Intelligent Design

Tonight’s Feature Presentation: Epigenetics, The Next Evolutionary Cliff

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We’ve discussed epigenetics, those incredible genetic regulation mechanisms such as molecular barcodes stamped onto DNA,histones, those incredible DNA packaging proteins that also have their own barcodes, the different kinds of barcodes, and how these marvels have falsified so many evolutionary predictions. If it all went by too fast then maybe tonight’s Feature Presentation will help tell a thousand words. You may need to view it a few times to follow the details, but the underlying plot should be clear.  Read more

20 Replies to “Tonight’s Feature Presentation: Epigenetics, The Next Evolutionary Cliff

  1. 1
    bornagain77 says:

    The problems that epigenetics presents to Darwinian processes are simply devastating. Especially devastating to the ‘central dogma’ (DNA makes RNA makes Proteins) of evolution, since some epigenetic modifications reach all the way down to the genetic text of DNA:

    Does the central dogma still stand? – Koonin EV. – 23 August 2012
    Excerpt: Thus, there is non-negligible flow of information from proteins to the genome in modern cells, in a direct violation of the Central Dogma of molecular biology. The prion-mediated heredity that violates the Central Dogma appears to be a specific, most radical manifestation of the widespread assimilation of protein variation into genetic variation. The epigenetic variation precedes and facilitates genetic adaptation through a general ‘look-ahead effect’ of phenotypic mutations.,,,
    http://www.ncbi.nlm.nih.gov/pubmed/22913395

    If that was not bad enough, there is even growing evidence that ‘mind’ can influence epigenetic modifications to the genome:

    Anxiety May Shorten Your Cell Life – July 12, 2012
    Excerpt: These studies had the advantage of large data sets involving thousands of participants.
    If the correlations remain robust in similar studies, it would indicate that mental states and lifestyle choices can produce epigenetic effects on our genes.
    http://crev.info/2012/07/anxie.....cell-life/

    Genie In Your Genes – video
    http://www.genieinyourgenes.com/ggtrailer.html

    ,,, This is simply completely devastating to what Darwinism presupposed:

    of related interest:

    The Mysterious Epigenome. What lies beyond DNA – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

    “The Mysterious Epigenome: What Lies Beyond DNA” – May 2012 – podcast
    http://intelligentdesign.podom.....7_28-07_00

    Epigenetics and the “Piano” Metaphor – January 2012
    Excerpt: And this is only the construction of proteins we’re talking about. It leaves out of the picture entirely the higher-level components — tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players.
    http://www.evolutionnews.org/2.....54731.html

  2. 2
    bornagain77 says:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.

    New Research Elucidates Directed Mutation Mechanisms – Cornelius Hunter – January 7, 2013
    Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,,
    These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,,
    http://darwins-god.blogspot.co.....ected.html

    Shapiro on Random Mutation:
    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”
    http://www.huffingtonpost.com/.....11144.html

    But if the vast majority of mutations are not truly random then that means neo-Darwinism has no ultimate source for creativity in its RV&NS scenario.

  3. 3
    William J Murray says:

    Darwinists might as well be standing around in a room full of top of the line computers loaded with high-end software, connected to and directing the operations of an automated factory,all the while insisting that the whole thing came together via undirected, unintelligent forces.

    There comes a time when a person is faced with what is both a profound challenge to their existing worldview and an amazing opportunity for them to incorporate transformational information into their understanding of existence; the question is, who is up to the challenge?

    Why insist on anything and everything, no matter how unfounded and far-fetched, just to ignore the obvious – that the best, current, provisional explanation for these things is that they were probably designed by an intelligence of some sort?

  4. 4
    JourneytotheLight says:

    I think it is supreme arrogance. Those who refuse to give intelligent design a fraction of a moment’s thought, subconsciously find it utterly inconceivable that there is Someone more intelligent than a human being.

    I strongly doubt they will admit it, not even to themselves.

  5. 5
    billmaz says:

    Bornagain77,

    Would such ideas as the Inverse Quantum Zeno Effect (Aharonov, Y., Vardi, M., 1980 Meaning of an individual ‘Feynman path.’ Phys. Rev. D 21, 2235-2240.) provide some possibility for directed mutations which could answer some of the concerns regarding non-random evolution? If so, would that be consistent with ID or evolution?

