Intelligent Design

Alternate RNA Polymerases

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Over at PhysOrg.com, a new summary discusses a paper on the newly published finding that different protein subunits of RNA polymerases exist side-by-side within the Arabidopsis thaliana’s genes, and that dependent on which protein sub-unit is used, the morphology of the organism changes.

Here’s a quote:

When you remove both proteins, the plants die as embryos; but if they lack just one of the proteins, they still survive, which is evidence that the two alternative forms of the protein are redundant for survival, . . . But despite this, plants missing either 9a or 9b have different physical characteristics, such as leaf shape, suggesting that Pol II built using 9a does not function exactly the same as Pol II assembled using 9b.”

Here is instant “speciation”. Except that gene frequencies haven’t changed in the slightest. It would appear that Nature stores many phenotypic expressions within its genes at all times. I have, for years, been an advocate of the idea of environmental stimulation/activation of different phenotypic expressions. This certainly points us in that direction.

22 Replies to “Alternate RNA Polymerases

  1. 1
    bornagain77 says:

    PaV, this paper, which also came out today on Physorg today, may be of interest to you;

    Protein complex affects cells’ ability to move, respond to external cues
    Excerpt: “Cells sense a wide variety of soluble chemical cues through ‘chemotaxis’ – a process that is the basis behind many drugs that target cell behavior. They also respond to attached cues from the surface that they are crawling upon – a much less well understood process called haptotaxis,”,,,
    “This experiment – which was possible only with the help of many diverse UNC colleagues ranging from genetics to biomedical engineering – finally tells us what lamellipodia and the ARP 2/3 protein complex do: help the cell respond to clues from the extracellular environment. It has long been assumed that the protein was important for chemotaxis, but that is not the case.”
    http://www.physorg.com/news/20.....ility.html

  2. 2
    bornagain77 says:

    As to

    It would appear that Nature stores many phenotypic expressions within its genes at all times.

    , I’m afraid I have to disagree with you a bit on this PaV. I believe that the information for Body Plans (phenotypes) exist almost completely outside of the genes of the DNA:

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

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype (Body Plan).”
    Michael John Denton page 172 of Uncommon Dissent

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2....._answ.html

    Cortical Inheritance: The Crushing Critique Against Genetic Reductionism – Arthur Jones – video
    http://www.metacafe.com/watch/4187488

    The Case Against Molecular Reductionism – Rupert Sheldrake and Bruce Lipton – video
    http://www.metacafe.com/watch/4899469

    Not in the Genes: Embryonic Electric Fields – Jonathan Wells – December 2011
    Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels — which determines the form of the endogenous electric field — constitutes an independent source of information in the developing embryo.
    http://www.evolutionnews.org/2.....54071.html

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer
    “Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Dr. Stephen Meyer comments at the end of the preceding video,,,

    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ – Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Myself, I actually believe that the highest level of information for body plans (phenotypes) is ‘non-local’ quantum information, which exist throughout the entirety of the cell, and which, though it may require molecules to be expressed in the cell, is not reducible to, nor producible by, the molecules of the cell.

    A few comments on ‘non-local’ ‘epigenetic’ information implicated in 3-D spatial organization of Body Plans:
    https://docs.google.com/document/pub?id=1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY

    Verse and Music:

    Psalm 139:13
    For you created my inmost being; you knit me together in my mother’s womb.

    High School Musical 2 – You are the music in me
    http://www.youtube.com/watch?v=IAXaQrh7m1o

  3. 3

    ba77, I’m not sure your observations are inconsistent with PaV’s comment.

    It sounds like the Arabidopsis thaliana’s situation is indeed an example of different phenotypic expression being driven by different expressions of what is essentially the same DNA. This is an interesting specific example that raises the question about pre-programming, environmental response, the very definition of what a “species” is, etc.

    At the same time, I understand what you’re saying about other information outside DNA being critical. One question I’ve been contemplating is whether *all* the information for an organism is in fact contained in its DNA. Specifically, there is a lot of non-DNA information in a living cell, but the living cell was arguably built, at least at some point in the replication process, by instructions from the DNA. Further, although the cellular machinery exists and is necessary in order for DNA to do anything, do we know for sure whether DNA contains all the information to build the cellular machinery?

