheels, axles, levers and clutches at the molecular level in biological systems? Or do you not think that step-by-step procedures are necessary for consistently turning a single gene into thousands of different proteins (i.e. decompression)? Is semiotic convention not a human construct (e.g. runes)?


      Nope. The comparison between all those biological things you list and their human designed counterparts are analogies. They have superficial similarities in form and function, but that doesn't make them both designed. All analogies break down when the details are studied, and yours are no different.

      Or maybe I should ask this: supposing there was actually algorithmically compressed machine code regulating sophisticated compound machinery at the root of biological life, would that give you pause, and cause you to say to yourself “you know, humans have devised techniques just like this in our modern world of computing, perhaps we were designed by someone of like mind”. Or would it be just another “ho-hum” if you were to suddenly realize this were the case? I guess we all know the answer to that one.

      A human designed lawn sprinkler and a rain cloud both perform the same function of watering my grass. Does that mean rain clouds are designed? If not, why not?

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  5. CH: Needless to say there is no scientific explanation for how this marvel could have evolved.

    Really? What's wrong with evolution?

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    1. EL:

      CH: Needless to say there is no scientific explanation for how this marvel could have evolved.

      EL: Really? What's wrong with evolution?


      I said "scientific".

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    2. And evolutionary theory, as you well know, Cornelius, is a scientific theory.

      So I ask you again: what is wrong with the theory of evolution as a explanation of "how this marvel could have evolved"?

      What do you think is unevolvable about it?

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    3. Elizabeth Liddle: And evolutionary theory, as you well know, Cornelius, is a scientific theory. So I ask you again: what is wrong with the theory of evolution as a explanation of "how this marvel could have evolved"?

      True scientists should not just say that ‘evolution did it’, but they should present plausible models on 'how evolution did it'.

      To my knowledge, not such models have been advanced by the current science establishment. Even worse, apparently, this issue has not been even been seriously raised, so we should thank Cornelius for raising it!

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    4. EL:

      "What do you think is unevolvable about it?"

      Nothing. I never said is is unevolvable. Again, you can't claim the evidence is overwhelming and compelling for evolution, and then when questioned about *your* claim, place the burden on the questioner to falsify evolution. Remember, evolutionists are the ones making the claim.

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    5. Nothing. I never said is is unevolvable.

      But you said that there was "no scientific explanation". And yet we have, to hand, a very nice scientific explanation as to how sequences that result in phenotypic effects that benefit the organism accumulate over time, and clearly sequences that govern gene expression benefit the organism.

      So where is the problem?

      Again, you can't claim the evidence is overwhelming and compelling for evolution, and then when questioned about *your* claim, place the burden on the questioner to falsify evolution. Remember, evolutionists are the ones making the claim.

      As usual, you equivocate. Clearly there are a tiny number of specific features for which we have a definitive evolutionary pathway. Nobody is claiming otherwise. On the other hand we have a powerful principle, which we know works (because we have observed it working, in real time), and abundant evidence of exactly the kind of adaptation over time and down bifurcating lineages that are in principle accountable for by descent with modification and heritable reproductive success.

      Now, if you had some reason to think that gene expression mechanisms were unevolvable, then there might be some point in writing a headline like the one for this post.

      But as it stands, all you have is your own incredulity, while, far from being "stunned and bewildered", the "evolutionists" are the ones doing the actual research that you keep citing as problematic for evolution.

      Giving no rationale at all.

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  6. If evolution is true then we expect codes to be universal.

    Baloney. Who said so?

    There are "codes" and then there are "codes." The genetic "code" is one. The histone "code" is another. The referenced splicing "code" is yet another. They are all human interpretations of the data. Equivocating among them to make cheap rhetorical points is just deceitful.

    Business as usual here.

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    1. And none of those "codes" bear any resemblance to the Morse code of computer machine code or any other code designed by human beings.

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    2. "And none of those "codes" bear any resemblance to the Morse code of computer machine code or any other code designed by human beings."

      Denying a code is a code, denying information is information. yada, yada, yada yawn, business as usual from Darwinists,,, nothing to see here move along. :)

      Every Bit Digital DNA’s Programming Really Bugs Some ID Critics - March 2010
      Excerpt: In 2003 renowned biologist Leroy Hood and biotech guru David Galas authored a review article in the world’s leading scientific journal, Nature, titled, “The digital code of DNA.”,,, MIT Professor of Mechanical Engineering Seth Lloyd (no friend of ID) likewise eloquently explains why DNA has a “digital” nature: "It’s been known since the structure of DNA was elucidated that DNA is very digital. There are four possible base pairs per site, two bits per site, three and a half billion sites, seven billion bits of information in the human DNA. There’s a very recognizable digital code of the kind that electrical engineers rediscovered in the 1950s that maps the codes for sequences of DNA onto expressions of proteins."
      http://www.salvomag.com/new/articles/salvo12/12luskin2.php

      Stephen C. Meyer - Signature In The Cell:
      "DNA functions like a software program," "We know from experience that software comes from programmers. Information--whether inscribed in hieroglyphics, written in a book or encoded in a radio signal--always arises from an intelligent source. So the discovery of digital code in DNA provides evidence that the information in DNA also had an intelligent source."
      http://www.evolutionnews.org/2009/07/leading_advocate_of_intelligen.html

      Extreme Software Design In Cells - Stephen Meyer - video
      http://www.metacafe.com/watch/5495397/

      The Digital Code of DNA - 2003 - Leroy Hood & David Galas
      Excerpt: The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science.
      http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html

      Judge Rules DNA is Unique (and not patentable) Because it Carries Functional Information - March 2010
      “Today the idea that DNA carries genetic information in its long chain of nucleotides is so fundamental to biological thought that it is sometimes difficult to realize the enormous intellectual gap that it filled.... DNA is relatively inert chemically.”
      http://www.uncommondescent.com/intelligent-design/judge-rules-dna-is-unique-because-it-carries-information/

      etc.. etc.. etc...

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    3. Pendant you may enjoy this:

      The Ribosome of the cell is found to be very similar to a CPU in a electronic computer:

      Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012
      David J D’Onofrio1*, David L Abel2* and Donald E Johnson3
      Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,,
      An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,,
      The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm.
      It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive.
      http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf

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    4. Pedant:

      CH: If evolution is true then we expect codes to be universal.

      Pedant: Baloney. Who said so? There are "codes" and then there are "codes." The genetic "code" is one. The histone "code" is another. The referenced splicing "code" is yet another. They are all human interpretations of the data. Equivocating among them to make cheap rhetorical points is just deceitful. Business as usual here.


      Oh I forgot. When a code is universal then evolution predicted it to be universal. When a code is different everywhere you look, then evolution predicted it to be everywhere different. Got it.

      And how did those codes arise again? Oh right, random mutations. Of course.

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    5. Cornelius,

      Poisson's spot has surely falsified geometrical optics. Why is geometrical optics still with us?

      Classical physics says that electrons orbiting an atomic nucleus must radiate and fall into the nucleus. Why are we still teaching classical physics?

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    6. oleq, could you please tell us the exact demarcation criterion by which Darwinism can even be describe as scientific in the first place???

      Science and Pseudoscience – Imre Lakatos
      “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

      Discerning Science from Pseudoscience – Lakatos – audio
      http://richmedia.lse.ac.uk/philosophy/2002_LakatosScienceAndPseudoscience128.mp3

      ‘Before you can ask ‘Is Darwinian theory correct or not?’, You have to ask the preliminary question ‘Is it clear enough so that it could be correct?’. That’s a very different question. One of my prevailing doctrines about Darwinian theory is ‘Man, that thing is just a mess. It’s like looking into a room full of smoke.’ Nothing in the theory is precisely, clearly, carefully defined or delineated. It lacks all of the rigor one expects from mathematical physics, and mathematical physics lacks all the rigor one expects from mathematics. So we’re talking about a gradual descent down the level of intelligibility until we reach evolutionary biology.’
      David Berlinski

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    7. ba77,

      Two points.

      1. My name is Oleg, not Oleq. Please make a note of it.

      2. If you are interested in understanding evolutionary biology (apropos of the last paragraph of your comment), why don't you take a course at your local university? It is well worth the effort.

      Delete
    8. Shorter Cornelius:

      "ZOMG it's SOOOOOOOOO complex, therefore MY CHRISTIAN GAWD designed it!!"

      CH mails in another snoozer. Film at 11.

      Delete
    9. Because many grown ups have evolved the skill to learn without disciplinarians. Of course, if you have ascertained where ba77's misunderstanding of evolution lies, you then have the ability to provide the needed correction.

      Can you explain which super nuanced facet of evolution he has mis-characterized? Is it the part that says "thing change"?

      Also, is there some mechanism in evolution that is as reliable in its predictive power as for example, specular reflection is in geometrical optics?

      Delete
    10. oleg, as to your comment that I take a class at college so as to understand evolution, ,,,

      Argument Ad Hominem (William Lane Craig) - video
      http://www.youtube.com/watch?v=IX3beh6g1Qg

      As to Lakato's comment that there is no demarcation criterion for Darwinism, well after years of debating dogmatic neo-Darwinists such as you, I fully agree with his statement. There is absolutely nothing in the entire framework of Darwinism that can withstand scrutiny and to which one can point and can say 'but at least this part is scientifically true of Darwinism'. Whatever Darwinism is, it certainly is not science in any meaningful sense of the word!