  6. 6
    bornagain77 says:

    billmaz, let’s see:

    The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay.
    http://en.wikipedia.org/wiki/Quantum_Zeno_effect

    Hmmm, some pretty heavy implications there for consciousness there, eh billmaz? i.e. Exactly why should conscious observation override thermodynamic considerations for a ‘particle’??? Very Interesting!!!

    Now,,,

    From the Quantum Zeno (Effect) to the Inverse Quantum Zeno Effect
    Excerpt: The temporal evolution of a quantum mechanical system undergoing repeated measurements (observations) is investigated. In general, by changing the time interval between successive measurements, the decay can be accelerated (Inverse Quantum Zeno Effect), or slowed down (Quantum Zeno Effect),,,
    http://www.ba.infn.it/~pascazi.....clitus.pdf

    As to your Question if this will provide a mechanism for ‘directed’ mutations,,, seeing that directed mutations are, as far as I know, for the most part accomplished by molecular machines, I don’t see how an increase of entropic decay, due to lack of observation, could possibly held explain ‘non-random evolution. As far as the question of if the Zeno effect, or its inverse, helps ID or Darwinism, at first glance I consider conscious observation preventing entropic decay of a particle to be crushing against Darwinism, simple because consciousness is held to ’emerge’ from particles in the materialistic framework, and here we have consciousness demonstrating a certain level of dominion over the actions of a particle.

  7. 7
    billmaz says:

    Bornagain, On my blogBill Maz: Adaptive Mutations and Quantum Mechanics I review how quantum mechanics, and specifically the Inverse Quantum Zeno Effect, is invoked to try to explain directed mutations. Specifically, the idea in the Inverse Quantum Zeno Effect is that a series of measurements along a particular path has been shown to force the quantum system to evolve along that path.

  8. 8
    bornagain77 says:

    Well, billmaz, at first glance, I would say that having a particle, or quantum system, ‘evolve’ along a certain path of motion, is a long way from explaining how a molecular machine knows how to make a specific ‘directed’ mutation in a particular section of a genome out of billions of base pairs. Moreover, you have the problem of consciousness having to be present in the system in order to ‘make a series of measurements’. From whence and where is this consciousness deciding to make a particular series of measurements so as to force the path of the quantum system in a particular direction. Not to say that it is not feasible from a ID perspective (and is certainly not feasible from the neo-Darwinian perspective), but there are a lot of unanswered questions at the outset that make it seem you will have quite a bit of trouble establishing it rigorously if it is indeed true. I think a more promising area of investigation, at the present moment, as to rigorously establishing a coherent mechanism for what is directing the mutations to the precisely correct areas of the genome, that are necessary to deal with a particular environmental stress ,is quantum computation:

    Notes:

    Is DNA a quantum computer? Stuart Hameroff
    Excerpt: DNA could function as a quantum computers with superpositions of base pair dipoles acting as qubits. Entanglement among the qubits, necessary in quantum computation is accounted for through quantum coherence in the pi stack where the quantum information is shared,,,
    http://www.quantumconsciousnes.....puter1.htm

    Quantum Computing in DNA – Stuart Hameroff
    Excerpt of Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist).
    Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement.
    http://www.quantumconsciousnes.....InDNA.html

    further notes of interest:

    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/re.....104244.htm

    DNA as classical and quantum information system – Dec. 2005
    Excerpt (pg. 118): Basic point to understand biological communication is synergy of classical and quantum process based on perfect numbers and the golden mean laws.
    http://www.doiserbia.nb.rs/img.....04115K.pdf

    Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009
    Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus.
    http://www.sciencemag.org/cgi/.....6/5950/289

    Scientists’ 3-D View of Genes-at-Work Is Paradigm Shift in Genetics – Dec. 2009
    Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these ‘hot spots’. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory.
    http://www.sciencedaily.com/re.....160649.htm

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

  9. 9
    billmaz says:

    BA, I believe the authors view the change in the cytoplasm (adding lactose to a cell unable to metabolize lactose) as being equivalent to a “measurement” or interaction between the cytoplasm and the DNA, thus obviating the need for a consciousness to measure but still meeting the requirements for a quantum entanglement between the DNA and the lactose/cytoplasm. The idea is that by simply stressing the system with lactose, a quantum entanglement is created which would then lead to a change in the DNA.

