Here’s That New Paper Showing the Genetic Regulation Hiearchy

_{Cornelius Hunter

September 23, 2012

Intelligent Design}

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Ever since Mendelian genetics was incorporated into Darwinism, evolutionists have believed that the gene is king. Genes, they thought, determine an organism’s design or, in technical jargon, the genotype specifies the phenotype. This fit their view that the species originated from the natural selection of biological change which did not arise initially as a consequence of need but rather as a consequence of random, spontaneous events. Those random, spontaneous, events were, for example, mutations in the genes. And later when the genetic code, which translates the information in those genes into proteins, was found to be essentially universal throughout biology, the story seemed complete. For if the species were designed why would their genetic codes be identical? But today, so many problems with this story have emerged it is difficult to keep track. And new research continues to add yet more problems. Read more

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of related interest:
Understanding ENCODE - gene regulation is similar to adding punctuation and spacing to a paragraph of written text - video http://www.youtube.com/watch?v=yjpW30z-SB8
I like the analogy in the preceding video of comparing the genetic text in the DNA to the written text of humans, but I would hold that the regulation of genes they have uncovered by the ENCODE project, thus far, is much better to be compared to as constructing entire paragraphs, whole cloth, complete with punctuation and spelling, from a dictionary of a very basic set of 23,000 'gene words'. That would be much more realistic to what ENCODE has actually found!bornagain77_{September 25, 2012
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I'm sorry for any confusion I may have caused, but I posted the preceding video before watching it, and it appears the video, for whatever reason, is not at all what it was described to be in the video description. In fact the video appears to be a rehash of one of Sanford's talks from a few years earlier on the '4 pillars of atheism'.bornagain77_{September 25, 2012
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of semi-related note, this video was recently uploaded:
Biological Information - the Signature of Life - Dr. John Sanford (inventor of 'the gene gun') - video http://www.youtube.com/watch?v=z9xmns7KeaI video description: Dr John Sanford http://creation.com/john-sanford | There is a growing awareness that information is the unique non-material force which makes life possible. This growing awareness comes as we are discovery the labyrinth of informational networks in even the simplest cells. This cellular network is similar to today's Internet. There is rapidly growing evidence that the principles of information run parallel to the laws of thermodynamics. The first law of thermodynamics essentially says that matter and energy cannot just arise from nothing. This is also true of information - it does not arise spontaneously from matter, it only arise through the operation of intelligence. The second law of thermodynamics essentially says that useful things always degenerate into useless things, apart from intelligent intervention. This is also true of information - apart from intelligent intervention, information always degenerates. All this strongly indicates that the biological information networks within cells and organisms must have been intelligently designed, but should now be decaying. This growing new consensus provides astounding affirmation of the Biblical view of reality - that is a recent and miraculous creation, a fallen and dying world, and a profound need for a Saviour. Dr John Sanford, Ph.D. (University of Wisconsin) Biography Dr John Sanford, A Cornell University Professor for more than 25 years, John has been semi-retired since 1998. His Ph.D. was in plant breeding and plant genetics. While a professor at Cornell, John has trained graduate students and conducted genetic research at the New York State Agricultural Experiment Station in Geneva, NY. During this time, John bred new crop varieties using conventional breeding and then became heavily involved in the newly-emerging field of plant genetic engineering. John has published over 80 scientific publications and has been granted over 30 patents. His most significant scientific contributions involve three inventions, the biolistic ("gene gun") process, pathogen-derived resistance, and genetic immunization. A large fraction of the transgenic crops (in terms of numbers and acreage) grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. John also started two biotech enterprises derived from his research, Biolistics, Inc., and Sanford Scientific, Inc. John still holds a position at Cornell (Courtesy Associate Professor), but has largely retired from Cornell and has started a small non-profit organization, Feed My Sheep Foundation.
bornagain77_{September 25, 2012
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dennis, is this something you recall from one of his books? I have them, but glancing through I don't immediately find anything clearly laid out in terms of 5 requirements for genetic information. We could probably come up with 5, though I don't know if they would match Dr. Johnson's. http://www.scienceintegrity.org/ http://www.scienceintegrity.net/Mung_{September 24, 2012
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dennis clarke, I don't remember anything specifically about 5 criteria, then again it's been a while since I have read any of his work, but this is Dr. Johnson's main site that has all his major work listed where you might find what you need:
Science Integrity http://www.scienceintegrity.org/
Perhaps the information you need is in this lecture video of Dr. Johnson's:
Bioinformatics: The Information in Life - video https://vimeo.com/11314902
I recall that Dr. Don Johnson explains the difference between Shannon Information and Prescriptive Information, as well as explaining 'the cybernetic cut', in this following Podcast:
Programming of Life - Dr. Donald Johnson interviewed by Casey Luskin - audio podcast http://www.idthefuture.com/2010/11/programming_of_life.html
here is a video along the same lines:
Programming of Life - Information - Shannon, Functional & Prescriptive - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/1/h3s1BXfZ-3w
As to broadly classifying sequential information, perhaps this is what you are looking for???
Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, (of note: 4 Null Hypothesis are laid out in the paper) http://www.tbiomed.com/content/2/1/29
Supplemental notes: Here is a very well done video (with animations) that was made using one of Dr. Johnson's books as its basis:
Programming of Life - video http://www.youtube.com/watch?v=00vBqYDBW5s&list=UUBeaK_xN_1SkG1oyPMzF2TQ&index=3
Here is a chapter Dr. Johnson had in David Abel's book 'The First Gene':
What Might Be a Protocell's Minimal Genome - Don Johnson http://www.scienceintegrity.org/FirstGeneCh10.pdf
Here is a interesting paper that Dr. Johnson coauthored with Dr. Abel where they found, from a information point of view, that The ribosome of the cell to operate very similarly to a CPU in a electronic computer:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
Hope you find what you need dennis clarke:bornagain77_{September 24, 2012
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Can someone here list the five (5) criteria that Dr. Don Johnson insists that something must satisfy in order to be validly termed as "information", more specifically, "genetic information"?dennis clarke_{September 24, 2012
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I am absolutely sure that the network of transcription factors in the cell will be shown to be a level of complex integration of extreme functional complexity. This is the true new frontier of biological research. Transcription factors will give us a window onto what has been completely missing in our undertsanding of genomic information: the procedures. Protein coding genes are only the final effectors of cellular functional complexity, and yet they cannot be explained by neo darwinian theory, not even a single one of them. But if and when we understand how different procedures are implemented in the genome and the cell, we will have a completely new level of integrated design. Papers like the one referenced here are the promising start of a new biological era. And guess which theory is going to benefit from all that?gpuccio_{September 24, 2012
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footnote: ,,,Encoded ‘classical information', such as what Dembski and Marks demonstrated the conservation of, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following proof:,,,
Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm
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The second level of information in the overall hierarchy of information in the cell is the 'biophoton' information:
The Real Bioinformatics Revolution - Proteins and Nucleic Acids 'Singing' to One Another? Excerpt: the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see' and ‘hear' each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).,,, More than 1,000 proteins from over 30 functional groups have been analysed. Remarkably, the results showed that proteins with the same biological function share a single frequency peak while there is no significant peak in common for proteins with different functions; furthermore the characteristic peak frequency differs for different biological functions.,,, The same results were obtained when regulatory DNA sequences were analysed. http://www.i-sis.org.uk/TheRealBioinformaticsRevolution.php The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems – May 2012 Excerpt: From the energy spectra, it was determined that the protein molecules could both radiate and absorb bio-photons with wavelengths of less than 3 micrometers and 5–7 micrometers, consistent with the energy level transitions of the excitons.,,, http://jap.aip.org/resource/1/japiau/v111/i9/p093519_s1?isAuthorized=no Are humans really beings of light? Excerpt: Dr. Popp exclaims, "We now know, today, that man is essentially a being of light.",,, "There are about 100,000 chemical reactions happening in every cell each second. The chemical reaction can only happen if the molecule which is reacting is excited by a photon... Once the photon has excited a reaction it returns to the field and is available for more reactions... We are swimming in an ocean of light." http://viewzone2.com/dna.html
The following video gives a 'jaw dropping' look at the biophotonic information in action:
An Electric Face: A Rendering Worth a Thousand Falsifications - Cornelius Hunter PhD. Biophysics - September 2011 Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.” http://darwins-god.blogspot.com/2011/09/electric-face-rendering-worth-thousand.html The (Electric) Face of a Frog - video http://www.youtube.com/watch?v=ndFe5CaDTlI 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/2011/12/not_in_the_gene054071.html
and lastly, The third 'bottom' level of information found in life is the 'classical information' which is encoded onto the material/molecular substrates of the cell (DNA, RNA and proteins). Furthermore, the hierarchical organization of this 'bottom level' of information is anything but simple, with at the very bottom of the organization structure being the linear (one dimensional) sequences of DNA:
Multidimensional Genome – Dr. Robert Carter – video (Notes in video description) http://www.metacafe.com/w/8905048
Of course all this could be further hashed out in far more detail, but for now, I think this basic overview gives a good brief outline as to just how far detached from reality the 'bottom up' model of neo-Darwinism is:bornagain77_{September 24, 2012
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Since the 'bottom up' molecular reductionism model of neo-Darwinism is a complete failure as to explaining body-plan morphogenesis,,,