      Is evolution pseudoscience?
      Excerpt:,,,
      1. Some pseudoscientific theories are based upon an authoritative text rather than observation or empirical investigation.
      2. Some pseudoscientific theories explain what non-believers cannot even observe.
      3. Some can’t be tested because they are consistent with every imaginable state of affairs in the empirical world.
      The next is essentially the same:
      4… [or] are so vague and malleable that anything relevant can be shoehorned to fit the theory.
      5. Some theories have been empirically tested and rather than being confirmed they seem either to have been falsified or to require numerous ad hoc hypotheses to sustain them.
      6. Some pseudoscientific theories rely on ancient myths and legends …
      Okay, one that doesn’t particularly describe evolution, although evolutionary notions can be traced back to ancient pagan Greek
      7.Some pseudoscientific theories are supported mainly by selective use of anecdotes, intuition, and examples of confirming instances.
      8. Some pseudoscientific theories confuse metaphysical claims with empirical claims.
      9. Some pseudoscientific theories … contradict known scientific laws and use ad hoc hypotheses to explain their belief.
      10. Pseudoscientists claim to base their theories on empirical evidence, and they may even use some scientific methods, though often their understanding of a controlled experiment is inadequate.
      Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other pseudosciences — astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
      http://creation.com/is-evolution-pseudoscience

      C.S. Lewis: creationist and anti-evolutionist
      Excerpt: "In 1951 C S Lewis wrote that evolution was “the central and radical lie in the whole web of falsehood that now governs our lives” and modern civilization. Evolution, Lewis explained, is a picture of reality that has resulted from imagination and is “not the logical result of what is vaguely called ‘modern science’.”
      http://creation.com/c-s-lewis

      "Evolution is the only 'scientific theory' that needs laws to protect it!" Author Unknown

      How Do We Know Intelligent Design Is a Scientific "Theory"? - Casey Luskin - October 2011
      Excerpt: ID is supported by a vast body of evidence ranging from physics and cosmology to biochemistry to animal biology to systems biology to epigenetics and paleontology. ID more than exceeds the NAS's definitions of "theory."
      http://www.evolutionnews.org/2011/10/how_do_we_know_intelligent_des051841.html

      Delete
    11. ba77,

      How do you twist a suggestion to learn some science into an ad hominem argument? That's quite a feat! You should observe that Cornelius Hunter studied biophysics at a major research university. Follow his lead!

      Delete
    12. oleg

      ba77,

      How do you twist a suggestion to learn some science into an ad hominem argument? That's quite a feat! You should observe that Cornelius Hunter studied biophysics at a major research university. Follow his lead!


      Studying the topic isn't enough - just look at the laughably bad quality of "science" CH cranks out here on a regular basis. You also have to have the intellectual honesty to go where the evidence leads.

      Every IDCer I've ever seen is driven by a single thought - "I'm specially created by my GAWD!". They just *know* they can't be related to any stinkin' monkeys, so everything about evolutionary theory must be false. Millions of studies by millions of scientists in hundreds of fields over 150+ years - all wrong. Even though they can't say why, or provide any alternate explanations for the data.

      IDCers don't have the intellectual honesty or the critical thinking skills to overcome the religious indoctrination they received as youth. In batspit77's case I sometimes think he's having weird acid flashbacks to boot.

      Delete
    13. Well oleg, Perhaps you can save me a ton of tuition and just point me to the one experiment where they evolved JUST ONE molecular machine from scratch? This should be no problem for such a big brained Darwinist as you!

      "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject."
      James Shapiro - Molecular Biologist

      ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’
      Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
      *Professor Emeritus of Biochemistry, Colorado State University, USA

      Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
      http://www.metacafe.com/watch/5302950/

      “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.”
      David Ray Griffin - retired professor of philosophy of religion and theology

      Delete
    14. Perhaps one of these?

      Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video
      http://www.metacafe.com/watch/3994630

      The ATP Synthase Enzyme - exquisite motor necessary for first life - video
      http://www.youtube.com/watch?v=W3KxU63gcF4

      Powering the Cell: Mitochondria - video
      http://www.youtube.com/watch?v=RrS2uROUjK4

      Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video
      http://www.metacafe.com/watch/4261990

      Kinesin Linear Motor - Video
      http://www.youtube.com/watch?v=kOeJwQ0OXc4

      Ribosome Translation High Quality - video
      http://pubs.acs.org/cen/multimedia/85/ribosome/translation_bacterial.html

      Myosin - video
      http://www.youtube.com/watch?v=j8F5GGPACkQ

      The Virus - Assembly Of A Molecular "Lunar Landing" Machine - video
      http://www.metacafe.com/watch/4023122

      The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell:

      Molecular Machines in the Cell -
      http://www.discovery.org/a/14791

      Delete
    15. I can't make you learn, ba77. It's an entirely voluntary activity. I can only encourage you to. But hey, it's a free world. Everyone is free to pick up slogans on the internet and paste them all over the place. And it doesn't cost anything.

      Delete
    16. oleq, but you got the big Darwinian brain that so much more evolved than ours, aren't you going to share the Darwinian origination of even one molecular machine with us? Oh well, I know you probably think its just to precious a secret to share. But others may get the wrong idea and think that you don't have any evidence at all oleg? Oh well perhaps we can just start a fund drive to forcebly educate the majority of the American public who think you guys are full of BS.

      Delete
    17. he called your post "slogans". That's funny. But I guess as he said, "it's a free world" :D

      Delete
    18. ba77,

      I doubt that someone who can't even remember the 4 letters of my name for one day has any capacity to learn.

      Delete
    19. Thorton:

      "ZOMG it's SOOOOOOOOO complex, therefore MY CHRISTIAN GAWD designed it!!"

      What's with the insane obsession with Christians? I suspect you had a fundamentalist upbringing like PZ Myers and you got this big chip on your shoulders that you need to get rid of. Nothing is more pathetic and annoying than an atheist who hates God.

      Besides, complexity is an extremely powerful argument against evolution, your feeble and hypocritical protestations to the contrary notwithstanding.

      Delete
    20. "I doubt that someone who can't even remember the 4 letters of my name for one day has any capacity to learn."

      So instead of evidence I get belittled. Is this what they taught you in your college courses on evolution oleg?

      Lesson 1 in Evolution 101: No matter what the evidence say, proclaim evolution did it!

      Lesson 2: When pressed for actual evidence belittle the questioner!

      Lesson 3: Wash, Rinse, and Repeat as often as necessary!

      Do I get my college degree now oleg?

      Delete
    21. Louis Savain

      Thorton: "ZOMG it's SOOOOOOOOO complex, therefore MY CHRISTIAN GAWD designed it!!"

      What's with the insane obsession with Christians?


      Don't blame me, I'm not one who posts scripture and links to corny Xian music every day as a "scientific" refutation.

      Besides, complexity is an extremely powerful argument against evolution, your feeble and hypocritical protestations to the contrary notwithstanding.

      How so? Evolutionary processes are empirically observed to create complexity. That means complexity by itself is not a positive indication of design. Science has been pointing out that fact to the IDCers since day one but apparently you're all too dense to get it.

      Delete
    22. oleg I just remembered, I can think of a lot of 4 letter words that come to mind for your name that don't even use any of the the 4 letters o,l,e, or g! :) Do I get bonus points? Will you tell me where the experimental evidence for the molecular machines are now?

      Delete
    23. "Evolutionary processes are empirically observed to create complexity"

      No they have not been observed:

      “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010
      Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit')
      http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

      Michael Behe talks about the preceding paper on this podcast:

      Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010
      http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

      Where's the substantiating evidence for neo-Darwinism?
      https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

      Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors
      Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,,
      http://www.tbiomed.com/content/2/1/29

      Delete
    24. Thorton:

      How so? Evolutionary processes are empirically observed to create complexity.

      No process can create complexity unless it was designed to create complexity. Where did these evolutionary processes come from? Did they evolve themselves before they could evolve? You're a silly man.

      That means complexity by itself is not a positive indication of design.

      No it doesn't. See above.

      Science has been pointing out that fact to the IDCers since day one but apparently you're all too dense to get it.

      Actually, you mean your chicken feather voodoo "science". Thanks for the laughs.

      Delete
    25. Louis Saverain

      No process can create complexity unless it was designed to create complexity.


      Go ahead Louis, give us all a laugh. Try to prove your negative.

      Delete
    26. We all know that it is logically impossible to prove a negative. We all know too that a single counterexample would disprove the statement. Can you provide one?

      Delete
    27. ba77: oleg I just remembered, I can think of a lot of 4 letter words that come to mind for your name that don't even use any of the the 4 letters o,l,e, or g! :) Do I get bonus points? Will you tell me where the experimental evidence for the molecular machines are now?

      Why don't you ask your favorite author Michael Behe? He claimed at some point that the HIV virus has not developed any new "molecular machines" since jumping from apes to humans. He was then taken to school by a grad student named Abbie Smith.