  10. 10
    bornagain77 says:

    “thus obviating the need for a consciousness to measure”

    Well if they truly did “obviate the need for a consciousness to measure” a quantum system then they will have overturned this proof:

    Can quantum theory be improved? – July 23, 2012
    Excerpt: However, in the new paper, the physicists have experimentally demonstrated that there cannot exist any alternative theory that increases the predictive probability of quantum theory by more than 0.165, with the only assumption being that measurement (conscious observation) parameters can be chosen independently (free choice assumption) of the other parameters of the theory.,,,
    ,, the experimental results provide the tightest constraints yet on alternatives to quantum theory. The findings imply that quantum theory is close to optimal in terms of its predictive power, even when the predictions are completely random.
    http://phys.org/news/2012-07-quantum-theory.html

    i.e. conscious observation and free will are ‘built into’ our understanding of quantum mechanics as starting assumptions. To “obviate the need’ for consciousness in quantum mechanics one would have to completely different theory than quantum theory to explain quantum theory’s unmatched predictive power.

  11. 11
    bornagain77 says:

    ,,,one would have to HAVE A,,,

  12. 12
    bornagain77 says:

    billmaz, I’m just fascinated by this Quantum Zeno effect that you brought to my attention:

    Quantum Zeno effect
    Excerpt: The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay.
    http://en.wikipedia.org/wiki/Quantum_Zeno_effect

    The reason why I am fascinated with this effect is, for one thing, that Entropy is, by a wide margin, the most finely tuned of initial conditions of the Big Bang:

    According to esteemed British mathematical physicist Roger Penrose (1931-present), the odds of one particular individual constant, the ‘original phase-space volume’ of the universe, required such precision that the “Creator’s aim must have been to an accuracy of 1 part in 10^10^123”. This number is gargantuan. If this number were written out in its entirety, 1 with 10^123 zeros to the right, it could not be written on a piece of paper the size of the entire visible universe, even if a number were written down on each sub-atomic particle in the entire universe, since the universe only has 10^80 sub-atomic particles in it.

    Roger Penrose discusses initial entropy of the universe. – video
    http://www.youtube.com/watch?v=WhGdVMBk6Zo

    The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose
    Excerpt: “The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).”

    How special was the big bang? – Roger Penrose
    Excerpt: This now tells us how precise the Creator’s aim must have been: namely to an accuracy of one part in 10^10^123.
    (from the Emperor’s New Mind, Penrose, pp 339-345 – 1989)

    For another thing, it is interesting to note just how foundational entropy is in its explanatory power:

    Shining Light on Dark Energy – October 21, 2012
    Excerpt: It (Entropy) explains time; it explains every possible action in the universe;,,
    Even gravity, Vedral argued, can be expressed as a consequence of the law of entropy. ,,,
    The principles of thermodynamics are at their roots all to do with information theory. Information theory is simply an embodiment of how we interact with the universe —,,,
    http://crev.info/2012/10/shini.....rk-energy/

    Evolution is a Fact, Just Like Gravity is a Fact! UhOh! – January 2010
    Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.
    http://www.uncommondescent.com.....fact-uhoh/

    In fact, entropy is the primary reason why our physical bodies grow old and die,,,

    And yet, to repeat the paper,,,

    Quantum Zeno effect
    Excerpt: The quantum Zeno effect is,,, an unstable particle, if observed continuously, will never decay.
    http://en.wikipedia.org/wiki/Quantum_Zeno_effect

    This is just fascinating! Why in blue blazes should conscious observation put a freeze on entropic decay, unless consciousness was/is more foundational to reality than entropy is? And seeing as to how entropy is VERY foundational to reality, I think the implications are fairly obvious:

    Verse and Music:

    Romans 8:18-21
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. The creation waits in eager expectation for the sons of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the glorious freedom of the children of God.

    Evanescence – The Other Side (Lyric Video)
    http://www.vevo.com/watch/evan.....tantsearch

  13. 13
    billmaz says:

    BA,
    Everything is mind-blowing.

    Further quote from Wikipedia:

    “The meaning of the term has since expanded, leading to a more technical definition in which time evolution can be suppressed not only by measurement: the quantum Zeno effect is the suppression of unitary time evolution caused by quantum decoherence in quantum systems provided by a variety of sources: measurement, interactions with the environment, stochastic fields, and so on.[2] As an outgrowth of study of the quantum Zeno effect, it has become clear that applying a series of sufficiently strong and fast pulses with appropriate symmetry can also decouple a system from its decohering environment.[3]”

    So here is the point I was making before, that an “interaction with the environment” can cause the system to decouple. If you read the paper I cited, the interaction with the environment (the introduction of lactose in a cell unable to metabolize lactose) is hypothesized to have caused the decoupling with the DNA and then caused a directed mutation (Inverse Quantum Zeno Effect). You can thus imagine a quantum system that responds “appropriately” to a stimulus causing it to “evolve” in the needed direction to “adapt” to the new environment. All this without the need for the designer to interfere, unless creating the laws of quantum physics counts.

