DNA as the “littlest origami”

a few related notes to "DNA as the “littlest origami”"

There’s a Mystery Machine That Sculpts the Human Genome -Oct 20, 2015 Excerpt: Consider that the human genome is longer than the average human. It consists of around two meters of DNA, which must somehow fit into cells, whose nuclei are about 200,000 times narrower. So it folds. And it folds in such a way that any given stretch can be easily unfolded, so the genes within it can be read and used. Knots are verboten,,, In the 1970s, biochemists showed that this feat of extreme origami begins when DNA is wrapped around proteins called histones, creating what looks like a string of beads. This reduces the packing problem, but doesn’t come close to solving it. The wrapped DNA must be folded and twisted in ever more complicated (and as yet unknown) ways. Eventually, it forms large loops.,,, “That was a total bombshell,” says student Suhas Rao who worked on the project. He, like many others, had assumed that loops form when two stretches of free-floating DNA randomly find each other and are fastened by a pair of CTCF proteins. But that can’t be right. If it was, the CTCF landing sequences would align in all four possible orientations, rather than the very specific one that Rao saw in his data. The loops must be forming in a completely different way, one that’s deliberate and controlled. ,,, “This is an important milestone in understanding the three dimensional structure of chromosomes, but like most great papers, it raises more questions than it provides answers,” http://www.theatlantic.com/science/archive/2015/10/theres-a-mystery-machine-that-sculpts-the-human-genome/411199/ First 3-D structure of the enzymatic role of DNA - March 2, 2016 Excerpt: DNA does not always adopt the form of the double helix which is associated with the genetic code; it can also form intricate folds and act as an enzyme: a deoxyribozyme. Scientists have solved the first three-dimensional structure of this biomolecule that has proved much more flexible than previously thought. Chemists successfully isolated deoxyribozymes over 20 years ago – a DNA with the ability to act as an enzyme. However, until now they had not been able to associate its catalytic activity with the three-dimensional structure that provides such function to this DNA. DNA does not always adopt the form of the double helix which is associated with the genetic code; it can also form intricate folds and act as an enzyme: a deoxyribozyme. A researcher from Spain and other scientists from the Max Planck Institute for Biophysical Chemistry (Germany) have solved the first three-dimensional structure of this biomolecule that has proved much more flexible than previously thought. Chemists successfully isolated deoxyribozymes over 20 years ago -- a DNA with the ability to act as an enzyme. However, until now they had not been able to associate its catalytic activity with the three-dimensional structure that provides such function to this DNA. Now, European scientists from the Max Planck Institute for Biophysical Chemistry in Göttingen (Germany) have succeeded after having bombarded this molecule with X-rays in the SLS synchrotron in Switzerland. The results, published in the journal 'Nature', have made it possible to build the crystal structure of this 'DNAzyme' using computers. "We have uncovered the first structure of a deoxyribozyme, and for the first time we can see that this DNA is capable of taking on forms as complex as those of protein enzymes or ribozymes ?an RNA capable of catalytic activity," points out the Spanish scientist Almudena Ponce-Salvatierra, a member of the European group responsible for accomplishing this breakthrough. The researchers have broken the paradigm of the supposed stiffness of DNA -a sort of symbol that is popularly associated with the double helix of Watson and Crick-, by demonstrating that this molecule can also adopt complicated three-dimensional structures in addition to being much more flexible than what was previously thought. https://www.sciencedaily.com/releases/2016/03/160302094511.htm 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm 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/releases/2009/12/091215160649.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/releases/2010/03/100311123522.htm

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as to:

“The paper turns the problem around from one in which an expert designs the DNA needed to synthesize the object, to one in which the object itself is the starting point, with the DNA sequences that are needed automatically defined by the algorithm,” says Mark Bathe, associate professor of biological engineering at MIT, and lead researcher for the study.

