Intelligent Design Irreducible Complexity

Challenge to Uncommon Descenters from ID Facebook page

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The over 3500-member page’s Timothy Kershner has sent us a request at UD, asking for responses to this article in American Society for Microbiology, “Evolution of the Bacterial Flagellum: Cumulative evidence indicates that flagella developed as modular systems, with many components deriving from other systems”,

Proponents of the intelligent design (ID) explanation for how organisms developed claim that the bacterial flagellum (BF) is irreducibly complex. They argue that this structure is so complicated that it could not have emerged through random selection but had to be designed by an intelligent entity. One part of this claim is that each flagellar component is used solely for the purpose of making a flagellum that, in turn, is used only for motility. Further, each flagellar protein is assumed to have appeared independently of the other component proteins.

Here, we summarize evidence from hundreds of laboratories, including our own, showing that these assumptions are false. Instead of by design, BF developed as modular systems, with components deriving from many different sources. Each BF module evolved independently from various primordial systems, which, in most cases, had nothing to do with cell motility. Complexity within BF arose by domain and protein recruitment, by intragenic and extragenic duplication events, and by superimposition of various modules onto others. The net result was coevolution of many types of structurally and functionally distinct flagella in various bacterial species. Although these different flagella are all used for motility, they share only about half of their protein constituents.

He references a pinned post here. All just sorta happened? Or not? Comments welcome.

40 Replies to “Challenge to Uncommon Descenters from ID Facebook page

  1. 1
    Mung says:

    They argue that this structure is so complicated that it could not have emerged through random selection but had to be designed by an intelligent entity.

    sigh

    It’s not how “complicated” the flagellum is that makes it IC.

    And random selection, really?

    One part of this claim is that each flagellar component is used solely for the purpose of making a flagellum that, in turn, is used only for motility. Further, each flagellar protein is assumed to have appeared independently of the other component proteins.

    I can’t wait to get to the sources and methods section, because I’d sure like to know their sources.

  2. 2
    Axel says:

    I bet you wouldn’t scruple to tell them Father Christmas doesn’t exist, too, Mung

  3. 3
    Axel says:

    Better that they keep a little magic star-dust in their eyes for as long as possible, isn’t it? If you wish upon a star…. – a nice atheistic/New Agey type of song.

  4. 4
    Mung says:

    Axel,

    Growing up I did have occasion to question Santa’s sources on which children were naughty and which were nice. I, of course, being the middle child, was perfect.

    It seemed highly unjust to me at the time that when my elder brother discovered who Santa really was he was given special gifts, but I was not.

    Bah humbug.

  5. 5
    Loghin says:

    Please start actually discussing the technical merits of the paper with some real probabilistics, genetics and other points regarding the paper. The sole reason Darwinists are respected more is because they work harder. Find a pozitive, technical non-materialistic workable mechanism and you win. It is like the critic who sits in the chair and laugths at the failing acrobats. Work a little.

  6. 6
    Mung says:

    @5

    The paper starts out misrepresenting ID and irreducible complexity. What’s to discuss?

  7. 7
    Upright BiPed says:

    What year is this? Behe answered this misrepresentationt long ago.

    Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions:
    A Response to Sharon Begley’s Wall Street Journal Column
    By: Michael J. Behe
    Discovery Institute
    February 18, 2004

    In a recent column in the Wall Street Journal (February 13, 2004, Science Journal, page B1, “Evolution Critics Come Under Fire for Flaws In ‘Intelligent Design'”) science writer Sharon Begley repeated some false claims about the concept of irreducible complexity (IC) that have been made by Darwinists, in particular by Kenneth Miller, a professor of biology at Brown University. After giving a serviceable description in her column of why I argue that a mousetrap is IC, Begley added the Darwinist poison pill to the concept. The key misleading assertion in the article is the following: “Moreover, the individual parts of complex structures supposedly serve no function.” In other words, opponents of design want to assert that if the individual parts of a putatively IC structure can be used for anything at all other than their role in the system under consideration, then the system itself is not IC. So, for example, Kenneth Miller has seriously argued that a part of a mousetrap could be used as a paperweight, so not even a mousetrap is IC. Now, anything that has mass could be used as a paperweight. Thus by Miller’s tendentious reasoning any part of any system at all has a separate “function”. Presto! There is no such thing as irreducible complexity.

    That’s what often happens when people who are adamantly opposed to an idea publicize their own definitions of its key terms—the terms are manipulated to wage a PR battle. The evident purpose of Miller and others is to make the concept of IC so brittle that it easily crumbles. However, they are building a straw man. I never wrote that individual parts of an IC system couldn’t be used for any other purpose. (That would be silly—who would ever claim that a part of a mousetrap couldn’t be used as a paperweight, or a decoration, or a blunt weapon?) Quite the opposite, I clearly wrote in Darwin’s Black Box that even if the individual parts had their own functions, that still does not account for the irreducible complexity of the system. In fact, it would most likely exacerbate the problem, as I stated when considering whether parts lying around a garage could be used to make a mousetrap without intelligent intervention.

    In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn’t form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system.

    Darwin’s Black Box, page 66.

    The reason why a separate function for the individual parts does not solve the problem of IC is because IC is concerned with the function of the system:

    By irreducibly complex I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.

    Darwin’s Black Box, page 39.

    The system can have its own function, different from any of the parts. Any individual function of a part does not explain the separate function of the system.

    Miller applies his crackerjack reasoning not only to the mousetrap, but also to the bacterial flagellum—the extremely sophisticated, ultra complex biological outboard motor that bacteria use to swim, which I had discussed in Darwin’s Black Box and which has becoming something of a poster child for intelligent design. No wonder, since anyone looking at a drawing of the flagellum immediately apprehends the design. Since the flagellum is such an embarrassment to the Darwinian project, Miller tries to distract attention from its manifest design by pointing out that parts of the structure can have functions other than propulsion. In particular, some parts of the flagellum act as a protein pump, allowing the flagellum to aid in its own construction—a level of complexity that was unsuspected until relatively recently.

    Miller’s argument is that since a subset of the proteins of the flagellum can have a function of their own, then the flagellum is not IC and Darwinian evolution could produce it. That’s it! He doesn’t show how natural selection could do so; he doesn’t cite experiments showing that such a thing is possible; he doesn’t give a theoretical model. He just points to the greater-than-expected complexity of the flagellum (which Darwinists did not predict or expect) and declares that Darwinian processes could produce it. This is clearly not a fellow who wants to look into the topic too closely.