  14. 14
    billmaz says:

    BA: Abstract mentioning the Inverse Quantum Zeno Effect:

    APS » Journals » Phys. Rev. A » Volume 48 » Issue 1

    Phys. Rev. A 48, 70–79 (1993)
    Dynamics by measurement: Aharonov’s inverse quantum Zeno effect
    Abstract
    References
    Citing Articles (23)
    Page Images
    Download: PDF (404 kB) Buy this article Export: BibTeX or EndNote (RIS)
    Thomas P. Altenmüller and Axel Schenzle
    Sektion Physik der Universität München, Theresienstrasse 37, 8000 München, Germany
    Max-Planck-Institut für Quantenoptik, Ludwig-Prandtl-Strasse 10, 8046 Garching, Germany
    Received 13 July 1992; published in the issue dated July 1993

    The quantum Zeno effect is known as the inhibition of a system’s reversible dynamics by frequent measurements. Aharonov and Vardi [Phys. Rev. D 21, 2235 (1980)] proposed a scheme intimately related to the quantum Zeno effect. They showed that, by performing a dense sequence of measurements along a presumed path, the system is found to follow this—arbitrarily chosen—trajectory. The proof was based on the von Neumann projection hypothesis. In this paper we investigate whether this effect still holds if we model a realistic measurement process instead of the artificial instantaneous von Neumann collapse. We test the orientation of the Bloch vector of a two-level system using a third level and resonance fluorescence as the measuring apparatus. Therefore we are able to use a dynamical collapse governed by the three-level master equations. We show that a sequence of orientation measurements designed to monitor a particular trajectory indeed induces a dynamics exactly along this trajectory.
    © 1993 The American Physical Society
    URL: http://link.aps.org/doi/10.1103/PhysRevA.48.70
    DOI: 10.1103/PhysRevA.48.70
    PACS: 06.20.Dk, 42.50.Wm

  15. 15
    Box says:

    Billmaz (9): The idea is that by simply stressing the system with lactose, a quantum entanglement is created which would then lead to a change in the DNA.

    But how does this entanglement with lactose lead to the right change in the DNA? How does it lead to the correct code for a protein?

  16. 16
    billmaz says:

    Box, The way I understand it is that the Inverse Quantum Zeno Effect says that by measuring (or even just having an interaction) a certain path you can cause the quantum system to travel down that path (see above). So the introduction of lactose in a non-lactose metabolizing system constitutes an interaction (which the definition above says it doesn’t have to be a measurement as we know it) that “causes” the quantum system, which is supposedly entangled between the DNA and cytoplasm, to evolve down the needed path (create a mutation that will create a protein which will metabolize lactose). It’s a stretch, I grant you. But some researchers are taking it seriously.

  17. 17
    bornagain77 says:

    billmaz, this is all interesting, save for the fact that I firmly believe that the example you cited is an example that, much like nylonase, and Lenski’s citrate digesting bacteria, will be found to well within the Edge Of Evolution of Dr. Behe as well as well within the UPB of Dr. Demsski ,,, If not, which I highly doubt, you can produce your evidence for functional information being produced above those limits, (1 novel functional protein by purely material processes would suffice in my book), and, to quote what you said earlier, you could “dispense with ID”.

  18. 18
  19. 19
    bornagain77 says:

    billmaz, in the following peer reviewed paper, on page 424, on the table, under listing #6, you will find Hall’s lactose e-coli. It is identified as a modification and a loss of function mutation, it is not listed as a gain of function mutation:

    The first rule of adaptive evolution – Michael Behe
    http://www.lehigh.edu/~inbios/....._paper.pdf

  20. 20
    Box says:

    @Billmazz
    I understand the hypothesis that DNA can be changed by this entanglement. What I do not understand is that this entanglement can explain the creation of the correct DNA code for a protein that can metabolize lactose. This entanglement may explain why DNA evolves down a path – but it does not explain the needed path.

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