This is another example of 'top down' Intelligent Design solving a problem instead of 'bottom up' Darwinian processes solving it. George Ellis comments on 'top down' causation here:

Physicist George Ellis on the importance of philosophy and free will - July 27, 2014 Excerpt: And free will?: Horgan: Einstein, in the following quote, seemed to doubt free will: “If the moon, in the act of completing its eternal way around the Earth, were gifted with self-consciousness, it would feel thoroughly convinced that it was traveling its way of its own accord…. So would a Being, endowed with higher insight and more perfect intelligence, watching man and his doings, smile about man’s illusion that he was acting according to his own free will.” Do you believe in free will? Ellis: Yes. Einstein is perpetuating the belief that all causation is bottom up. This simply is not the case, as I can demonstrate with many examples from sociology, neuroscience, physiology, epigenetics, engineering, and physics. Furthermore if Einstein did not have free will in some meaningful sense, then he could not have been responsible for the theory of relativity – it would have been a product of lower level processes but not of an intelligent mind choosing between possible options. I find it very hard to believe this to be the case – indeed it does not seem to make any sense. Physicists should pay attention to Aristotle’s four forms of causation – if they have the free will to decide what they are doing. If they don’t, then why waste time talking to them? They are then not responsible for what they say. https://uncommondesc.wpengine.com/intelligent-design/physicist-george-ellis-on-the-importance-of-philosophy-and-free-will/

and also here

Recognising Top-Down Causation - George Ellis, University of Cape Town 1: The Theme A key assumption underlying most present day physical thought is the idea that causation is bottom up all the way: particle physics underlies nuclear physics, nuclear physics underlies atomic physics, atomic physics underlies chemistry, and so on. Thus all the higher level subjects are at least in principle reducible to particle physics, which is therefore the only fundamental science; as famously claimed by Dirac, chemistry is just an application of quantum physics[1]. However there are many topics that one cannot understand by assuming this one-way flow of causation. The flourishing subject of social neuroscience makes clear how social influences act down on individual brain structure[2]; studies in physiology demonstrate that downward causation is necessary in understanding the heart, where this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes[3]; epigenetic studies demonstrate that biological development is crucially shaped by the environment[4]. What about physics? In this essay I will make the case that top-down causation is also prevalent in physics, even though this is not often recognised as such. This does not occur by violating physical laws; on the contrary, it occurs through the laws of physics, by setting constraints on lower level interactions. Thus my theme is that the foundational assumption that all causation is bottom up is wrong, even in the case of physics[5]. Some writers on this topic prefer to refer to “contextual effects” or “whole-part constraints”. These are perfectly acceptable terms, but I will make the case that the stronger term “top-down causation” is appropriate in many cases. http://fqxi.org/data/essay-contest-files/Ellis_FQXI_Essay_Ellis_2012.pdf

Of related note:

What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: "Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements... take unique meaning from their context.[3]",,, http://www.thenewatlantis.com/publications/what-do-organisms-mean The face of a frog: Time-lapse video reveals never-before-seen bioelectric pattern - July 2011 Excerpt: For the first time, Tufts University biologists have reported that bioelectrical signals are necessary for normal head and facial formation in an organism and have captured that process in a time-lapse video that reveals never-before-seen patterns of visible bioelectrical signals outlining where eyes, nose, mouth, and other features will appear in an embryonic tadpole.,,, "When a frog embryo is just developing, before it gets a face, a pattern for that face lights up on the surface of the embryo,",,, "We believe this is the first time such patterning has been reported for an entire structure, not just for a single organ. I would never have predicted anything like it. It's a jaw dropper.",,, http://www.physorg.com/news/2011-07-frog-time-lapse-video-reveals-never-before-seen.html 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 Getting Over the Code Delusion (Epigenetics) - Talbott - November 2010 Excerpt: The standard doctrine has it that functionally important sequences, precisely because they are important to the organism, will generally be conserved across considerable evolutionary distances. But the emerging point of view holds that architecture can matter as much as sequence. As bioinformatics researcher Elliott Margulies and his team at the National Human Genome Research Institute put it, “the molecular shape of DNA is under selection” — a shape that can be maintained in its decisive aspects despite changes in the underlying sequence. It’s not enough, they write, to analyze “the order of A’s, C’s, G’s, and T’s,” because “DNA is a molecule with a three-dimensional structure.”[14] Elementary as the point may seem, it’s leading to a considerable reallocation of investigative resources. http://www.thenewatlantis.com/publications/getting-over-the-code-delusion Ask an Embryologist: Genomic Mosaicism - Jonathan Wells - February 23, 2015 Excerpt: humans have a "few thousand" different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,, The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It's called genomic mosaicism. In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,, ,,,(then) "genomic equivalence" -- the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA -- became the accepted view. I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common. I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It's the organism controlling the DNA, not the DNA controlling the organism. per ENV Body Plans Are Not Mapped-Out by the DNA - Jonathan Wells - video http://www.youtube.com/watch?v=meR8Hk5q_EM The Insurmountable Problem of “Form/Shape” for Darwinian Explanations – video (2016) https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1138468566166075/?type=2&theater

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