      Here is Behe, conceding the point. (He can't bring himself to acknowledge losing to a lowly grad student, so he refers solely to Dr. Ian Musgrave.)

      And now let’s talk about Dr. Musgrave’s “core argument,” that subsequent to the virus leaping to humans from chimps Vpu developed the ability to act as a viroporin, allowing the leakage of cations which helps release the virus from the cell membrane. Yes, I’m perfectly willing to concede that this does appear to be the development of a new viral protein-viral protein binding site, one which I overlooked when writing about HIV. So the square point in Figure 7.4 representing HIV should be placed on the Y axis at a value of one, instead of zero, and Table 7.1 should list one protein-binding site developed by HIV instead of zero.

      Hope this helps.

      Delete
    28. Daniel

      T: "Evolutionary processes are empirically observed to create complexity."

      We all know that it is logically impossible to prove a negative. We all know too that a single counterexample would disprove the statement. Can you provide one?


      evolutionary algorithms

      Before you start with he normal IDCer squawk "but the computer program was DESIGNED!!", please note that while the program was human designed, the processes being used are not human designed but are naturally occurring evolutionary ones.

      Delete
    29. "evolutionary algorithms":

      Refutation Of Evolutionary Algorithms

      "Darwin or Design" with Dr. Tom Woodward with guest Dr. Robert J. Marks II - video
      http://www.youtube.com/watch?v=Yoj9xo0YsOQ

      LIFE’S CONSERVATION LAW - William Dembski - Robert Marks - Pg. 13
      Excerpt: Simulations such as Dawkins’s WEASEL, Adami’s AVIDA, Ray’s Tierra, and Schneider’s ev appear to support Darwinian evolution, but only for lack of clear accounting practices that track the information smuggled into them.,,, Information does not magically materialize. It can be created by intelligence or it can be shunted around by natural forces. But natural forces, and Darwinian processes in particular, do not create information. Active information enables us to see why this is the case.
      http://evoinfo.org/publications/lifes-conservation-law/

      The Evolutionary Informatics Lab: Putting Intelligent Design Predictions to the Test - Casey Luskin - February, 2012
      Excerpt: The work of the Evolutionary Informatics Lab demonstrates that ID proponents are capable of producing innovative techniques for tackling questions related to intelligent design and evolution. First, the lab developed a methodology for studying the degree to which information is smuggled into evolutionary algorithms. Then, the researchers applied that methodology to various well-known programs like ev, Avida, and Dawkins' "Weasel Simulation," and successfully identified sources of "active information" in each. As the lab's website promised, their research has shown that even the best efforts of ID-critics cannot escape the fact that intelligence is required to generate new information.
      http://www.evolutionnews.org/2012/02/the_evolutionar056061.html

      Climbing the Steiner Tree--Sources of Active Information in a Genetic Algorithm for Solving the Euclidean Steiner Tree Problem - 2012 - Winston Ewert, William A Dembski, Robert J Marks II
      http://bio-complexity.org/ojs/index.php/main/article/view/50

      Delete
    30. related notes:

      Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism - Dembski - Marks - Dec. 2009
      Excerpt: The effectiveness of a given algorithm can be measured by the active information introduced to the search. We illustrate this by identifying sources of active information in Avida, a software program designed to search for logic functions using nand gates. Avida uses stair step active information by rewarding logic functions using a smaller number of nands to construct functions requiring more. Removing stair steps deteriorates Avida’s performance while removing deleterious instructions improves it.
      http://evoinfo.org/publications/evolutionary-synthesis-of-nand-logic-avida/

      Kurt Gödel - Incompleteness Theorem - video
      http://www.metacafe.com/w/8462821

      Alan Turing & Kurt Godel - Incompleteness Theorem and Human Intuition - video (notes in video description)
      http://www.metacafe.com/watch/8516356/

      Here is what George Chaitin, a world-famous mathematician and computer scientist, said about the limits of his computer program trying to prove evolution was mathematically feasible:

      At last, a Darwinist mathematician tells the truth about evolution - VJT - November 2011
      Excerpt: In Chaitin’s own words, “You’re allowed to ask God or someone to give you the answer to some question where you can’t compute the answer, and the oracle will immediately give you the answer, and you go on ahead.”
      http://www.uncommondescent.com/intelligent-design/at-last-a-darwinist-mathematician-tells-the-truth-about-evolution/

      Here is the video where, at the 30:00 minute mark, you can here the preceding quote from Chaitin's own mouth in full context:

      Life as Evolving Software, Greg Chaitin at PPGC UFRGS
      http://www.youtube.com/watch?v=RlYS_GiAnK8

      Moreover, at the 40:00 minute mark of the video Chaitin readily admits that Intelligent Design is the best possible way to get evolution to take place, and at the 43:30 minute mark Chaitin even tells of a friend pointing out that the idea Evolutionary computer model that Chaitin has devised does not have enough time to work. And Chaitin even agreed that his friend had a point, although Chaitin still ends up just 'wanting', and not ever proving, his idea Darwinian mathematical model to be true!

      Delete
    31. Daniel, responding to Thorton:

      We all know that it is logically impossible to prove a negative.

      But this is not true. Don't let evolutionists pull a wool over your eyes, amigo. First of all, evolutionists continually use negative arguments to support their silly theory; they argue, for example, that it could not have been done any other way but their way. This metaphysical argument on the part of evolutionists is the crux of Hunter's blog. The evolutionist's argument always comes down to "God could not have done it a certain way". It's a perfect example of a bad negative argument.

      Second, negatives are proven all the time. In logic, we use statements such as, a set contains or does not contain a number or variable or, a given problem has no solutions. The halting problem is a case in point. Alan Turing proved that a general algorithm to solve the halting problem for all possible program-input pairs cannot exist.

      Thorton has a chicken sh!t religion to defend and he uses every stupid trick in the book to do so. Don't let him BS you. Don't ever allow evolutionists to intimidate you. They've got excrement for brains.

      Delete
    32. Thorton:

      Before you start with he normal IDCer squawk "but the computer program was DESIGNED!!", please note that while the program was human designed, the processes being used are not human designed but are naturally occurring evolutionary ones.

      Talk about pulling BS out of one's asteroid orifice. And you proved that those processes were not designed how again?

      Delete
    33. CH:Oh I forgot. When a code is universal then evolution predicted it to be universal. When a code is different everywhere you look, then evolution predicted it to be everywhere different. Got it.

      No, you haven't got it, Cornelius, and it is dawning on me just how profound your misunderstanding of scientific methodology actually is, which is extraordinary given that you have PhD level training in empirical science.

      As you should (but apparently do not) know, the word "theory" usually refers to an explanatory model that accounts for our observations. It is not usually predictive. A "law" on the other hand, is usually a mathematical model that reliably predicts new observations, but is not, in itself, explanatory.

      A good theory will generate testable hypotheses - postulated explanations hypotheses that do make specific predictions. These generally flesh out the theory, and if a hypothesis is infirmed, do not necessarily infirm the entire theory from which they are derived, but, if confirmed, contribute to the overall explanatory model. However, if a theory consistently fails to generate successful hypothesis, it may be rejected in favour of a more fecund theory.

      The theory of evolution is a large body of theory, which, in Darwin's original conception, proposed that living organisms were descended from "a few forms or one", and diversified down branching lineages by means of descent with modification and natural selection.

      This theory was presented as an explanation of the patterns of features of living organisms he had himself observed on his voyages, and also as recorded and organised by Linnaeus.

      From it, since, have been derived many testable hypotheses, i.e. predictions of the form: IF this is true THEN we should see this. Some of these hypotheses have been confirmed; some infirmed; most get the answer "yes, but...." where the "but..." is something more interesting and more complex than the original hypothesis.

      As a result, the "theory of evolution" is now hugely more complex than Darwin's original theory, and has spawned many explanatory mechanisms that were beyond Darwin's wildest imaginings. Darwin, after all, did not know the basic mechanism of heredity, nor did he have any idea of what might cause the variation on which his theory depended.

      So your continued allegations that Darwin's theory is full of "failed predictions" is not only false, but silly. Darwin's theory neither predicted a common code nor different codes. What it postulated was common ancestry, and descent with modification plus natural selection. Descent turns out to have a lot to do with molecular "codes", but it also turns out that those molecular "codes" are transferred by mechanisms other than descent, and that the codes themselves are modified during transfer, and have phenotypic effects that affect reproductive success (i.e. are subject to natural selection).

      i.e. nothing in any of that "falsifies" the theory, nor violates predictions of the theory (which is not itself predictive anyway, but explanatory).


      And how did those codes arise again? Oh right, random mutations. Of course.


      You forgot selection. Also, I suspect you of equivocating with the word "random".