    I’m not just talking about a timing element here (obviously there is a chicken-and-egg problem if we are talking about origins, which I’m ignoring here). I’m just talking about whether DNA in fact contains all the instructions necessary to build an organism, or if there is information in the structure of the organism itself — how the cell is arranged, for example — that exists completely independently of the DNA and is not reproduced by reference to the DNA?

  4. 4
    bornagain77 says:

    Well Eric, as noted here:

    plants missing either 9a or 9b have different physical characteristics, such as leaf shape,

    thus it is loss of the epigenetic information (outside of DNA) information contained, apparently and solely, within those proteins, that drove the plasticity of the phenotype, clearly it is not the DNA that drove the plasticity of phenotype. But you were wondering here,,

    is information in the structure of the organism itself — how the cell is arranged, for example — that exists completely independently of the DNA and is not reproduced by reference to the DNA?

    Yes! We now have evidence of transcendent ‘non-local’, beyond space and time, quantum information within the cell, outside of the DNA, that is not reducible to any molecules of the cell (DNA, protein, or otherwise, molecules)

    i.e. transcendent quantum information has been confirmed to be in protein structures;

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

    Quantum states in proteins and protein assemblies:
    The essence of life? – STUART HAMEROFF, JACK TUSZYNSKI
    Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign.
    http://www.tony5m17h.net/SHJTQprotein.pdf

    Eric, this quantum information/entanglement found in protein structures (and even in DNA) is simply not reducible to a molecular basis. In fact quantum entanglement was what was used to falsify the reductive material basis of ‘local realism’ in the first place:

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    This following video is very good for showing just how ‘spooky’, to use Einstein’s infamous word, it is to find quantum entanglement on a massive scale within molecular biology:

    Light and Quantum Entanglement Reflect Some Characteristics Of God – video
    http://www.metacafe.com/watch/4102182

    further notes:

    Falsification Of Neo-Darwinism by Quantum Entanglement/Information
    https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US

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

  5. 5
    bornagain77 says:

    Eric, to try to make the preceding a bit easier to understand. The experimental falsification of ‘local realism’, by quantum entanglement, forces one to have to appeal to a ‘non-local’ (transcendent, beyond space and time) cause to explain quantum entanglement. It is simply impossible for the ‘local realism’ (within space and time reality) of material particles to be the cause of non-local quantum entanglement.

  6. 6

    Thanks, ba77:

    I saw that about the proteins. But isn’t the coding for them contained in the DNA? If so, we obviously can’t say they are “outside” of the DNA. Otherwise, we end up with an argument ad absurdum, because all the cellular machinery, once it is built, is “outside” the DNA.

    I’m just wondering how much information, if any, for an organism is not contained in DNA at all.

    —–

    As to the other point, I know you’ve talked a lot on this blog about entanglement. I haven’t spent a lot of time looking into that issue as it applies to biology. If I get a chance I’ll try to check it out.

  7. 7
    bornagain77 says:

    Eric, I also use to have the view that DNA was be all and end all of information in the cell. But I have come to realize that the sequential information in DNA (A,T,C & G’s) is much more limited in its scope of 3-Dimensional influence than I had once thought. For instance, this very ‘un-central dogma’ finding;

    Researchers Uncover New Kink In Gene Control: – Oct. 2009
    Excerpt: a collaborative effort,, has uncovered more than 300 proteins that appear to control genes, a newly discovered function for all of these proteins previously known to play other roles in cells.,,,The team suspects that many more proteins encoded by the human genome might also be moonlighting to control genes,,,
    http://www.sciencedaily.com/re.....125536.htm

    As well, I have seen no evidence that the one dimensional sequence of information in the DNA decides the ultimate 3-Dimensional shape of organisms,

    Response to John Wise – October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    nor evidence of DNA dictating, in a overriding fashion, the 3-Dimensional shape of proteins, since proteins with the exact same sequences can have vastly different shapes and functions in different settings within the cell.

    The Complexity of Gene Expression, Protein Interaction, and Cell Differentiation – Jill Adams, Ph.D. – 2008
    Excerpt: it seems that a single protein can have dozens, if not hundreds, of different interactions,,
    http://www.nature.com/scitable.....tion-34575

    Simplest Microbes More Complex than Thought – Dec. 2009
    Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes.”
    http://www.creationsafaris.com.....#20091229a

    In fact even the 3-Dimensional shape of the DNA molecule itself is found to be governed by ‘non-local’ quantum information/entanglement;

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    The relevance of continuous variable entanglement in DNA – July 2010
    Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix.
    http://arxiv.org/abs/1006.4053v1

    The preceding is confirmed empirically:

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: 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.
    http://www.dailygalaxy.com/my_.....ave-t.html

    Thus Eric, I have to view the DNA as merely a parts list of sorts for the cell, and have come to view the non-local quantum information permeating the cell as the overriding ‘dynamic blueprint’ that governs the overall shape and 3-Dimensional structure of the cell.