The Fate of Darwinism: Evolution After the Modern Synthesis - January 2012 Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. http://www.springerlink.com/content/845x02v03g3t7002/
,,, I think it would be helpful to elucidate a basic sketch of the actual 'top down' hierarchy of information being found in life. There are three distinct levels of information in the cells of life. The very top level of information found in life is 'quantum' information: First, ‘spooky action at a distance' (as Einstein called it) quantum entanglement/information, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality (Bohr, Einstein, Bell, Aspect, Zeilinger, etc..), is now being found in molecular biology on a massive scale!
Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ 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 (arxiv.org/abs/1006.4053v1). “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.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/
Quantum Entanglement/Information is confirmed in DNA and proteins by direct observation here;
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. http://www.dailygalaxy.com/my_weblog/2009/04/does-dna-have-t.html 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/releases/2011/03/110331104014.htm 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/quantum-coherence-living-cells-and-protein/
Moreover:
Quantum no-hiding theorem experimentally confirmed for first time - March 2011 Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html
bornagain77_{September 24, 2012
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as to this:
Here’s That New Paper Showing the Genetic Regulation Hierarchy - Cornelius Hunter - September 2012 Excerpt: a massive study of the interactions between transcription factors and DNA. The study found that the action of transcription factors falls into three distinct, hierarchical, categories. There are interactions that specify the basic cell type (muscle, skin, nerve, and so forth). Then there are interactions that specify the cell’s sub-identity (the particular type of muscle cell, for example). And finally there are interactions that specify the cell’s response to the current environmental challenges. http://darwins-god.blogspot.com/2012/09/heres-that-new-paper-showing-genetic.html
Different hierarchies of regulation networks that specify cell type, sub cell types, as well as specifying the specific cell type's response to differing environmental conditions??? As PaV would say, "another day, another extremely bad day for Darwinism!" If all that was not bad enough for Darwinists and their 'bottom up' molecular reductionism model:
New level of genetic diversity in human RNA sequences uncovered Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person's genetic material." http://www.physorg.com/news/2011-05-genetic-diversity-human-rna-sequences.html
OK where is the phenotype (body-plan) information coming from if it is not coming from the genes (genotype)??? also of related note,
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/2012/01/epigenetics_and054731.html Mathematician Alexander Tsiaras on Human Development: "It's a Mystery, It's Magic, It's Divinity" - March 2012 Excerpt: 'The magic of the mechanisms inside each genetic structure saying exactly where that nerve cell should go, the complexity of these, the mathematical models on how these things are indeed done, are beyond human comprehension. Even though I am a mathematician, I look at this with the marvel of how do these instruction sets not make these mistakes as they build what is us. It's a mystery, it's magic, it's divinity.' http://www.evolutionnews.org/2012/03/mathematician_a057741.html
Here are two articles that gives a small glimpse at the extreme organizational complexity, that is thus far completely unaddressed by the genetic reductionism model of neo-Darwinism, that goes into crafting 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. http://ai.stanford.edu/~serafim/CS374_2006/papers/Mattick_NRG2004.pdf To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, ,,,One cell. One division. Half a gig of data. Now figure that millions of bacteria could fit on the head of a pin and that many of them are an order of magnitude more complex than M. genitalium. Or ponder the idea that the human body is made up of 10 trillion (big, complex) human cells, plus about 90 or 100 trillion bacterial cells. That's about 100,000,000,000,000 cells in total. That'd take a lot of computers to model, eh? If it were possible, that is. http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/ "Complexity Brake" Defies Evolution - August 2012 Excerpt: "This is bad news. Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology speeds up by an order of magnitude each year.",,, Even with shortcuts like averaging, "any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system," Koch said. "It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner." He described the concept of the Complexity Brake:,,, "Allen and Greaves recently introduced the metaphor of a "complexity brake" for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.",,, Why can't we use the same principles that describe technological systems? Koch explained that in an airplane or computer, the parts are "purposefully built in such a manner to limit the interactions among the parts to a small number." The limited interactome of human-designed systems avoids the complexity brake. "None of this is true for nervous systems.",,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html
Moreover there another whole level of information on a cell's surface that is scarcely even beginning to be understood:
Glycan Carbohydrate Molecules - A Whole New Level Of Scarcely Understood Information on The Surface of Cells https://docs.google.com/document/d/1bO5txsOPde3BEPjOqcUNjL0mllfEc894LkDY5YFpJCA/edit Psalm 139:15 My frame was not hidden from You, When I was made in secret, And skillfully wrought in the depths of the earth; Multidimensional Genome - Dr. Robert Carter - video (Notes in video description) http://www.metacafe.com/w/8905048
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