      Delete
  7. Of related note:

    Evolutionists have long argued that the genetic code is universal for all lifeforms, and maintain that that fact is strong evidence for evolution from a universal common anscestor, yet it appears they were wrong once again:

    No Darwin Tree of Life (Craig Venter vs. Richard Dawkins)- video
    http://www.youtube.com/watch?v=zqaXVqmcDVI

    Venter vs. Dawkins on the Tree of Life - and Another Dawkins Whopper - March 2011
    Excerpt:,,, But first, let's look at the reason Dawkins gives for why the code must be universal:
    "The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation...this would spell disaster." (2009, p. 409-10)
    OK. Keep Dawkins' claim of universality in mind, along with his argument for why the code must be universal, and then go here (linked site listing 23 variants of the genetic code).
    Simple counting question: does "one or two" equal 23? That's the number of known variant genetic codes compiled by the National Center for Biotechnology Information. By any measure, Dawkins is off by an order of magnitude, times a factor of two.
    http://www.evolutionnews.org/2011/03/venter_vs_dawkins_on_the_tree_044681.html

    Actually there is a more 'technical' reason, than the reason Dawkins gave, for why codes cannot be changed to become more complex once they are in place:

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

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

    Though I'm certain Darwinists will disagree (as they always do), I'm fairly certain that Shannon channel capacity will apply to other codes such as the splicing code as well as it does to the genetic code. (At least that is the take home message I took from Perry Marshall's video)

    Further notes:

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

    ReplyDelete
  8. Hunter:

    Oh I forgot. When a code is universal then evolution predicted it to be universal. When a code is different everywhere you look, then evolution predicted it to be everywhere different. Got it.

    I repeat: Baloney. Who said so?

    Our historian of science could enhance his credibility by providing references from the scientific literature that support his claims, bearing in mind that hindsight is not predictive.

    ReplyDelete
    Replies
    1. Pendant, So evolution never claimed anything particular about codes in life? Thanks for clearing that up pendant! :)

      Guess Talk Origins 29 evidences for macroevolution, Rational wiki, and wikipedia can take stuff like this out:

      Rational wiki
      Excerpt: The most powerful evidence for common descent includes , DNA and RNA code - Almost all organisms use the same three-letter code for translating RNA into proteins. There are variations, such as the code used by mitochondria and some bacteria and fungi, but the differences are only minor. Regardless of the slight differences, all organisms use the same coding mechanism for translating the code into amino acid sequences.,,,, All life significantly shares the genetic code based on the molecule DNA and its related molecule RNA. The translation between DNA and RNA codons (groups of three bases) and the corresponding amino acids is almost the same in all known forms of DNA-based life on earth, from humans to bacteria. If the translation between DNA, RNA, and amino acid differs, it allows scientists to probe how creatures have evolved and how different taxonomic groups branched apart.
      http://rationalwiki.org/wiki/Common_descent

      http://rationalwiki.org/wiki/Common_descent#RNA_.2F_DNA_code

      Pendant an Interesting thing about codes is that they are abstract and cannot be reduced to a material basis. Moreover this argument follows from 'abstract concepts':

      Here is a sound argument from the preceding observation:.
      1. We know what a thing is by observing how it acts.
      2. The mind/soul acts to produce abstract immaterial concepts (such as codes) and rational arguments that no material entity can produce.
      3. Therefore, the mind/soul is not a material entity, but must be immaterial. Furthermore, this tells us that not only is it possible for immaterial entities to exist, based on our own experience and reason immaterial entities do in fact exist and some form of dualism is true.
      http://www.uncommondescent.com/neuroscience/memo-from-materialists-science-is-over-oh-and-by-the-way-consciousness-doesnt-matter/#comment-421418

      Alvin Plantinga and the Modal Argument (for the existence of the soul) - video
      http://www.youtube.com/watch?v=WOTn_wRwDE0

      Delete
    2. As well:

      The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video
      http://www.metacafe.com/watch/4060532

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

      Delete
  9. oleg, you are actually claiming ONE SINGLE novel protein-protein binding site as a entire molecular machine??? WOW just WOW!

    oleg Perhaps you should take a course at your local college in electrical motors, machine shop, or automotive class, or something similar to learn what a machine actually is, how it is composed of many different parts working together to perform usually a single function!

    As well oleg, Perhaps you should also take a closer look at what that ONE protein-protein binding site in HIV actually accomplished before you go crowing about it:

    Michael Behe defends the one 'overlooked' protein/protein binding site generated by the HIV virus, that Abbie Smith and Ian Musgrave had found, by pointing out it is well within the 2 binding site limit he set in "The Edge Of Evolution" on this following site:

    Response to Ian Musgrave's "Open Letter to Dr. Michael Behe," Part 4
    "Yes, one overlooked protein-protein interaction developed, leading to a leaky cell membrane --- not something to crow about after 10^20 replications and a greatly enhanced mutation rate."
    http://behe.uncommondescent.com/page/4/

    An information-gaining mutation in HIV? NO!
    http://creation.com/an-information-gaining-mutation-in-hiv

    In fact, I followed this debate very closely and it turns out the trivial gain of just one protein-protein binding site being generated for the non-living HIV virus, that the evolutionists were 'crowing' about, came at a staggering loss of complexity for the living host it invaded (People) with just that one trivial gain of a 'leaky cell membrane' in binding site complexity. Thus the 'evolution' of the virus clearly stayed within the principle of Genetic Entropy since far more functional complexity was lost by the living human cells it invaded than was ever gained by the non-living HIV virus. A non-living virus which depends on those human cells to replicate in the first place. Moreover, while learning HIV is a 'mutational powerhouse' which greatly outclasses the 'mutational firepower' of the entire spectrum of higher life-forms combined for millions of years, and about the devastating effect HIV has on humans with just that one trivial binding site being generated, I realized if evolution were actually the truth about how life came to be on Earth then the only 'life' that would be around would be extremely small organisms with the highest replication rate, and with the most mutational firepower, since only they would be the fittest to survive in the dog eat dog world where blind pitiless evolution rules and only the 'fittest' are allowed to survive.

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    Replies
    1. related note: The Problem of Information for the Theory of Evolution – debunking Schneider's ev computer simulation
      Excerpt: In several papers genetic binding sites were analyzed using a Shannon information theory approach. It was recently claimed that these regulatory sequences could increase information content through evolutionary processes starting from a random DNA sequence, for which a computer simulation was offered as evidence. However, incorporating neglected cellular realities and using biologically realistic parameter values invalidate this claim. The net effect over time of random mutations spread throughout genomes is an increase in randomness per gene and decreased functional optimality.
      http://www.trueorigin.org/schneider.asp

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    2. Yeah, ba77, this is how the debate has been progressing. Creationists draw a line in the sand that evolution cannot cross, biologists find evidence to the contrary, creationists redraw a new line. If one binding site can develop naturally (and apparently more than once in HIV) then why can't two and three? What stops the virus from doing so? Your own word?

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    3. oleq, Is one binding site a molecular machine to you? Is one binding site past the 2 binding site limit Dr. Behe set for the 'edge of evolution'? i.e. Have you given me empirical evidence of a molecular machine arising by Darwinian processes? If you believe one binding site is a molecular machine, can I interest you in some ocean front property in Arizona?

      Delete
    4. ba77,

      1. You forgot how to spell my name again.

      2. Is there a definition of "molecular machine" somewhere that you can point me to? If not then each of us is free to come up with one's own.

      Delete
    5. Hmmm oleg, so one protein binding site generated in 10^20 tries is a molecular machine for you and you believe that all life arose via undirected processes because of this 'unlimited' ability???

      On a more sober note, methinks you may have overlooked something:

      "The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable."
      Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")

      The Sheer Lack Of Evidence For Macro Evolution - William Lane Craig - video
      http://www.metacafe.com/watch/4023134

      So, how many protein-protein binding sites are found in life?

      Dr. Behe, on the important Table 7.1 on page 143 of Edge Of Evolution, finds that a typical cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites in a multicellular creature is,,,

      Largest-Ever Map of Plant Protein Interactions - July 2011
      Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker.
      http://www.sciencedaily.com/releases/2011/07/110728144936.htm

      So taking into account that they only covered 2%, of the full protein-protein "interactome", then that gives us a number, for different protein-protein interactions, of 310,000. Thus, from my very rough 'back of the envelope' calculations, we find that this is at least 30 times higher than Dr. Behe's estimate of 10,000 different protein-protein binding sites for a typical single cell (Page 143; Edge of Evolution; Behe). Therefore, at least at first glance from my rough calculations, it certainly seems to be a gargantuan step that evolution must somehow make, by purely unguided processes, to go from a single cell to a multi-cellular creature. To illustrate just how difficult of a step it is, the order of difficulty, of developing a single protein-protein binding site, is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

      Delete
    6. Dr. Behe's empirical research agrees with what is found if scientists try to purposely design a protein-protein binding site:

      Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011
      Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:
      "...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2"
      If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?
      In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick!
      http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool

      Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012
      Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder.
      http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.html

      Moreover, there is, 'surprisingly', found to be 'rather low' conservation of Domain-Domain Interactions occurring in Protein-Protein interactions:

      A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms
      Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,,
      http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005096

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    7. Two Domain Protein - video (several binding sites required)
      http://www.facebook.com/photo.php?v=421708024519477

      Why Proteins (Protein Domains) Aren't Easily Recombined - Ann Gauger - May 2012
      Excerpt: each particular helix or sheet has a distinct set of side chains sticking out from it, requiring a distinct set of chemical interactions with any nearby protein sequence. Thus, helices and sheets are sequence-dependent structural elements within protein folds. You can’t swap them around like lego bricks. This necessarily means that when you bring new secondary structure elements into contact by some sort of rearrangement, they will be unlikely to form a stable three dimensional fold without significant modification.
      http://www.biologicinstitute.org/post/22595615671/why-proteins-arent-easily-recombined