  8. 8

    Thanks, ba77. I don’t view DNA as the be all and end all of information. I agree with you that it appears to be more of a database, “a parts list,” as you say, although I think it is more than just a parts list because it is not only the data, but the embodiment of the data in a 3-dimensional storage medium, the structure of which itself appears to be important for function.

    I guess I’m raising a narrower point, namely how much information is in the DNA itself. I don’t think we know the answer, but the things you are pointing to seem to suggest that there is a lot of information not in DNA.

    Think of it this way. If we find some wolly mammoth DNA and insert it into an elephant egg and let it gestate within a female elephant, what will be born? An elephant or a wolly mammoth? How much of the ultimate organism is determined by the DNA as opposed to the structure of the initial egg?

  9. 9
    bornagain77 says:

    Eric you ask:

    If we find some wolly mammoth DNA and insert it into an elephant egg and let it gestate within a female elephant, what will be born?

    Well It certainly will not be a 100% wolly mammoth, although it may recover some of its information that it lost in its sub-speciation to becoming an elephant, it will be some sort of hybrid, but how much?:

    Notes:

    “There is now considerable evidence that genes alone do not control development. For example when an egg’s genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.”
    The Design of Life – William Dembski, Jonathan Wells Pg. 50
    http://books.google.com/books?.....38;f=false

    And even Venter’s work of implanting a ‘synthetic genome’ into a bacteria was far more modest than the sensational headlines touting that Venter had ‘created life’. Here are some more ‘restrained’ articles on what Venter’s work actually accomplished:

    Partially synthetic cell created – Washington Post / May 21, 2010
    Excerpt: Venter and his 24-member team used off-the-shelf chemicals and the known DNA sequence of Mycoplasma mycoides’s genes to manufacture a copy of the bacterium’s genome. They then transplanted the genome into a different (but closely related) bacterial species. The donor genome reprogrammed the recipient cell, which then replicated and divided. The result was new colonies of Mycoplasma mycoides, which Venter terms “synthetic cells.’’
    Other scientists, however, characterize the experiment in less revolutionary terms. They note that only the genome was synthetic.
    http://www.boston.com/news/sci.....l_created/

    Is Craig Venter’s Synthetic Cell Really Life? – July 2010
    Excerpt: David Baltimore was closer to the truth when he told the New York Times that the researchers had not created life so much as mimicked it. It might be still more accurate to say that the researchers mimicked one part and borrowed the rest.
    http://www.uncommondescent.com.....ally-life/

    Stephen Meyer Discusses Craig Venter’s “Synthetic Life” on CBN – video
    http://www.evolutionnews.org/2.....35991.html

    Another fact that argues against a DNA centric view of organisms is this:

    150 human animal hybrids grown in UK labs: Embryos have been produced secretively for the past three years – July 2011
    Excerpt: ‘At every stage the justification from scientists has been: if only you allow us to do this, we will find cures for every illness known to mankind. This is emotional blackmail.
    ‘Of the 80 treatments and cures which have come about from stem cells, all have come from adult stem cells – not embryonic ones.
    ‘On moral and ethical grounds this fails; and on scientific and medical ones too.’
    http://www.dailymail.co.uk/sci.....years.html

    Of related note, the man who first cloned a animal (Dolly) recently surprised people with this:

    Dolly Scientist Says Abandon Embryonic Stem Cell Research – December 2011
    Excerpt: Ian Wilmut, the scientist who achieved international notoriety for cloning the sheep Dolly, is now urging his fellow scientists and researchers to abandon embryonic stem cell research.
    His comments at a conference follow on the major news that Geron, a cloning company the Obama administration funded to undertake the first human clinical trials involving embryonic-like stem cells, abruptly canceled the trials and got out of the embryonic stem cell research business.
    http://www.lifenews.com/2011/1.....-research/

    Further notes

    DNA: The Alphabet of Life – David Klinghoffer
    Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell’s building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn’t there. Instead, “It is as if the ‘idea’ of the fly (or any other organism) must somehow permeate the genome that gives rise to it.”
    http://www.evolutionnews.org/2....._life.html