    In fact, the function of a pump has essentially nothing to do with the function of the system to act as a rotary propulsion device, anymore than the ability of parts of a mousetrap to act as paperweights has to do with the trap function. And the existence of the ability to pump proteins tells us nil about how the rotary propulsion function might come to be in a Darwinian fashion. For example, suppose that the same parts of the flagellum that were unexpectedly discovered to act as a protein pump were instead unexpectedly discovered to be, say, a chemical factory for synthesizing membrane lipids. Would that alternative discovery affect Kenneth Miller’s reasoning at all? Not in the least. His reasoning would still be simply that a part of the flagellum had a separate function. But how would a lipid-making factory explain rotary propulsion? In the same way that protein pumping explains it—it doesn’t explain it at all.

    The irreducible complexity of the flagellum remains unaltered and unexplained by any unintelligent process, despite Darwinian smoke-blowing and obscurantism.

    I have pointed all this out to Ken Miller on several occasions, most recently at a debate in 2002 at the American Museum of Natural History. But he has not modified his story at all.

    As much as some Darwinists might wish, there is no quick fix solution to the problem of irreducible complexity. If they want to show their theory can account for it (good luck!), then they’ll have to do so by relevant experiments and detailed model building—not by wordplay and sleight-of-hand.

  8. 8
    Mung says:

    That’s what “peer review” gets you.

  9. 9
    Optimus says:

    Mung @ 1
    I noticed that same problem right off. That paper is off to such a poor start that it hardly deserves serious consideration. How can anyone refute a concept that they cannot define properly?

  10. 10
    Barb says:

    The challenge is to show how a small rotary engine–the flagellum–assembles itself in 20 minutes with all these parts (rotor, bushing, universal joint, propeller, and flagella) in place and functional. All by means of random mutations and natural selection.

    I thought it interesting that New Scientist magazine calls the bacterial flagellum “a prime example of a complex molecular system—an intricate nanomachine beyond the craft of any human engineer.”

    Highly educated human engineers can’t build one, but blind, undirected selection and mutations can. Sounds perfectly reasonable.

  11. 11
    bornagain77 says:

    I seriously want to know where this wondrous Darwinian tinker-shop is. Where parts serving some other purpose, for no particular reason at all, decide (or is that randomly select) that they can also serve a specific purpose elsewhere. And to ‘accidentally’ do it far better that human engineers can imitate.,, Darwinists cannot even explain how a single protein came about by such a trial and error mechanism, much less an entire molecular machine,,

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

    So that is what Darwinian evolution would need to find the ‘tiniest of function’, but what do we find instead???

    The Ribosome: Perfectionist Protein-maker Trashes Errors
    Excerpt: The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.
    per – Science Daily

    And exactly how is the evolution new life forms suppose to ‘randomly’ occur if it is prevented from ‘randomly’ occurring to the proteins in the first place?

    Well perhaps DNA will give us some leeway for this magical Darwinian tinker-shop,, where things can just magically fall together?

    Repair mechanisms in DNA include:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass
    http://www.newgeology.us/presentation32.html

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.”
    http://www.arn.org/blogs/index....._contradic

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    The Bacterial Flagellum certainly gives no indication that it is a happenstance cobbled together piece of machinery. Indeed, as the following video shows,,,

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

    ,,,that the flagellum operates at near 100% efficiency (something human engineers can only dream about) and rotates far faster that a formula one race car. Moreover, the assembly process is so sophisticated that researchers are trying to model it in hopes of enhancing industrial operations,,

    The Bacterial Flagellum: A Paradigm for Design – Jonathan M. – Sept. 2012
    Excerpt: Indeed, so striking is the appearance of intelligent design that researchers have modelled the assembly process (of the bacterial flagellum) in view of finding inspiration for enhancing industrial operations (McAuley et al.). Not only does the flagellum manifestly exhibit engineering principles, but the engineering involved is far superior to humanity’s best achievements. The flagellum exhibits irreducible complexity in spades. In all of our experience of cause-and-effect, we know that phenomena of this kind are uniformly associated with only one type of cause – one category of explanation – and that is intelligent mind. Intelligent design succeeds at precisely the point at which evolutionary explanations break down.
    http://www.scribd.com/doc/1067.....-Flagellum

    Perhaps Darwinists have no problem imagining how all that just accidentally came together to produce such a sophisticated machine, but I certainly do! As to actual empirical evidence, i.e. an actual demonstration, from Darwinists that such sophistication can happen by ‘random’ Darwinian processes, well you will be waiting a long, long, time for such hard evidence,,

    “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/

    Also of note, Dr. James Tour, who, in my honest opinion, currently builds some of the most sophisticated man-made molecular machines in the world (though they still pale in comparison to what is actually found in biological life),,,

    Science & Faith — Dr. James Tour – video (At the two minute mark of the following video, you can see a nano-car that was built by Dr. James Tour’s team)
    http://www.youtube.com/watch?v=CdU5ojTpyzg

    ,,states that he will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:

    “I build molecules for a living, I can’t begin to tell you how difficult that job is. I stand in awe of God because of what he has done through his creation. Only a rookie who knows nothing about science would say science takes away from faith. If you really study science, it will bring you closer to God.”
    James Tour – one of the leading nano-tech engineers in the world – Strobel, Lee (2000), The Case For Faith, p. 111

    Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video
    http://www.youtube.com/watch?v=WCyAOCesHv0

  12. 12
    KD says:

    Just took a quick look at the paper and was really surprised to see how short it is. Experimental results seem to be non-existent. Instead, it appears to be a hypothesis (it is actually an example of creative story telling, but to be charitable, I’ll call it a hypothesis) with some serious blanks to fill in. For example, here is a major blank to fill in, ‘One simple explanation is that the evolutionary precursor of these proteins resembled the smaller ones (FlgG and FlgF), and that a novel domain was inserted into FlgE to generate the larger one.’

