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A stunningly elegant solution to storing information


 Chromosomes have yet another level of complexity and are even better designed than previously thought.   Erez Lieberman-Aiden et al 

By probing the three-dimensional architecture of whole genomes, the authors constructed spatial proximity maps of the human genome that confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. They identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. 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.

Imagine a fine hair 2 meters long. Imagine balling it up in such a way that it can fit on the head of pin — and be unraveled and knot-free, at a moment’s notice. A similar engineering feat is at work inside each cell in our body. The genome is over two meters long and must be carefully packed into the confines of a space (called the “nucleus”) several times narrower than a human hair.

First co-author Erez Lieberman-Aiden, says “Scientists have not really understood how the double helix folds to fit into the nucleus of a human cell, which is only about a hundredth of a millimeter in diameter.”

They discovered an unusual compartmental structure to DNA within the nucleus: active genes tend to localize to one area and inactive ones to another. Also the genomic regions appear to flow in and out of these two nuclear compartments as the genes within them are turned on or off.

“Cells cleverly separate the most active genes into their own special neighborhood, to make it easier for proteins and other regulators to reach them,” said Dekker, an associate professor of biochemistry and molecular pharmacology. The finer-scale organization of the genome inside nucleus is achieved by folding into what is known as a “fractal globule,” DNA condenses into an exceedingly dense structure, entirely devoid of knots, that can easily unfold and refold as needed.

“Nature’s devised a stunningly elegant solution to storing information – a super-dense, knot-free structure,” said senior author Eric Lander, who is also professor of biology at MIT, and professor of systems biology at Harvard Medical School. It is well known that DNA elements separated by vast genomic distances can – and do – interact with each other, but it has only recently become possible to map these interactions on a genome-wide scale.