      "Why Proteins Aren't Easily Recombined, Part 2" - Ann Gauger - May 2012
      Excerpt: "So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required."
      http://www.biologicinstitute.org/post/23170843182/why-proteins-arent-easily-recombined-part-2

      There simply isn't any evidence in the fossil record indicating that single cells ever formed anything other than 'simple aggregates':

      "We go from single cell protozoa. which would be ameoba and things like that. Then you get into some that are a little bit bigger, still single cell, and then you get aggregates, they're still individual cells that aggregate together. They don't seem to have much in the way of cooperation,,, but when you really talk about a functioning organism, that has more than just one type of cell, you are talking about a sponge and you can have hundreds, thousands, tens of thousands of cells. So we don't really have organisms that function with say two different types of cells, but there is only five total. We don't have anything like that."
      - Dr. Raymond G. Bohlin - quote taken from 31:00 minute mark of this following video
      Natural Limits to Biological Change 2/2 - video
      http://www.youtube.com/watch?v=vo3OKSGeFRQ

      Nor does the experimental evidence suggest that such a transition from single cell aggregates to multicellular organisms is possible:

      More Darwinian Degradation - M. Behe - January 2012
      Excerpt: Recently a paper appeared by Ratcliff et al. (2012) entitled “Experimental evolution of mulitcellularity” and received a fair amount of press attention, including a story in the New York Times.,,, It seems to me that Richard Lenski, who knows how to get the most publicity out of exceedingly modest laboratory results, has taught his student well. In fact, the results can be regarded as the loss of two pre-existing abilities: 1) the loss of the ability to separate from the mother cell during cell division; and 2) the loss of control of apoptosis.
      http://behe.uncommondescent.com/2012/01/more-darwinian-degradation/

      In fact Dr. Stephen Meyer's next book is going to be on the sheer impossibility of neo-Darwinian processes to explain the origination of 'Body-Plan information' from single cells to multicellular organisms in the Cambrian Explosion:

      Here is a sneak peek at his forthcoming book:

      Dr. Stephen Meyer: Why Are We Still Debating Darwin? pt. 2 - podcast
      http://intelligentdesign.podomatic.com/entry/2012-05-23T13_26_22-07_00

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    8. ba77,

      1 in 10^20 was Behe's estimate for the chances of chloroquine resistance developing naturally. He thought the chances would be even worse for a single protein binding site. In his own words,

      Generating a single new cellular protein-protein binding site is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.

      I guess his math was wrong.

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    9. This comment has been removed by the author.

      Delete
    10. oleg, the limit Behe set is not 1 protein binding site is it? Have you presented evidence that the limit he set in the 'edge of evolution' is broken? NO! So since you have not presented any evidence of the 2 binding site limit being broken why do you not accept what the scientific evidence itself is telling you? You are about science are you not?

      Delete
    11. And if I present evidence for 2 binding sites developing naturally then what happens?

      Delete
    12. Excerpt: Behe summarizes the statistical problems for the evolutionary scenario in an important Table 7.1 (p. 143). A typical cell might have some 10,000 protein-binding sites, but in all the cases surveyed, perhaps one protein-protein binding site has arisen by mutation: the sickle cell condition in humans, which is quite non-specific and actually destroys the normal structure of the hemoglobin tetrad and causes disease not evolutionary advancement (and HIV). So Behe is being generous in granting one example. Considering the number of organisms that have ever lived, it is clear that evolution could have created only two at most of the ~10,000 binding sites in a cell. And definitely no complexes of three or more proteins (of which there are many in a cell).
      http://creation.com/review-michael-behe-edge-of-evolution

      There you have it oleg, 2 is the limit set, and 3 would falsify Behe's claim.

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    13. Moving the goal posts further, ba77? 2 binding sites aren't good enough?

      Delete
    14. oleg

      Moving the goal posts further, ba77? 2 binding sites aren't good enough?


      Well, it's not like batspit77 understands a single word of the Creationist crap he C&Ps. He's just witnessing for Jesus. It doesn't have to be honest or make sense.

      Delete
    15. Well since Behe said 2 is the limit and 3 would break it, and you have college education, what does your advanced math tell you you need to do to falsify Behe's claim?

      Delete
    16. My advanced math tells me that you are off by one. Behe wrote of complexes consisting of three proteins. They require two binding sites.

      Delete
    17. Well let's see exactly where Behe set the bar. He wrote on page 146 0f "Edge";

      "The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable."

      I followed Dr. Behe's defense of this claim for a few years. Here is the archive of the exchanges (you may have to go a few years back to find the start):

      Behe's UD Blog
      http://behe.uncommondescent.com/

      The closest I saw anyone get to falsifying Dr. Behe was the single HIV binding site you mentioned. Perhaps you know better than all those PhD's who tried to refute Dr. Behe in peer review for the years I followed the debate. I doubt it though. But if not, I'm sure Dr. Behe would welcome a serious challenge since he is sincerely seeking what the "Edge' truly is for evolutionary processes, and does not seek to mislead people as Darwinists are notorious for.

      Delete
    18. Just to be clear that we understand each other, ba77. Behe is saying that complexes of three or more proteins, which require two or more protein-binding sites, cannot arise naturally. That is why I am asking you what you would say if we find two or more protein-binding sites evolving.

      Delete
    19. oleg, you state:

      which require two or more protein-binding sites

      And yet Behe states:

      "The immediate, most important implication is that complexes with more than two different binding sites

      So the bar is clearly set at MORE THAN TWO

      Since I certainly am not qualified to defend whatever assertion you bring forth, I look forward to your peer reviewed article and Behe's response.

      Notes:

      Here is another article that I found made a valiant effort to challenge Dr. Behe's "Edge", but in the end failed; Art Hunt's attempt to refute Dr. Behe:

      Here is a defense of Dr. Behe's binding site limit from the T-urf13 gene/protein that was argued, by neo-Darwinists, to be a 'new' gene/protein that refuted Behe's limit:

      How Arthur Hunt Fails To Refute Behe (T-URF13)- Jonathan M - February 2011
      http://www.uncommondescent.com/intelligent-design/on-the-non-evolution-of-irreducible-complexity-how-arthur-hunt-fails-to-refute-behe/#comment-373010

      On the non-evolution of Irreducible Complexity – How Arthur Hunt Fails To Refute Behe - PaV
      Excerpt: furthermore, T-urf 13 involves a kind of degradation of maize. In the case of the Texas maize–hence the T—the T-urf 13 was located by researchers because it was there that the toxin that decimated the corn grown in Texas in the late 60′s attached itself. So the “manufacturing” of this “de novo” gene proved to make the maize less fit. This is in keeping with Behe’s latest findings.
      http://www.uncommondescent.com/intelligent-design/on-the-non-evolution-of-irreducible-complexity-how-arthur-hunt-fails-to-refute-behe/comment-page-3/#comment-373178

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    20. ba77,

      Further down in the text he mentions three-protein complexes: "In short, complexes of just three or more different proteins are beyond the edge of evolution" (p. 135). That's two binding sites or more.

      Behe's estimate of 1 in 10^40 refers to two protein-binding sites (p. 143). He notes that the total number of organisms in the Earth's entire history was 10^40 and concludes that the chances of developing two protein-binding sites on any reasonable time scale are unlikely.

      He gets even bolder on p. 145 saying:

      "Could the edge of evolution be as close as a single cellular protein-binding site, rather than two? After all, no new such interactions have been uncovered in malaria and HIV. Could it be that shape-space reasoning has significantly underestimated the difficulty of developing a single new binding site in a crowded, tightly regulated interior of a cell?"

      So Behe initially put two protein-binding sites beyond the edge of evolution, then tentatively moved the boundary even closer, suggesting that even a single binding site is inaccessible to natural processes. We know how that turned out. :) So now his edge is between one and two new binding sites.

      Agree?

      Delete
    21. Oleg, the graph on 144 is set at two (Shaded below 2, clear on top of 2). If you disagree, e-mail Dr. Behe. I certainly can't speak for him. As for myself, I am not versed in all the subtle intricacies of molecular biology and thus I will personally need you to evolve JUST ONE molecular machine for me by purely Darwinian processes, as I originally requested, to satisfy my criteria. (Why is such a 'trivial' thing so hard for you to produce ant evidence?) Any of these following molecular machines evolved from scratch will quench the questions I have toward your sanity for believing in neo-Darwinism so fervently without any compelling proof:

      Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video
      http://www.metacafe.com/watch/3994630

      The ATP Synthase Enzyme - exquisite motor necessary for first life - video
      http://www.youtube.com/watch?v=W3KxU63gcF4

      Powering the Cell: Mitochondria - video
      http://www.youtube.com/watch?v=RrS2uROUjK4

      Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video
      http://www.metacafe.com/watch/4261990

      Kinesin Linear Motor - Video
      http://www.youtube.com/watch?v=kOeJwQ0OXc4

      Ribosome Translation High Quality - video
      http://pubs.acs.org/cen/multimedia/85/ribosome/translation_bacterial.html

      Myosin - video
      http://www.youtube.com/watch?v=j8F5GGPACkQ

      The Virus - Assembly Of A Molecular "Lunar Landing" Machine - video
      http://www.metacafe.com/watch/4023122

      The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell:

      Molecular Machines in the Cell -
      http://www.discovery.org/a/14791

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    22. Dr. Behe comments here:

      Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe

      Michael Behe on Falsifying Intelligent Design - video
      http://www.youtube.com/watch?v=N8jXXJN4o_A

      By the way what is the falsification criteria of Darwinism once again? Seems Darwinists keep forgetting to mention it.