    ‘Simple explanation’? A ‘novel domain was inserted’? The lack of rigour is really quite discouraging here. There does not seem to be any attempt whatsoever to quantify just how easy or difficult the sudden appearance of a novel domain is. I and my colleagues have laid out a way to quantify the degree of difficulty here http://www.ncbi.nlm.nih.gov/pubmed/18062814 . The degree of difficulty in obtaining a ‘novel domain’ is so great, it is unlikely it will occur in the history of the planet earth, yet this piece of creative story telling casually suggests this extremely improbable ‘simple explanation’ as if these things are just appearing all the time in the evolution of life. Science should be testable. The authors need to test the hypothesis that novel, structural domains can appear under anything remotely similar to real life conditions on the planet. This article by Wong et al. is not science; it is creative story telling. If I recall correctly, an earlier paper by Matzke stated that there are 15 ‘unique’ proteins (no known homologs) and of those, 2 are ‘indispensable’. Not so much as the faintest hint of breaking out in a sweat about the degree of difficulty in having novel protein families appear. Just one indispensable protein family that has no known homolog is a show stopper, yet the average Darwinist does not seem to have the wit to understand the problem, usually responding with some sort of creative story where magic provides the coding sequence for a novel protein family when needed. Of course, the word ‘magic’ is not used ….. the protein or, in this case, the novel domain, just simply appears.

    I wondered how this paper got through review and who could possibly have been so out of touch with the real life problems of generating novel protein domains. Then I noticed that most of the authors were undergraduate students. I assume these are not science students, because science must be testable, falsifiable and verifiable, to say the least. These students (and the journal) are confused in the difference between doing science and creative story telling. This paper does not qualify as ‘doing science’ and if Darwinists are incontinent with ecstasy that someone has finally presented a creation myth as to how the flagellum came to be, then there is a crisis of science in the field of evolutionary biology.

  13. 13
    Mung says:

    Welcome back KD.

    If it’s not too far afield, what’s your take in “Shannon Information.” Is it a measure of “meaningless” information?

    Is “meaningless information” an oxymoron?

  14. 14
    Upright BiPed says:

    Thank you for responding Dr Durston.

  15. 15
    Mung says:

    How can anyone refute a concept that they cannot define properly?

    By blaming their failure to refute on the definition!

    Just ask Upright BiPed.

  16. 16
    Querius says:

    That evolution is called upon to act as a materialistic explanation for self-organization and self-replication to a level of complexity that makes a computer look trivial by comparison is nothing short of a scientific sounding way of saying “Once upon a time” or “Within the first billion years, a series of miracles must have occurred.”

    I just don’t buy into it anymore.

  17. 17
    Querius says:

    And what’s wrong with simply saying, “We simply don’t know how life began, nor RNA and DNA (and why they seem to be encrypted), major body plans, organs and organelles, a vast array of really complicated chemical cycles, cell walls, and so on. It could have been God, or aliens, or some strange natural process that we haven’t been able to reproduce.”

    There’s a certain integrity and dignity in an admission like that. Then, we can continue experimenting around the edges of the unknown to see how things are put together, and how they work. Label the rest speculation.

  18. 18
    Jerad says:

    I don’t know of anyone who says we DO know how life began on Earth. Which is why they’re doing research trying to figure it out!!

  19. 19
    bornagain77 says:

    Jerad states,,,

    I don’t know of anyone who says we DO know how life began on Earth. Which is why they’re doing research trying to figure it out!!

    Well, what does our research tell us? It is not nearly as conducive to a materialistic/atheistic view of reality as atheists presuppose. As Stephen Meyer points out here,,,

    The DNA Enigma – Where Did The Information Come From? – Stephen C. Meyer – video
    http://www.metacafe.com/watch/4125886

    and also points out here,,,

    Dr. Stephen Meyer: Chemistry/RNA World/crystal formation can’t explain genetic information – video
    http://www.youtube.com/watch?v=yLeWh8Df3k8

    ,, the primary problem for Origin of Life research (and the ‘random’ evolution of organic life in general) always boils down to an ‘information problem’. Yet the only source that we know of that is capable of generating functional information is mind. Thus to address the ‘information problem’ properly it is first necessary to see if mind might have preceded the formation of organic life on Earth. One might imagine, as the late Francis Crick did,,

    At the 37 min. 15 sec. mark of this following video, Dr. Walter Bradley talks a little bit about the OOL problem and Watson and Crick’s, the co-discoverers of the DNA helix, disbelieving reactions to the DNA, RNA, Protein, ‘translation complexity’ they found themselves to be dealing with:

    Evidence for an Engineered Universe – Walter Bradley – video
    http://www.youtube.com/watch?v=nLd_cPfysrE

    ,,,and as Richard Dawkins also does in the movie EXPELLED,,

    Ben Stein vs. Richard Dawkins Interview – video
    http://www.youtube.com/watch?v=GlZtEjtlir

    ,,,one might imagine as they did that some type of Extra-Terrestrial aliens (ETs) created the first life on Earth and thus try to circumvent the ‘information problem’. It would hardly be observational science but one could imagine that scenario. On the other hand if one demanded a little more rigor to one’s science then one could look to the cutting edge of science in quantum mechanics and find that breakthroughs in quantum mechanics have given us clear, unambiguous, evidence that mind/consciousness precedes not only life on earth but precedes all of material reality altogether. The enigma of conscious observation being central in the double slit experiment, and elsewhere in quantum mechanics, is now born out to an impressive level of ‘scientific’ detail,,

    Quantum Mechanics – Double Slit Experiment. Is anything real? (Prof. Anton Zeilinger) – video
    http://www.youtube.com/watch?v=ayvbKafw2g0

    A team of physicists in Vienna has devised experiments that may answer one of the enduring riddles of science: Do we create the world just by looking at it? – 2008
    Excerpt: In mid-2007 Fedrizzi found that the new realism model was violated by 80 orders of magnitude; the group was even more assured that quantum mechanics was correct.
    http://seedmagazine.com/conten....._tests/P3/

    This, and several other lines of evidence from quantum mechanics, intersect to produce this argument for God:

    1. Consciousness either preceded all of material reality or is a ‘epi-phenomena’ of material reality.
    2. If consciousness is a ‘epi-phenomena’ of material reality then consciousness will be found to have no special position within material reality. Whereas conversely, if consciousness precedes material reality then consciousness will be found to have a special position within material reality.
    3. Consciousness is found to have a special, even central, position within material reality.
    4. Therefore, consciousness is found to precede material reality.

    Four intersecting lines of experimental evidence from quantum mechanics that shows that consciousness precedes material reality (Wigner’s Quantum Symmetries, Wheeler’s Delayed Choice, Leggett’s Inequalities, Quantum Zeno effect):
    https://docs.google.com/document/d/1G_Fi50ljF5w_XyJHfmSIZsOcPFhgoAZ3PRc_ktY8cFo/edit

    Colossians 1:17
    And he is before all things, and by him all things consist.