Adapted from a press release written by Steve Bradt, Harvard University

Sorry for all my typos. Another issue with the problem is this: With the atronomically generous asusmption that you could have all the right parts, that would fit to form the flagellum. To co-opt them they would have to be made at the same time, yet "installed" in the correct sequence, with the correct three dimensional orientation relative to each other and the cell membrane. A large protein is 10nm. A small bacteria is maybe 1000 nm. If the cell were a sphere with the diameter of a football field. And a protein were the size of a barrel. What are the odds you would randomly assign 40 barrel sized parts to assemble at the same time and proper order at any localized spot on the surface of that sphere? Good luck! JGuy
This is all relevant enough to remind me of the facets of the bacterial flagellum problem. One angle of the overall origin problem, regarding any attempted Darwinian explanation, is mostly overlooked - though maybe not in principle - and daming to the any attempted gradualistic explanation: So, there are about 40 highly integrated, exactly sized, protein parts that make up the bacterial flagellum. If an attempted Darwinian explanation invokes co-option, it still does not take into account that the prts actually fit. Afterall, three is no reason that the stator should accomodate the shaft which should fit the proton drive motor which should accomodate a sensory feedback & control mechanism (which has it's own issues fo that matter). For exmple, if I gave you most of the parts for a gasoline powered lawnmowever engine, but the provided piston was from a tractro trailer truck, and a piston cylinder was from a model airplane engine... Do you really think you could co-opt the parts? Same for the flagellum, even if you could derive all these parts in the cell, whose to say that they will fit? IF you say they fit all at the same time on the fist try, then you are violating gradulism. If you say they evolve to fit, then you are defying the notion that evolution is not forward looking. Afterall, to think they still happen to evolve and happen [fortuitoutly; by chance] upon a function much greater than the sum of their parts(i.e.locomotion system) is inane & unwittingly(?) begging for hopeful monsters. JGuy
With every new discovery about the internal workings of living things, one impression becomes more and more confirmed: There is no way that these things are entirely the product of natural selection. EvilSnack
Off Topic L White at 4: See: Evolution News mp3s and ARN mp3s DLH
Darwin was from a different culture, one that was still on the way up the hill of science - not one that had become drunken and lazy. I have no doubt he would be absolutely horrified by way in which his theory has been used to abuse the institution. Upright BiPed
William J. Murray @ 9: "One wonders if Darwin himself would be as obstinant as his successors in denying the obvious engineering design of the cell if modern information were presented to him." Good question. Difficult to answer. The last sentence of The Origin of Species leaves open the idea that the original form(s) of life was/were designed. If there was sincerity in that declaration, he might opt for some type of front loaded design, where these incredible features were built in from the start, with the option to diversify as he described. On the other hand, he took the death of one of his children quite hard, and this affected his views regarding God. If someone doesn't want God in the picture, no amount of evidence may seem sufficient to warrant letting that Divine Foot in the door. ericB
Phillip @ 6 Makes sense. But notwithstanding the reasonnig, Darwinist can always come up with some fanciful just-so stories to explain them, or attempt to downplay the findings. Such as, what design, it only appears designed! But for some reason, it warrants explanation... or maybe, music only appears to be enoyable becasue we evovled to enjoy it... and developoing the use of calculus was just an insignificant side effect of knowing how to rub two sticks together for fire under a cave (cave...curve...under the curve...yeah! see!!! oh joy, Darwin would be delighted!)...anyway...and then get them peer reviewed in the process! LOL ... membership benefits. :P JGuy
A far cry from the bags of primordial protoplasm Darwin and his peers envisioned as the building blocks of life. One wonders if Darwin himself would be as obstinant as his successors in denying the obvious engineering design of the cell if modern information were presented to him. My guess would be that such denial can only be purchased with 150 years of accumulated blinding numbness, like frogs slow-cooked to a friendly boil. Darwin would probably have torn his manuscript up if he were faced with what we now know about the cell. William J. Murray
This is really amazing. Somehow, the more we become ourselves technologically advanced, the more we are realising that nature is far more advanced that we are. The designer used a technology so sophisticated that we are still not able to understand it completely. Kyrilluk
Sorry, I meant JGuy@4 PhilipW
JGuy @3 Speaking of fitness traits which translates to survival traits: Why are humans as advanced as they are? Is there a survival advantage to being able to discover and use the calculus? Do we need to be able to write music in order to better survive the ravages of nature and to defend ourselves and find food. We are weak and naked so we need clothing and shelter. A bow and arrow, fire, and the ability to make these things along with a few more abilities I can understand. However, this does not in any way mean that we need advanced mathematics, music, literature (or even a written language) to do very well in the world. Nature has no need of philosophers so far as survival in concerned. PhilipW
This should not come as a surprise to anyone familiar with the fine structure of matter and the continuing search for fundamental particles, etc. The more we are able to observe nature at smaller and more detailed levels the more we discover about the true genius of the designer. This discovery will be eclipsed in the future by the discovery of even smaller and more sophisticated design features, maybe next year, maybe in ten years. We have been looking at the world searching for natures secrets for only a few years and every question that is answered opens a whole host of new and unsuspected questions. We know far less than we would like to believe about the workings and construction of the universe, including biology. This is true on the micro and macro scales as exemplified by the Large Hadron Collider and the Hubble telescope. We know nothing about dark matter and we know little about the most elementary particles. Deeper and deeper we plumb for natures secrets and deeper and deeper we will continue. The real head scratcher is that there are still those who deny ID. Will we ever discover all of natures secrets and finally be able to close up shop? Richard Feynman said he did not know. He refused to attempt an answer as to whether there were an infinite number of layers in the onion of physics or not. In our continuing search for more answers there are some very important points to remember and ponder. They may or may not have application to biology but I suspect they do on some level. Physics and biology are related and entwined disciplines. We do not even know how gravity is propagated or whether it is particles or waves or something completely unknown. The same is true of magnetism as in a permanent magnet. Learning to manipulate something is not at all the same as knowing the source and true nature of it. PhilipW
LOL @ 3 Amazing Design. Natural Selection can carve a design like this yet can’t make a shorter recurrent laryngeal nerve in mammals? Something is amiss in that whole scenario. I've wondered similar questions to myself... like... Old people give birth to young people. And if evolution were good enough to "fine tune" ultra subtle details, like eye lashes, then why aren't we immortal already... That would be the uiltimate fitness trait...call me crazy. JGuy
Sorry to barge in on this conversation, but is there a place where I can get lots of mp3 files of discussion of ID--both pro and con? L White
Sounds almost like a Splay Tree in computer science, where you push frequently accessed nodes on a tree towards one section of the tree, for easy subsequent access. The reasoning is that if you access something once, you're likely to access it again. Amazing Design. Natural Selection can carve a design like this yet can't make a shorter recurrent laryngeal nerve in mammals? Something is amiss in that whole scenario. Atom Atom
Eric Lander is a big name. He was part of the Human Genome Project. tragic mishap
I wonder how this work correlates with the research on the distribtion of genetic material in the nucleus of nerve cells in the retina. I recall that this distribution is inverted from the normal, in order to use the nucleus as a primitive lens. Unless this globular structure can be turned inside out, there is still a lot to be learned here. Nakashima

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