      “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

      Notes:

      The Bacterial Flagellum – Truly An Engineering Marvel! - December 2010
      http://www.uncommondescent.com/intelligent-design/the-bacterial-flagellum-truly-an-engineering-marvel/

      Michael Behe Hasn't Been Refuted on the Flagellum - March 2011
      http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.html

      Of particular interest:

      INFORMATION AND ENERGETICS OF QUANTUM FLAGELLA MOTOR
      Hiroyuki Matsuura, Nobuo Noda, Kazuharu Koide Tetsuya Nemoto and Yasumi Ito
      Excerpt from bottom page 7: Note that the physical principle of flagella motor does not belong to classical mechanics, but to quantum mechanics. When we can consider applying quantum physics to flagella motor, we can find out the shift of energetic state and coherent state.
      http://www2.ktokai-u.ac.jp/~shi/el08-046.pdf

      Persistent dynamic entanglement from classical motion: How bio-molecular machines can generate non-trivial quantum states – November 2011
      Excerpt: We also show how conformational changes can be used by an elementary machine to generate entanglement even in unfavorable conditions. In biological systems, similar mechanisms could be exploited by more complex molecular machines or motors.
      http://arxiv.org/abs/1111.2126

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    23. Well, that's too bad, ba77. Behe makes it pretty clear in the book that two binding sites are out of reach for evolution. And guess what? That has been observed. See Nick Matzke's comments at Telic Thoughts and his more detailed post at Panda's Thumb. The paper he mentions [6] is available for free on the publisher's site: doi:10.1093/protein/15.11.943.

      Delete
    24. oleg, Like I said e-mail Behe if you disagree! Once again here is his site where he defends against the peer-reviewed challenges:

      http://behe.uncommondescent.com/page/8/

      Moreover oleg, if you really think that even 2,3,4 or whatever, randomly stuck 'wads of gum' binding sites proves that unfathomed integrated complexity, which man can only dream of imitating to any meaningful degree, can be built in a stepwise, non-directed, fashion, then you are clearly living in a atheistic fantasy land:

      I think you referenced a phage paper with some kind of weird protein that had many 'sticky sites' exposed. OK oleq, try to be honest instead of playing games with 'wads of gum' sticking randomly here and there, show me exactly how the phage virus came to be by purely Darwinian processes:

      The Bacteriophage Virus - Assembly Of A Molecular "Lunar Landing" Machine - video
      http://www.metacafe.com/watch/4023122

      Moreover, as to a protein binding to a specific site on a virus, in order to accomplish something meaningful, instead of just sticking anywhere, like wads of gum, and not accomplishing anything meaningful at all (as you seem more than willing to accept as concrete proof for Darwinism), here is what is found for the difficulty involved:

      Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011
      Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:
      "...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2"
      If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?
      In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick!
      http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool

      Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012
      Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder.
      http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.html

      Now oleg, the honest person would definitely notice that that took an inordinate amount of effort to accomplish a 'simple' specific protein binding to accomplish something meaningful. Why can't you recognize the same?

      Delete
  10. Just once it would be nice to have a thread that wasn't completely trashed by Philip "batspit77" Cunningham's clueless C&Ped projectile vomiting.

    Just once.

    ReplyDelete
    Replies
    1. batspit77 probably thinks the YEC version of Jeebus saved him from his former substance abuse and homosexual tendencies and now he feels he owes Jeebus a big one. He has a big man-crush on Jeebus and this is his twisted way of thanking him.

      Until BA77 figures out he saved himself, or if the destruction he visited upon himself for many years takes its tole, fat chance he will cease spamming.

      Delete
  11. CH: Hunter: If evolution is true then we expect codes to be universal. Here we have an obvious example of a code that most definitely is not universal, so the prediction is false. And if a prediction is false, then either the theory is false, or it must be modified.

    So, I take it that you're an instrumentalist, in that science is merely a useful instrument for undersigning the world, but can tell us noting about reality?

    Again, we not only take the theory in question seriously, in that it's true in reality, but we take into account all of the rest of our most current, best explanations as a coherent whole for the purpose of criticism (evaluating predictions.) We do this because other theories make assertions about how things *are* in reality. If's from these other theories that we deduce what effect they would have on what we would experience.

    So, a prediction made 50 years ago might not be observed because the underlying explanation for some other theory that effected it became more accurate. In turn, this changes what we will experience without necessarily changing the underlying explanation behind the theory in question.

    No theory contains a laundry list of possible caveats that effect its predictions. That would be, well, impossible because there are an infinite number of parallel, yet unrelated events, in reality, that could effect what we'd experience at the time we evaluate the prediction. It's unreasonable to expect anyone to be take into account these possibilities.

    To think otherwise would be to mistake the predictions of scientific theories as prophecy.

    Nor could we predict what other knowledge that might be created, the effect it could have on reality, etc. We simply cannot know this at the time the theory was formed. Yet, the underlying explanation that theory could still not have been falsified because we'd have an explanation as to why we didn't observe the original prediction.

    Furthermore, you omitted the option that a theory could become more accurate.

    For example, the underlying explanation for a man traveling from point A to point B could start out as some kind of self propelled vehicle. We would then take this theory seriously, in that we assume it was true, in reality, along with all of our current, best explanations, in that all observations should conform to them. Again, this would represent an explanatory whole for the purpose of criticism.

    Based on criticism, we could go from a self propelled vehicle, to a four wheeled self propelled vehicle, to an electric four wheeled vehicle, to a Tesla Model S. This would example of a theory becoming more and more accurate.

    ReplyDelete
  12. I have gone thru some of the titles on this blog and i was not surprised to see that most of the titles start with " you wont believe evolutionists say....."

    I wonder if there is a good reason to explain this.? I think believing or not believeing in a scientific theory should not even bother the readers here. Whether someone believes ina scientific theory or not doesnt make a fact anything else. believeing in earth is flat doesnt make earth flat, does it?

    ReplyDelete
  13. It's very clear that Dr Hunter has long ago given up on fighting evolution on scientific merits. He's just a useful idiot now, a tool used by his theocratic employers in the propaganda war against any science that might shed some doubt on the creation stories his employers prefer to believe. Hunter is just a cheap gun for hire. His supporters on this blog are all obviously lunatics (e.g. Louis Savain, BA77) or just stupid (e.g. Lino/PaV).

    cheers

    ReplyDelete
    Replies
    1. "It's very clear that Dr Hunter has long ago given up on fighting evolution on scientific merits."

      And since when did neo-Darwinian evolution ever have a foundation within science to begin with?

      "But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881

      The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);

      Evolutionary guru: Don't believe everything you think - October 2011
      Interviewer: You could be deceiving yourself about that.(?)
      Evolutionary Psychologist: Absolutely.
      http://www.newscientist.com/article/mg21128335.300-evolutionary-guru-dont-believe-everything-you-think.html

      Which also begs the question of how can Darwinism ever be considered scientific if you can never be sure what you are thinking is true:

      Should You Trust the Monkey Mind? - Joe Carter
      Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
      http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind

      What is the Evolutionary Argument Against Naturalism? ('inconsistent identity' of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) - video
      http://www.youtube.com/watch?v=5yNg4MJgTFw

      Alvin Plantinga - Science and Faith Conference - video
      http://www.youtube.com/watch?v=mVlMK9Ejhb0

      Philosopher Sticks Up for God
      Excerpt: Theism, with its vision of an orderly universe superintended by a God who created rational-minded creatures in his own image, “is vastly more hospitable to science than naturalism,” with its random process of natural selection, he (Plantinga) writes. “Indeed, it is theism, not naturalism, that deserves to be called ‘the scientific worldview.’”
      http://www.nytimes.com/2011/12/14/books/alvin-plantingas-new-book-on-god-and-science.html?_r=1&pagewanted=all

      This following site is a easy to use, and understand, interactive website that takes the user through what is termed 'Presuppositional apologetics'. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in God who guarantees our perceptions and reasoning are trustworthy in the first place.

      Presuppositional Apologetics - easy to use interactive website
      http://www.proofthatgodexists.org/index.php

      Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer - video – (Notes in description)
      http://vimeo.com/32145998

      Why should the human mind be able to comprehend reality so deeply? - referenced article
      https://docs.google.com/document/d/1qGvbg_212biTtvMschSGZ_9kYSqhooRN4OUW_Pw-w0E/edit

      Delete
    2. Hallelujah! Hallelujah!

      Preach it batspit77!

      All science so far!