    Richard Conn Henry, PhD. Physics, puts it this way:

    Quantum Enigma:Physics Encounters Consciousness – Richard Conn Henry – Professor of Physics – John Hopkins University
    Excerpt: It is more than 80 years since the discovery of quantum mechanics gave us the most fundamental insight ever into our nature: the overturning of the Copernican Revolution, and the restoration of us human beings to centrality in the Universe.
    And yet, have you ever before read a sentence having meaning similar to that of my preceding sentence? Likely you have not, and the reason you have not is, in my opinion, that physicists are in a state of denial…
    http://www.uncommondescent.com.....-designer/

    Scott Aaronson PhD, MIT Quantum Computation, humorously puts it this way,,,

    Lecture 11: Decoherence and Hidden Variables –
    Scott Aaronson
    Excerpt: “Look, we all have fun ridiculing the creationists who think the world sprang into existence on October 23, 4004 BC at 9AM (presumably Babylonian time), with the fossils already in the ground, light from distant stars heading toward us, etc. But if we accept the usual picture of quantum mechanics, then in a certain sense the situation is far worse: the world (as you experience it) might as well not have existed 10^-43 seconds ago!”
    http://www.scottaaronson.com/democritus/lec11.html

  20. 20
    bornagain77 says:

    Moreover, as if mind preceding matter was not enough to refute any materialistic/atheistic origin of life scenario, it is now found that not only have material processes never been observed to generate functional information in the first place,,

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    But it now also found that material particles can be reduced to functional ‘quantum’ information instead of vice versa. Reducing material particles to quantum information is accomplished by a subtle nuance in quantum entanglement experiments,,,

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    – Per Free Republic

    Physicists set new record for quantum teleportation with matter qubits – Apr 16, 2013
    Excerpt: “The greatest significance of our work is the dramatic increase in efficiency compared to previous realizations of matter-matter teleportation,” Nölleke said. “Besides, it is the first demonstration of matter-matter teleportation between truly independent systems and constitutes the current record in distance of 21 m. The previous record was 1 m.”
    Per Physorg

    How Teleportation Will Work –
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://science.howstuffworks.c.....ation1.htm

    Quantum Teleportation – IBM Research Page
    Excerpt: “it would destroy the original (photon) in the process,,”
    http://researcher.ibm.com/view_project.php?id=2862

    Unconditional Quantum Teleportation – abstract
    Excerpt: This is the first realization of unconditional quantum teleportation where every state entering the device is actually teleported,,
    http://www.sciencemag.org/cont.....6.abstract

    Quantum Computing – Stanford Encyclopedia
    Excerpt: Theoretically, a single qubit can store an infinite amount of information, yet when measured (and thus collapsing the Quantum Wave state) it yields only the classical result (0 or 1),,,
    http://plato.stanford.edu/entr.....tcomp/#2.1

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

  21. 21
    bornagain77 says:

    In fact, in the following video, the theoretical feasibility of reducing an entire human to quantum information and teleporting him/her to another location in the universe is discussed:

    New Breakthrough in (Quantum) Teleportation – video
    http://www.youtube.com/watch?v=6xqZI31udJg
    Quote from video:
    “There are 10^28 atoms in the human body.,, The amount of data contained in the whole human,, is 3.02 x 10^32 gigabytes of information. Using a high bandwidth transfer that data would take about 4.5 x 10^18 years to teleport 1 time. That is 350,000 times the age of the universe.”
    for comparison sake:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.” (a zettabyte is one billion trillion or 10^21 bytes of digital data)
    Sriram Kosuri PhD. – Wyss Institute

    In the preceding video they speak of having to entangle all the material particles of the human body on a one by one basis in order to successfully teleport a human. What they failed to realize in the video is that the human body is already ‘teleporatation ready’ in that all the material particles of the human body are already ‘quantumly entangled’:

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    per Daily Galaxy

    Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
    http://www.metacafe.com/watch/5936605/

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....n-folding/

    Also of note, quantum entanglement requires a non-local, beyond space and time, cause in order to explain its effect:

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    Per Science Daily

    The implications of finding ‘non-local’, beyond space and time, quantum information/entanglement in our body on a massive scale are fairly self evident:

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video (notes in description)
    http://vimeo.com/29895068

    Quantum Entangled Consciousness (Permanence/Conservation of Quantum Information) – Life After Death – Stuart Hameroff – video
    https://vimeo.com/39982578

    One more line of evidence that God was directly involved in the formation of the first life on earth is photosythesis:

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    At the 21:00 minute mark of the following video, Dr Suarez explains why photosynthesis needs a ‘non-local’, beyond space and time, cause to explain its effect:

    Nonlocality of Photosynthesis – Antoine Suarez – video – 2012
    http://www.youtube.com/watch?v.....ge#t=1268s

    Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Gregory S. Engel, Nature (12 April 2007)
    Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated.,,,, This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path. —- Conclusion? Obviously Photosynthesis is a brilliant piece of design by “Someone” who even knows how quantum mechanics works.
    http://www.ncbi.nlm.nih.gov/pubmed/17429397

    Quantum Mechanics at Work in Photosynthesis: Algae Familiar With These Processes for Nearly Two Billion Years – Feb. 2010
    Excerpt: “We were astonished to find clear evidence of long-lived quantum mechanical states involved in moving the energy. Our result suggests that the energy of absorbed light resides in two places at once — a quantum superposition state, or coherence — and such a state lies at the heart of quantum mechanical theory.”,,, “It suggests that algae knew about quantum mechanics,, billion(s) of years before humans,” says Scholes.
    http://www.sciencedaily.com/re.....131356.htm

  22. 22
    bornagain77 says:

    Thus not only is God somehow directly involved in the formation of all the biological molecules of life on earth through non-local quantum entaglment, but He is apparently also responsible for feeding all higher life on earth since all higher life on earth is ultimately dependent on ‘non-local’ photosynthesis for food.

    Verse and Music:

    John 1:4
    In him was life, and that life was the light of all mankind.

    Natalie Grant – Alive (Resurrection music video)
    lyric: “Death has lost and love has won!”,,
    http://www.godtube.com/watch/?v=KPYWPGNX

    My question to materialistic atheists who look for life to accidentally ‘emerge’ for a tarry soup lifeless chemicals,,,,

    Luke 24:5
    ,,,“Why do you look for the living among the dead?