    In the case of DNA, the package can be as important as its contents: study
    modENCODE (the Model Organism ENCylopedia of DNA Elements)
    Excerpt: Instead of spewing out long strings of the As, Ts, Gs and Cs like the gene sequencing labs, the epigenetic labs are disgorging voluminous data about the proteins bound to the DNA and the many other gizmos and widgets that make up the machinery of gene expression.
    These widgets are collectively called the epigenome, because they provide a level of control in addition to, or beyond, the level provided by the genome. Whereas the genome is the same in every cell of an organism, the epigenome of every cell type is different. It is because of the epigenome that a liver cell is not a brain cell is not a bone cell.
    http://www.physorg.com/news/20.....tents.html

    Of related note: Here is a article that gives a small glimpse at the extreme organizational complexity that would go into precisely ‘orchestrating’ all the cells into one human body:

    How many different cells are there in complex organisms?
    Excerpt: The nematode worm Caenorhabditis elegans, the cellular ontogeny of which has been precisely mapped, has 1,179 and 1,090 distinct somatic cells (including those that undergo programmed cell death) in the male and female, respectively, each with a defined history and fate. Therefore, if we take the developmental trajectories and cell position into account, C. elegans has 10^3 different cell identities, even if many of these cells are functionally similar. By this reasoning, although the number of different cell types in mammals is often considered to lie in the order of hundreds, it is actually in the order of 10^12 if their positional identity and specific ontogeny are considered. Humans have an estimated 10^14 cells, mostly positioned in precise ways and with precise organization, shape and function, in skeletal architecture, musculature and organ type, many of which (such as the nose) show inherited idiosyncrasies. Even if the actual number of cells with distinct identities is discounted by a factor of 100 (on the basis that 99% of the cells are simply clonal expansions of a particular cell type in a particular location or under particular conditions (for example, fat, muscle or immune cells)), there are still 10^12 positionally different cell types.

    This following video gives a glimpse of this ‘higher level positional’ information in action (please note the seemingly ‘miraculous’ formation of blood vessels):

    Fearfully and Wonderfully Made – Glimpses At Human Development In The Womb – video
    http://www.metacafe.com/watch/4249713

  10. 10
    Starbuck says:

    Polymerases II, IV and V each have 12 subunits and those subunits seem to contribute to the functions of these enzymes. Numerous other proteins interact with the polymerases to recruit the polymerases to specific subsets of the thousands of genes present within the genome, or to regulate their activity after their recruitment to the genes. By using alternative subunits, I think that the polymerases interact with different protein partners, or have slightly different RNA synthetic capabilities, and this broadens their potential functions. It is very clear that different combinations of transcription factors are required to turn on specific genes at different times and in different cells via their recruitment or activation of RNA polymerases. The new data suggest that alterations in the composition of the polymerase itself add to this regulatory complexity.

  11. 11

    ba77:

    Thanks.

    I like this: “Whereas the genome is the same in every cell of an organism, the epigenome of every cell type is different. It is because of the epigenome that a liver cell is not a brain cell is not a bone cell.”

    I’ve also thought a lot about what would be required to build the organism as a whole — cell types and positionally — as in your second-to-last quote. If there are even a fraction of the cell identities they are talking about, that is astounding.

    Thanks for sharing.

  12. 12
    PaV says:

    BA77:

    I’m afraid I have to disagree with you a bit on this PaV. I believe that the information for Body Plans (phenotypes) exist almost completely outside of the genes of the DNA

    The kinds of variation we’re dealing with in this experiment is not at the level of a Bauplan. Rather, it involves a portion of a protein having two forms of expressing itself. This should remind us of Mendelian genetics. And, in fact, the kind of change they observe is that of a change in leaf shape, which, again, should remind us of the kind of experiments that Mendel undertook.

    In agreement with you, I see “genes” as simply being basic ‘building blocks’ for the cell. And, as to Bauplans=Body Plans, I’m in full agreement with you that this is the provenance of gene regulatory networks and epigentic mechanisms and phenomena of all types.

    It strikes me as being significant that you have a mechanism that provides two forms to a particular trait much like Mendelian ‘alleles’, and yet does not involve the ‘replacement’ of one ‘allele’ by another. So, while affirming basic Mendelian genetics, it at the same time undermines conventional population genetics thinking, wherein “frequencies” are changed. What this set of experiments suggests is that the “frequencies” remain relatively constant, and that other, epigenetic effects, are the cause of the differing forms on phenotypic expression.