      Delete
    3. This comment has been removed by the author.

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    4. bornagain 77June 24, 2012 12:20 PM

      [...]

      And since when did neo-Darwinian evolution ever have a foundation within science to begin with?


      Since 1859, wasn't it?

      The following interview is sadly comical as a evolutionary psychologist realizes that neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth, not even for the truth that he is purporting to give in the interview, (which begs the question of how was he able to come to that particular truthful realization, in the first place, if neo-Darwinian evolution were actually true?);

      Evolutionary guru: Don't believe everything you think - October 2011
      Interviewer: You could be deceiving yourself about that.(?)
      Evolutionary Psychologist: Absolutely.
      http://www.newscientist.com/article/mg21128335.300-evolutionary-guru-dont-believe-everything-you-think.html


      That interview, with Robert Trivers, was about possible explanations for the human capacity for self-deception. In other words, why do humans, having reason to believe something to be true - to some extent - pretend other wise to themselves, let alone to others?

      As for this silly argument about the unreliability of our faculties of reasoning, Quine, as you know, skewered it pithily this:

      Creatures inveterately wrong in their inductions have a pathetic, but praiseworthy, tendency to die before reproducing their kind.

      Delete
    5. 'Creatures inveterately wrong in their inductions have a pathetic but praiseworthy tendency to die before reproducing their kind.'

      Yet we find,,,

      Children are born believers in God, academic claims - Telegraph - November 2008
      Excerpt: "The preponderance of scientific evidence for the past 10 years or so has shown that a lot more seems to be built into the natural development of children's minds than we once thought, including a predisposition to see the natural world as designed and purposeful and that some kind of intelligent being is behind that purpose,"
      http://www.telegraph.co.uk/news/religion/3512686/Children-are-born-believers-in-God-academic-claims.html

      'Believers' gene' will spread religion , says academic - January 2011
      Excerpt: The World Values Survey, which covered 82 nations from 1981 to 2004, found that adults who attended religious services more than once a week had 2.5 children on average; while those who went once a month had two; and those who never attended had 1.67.
      Prof Rowthorn wrote: "The more devout people are, the more children they are likely to have."
      http://www.telegraph.co.uk/science/8252939/Believers-gene-will-spread-religion-says-academic.html

      Thus either the atheist is right and evolution is producing a true belief, and that true belief is Theism, since atheists have a 'praiseworthy tendency to die before reproducing their kind', or Dr. Plantinga is right and there is no guarantee that the results of Darwinian evolution will produce true beliefs about the nature of reality! Which is it? Either answer is a self defeater for evolutionary naturalism!

      Delete
    6. bornagain77 June 24, 2012 3:26 PM

      [...]

      Yet we find,,,

      Children are born believers in God, academic claims - Telegraph - November 2008


      Question: is there anything in that report - other than spelling God with a capital G which implies the Christian god - to suggest that we are genetically predisposed to believe in Christianity or will any old religion do? If the latter is the case then I see little comfort for you in this research.

      [..]

      'Believers' gene' will spread religion , says academic - January 2011
      Excerpt: The World Values Survey, which covered 82 nations from 1981 to 2004, found that adults who attended religious services more than once a week had 2.5 children on average; while those who went once a month had two; and those who never attended had 1.67.
      Prof Rowthorn wrote: "The more devout people are, the more children they are likely to have."


      The poorer they are the more children people have. Perhaps poverty is more important for fertility than religion.

      And, yet again, the research doesn't show that it's only Christianity that has this effect, apparently any old religion will do.

      Thus either the atheist is right and evolution is producing a true belief, and that true belief is Theism, since atheists have a 'praiseworthy tendency to die before reproducing their kind', or Dr. Plantinga is right and there is no guarantee that the results of Darwinian evolution will produce true beliefs about the nature of reality! Which is it? Either answer is a self defeater for evolutionary naturalism!

      If people jump off the top of very tall buildings because they think this world is just a simulation like in The Matrix how long do you think that false belief will last? If Plantinga is actually making that case, which I doubt, then he's talking nonsense.

      What this actually shows, in my view, is that religion has survived and flourished because it provides great social benefits. Note that I said "religion" in general. The specific faith or creed doesn't really matter as long as it binds people together and makes them stronger and more resilient if the face of the many problems that inevitably befall us in this world.

      Delete
  14. BA77:

    neo-Darwinism can offer no guarantee that our faculties of reasoning will correspond to the truth

    Nothing can guarantee that, brain-damaged fruit loop. In fact, it's well known that our brains deceive us sometimes (Google optical illusions). You believe in YEC stuff that is demonstrably BS yet you are blind to that truth.

    ReplyDelete
    Replies
    1. "You believe in YEC stuff that is demonstrably BS yet you are blind to that truth."

      I am not a YEC and never have held that position since my Grandfather told me the six days in Genesis represented long periods of time. Moreover you hold to the atheistic materialistic philosophy even though it is demonstrably BS. Go figure, glass houses and all.

      You also state:

      "it's well known that our brains deceive us sometimes (Google optical illusions)."

      But alas with neo-Darwinian evolution the problem is much more foundational than you realize in that there is no way to know that you are being deceived because there is no 'you' that stands independent of the random fluctuations of the molecules in your brain in order to make the judgment:

      "Descartes remarks that he can continue to doubt whether he has a body; after all, he only believes he has a body as a result of his perceptual experiences, and so the demon could be deceiving him about this. But he cannot doubt that he has a mind, i.e. that he thinks. So he knows he exists even though he doesn’t know whether or not he has a body."
      http://cw.routledge.com/textbooks/philosophy/downloads/a2/unit4/descartes/DescartesDualism.pdf

      “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms.” J. B. S. Haldane ["When I am dead," in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209.

      Moreover:

      Alvin Plantinga and the Modal Argument (for the existence of the soul) - video
      http://www.youtube.com/watch?v=WOTn_wRwDE0

      Here is a sound argument from the man's use of 'information':.
      1. We know what a thing is by observing how it acts.
      2. The mind/soul acts to produce abstract immaterial concepts (such as codes and information) and rational arguments that no material entity can produce.
      3. Therefore, the mind/soul is not a material entity, but must be immaterial. Furthermore, this tells us that not only is it possible for immaterial entities to exist, based on our own experience and reason immaterial entities do in fact exist and some form of dualism is true.
      http://www.uncommondescent.com/neuroscience/memo-from-materialists-science-is-over-oh-and-by-the-way-consciousness-doesnt-matter/#comment-421418

      etc.. etc..

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    2. I am not a YEC and never have held that position since my Grandfather told me the six days in Genesis represented long periods of time.

      Well, if grandpa says it, it must be true, seeing as your grandpa was an eminent scientist.

      Yet you often quote the YEC Sandford's nonsensical ideas about genetic entropy. Have you considered being consistent?

      Delete
    3. well Troy I also quote neo-Darwinists even though I hold them to be completely wrong in their worldview. I'll even quote you if I feel like it.!

      Delete
    4. Haha, yeah go ahead and quote me if you feel like it. Doesn't make you any less insane.

      Delete
    5. Doesn't make you any less insane.

      And yet the irony in all this is that you, the atheist, deny that you even have a mind (consciousness) to begin with. How insane is that?

      God Versus Science: A Futile Struggle By J Roy Singham - May 2012
      Excerpt: Materialists believe that matter is unconscious, a tenable opinion. But they also believe that consciousness is an illusion. That belief is absurd, almost madness.
      http://ezinearticles.com/?God-Versus-Science:-A-Futile-Struggle&id=6940055

      Mind and Cosmos - Why the Materialist Neo-Darwinian Conception of Nature is Almost Certainly False - Thomas Nagel - November 2012 (projected publication date)
      Excerpt: If materialism cannot accommodate consciousness and other mind-related aspects of reality, then we must abandon a purely materialist understanding of nature in general, extending to biology, evolutionary theory, and cosmology. Since minds are features of biological systems that have developed through evolution, the standard materialist version of evolutionary biology is fundamentally incomplete. And the cosmological history that led to the origin of life and the coming into existence of the conditions for evolution cannot be a merely materialist history.
      http://ukcatalogue.oup.com/product/9780199919758.do

      Moreover Troy, you, the atheist/materialist, claim to be rational, logical, scientific, and all that, yet you can't even ground science, logic, or rationality, in the materilistic/atheistic worldview in the first place! How insane is that? Just how does one propose to logically prove atheism/materialism unversally true when atheism/materialism cannot ground universal logic? Dog, tail, chase, circle!

      Is Life Unique? David L. Abel - January 2012
      Concluding Statement: The scientific method itself cannot be reduced to mass and energy. Neither can language, translation, coding and decoding, mathematics, logic theory, programming, symbol systems, the integration of circuits, computation, categorizations, results tabulation, the drawing and discussion of conclusions. The prevailing Kuhnian paradigm rut of philosophic physicalism is obstructing scientific progress, biology in particular. There is more to life than chemistry. All known life is cybernetic. Control is choice-contingent and formal, not physicodynamic.
      http://www.mdpi.com/2075-1729/2/1/106/

      "Nonphysical formalism not only describes, but preceded physicality and the Big Bang
      Formalism prescribed, organized and continues to govern physicodynamics."
      http://www.mdpi.com/2075-1729/2/1/106/ag

      Delete
  15. Once more into the breach, dear friends, once more:

    Our historian of science could enhance his credibility by providing references from the scientific literature that support his claims, bearing in mind that hindsight is not predictive.