    Here is a clue as to where true life (i.e. eternal life) may truly be found;

    The absorbed energy in the Shroud body image formation appears as contributed by discrete values – Giovanni Fazio, Giuseppe Mandaglio – 2008
    Excerpt: This result means that the optical density distribution,, can not be attributed at the absorbed energy described in the framework of the classical physics model. It is, in fact, necessary to hypothesize a absorption by discrete values of the energy where the ‘quantum’ is equal to the one necessary to yellow one fibril.
    http://cab.unime.it/journals/i.....802004/271

    Scientists say Turin Shroud is supernatural – December 2011
    Excerpt: “The results show that a short and intense burst of UV directional radiation can colour a linen cloth so as to reproduce many of the peculiar characteristics of the body image on the Shroud of Turin,” they said. And in case there was any doubt about the preternatural degree of energy needed to make such distinct marks, the Enea report spells it out: “This degree of power cannot be reproduced by any normal UV source built to date.”
    http://www.independent.co.uk/n.....79512.html

    Music:

    K-LOVE – Steven Curtis Chapman “Love Take Me Over” LIVE
    http://www.youtube.com/watch?v=Qn5mi5G9RQY

    “In Christ Alone” / scenes from “The Passion of the Christ”
    http://www.youtube.com/watch?v=UDPKdylIxVM

  23. 23
    KD says:

    @Mung #13: One would think that the term ‘meaningless information’ is an oxymoron but, unfortunately, in the field of information theory, it is not. Classical information measures such as Shannon Information and Kolmogorov Complexity do not distinguish between meaningful and meaningless information (relevant to humans), or functional or non-functional information (relevant to non-sentient systems, such as the cell). My take on Shannon Information would be nicely summarized by Szostak in his brief article ‘Molecular Messages’, Nature, vol. 423, June 2003. In that article he introduces the need for a ‘new measure of information—functional information’. In a later paper by Hazen et al. (where Szostak is a coauthor), the concept of functional information is expanded upon (PNAS, vol. 104, ‘Functional Information and the Emergence of Biocomplexity’, 2007). That same year, our paper on functional complexity was also published, linked to in my previous post.

    @all: My first question to Wong et al. re. the review article under discussion would be:

    1. What is the estimated level of functional information/functional complexity required for the novel domain they mention?
    2. Given the answer to (1), what is the probability (Hazen’s M(Ex)/N) of obtaining said novel domain?

    There are at least two major problems to solve when one desires to obtain a molecular machine:

    a) Obtaining all the stable, folding proteins required for its parts and,
    b) getting those parts assembled to build the machine.

    There seems to be the thinking by Wong and also Matzke that if we can only explain where most of the parts came from, then we have the molecular machine. It is similar to the thinking (or lack thereof) that if we can explain where we get various nuts, bolts, wiring, etc. from, then we have explained how the latest aircraft engine is built. Not at all; we have only explained where the parts came from and, in the case of the bacterial flagellum, we have not even been offered an adequate explanation for that ….. in fact, not even an analysis of how hard it might be to get those parts in the first place. There has to be some sort of system (ultimately coded in the genome but interacting with various cell inputs) that governs the assembly of a molecular machine once we have production up and running for the individual parts. To read this review article, or Matzke’s article, one would think that all one has to do is to spoon all the right proteins into a test tube, give it a few shakes, and out comes a fully assembled molecular machine. Ultimately, I think it boils down to a problem of how such statistically impressive levels of functional information got encoded within the genomes of life. Much of it is not a hill-climbing problem (where selection might help). For novel protein domains, it is a needle-in-the-haystack problem where selection is of no help whatsoever.

    I am a bit incredulous that a ‘review’ article with eight authors/coauthors was published with a mere 10 ‘suggested reading’ references. True, they did claim that the evidence for their summary came from ‘hundreds of labs’. Normally, one would expect that these hundreds of labs have published results relevant to the topic and one would have actually read those papers and referenced them in the review article. No such thing here, just a mention of ‘hundreds of labs’. That the editors were happy with a ‘review’ paper written as a group project by undergraduate students, who supply no references to the results of these ‘hundreds of labs’ is a testimony to the quality of the journal, editor and referees that published the article, not to mention the low level of critical commitment to good science demonstrated by those 3,500 critical thinkers who are endorsing this review article … an article which, in my mind, would be a C+ undergraduate essay if it were written by one student, but an F for an eight student effort. The professor who has put his name on that paper has embarrassed himself. He should have required his students to supply at least five relevant references each. Five papers is not too much for an undergraduate student to read, especially if one wishes to submit the review for publication.

  24. 24
    Barry Arrington says:

    Loghin @ 5: “Darwinists are respected more is because they work harder.” Apparently they cannot be bothered to work hard enough to learn what a theory actually espouses before trying to refute it.

  25. 25
    Alan Fox says:

    Hi Dr Durston. Glad to see a representative from the more intellectual wing of the ID movement again.

    You write:

    There are at least two major problems to solve when one desires to obtain a molecular machine:

    a) Obtaining all the stable, folding proteins required for its parts and,
    b) getting those parts assembled to build the machine.

    Leaving aside “at least” and whether “machine” is an accurate description of cell organelles, let me first query what you mean by “assembled”? I get this mental image of tiny little builder people in hard hats guiding molecules into place. We know that molecules inherently self-assemble, witness bilipid layer cell membranes, for instance. And with regard to the E. coli flagellar filament, here is a paper describing the process. I think if you can get your a) then b) comes as a bonus.

    There has to be some sort of system (ultimately coded in the genome but interacting with various cell inputs) that governs the assembly of a molecular machine once we have production up and running for the individual parts.

    Not necessarily. Self-assembly enhanced by chaperones is an observed and powerful mechanism.

    For novel protein domains, it is a needle-in-the-haystack problem where selection is of no help whatsoever.

    I disagree. Proteins are not postulated to form from a “tornado in a junkyard” and we still don’t know how rare functional proteins are. You are obviously familiar with the work of Szostak so you must be aware of what evidence there is so far suggests there may be widespread functionality in unknown proteins.

  26. 26
    Alan Fox says:

    Apparently they cannot be bothered to work hard enough to learn what a theory actually espouses before trying to refute it.

    What theory do you allude to, Barry? If it is a positive, testable theory of “Intelligent Design” I, and many others, would be most interested to hear about it.

  27. 27
    Box says:

    KD #23: There has to be some sort of system (ultimately coded in the genome but interacting with various cell inputs) that governs the assembly of a molecular machine once we have production up and running for the individual parts.

