Cell biology Darwinism Intelligent Design

The Axe-ocalypse! It is coming!

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protein folding
Four Horsemen of Apocalypse (1887)/Viktor Vasnetsov

We told you so!

Four horsemen. No waiting. From Brian Miller at ENST:

One of the most significant projects for the intelligent design movement was Douglas Axe’s research testing the rarity of protein folds. Axe’s method represented the most accurate approach for addressing the problem to date, but his was actually one in a line of studies which concluded that amino acid sequences forming the stable proteins found in nature are exceedingly uncommon. As a consequence, most proteins seen in life could never have originated via random mutations and selection.

One of the early online critics of Axe’s work was Arthur Hunt, who wrote a lengthy critique at the Darwinian advocacy site Panda’s Thumb. His area of expertise is not the evolution of new protein folds, and his arguments revealed a general misunderstanding of Axe’s approach and the field in general. The reviewers of Axe’s JMBarticle which reported his results were experts in protein studies, so they would have identified any of the issues raised by Hunt if they were real. Instead, they published the article affirming both the design of Axe’s experiment and his conclusions. A more recent series of critiques, published by the online journal Sapientia, was aimed at Axe’s book, Undeniable: How Biology Confirms Our Intuition That Life Is Designed. The four biologists offering these critiques I affectionately refer to as the four horsemen: Dennis Venema, Cara Wall-Scheffler, Joel Duff, and Keith Fox. As Axe pointed out in his response to these critiques, they mostly ignore the main argument of the book — a common-sense argument — choosing to get lost in scientific details instead. Here at Evolution News, Axe has responded specifically to Venema’s critique of his protein work.

Here, I want to flesh out some of the salient details of this discussion. … More.

Also from ENST:

Four Darwin Heretics: A Reader’s Roundup

One, two, three, four books — four recent titles by Darwin skeptics (three scientists, one journalist) in two short years. They are all heretics, all convinced of the same fact: Darwin’s house of cards is collapsing. Science, which is to say the future, is on the side of intelligent design. Let’s look at what they say about the linchpin of Darwinian theory: Charles Darwin’s famous “mechanism” of evolution, natural selection (aka, survival of the fittest). Many would consider Darwinism and natural selection synonymous. More.

4 Replies to “The Axe-ocalypse! It is coming!

  1. 1
    harry says:

    Defending the notion that the functional complexity of the self-replicating, digital-information-based nanotechnology of life came about mindlessly and accidentally is becoming more and more like defending the notion that self-replicating robotic equipment might come about that way. That is to say it is has become simply irrational to defend that notion.

  2. 2
    bornagain77 says:

    The ‘realistic’ estimates for finding functional proteins are all astronomically high:

    Yockey and a Calculator Versus Evolutionists – Cornelius Hunter PhD – September 25, 2015
    Excerpt: In a 1977 paper published in the Journal of Theoretical Biology, Hubert Yockey used information theory to evaluate the likelihood of the evolution of a relatively simple protein.,,,
    Yockey found that the probability of evolution finding the cytochrome c protein sequence is about one in 10^64. That is a one followed by 64 zeros—an astronomically large number. He concluded in the peer-reviewed paper that the belief that proteins appeared spontaneously “is based on faith.”
    Indeed, Yockey’s early findings are in line with, though a bit more conservative than, later findings. A 1990 study of a small, simple protein found that 10^63 attempts would be required for evolution to find the protein.
    A 2004 study found that 10^64 to 10^77 attempts are required, and a 2006 study concluded that 10^70 attempts would be required.
    These requirements dwarf the resources evolution has at its disposal. Even evolutionists have had to admit that evolution could only have a maximum of 10^43 such experiments. It is important to understand how tiny this number is compared to 10^70. 10^43 is not more than half of 10^70. It is not even close to half. 10^43 is an astronomically tiny sliver of 10^70.
    Furthermore, the estimate of 10^43 is, itself, entirely unrealistic. For instance, it assumes the entire history of the Earth is available, rather than the limited time window that evolution actually would have had.,,,

    Dr. Durston elaborates on how futile an evolutionary search is to find a single functional protein:
    Excerpt: From this, we can come up with a very rough estimate for the total number of stable, folding 3D sequences in 300 residue sequence space … roughly 10^74 sequences that will give stable 3D folds (this is very rough, but it will illustrate my point and help one see why scientists don’t search for novel stable 3D folds from a library of random sequences). One might think that 10^75 sequences is an enormous number, however, it is miniscule in comparison with 20^300, which is the total number of sequences in 300 –residue sequence space. This is why the theory that an evolutionary search, even if it involved all the planets in all the galaxies of the known universe, is utterly implausible.

    And even these ‘realistic’ estimates for finding functional proteins may be far to optimistic. As Kurt Durston explains, “interdependence” among amino acid sites in proteins greatly reduce the number of possible functional protein sequences by many orders of magnitude.

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.

    And amino acids in proteins are now found to be extremely interdependent:

    Proteins with cruise control provide new perspective:
    “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”

    The reason why the amino acids are extremely interdependent in a protein is because proteins are now found to operate on quantum principles, As the following paper explains, proteins “remain entangled as a single quantum state”

    Coherent Intrachain energy migration at room temperature – Elisabetta Collini & Gregory Scholes – University of Toronto – Science, 323, (2009), pp. 369-73
    Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.

    How many orders of magnitude does this interdependence of amino acids within a protein add to the already astronomical estimate for finding a functional protein? Well the following paper states that “finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,

    Quantum criticality in a wide range of important biomolecules
    Excerpt: “Most of the molecules taking part actively in biochemical processes are tuned exactly to the transition point and are critical conductors,” they say.
    That’s a discovery that is as important as it is unexpected. “These findings suggest an entirely new and universal mechanism of conductance in biology very different from the one used in electrical circuits.”
    The permutations of possible energy levels of biomolecules is huge so the possibility of finding even one that is in the quantum critical state by accident is mind-bogglingly small and, to all intents and purposes, impossible.,, of the order of 10^-50 of possible small biomolecules and even less for proteins,”,,,
    “what exactly is the advantage that criticality confers?”

    Moreover, as if all that was not bad enough for Darwinists, quantum entanglement is a ‘non-local’, beyond space and time, effect that requires a cause that is not limited to space and time.

    I’m pretty sure Darwinists do not want to go the route of looking for a ‘beyond space and time’ cause! 🙂 It pretty much defeats their whole reductive materialistic worldview!

    Whereas, Theists, on the other hand. should be very happy with these developments.

  3. 3
    harry says:

    bornagain77 @2,

    Great stuff, as usual.

    Have you ever thought about putting a list of the sources you cite online? Something users can search by topic.

  4. 4
    bornagain77 says:

    Harry, I have several pages of notes that I have collected through the years, but they are not in any kind of specific order that someone could easily search through. Of course, I know the basic order in which the notes are put together, but that would hardly be useful for anyone who does not know that basic order.

    Plus there are many notes that are somewhat obsolete that are interspersed within the pages of useful notes.

    It would be somewhat of a monumental task to go through those years of notes to make then easily searchable, concise, and therefore useful to others.

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