    ReplyDelete
  16. Will Dr Hunter defend his claim that

    If evolution is true then we expect codes to be universal.

    I'm not holding my breath. I suspect that Hunter knows full well that evolutionary theory doesn't make that claim at all. Just a little lying for Jesus, as usual. Gotta justify those expenses to the Dishonesty Institute.

    ReplyDelete
  17. troy,

    Holding your breath would be suicidal.

    I've repeatedly tried to get Dr Hunter to back up his claims, and he usually takes a powder.

    As you point out, he's blowing smoke on this one.

    ReplyDelete
    Replies
    1. Yes, Hunter isn't interested in discussing the "substance" of his "ideas". He just has to throw some bones to the creationists. Keeps the chimney smoking.

      Delete
    2. Pedant

      As you point out, he's blowing smoke on this one.


      This one? Has there been any claim of his in the last year he hasn't just blown smoke on?

      Delete
  18. Theobalds prediction. 1.1. 29 evidences of evolution.

    ReplyDelete
    Replies
    1. Nice catch, Tedford. But Theobald's history demonstrates how controversial the idea of a universal genetic code was before the code was fully described. Some quotations:

      "Crick urged on his companions two other simplifying assumptions of great audacity. ... they assumed, with some apprehension, that the genetic code would be the same for all living things. There was no evidence whatever for this; .... Yet universality seemed inevitable for an obvious reason: since a mutation that changed even one word or letter of the code would alter most of a creature's proteins, it looked sure to be lethal." (Judson 1996, p. 280-281)

      In fact, the assumption of a universal genetic code was instrumental in their success in solving the code. For instance, in 1957, nearly ten years before the genetic code was finally solved, Sydney Brenner published an influential paper in which he concluded that all overlapping triplet codes were impossible if the code was universal (Brenner 1957). This paper was widely considered a landmark work, since many researchers were leaning towards an overlapping code. Of course, it turned out that Brenner was correct about the nature of the true code.

      Delete
  19. Reading further in

    http://www.talkorigins.org/faqs/comdesc/section1.html

    In fact, in 1963—three years before the code was finally solved—Hinegardner and Engelberg published a paper in Science formally explaining the evolutionary rationale for why the code must be universal (or nearly so) if universal common descent were true, since most mutations in the code would likely be lethal to all living things. Note that, although these early researchers predicted a universal genetic code based on common descent, they also predicted that minor variations could likely be found. Hinegardner and Engelberg allowed for some variation in the genetic code, and predicted how such variation should be distributed if found:

    "... if different codes do exist they should be associated with major taxonomic groups such as phyla or kingdoms that have their roots far in the past." (Hinegardner and Engelberg 1963)

    Similarly, before alternate codes were found, Francis Crick and Leslie Orgel expressed surprise that minor variants of the code had not been observed yet:

    "It is a little surprising that organisms with somewhat different codes do not coexist." (Crick and Orgel 1973, p. 344)

    Crick and Orgel were correct in their surprise, and today we know of about a dozen minor variants of the standard, universal genetic code (see the grey, red, and green codons in Figure 1.1.1). As Hinegardner and Engelberg predicted, the minor variations in the standard genetic code are indeed associated with major taxonomic groups (vertebrates vs. plants vs. single-celled ciliates, etc.).


    Consider carefully the reasoning employed by those theoreticians.

    ReplyDelete
    Replies
    1. This comment has been removed by the author.

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

      DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011
      Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
      http://www.sciencedaily.com/releases/2011/01/110128104244.htm

      Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011
      Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer."
      http://www.evolutionnews.org/2011/09/ends_and_means050391.html

      Delete
    3. A Critique of Douglas Theobald’s - “29 Evidences for Macroevolution” by Ashby Camp
      Excerpt: There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature.
      - Biophysicist Cornelius G. Hunter
      http://www.trueorigin.org/theobald1b.asp

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

      DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011
      Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
      http://www.sciencedaily.com/releases/2011/01/110128104244.htm

      Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011
      Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer."
      http://www.evolutionnews.org/2011/09/ends_and_means050391.html

      Delete
  20. A Critique of Douglas Theobald’s - “29 Evidences for Macroevolution” by Ashby Camp
    Excerpt: There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature.
    - Biophysicist Cornelius G. Hunter
    http://www.trueorigin.org/theobald1b.asp

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

    DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011
    Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code,
    http://www.sciencedaily.com/releases/2011/01/110128104244.htm

    Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011
    Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer."
    http://www.evolutionnews.org/2011/09/ends_and_means050391.html

    ReplyDelete
  21. Pendant, and your evidence that even one code can arise by purely material processes is where exactly?

    The DNA Code - Solid Scientific Proof Of Intelligent Design - Perry Marshall - video
    http://www.metacafe.com/watch/4060532

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

    ReplyDelete
  22. CH: Evolutionists had no explanation for this incredible and profound molecular manufacturing system (which still out performs anything scientists can come up with), but they remained steadfast.

    That's odd. I keep proving an explanation, which you have yet to criticize. So, apparently, you don't have a problem with my explanation while at the same time rejecting it.

    CH: Indeed they argued all of this provided yet more proofs for evolution. Why? Because the DNA code was essentially universal.

    As someone who teaches biology at the college level, you seem to be quite confused about how science works. Science doesn't positively prove anything. That is, unless you happen to have formulated a "principle of induction" that actually works, in practice. Rather, evidence collaborates evolutionary theory.

    CH: As one evolutionist explained, while the genetic code is preserved across species, it would not be if the species had been created independently.

    Rather than paraphrasing Ridley, where is the actually quote?

    CH: If that’s true then the genetic code must have somehow evolved. Is that true?

    Even if your paraphrase is correct, how exactly does that follow merely from your quote? Please be specific. Second, evolutionary theory isn't abiogenesis.

    Third, Research has shown that synthetic base pairs (NaM and 5SICS) can be copied by DNA polymerase, which arranges them in the same Watson-Crick arrangement of base pairs current found in nature - even though these synthetic base pairs do not form hydrogen bonds.

    From the article.

    Romesberg said this unexpected finding has major implications for evolutionary theory. The ability of DNA polymerase to place NaM and 5SICS together (and presumably other base pairs held together by hydrophobic forces), doesn't seem likely to be just a coincidence. It may be possible that early life actually started out using such "artificial" base pairs, then discarded them for the four familiar ones found in living things today.

    Testing that hypothesis would be extremely difficult, Romesberg said. There's unlikely to be any direct evidence of this transition, only indirect evidence such as this hitherto unknown capacity of DNA polymerase.


    In other words, this sort of flexibility strongly collaborates the theory that other forms of genetic material can be interchanged and still replicated.

    ReplyDelete
  23. CH: Regulate each other and a whole network of other RNA binding proteins? Needless to say there is no scientific explanation for how this marvel could have evolved. And since this code is not universal but, quite the opposite, highly varying even between tissues, we can safely conclude the “universal code” prediction of evolution is falsified.

    Again, I've provided an explanation, which you have yet to criticize. As such, this objection rings hollow.

    Biological organism build themselves in the form of adaptations. Adaptations occur when the requisite knowledge of how to perform those adaptations are present. Different codes represent different forms of knowledge, which would build different tissue types. This represents non-explanatory knowledge created using a form of conjecture and refutation.

    Modern DNA is relatively uniform across all species because it made the jump to universality. Specifically, it's repertoire of combinations became such that it could be used to universally encode the information necessary to build a vast set of biological organisms. This is similar as to how computing systems because Universal Turing Machines (UTM), in that they could run a program that could run on any other another UTM.

    However, UTMs are not specific to any particular CPU architecture, how fast they can perform computations or if they store data on paper tape or magnetic media. They are all UTMs because of the repertoire of computations they can perform. In other words, no one "created" a UTM. UTMs emerged from a specific repertoire of computations when they made the leap to universality.

    We can say the same about number systems, which were initially only capable of repressing a very limited set of numbers, despite the fact that we could have easily implemented system that was universal out of the gate. Yet we did not because we initially didn't work with very large numbers. In fact, we started out with tallying, rather than number systems.

    It's only when the Arabic number system, which was ironically actually devised in India, that we had a universal number system. This represented yet another leap to universality. While we devised this number system, it's universal ability to represent any number is an emergent property of it.

    So, my point here is that we can explain why DNA evolved in the past, then became standardized, while also containing limited variation. And the variation we do observe can be explained in that it reflects different knowledge to build different adaptations.

    ReplyDelete
  24. CH:"If evolution is true then we expect codes to be universal."

    A blanket assertion, and wrong. We expect anything to be universal only if LUCA had it. Prior to LUCA, other schemes could have been tried, but failed to leave descendants because either chance or selection killed them off.

    But I agree with CH here - if we can figure out the splicing process (not a "code" in the sense of the genetic code) in many different species, we will find variation caused by the standard sources such as duplication, subsequent mutation, etc.

    ReplyDelete