    Alan Fox #25: Not necessarily. Self-assembly enhanced by chaperones is an observed and powerful mechanism.

    Alan, these ‘chaperones’ you are referring to, are they necessary for the assembly process? If so, one might say that there is a system of chaperones, that governs the assembly, in place. In which case I don’t see on what ground you disagree with KD.

  28. 28
    Alan Fox says:

    No, useful but not essential. Read Wikipedia for a basic explanation.

  29. 29
    bornagain77 says:

    Mr. Fox asks for evidence,,

    If it is a positive, testable theory of “Intelligent Design” I, and many others, would be most interested to hear about it.

    He is given evidence that ID does make testable predictions (some of which, such as functional junk DNA, which have been confirmed in stunning fashion i.e. ENCODE):

    A Positive, Testable Case for Intelligent Design – Casey Luskin – March 2011 – several examples of cited research
    http://www.evolutionnews.org/2.....45311.html

    A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design? – March 2010
    Excerpt: Regarding testability, ID (Intelligent Design) makes the following testable predictions:
    (1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).
    (2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.
    (3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.
    (4) Much so-called “junk DNA” will turn out to perform valuable functions.
    http://www.evolutionnews.org/2.....rom_a.html

    On the Origin of Protein Folds – Jonathan M. – September 8, 2012
    Excerpt: A common objection to the theory of intelligent design is that it makes no testable predictions, and thus there is no basis for calling it science at all. While recognizing that testability may not be a sufficient or necessary resolution of the “Demarcation Problem,” my article, which I invite you to download, will consider one prediction made by ID and discuss how this prediction has been confirmed.
    http://www.evolutionnews.org/2.....64081.html

    and yet Mr. Fox and other atheists when presented with such evidence respond as such,,

    The Atheist Doctor
    http://www.youtube.com/watch?v=FRQzQpnYhKI

    What is ironic in all this is that Darwinism is the theory that has no rigid demarcation criteria so as delineate it as ‘scientific’:

    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

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    (Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003)

    “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) – per ENV

    Whereas, on the other hand, ID does have a demarcation criteria to delineate it as ‘scientific’:

    Dembski’s original value for the universal probability bound is 1 in 10^150,
    10^80, the number of elementary particles in the observable universe.
    10^45, the maximum rate per second at which transitions in physical states can occur.
    10^25, a billion times longer than the typical estimated age of the universe in seconds.
    Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang.
    How many bits would that be:
    Pu = 10-150, so, -log2 Pu = 498.29 bits
    Call it 500 bits (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity)
    Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors
    http://www.tbiomed.com/content/2/1/29

    This short sentence, “The quick brown fox jumped over the lazy dog” is calculated by Winston Ewert, in this following video at the 10 minute mark, to contain 1000 bits of algorithmic specified complexity, and thus to exceed the Universal Probability Bound (UPB) of 500 bits set by Dr. Dembski
    Proposed Information Metric: Conditional Kolmogorov Complexity – Winston Ewert – video
    http://www.youtube.com/watch?v=fm3mm3ofAYU

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

    see also David Abel’s Null Hypothesis for information generation by material processes

  30. 30
    PaV says:

    Here’s the telling sentence of their article. (If you can actually call it an article. It seems to be wierdly put together.)

    Complexity within BF arose by domain and protein recruitment, by intragenic and extragenic duplication events, and by superimposition of various modules onto others. The net result was coevolution of many types of structurally and functionally distinct flagella in various bacterial species. Although these different flagella are all used for motility, they share only about half of their protein constituents.

    First: “doman and protein recruitment”? Nice words. What do they mean? It sounds like something decided that the various “modules” of the BF should cooperate and work together. But what was that something? Was it Darwinian selection? Well, describe the process? Describe the functional transitional precursors to the BF.

    Silence.

    Second: “by intragenic and extragenic duplications events”. Really? What is an “extragenic” duplication event? What controls it? What coordinated these “intragenic” and “extragenic” duplication events? Was it random processes being guided by NS? Well, how did this happen? What did it look like? What Darwinian mechanism can explain this coordination?

    Silence.

    Third: “by superimposition of various modules onto others”. Really? So these “various modules” just decided that they would “superimpose” themselves on one another. Very interesting. And, of course, what would be that Darwinian mechanism directing this superposition, all the while providing for functional intermediate stages? How did NS know to allow these superimpositions? How did this aggregation of separate modules come about? And, isn’t “irruducible complexity” the notion that a functional structure composed of “various modules” is NOT functional if one of these “modules” is removed? So, how then has it been proven that IC still applies without first proving that a pathway of functional intermediates can be proposed which lead to the final BF?

    Now it’s really silent.

    Are we to believe this is science? It sure looks like religion to me. I.e., I “believe” in Darwinism, and so I will come up with some kind of “just-so” story that I will then throw at critics who “don’t believe” in Darwinism. I’ll call it Darwinian apologetics. Maybe I’ll get a teaching position at some University.

  31. 31
    Phinehas says:

    KD:

    Just one indispensable protein family that has no known homolog is a show stopper, yet the average Darwinist does not seem to have the wit to understand the problem…

    Ooo. That seems a bit harsh. I prefer to give them the benefit of the doubt. It might not be that they lack wit so much as that they have immeasurable amounts of faith, an unshakable dogma, and very active imaginations.

  32. 32
    forexhr says:

    Let’s imagine that we have an independent super-machine that incorporates a complete production facility for 1886 Swift Safety Bicycles. All you need to do to produce the bicycle is put into a machine binary information that represents coordinates of the spatial atom arrangements of the bike components and their relations. Now imagine that someone tells you that all you have to do before each production cycle is to make a few hundred RANDOM CHANGES in the binary information, start production cycle, SELECT information that represents ready-made products with the best driveability, and at some future time Mercedes SLS will emerge. Mercedes SLS complexity will arose by metal component recruitment, by occasional information duplication events, and by superimposition of various modules onto others.

  33. 33
    KD says:

    @Alan Fox #25: Since we are discussing molecular machines, ‘machine’ is an accurate description of what we are discussing with regard to the nano-machine that propels the filament. An example of what I mean by ‘assembled’ is described here. It is likely true that simple structures can self assemble, but that is not likely to be true of molecular machines, where the right part must be produced and brought into position in the proper order for assembly to occur. Your example of the filament is not an example of self assembly, it needs the assistance of a proton motive force pump to drive the flagellin proteins up the central channel (rather than have flagellin floating by the end and fortuitously coming close enough to bond to the growing tip of the filament). Coming up the centre of the filament like that, they are properly positioned for attachment at the end. The polymerization of the filament is also assisted by another protein that ultimately forms a cap. This is just for something simple like the filament. When it comes to the stator, the rotor, the hook, etc. and the proper assembly of these components, we can be assured this is not a random process. It likely depends heavily upon gene regulation to start with, and some sort of transport mechanism, as well as protein ‘tools’ involved in the construction of the flagellum.