    And, as I point out, this rather conforms to my notions that it is the environment that is causitive, likely through its triggering of some sort of epigenetic effect.

  13. 13

    PaV, looks like this article is similar to what you are saying?

    http://www.uncommondescent.com.....ken-types/

  14. 14
    bornagain77 says:

    Eric and perhaps PaV: this recent paper may interest you:

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

    here is a analysis of the preceding paper:

    Testing quantum entanglement in protein
    Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement. ,,,In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules.
    http://www.quantum-mind.co.uk/.....-c288.html

  15. 15
    PaV says:

    BA77:

    I didn’t realize that the “previous orthodoxy . . . held that quantum effects could not exist in biological systems . . .”.

    To me, the only thing that makes sense in this regard is biological systems operating via quantum effects. What in the world do they think chemical bonding is?

    So, I think they didn’t present this precisely enough. They should have said something like: “Exotic elements of quantum theory were held . . . ‘not to exist in biological systems because of the amount of noise in these systems.'”

    What the Darwinists don’t understand, or don’t want to understand, is that each, and every, day brings dramatic new evidence of the utter complexity of the living cell. Each new element of complexity that is added has to somehow be explained without the presence of NS to ‘jimmy’ the equation. It gets worse and worse for them each day. ID exists, not directly because of Creationist thought, but because of the advances that molecular biology provides on a daily basis.

  16. 16
    bornagain77 says:

    PaV, the biggie of quantum phenomena to establish in biological systems is entanglement. For it is by quantum entanglement that quantum information channels are established. And it is through quantum information channels that quantum computation becomes very feasible to look for in molecular biology. I agree they should have been more precise so as to differentiate these aspects of quantum actions in molecular biology, but as you have alluded to, this finding ‘brings dramatic new evidence of the utter complexity of the living cell.’ Complexity that I am sure we have only seen the tip of the iceberg of yet, if even that much!

  17. 17
    PaV says:

    BA77:

    As to the article you’ve linked, here,IMO, is the pertinent summation:

    This can be explained since the spin gas environment also contains a built-in reset mechanism via spin flip: For the molecular con guration in which the two spins are spatially separated, the environment eff ectively lowers the system’s entropy and increases the ground state population. Thus, under these conditions and in accordance with what has been observed for thermal baths, dynamic entanglement is generated in the long time limit.

    I think what they’re saying here is that if you have two spin states, up and down, spread out over an intermediate “spin-gas lattice” of atoms, they can hold each other in balance, and increase the overall ‘orderliness’ (lowered entropy) of the system, and, simultaneously, spread out this ‘ordering’ over an increased population of other “spin-gas” atoms. So, in effect, the ‘energy’ of this spin ‘differential’ (the energy difference between these two quantum states) can actually be used to stabilize the system, and, hence, “dynamic entanglement is generated in the long time limit.” (i.e., it’s relatively stable.)

    So, superposition can actually be maintained via intermediate particles—which normally are thought of as producing “noise” (decoherence).

    Anyway, that’s my take. And this would mean that in biological systems, with huge polymers, such effects could be maintained. That’s my gist. [But it would be nice if some PhD in physics confirmed this view.]

    The “spin-gas lattice” model, I believe, is what scientists use to study possible quantum-computing scenarios. So, once again, we have information theory revealing so much more about the cell’s complexity!

  18. 18
    PaV says:

    I should have added this quote to the above in #17:

    The present model serves two purposes: On one hand, it provides a concrete route where to search for signatures of entanglement in biomolecular systems operating at room temperature. On the other hand, it indicates new directions to design molecular scale machines able to generate non-trivial quantum states even in noisy environments.

  19. 19
    bornagain77 says:

    a few notes as to quantum computation:

    Quantum Entanglement and Information
    Excerpt: 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.
    http://plato.stanford.edu/entries/qt-entangle/

    And quantum entanglement (information channels) have now been established running throughout entirety of the length of DNA;

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    And with quantum information channels now established in DNA, here is what I firmly believe is a clear example of ‘quantum computation’ in the cell involving the DNA:

    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

    Can Quantum Mechanics Play a Role in DNA Damage Detection? (Short answer; YES!) – video – as well at about 27 Minute mark in the video – Fröhlich Condensation and Quantum Consciousness
    http://www.scivee.tv/node/25476

    Of note: DNA repair machines ‘Fixing every pothole in America before the next rush hour’ is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. ‘Traveling salesman problems’ are notorious for keeping supercomputers busy for days.