    You will need to clarify how you are using ‘chaperones’. Are you referring to the chaperones that assist in protein folding? If so, these are not involved in the assembly of molecular machines.

    Regarding folding protein sequence space, we discussed this in a previous thread. In the Keefe and Szostak paper to which I think you are referring, they found that roughly 1 in 10^11 random sequence proteins bound to ATP. What that tells us is that ATP-binding is a relatively simple process such that random sequences that will bind to it are relatively common. This is not to be confused with biological functionality, where ATP must be transported and released as well. It would be fascinating to repeat the experiment to see what subset of the random sequences not only bound to ATP, but would release the ATP within biological requirements. ‘Functionality’ must be distinguished from ‘biological functionality’. The requirements of biological processes demand highly tailored proteins. For example, let us say we were given a particular 3-D structure that makes up one component of the flagellum rotor. Now it is up to us to find other proteins with the right 3D structure such that they will not only fit the first one and each other, but produce a functional rotary motor. As I am sure you can appreciate, the functional constraints are far higher than merely finding a random sequence that will bind to something. The constraints ramp up far higher still the moment we make our first choice of 3D structure, for all subsequent proteins will need to fit according to that first choice.

  34. 34
    Alan Fox says:

    This is not to be confused with biological functionality, where ATP must be transported and released as well.

    Just a brief comment. In a system small enough, Brownian motion takes care of transport. It may be inefficient and slow but, in a world where your only competitors have the same limitations, it can be good enough.

    Will pick up on other points tomorrow as past bed time.

  35. 35
    KD says:

    Alan, you might be right. It just seems awfully hit and miss to me, given the volume within which the right proteins have to accidentally bump into each other. I suspect there is still quite a bit more to be discovered in this area.

  36. 36
    Alan Fox says:

    I suspect there is still quite a bit more to be discovered in this area.

    Indeed!

  37. 37
    franklin says:

    Brownian motion is one process to bring various solutes into proximity there are also factors to consider as well. Aside from the absolute concentration of each of the solutes there is the hydrophilic and lipophilic nature of the phsycial chemical properties of each of the consituents. This simple structure relationship can drive low concentrations into regions where their concentration is thus increased. With the increased concentration comes the potential for chemical reactions to take place that would be unlikely with a homogeneous mix of solutes.

    If we think of the Earth as a cell as it relates to solute movement it took less than 50 years for PCB’s to migrate from industrial use in mid to ower latitudes to being being found in high levels in Artic mammals. Simple (c0nceptually) Global distillation processes was all it took to facilitate the movement of these compounds in a rapid fashion around the surface of the planet.

    Another simple non-cellular example of this is eutectic phases in ice which have been demonstrated to among other things, facilitate the non-enzymatic production of nucleotides.

  38. 38
    bornagain77 says:

    KD as to Mr. Fox’s comment:

    In a system small enough, Brownian motion takes care of transport. It may be inefficient and slow but, in a world where your only competitors have the same limitations, it can be good enough.

    to which:

    We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naïve as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB — and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. Consider an enzyme, for example. If its substrate molecule is present at a concentration of 0.5mM,which is only one substrate molecule for every 105 water molecules, the enzyme’s active site will randomly collide with about 500,000 molecules of substrate per second. And a typical globular protein will be spinning to and fro, turning about various axes at rates corresponding to a million rotations per second.
    But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”
    (Bruce Alberts, “The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists,” Cell, 92 (February 6, 1998): 291-294 (emphases added).)

    of note:

    Brownian motion or pedesis is the presumably random moving of particles suspended in a fluid (a liquid or a gas) resulting from their collision by the fast-moving atoms or molecules in the gas or liquid,,,
    http://en.wikipedia.org/wiki/Brownian_motion

    as to this comment by Mr. Fox

    in a world where your only competitors have the same limitations, it can be good enough.

    And please, pray tell Mr. Fox, where is your empirical evidence that this world actually exists anywhere save in your and other neo-Darwinists’ imagination?

    As to what reality tells us:

    James Shapiro on “dangerous oversimplifications” about the cell – August 6, 2013
    Excerpt: “Depending upon the energy source and other circumstances, these indescribably complex entities can reproduce themselves with great reliability at times as short as 10-20 minutes. Each reproductive cell cycle involves literally hundreds of millions of biochemical and biomechanical events. We must recognize that cells possess a cybernetic capacity beyond our ability to imitate. Therefore, it should not surprise us when we discover extremely dense and interconnected control architectures at all levels. Simplifying assumptions about cell informatics can be more misleading than helpful in understanding the basic principles of biological function.
    Two dangerous oversimplifications have been (i) to consider the genome as a mere physical carrier of hypothetical units called “genes” that determine particular cell or organismal traits, and (ii) to think of the genome as a digitally encoded Read-Only Turing tape that feeds instructions to the rest of the cell about individual characters [4].”
    http://www.uncommondescent.com.....-the-cell/

  39. 39
    bornagain77 says:

    as to franklin’s comment here:

    If we think of the Earth as a cell as it relates to solute movement it took less than 50 years for PCB’s to migrate from industrial use in mid to ower latitudes to being being found in high levels in Artic mammals. Simple (c0nceptually) Global distillation processes was all it took to facilitate the movement of these compounds in a rapid fashion around the surface of the planet.

    as to ‘Global distillation processes’, that is actually a fact that argues in favor of Intelligently Designed Terra-Forming:

    The Concentration of Metals for Humanity’s Benefit:
    Excerpt: They demonstrated that hydrothermal fluid flow could enrich the concentration of metals like zinc, lead, and copper by at least a factor of a thousand. They also showed that ore deposits formed by hydrothermal fluid flows at or above these concentration levels exist throughout Earth’s crust. The necessary just-right precipitation conditions needed to yield such high concentrations demand extraordinary fine-tuning. That such ore deposits are common in Earth’s crust strongly suggests supernatural design.
    http://www.reasons.org/TheConc.....tysBenefit

    Related assorted notes:

    The Creation of Minerals:
    Excerpt: Thanks to the way life was introduced on Earth, the early 250 mineral species have exploded to the present 4,300 known mineral species. And because of this abundance, humans possessed all the necessary mineral resources to easily launch and sustain global, high-technology civilization.
    per Reasons to believe

    “Today there are about 4,400 known minerals – more than two-thirds of which came into being only because of the way life changed the planet. Some of them were created exclusively by living organisms” –
    Bob Hazen – Smithsonian – Oct. 2010, pg. 54

    The Place of Life and Man in Nature: Defending the Anthropocentric Thesis – Michael J. Denton – February 25, 2013
    Summary (page 11)
    Many of the properties of the key members of Henderson’s vital ensemble —water, oxygen, CO2, HCO3 —are in several instances fit specifically for warm-blooded, air-breathing organisms such as ourselves. These include the thermal properties of water, its low viscosity, the gaseous nature of oxygen and CO2 at ambient temperatures, the inertness of oxygen at ambient temperatures, and the bicarbonate buffer, with its anomalous pKa value and the elegant means of acid-base regulation it provides for air-breathing organisms. Some of their properties are irrelevant to other classes of organisms or even maladaptive.
    It is very hard to believe there could be a similar suite of fitness for advanced carbon-based life forms. If carbon-based life is all there is, as seems likely, then the design of any active complex terrestrial being would have to closely resemble our own. Indeed the suite of properties of water, oxygen, and CO2 together impose such severe constraints on the design and functioning of the respiratory and cardiovascular systems that their design, even down to the details of capillary and alveolar structure can be inferred from first principles. For complex beings of high metabolic rate, the designs actualized in complex Terran forms are all that can be. There are no alternative physiological designs in the domain of carbon-based life that can achieve the high metabolic activity manifest in man and other higher organisms.
    http://bio-complexity.org/ojs/.....O-C.2013.1

    Elemental Evidence of Earth’s Divine Design – Hugh Ross PhD. – April 2010
    Table: Earth’s Anomalous Abundances – Page 8
    The twenty-five elements listed below must exist on Earth in specific abundances for advanced life and/or support of civilization to be possible. For each listed element the number indicates how much more or less abundant it is, by mass, in Earth’s crust, relative to magnesium’s abundance, as compared to its average abundance in the rest of the Milky Way Galaxy, also relative to the element magnesium. Asterisks denote “vital poisons,” essential elements that if too abundant would be toxic to advanced life, but if too scarce would fail to provide the quantities of nutrients essential for advanced life. The water measure compares the amount of water in and on Earth relative to the minimum amount the best planet formation models would predict for a planet the mass of Earth orbiting a star identical to the Sun at the same distance from the Sun.

    carbon* 1,200 times less
    nitrogen* 2,400 times less
    fluorine* 50 times more
    sodium* 20 times more
    aluminum 40 times more
    phosphorus* 4 times more
    sulfur* 60 times less
    potassium* 90 times more
    calcium 20 times more
    titanium 65 times more
    vanadium* 9 times more
    chromium* 5 times less
    nickel* 20 times less
    cobalt* 5 times less
    selenium* 30 times less
    yttrium 50 times more
    zirconium 130 times more
    niobium 170 times more
    molybdenum* 5 times more
    tin* 3 times more
    iodine* 3 times more
    gold 5 times less
    lead 170 times more
    uranium 16,000 times more
    thorium 23,000 times more
    water 250 times less
    http://www.reasons.org/files/e.....010-02.pdf

    Compositions of Extrasolar Planets – July 2010
    Excerpt: ,,,the presumption that extrasolar terrestrial planets will consistently manifest Earth-like chemical compositions is incorrect. Instead, the simulations revealed “a wide variety of resulting planetary compositions.
    per Reasons to Believe

    Privileged Planet – Observability Correlation – Gonzalez and Richards – video
    http://www.metacafe.com/watch/5424431

    The very conditions that make Earth hospitable to intelligent life also make it well suited to viewing and analyzing the universe as a whole.
    – Jay Richards

    Linked from Appendix C from Dr. Ross’s book, ‘Why the Universe Is the Way It Is’;
    Probability for occurrence of all 816 parameters – approx. 10^-1333
    dependency factors estimate – approx. 10^324
    longevity requirements estimate – approx. 10^45
    Probability for occurrence of all 816 parameters – approx. 10^-1054
    Maximum possible number of life support bodies in observable universe – approx. 10^22

    Thus, less than 1 chance in 10^1032 exists that even one such life-support body would occur anywhere in the universe without invoking divine miracles.
    http://www.reasons.org/files/c....._part3.pdf

    Hugh Ross – Evidence For Intelligent Design Is Everywhere (10^-1054) – video
    http://www.metacafe.com/watch/4347236

    Verse, video, and music:

    Isaiah 45:18-19
    For thus says the Lord, who created the heavens, who is God, who formed the earth and made it, who established it, who did not create it in vain, who formed it to be inhabited: “I am the Lord, and there is no other. I have not spoken in secret, in a dark place of the earth; I did not say to the seed of Jacob, ‘seek me in vain’; I, the Lord speak righteousness, I declare things that are right.”

    The Earth as You’ve Never Seen it Before: Atmosphere, Airglow and Aurora – video
    https://vimeo.com/42909676

    Casting Crowns – Until The Whole World Hears W/Lyrics
    http://www.youtube.com/watch?v=C9jVK9cZ2aw

  40. 40
    Mung says:

    KD@23:

    @Mung #13: One would think that the term ‘meaningless information’ is an oxymoron but, unfortunately, in the field of information theory, it is not. Classical information measures such as Shannon Information and Kolmogorov Complexity do not distinguish between meaningful and meaningless information (relevant to humans), or functional or non-functional information (relevant to non-sentient systems, such as the cell).

    Given that there is no such thing as meaningless information, how can anyone fault those information measures for not making a distinction where there is none?

    And if it’s a fact that those measures of information cannot distinguish between meaningful and meaningless information how does it follow that meaningless information is not an oxymoron?

    It does not follow. This is an error in logic. Meyer makes it in both his books. The sooner that ID theorists clarify this issue the better off ID will be.

    Shannon information is about something. It is not meaningless.

    Kolmogorov Complexity is about something. It is not meaningless.

    All information is about something. Information is never meaningless.

    A fundamental, but somehow forgotten fact, is that information is always information about something.

    – Jan Kahre. The Mathematical Theory of Information

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