    NP-hard problem
    http://en.wikipedia.org/wiki/NP-hard

    Since it is fairly obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion by crunching bits, and generating copious amounts of heat, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA;

    And to put all this in proper perspective, it is good to note just how trivial our advances into the field of quantum computation has been thus far, despite huge investment and despite the fact it would dwarf some of the computational capabilities of modern ‘classical’ computers:

    Scientists take another step towards quantum computing using flawed diamonds – March 2011
    Excerpt: Scientists have for years been intrigued by the idea of a quantum computer,,, Such a machine would dwarf the capabilities of modern computers,
    http://www.physorg.com/news/20.....monds.html

    IBM Research Announces New Advances in Quantum Computing – February 2012 – video
    http://www.youtube.com/watch?v=_NRmOe1b8_s

    Quantum Computing Promises New Insights, Not Just Supermachines – Scott Aaronson – NY Times – December 2011
    Excerpt: Unfortunately, while small quantum computations have already been demonstrated in the lab, they typically fall apart after only a few dozen operations. That’s why one of the most-celebrated quantum computations to date has been to factor 15 into 3 times 5 — with high statistical confidence! (With a lab full of equipment). The problem is decoherence: basically, stray interactions that intrude prematurely on the computer’s fragile quantum state, “collapsing” it like a soufflé. In theory, it ought to be possible to reduce decoherence to a level where error-correction techniques could render its remaining effects insignificant. But experimentalists seem nowhere near that critical level yet. (Of note: Now they have factored 143 into 13 times 11)

    Quantum life: The weirdness inside us – 03 October 2011 by Michael Brooks
    Excerpt: “It sounds harsh but we haven’t learned a thing apart from the obvious.” A better understanding of what is going on might also help us on the way to building a quantum computer that exploits coherent states to do myriad calculations at once. Efforts to do so have so far been stymied by our inability to maintain the required coherence for long – even at temperatures close to absolute zero and in isolated experimental set-ups where disturbances from the outside world are minimised.
    http://www.newscientist.com/ar.....?full=true

    Verse and Music:

    Isaiah 40:13
    Who is able to advise the Spirit of the LORD? Who knows enough to give him advice or teach him?

    Learning To Be The Light – Newworldson – video
    http://www.youtube.com/watch?v=pqs24i1RBQo

  20. 20
    PaV says:

    BA77:

    Since it is fairly obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely ‘material’ fashion by crunching bits, and generating copious amounts of heat, then it is readily apparent that this monster ‘traveling salesman problem’, for DNA repair, is somehow being computed by ‘non-local’ quantum computation within the cell and/or within DNA;

    We’re on the same page here. I couldn’t agree with you more. Everything interacts at the atomic/molecular level via quantum mechanical effects—pure chemical bonding. However, just as epigenetics represents a control level above that of strict genetics, so, too, it seems to me, does the cell participate in quantum computing, communicating and interacting via this physical phenomena. So—let us predict here—as more and more is learned in the build-up to quantum computing, more and more parallels to cellular activities will be discovered.

    And, of course . . . . . . this will all be attributed to the wonders of natural selection!!!

  21. 21

    ba77:

    Thanks for the link to the article summary: “Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010”. I don’t think the particular study has anything to do with quantum effects (the quantum dots were just used to track the proteins) in DNA.

    Thanks for the link, however, I hadn’t seen that before and have to say it is absolutely astounding. The more we learn the more I am convinced we are just barely scratching the surface. The existence of DNA and its functional information is incredible enough. The ability to detect and repair is a whole additional layer of astounding capability.

    Great stuff!

  22. 22
    bornagain77 says:

    Eric, Well that’s the second time someone has pointed out that the quantum dots are not proof of quantum action in DNA. 🙂 Well, I know that and never said that the quantum dots proved that particular point. The fact I maintain is that it is the repairing of the DNA itself (every pothole in America in 20 minutes) without recourse to classical computation in the cell, that warrants the inference to quantum computation in the cell to solve the dilemma as to how the cell could possibly efficiently coordinates such a monster repair process. Despite the way Darwinists practice science, there actually must be a coherent process to explain how this repair can happen so quickly!

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