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Scientists Discover How DNA Is Folded Within the Nucleus
mikael writes "Sciencedaily.com is reporting that scientists have discovered how DNA is folded within the nucleus of a cell such that active genes remain accessible without becoming tangled. The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded."
The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded.
Well OBVIOUSLY.
So, life figured out a form of a Hilbert Curve for storing data? Cool!
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Could all the "junk" DNA that we supposedly don't use maybe have some sort of structural stabilization function? It wouldn't actively code for any proteins but the coding structure itself might allow it to make these shapes and/or allow the globule to move without causing knots in the structure.
I used to have this problem, too, until I discovered that little white collar on the wire. When not in use, simply slide it all the way up. This prevents the majority of the knotting. Or, just get a pair that occupy 4 dimensional space -- that way it's impossible for them to get tangled up!
And it makes use of a primary cache. "That's hot."
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I'm confused, here. I'm certainly no biology expert, but I have taken a few courses, one of which the prof seemed to describe exactly how DNA folds. Indeed, it's spelled out in detail on this Wikipedia page on chromatin.
Is this information now obsolete?
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Anyone else wish they could read the actual publication? It's sad considering this is partly taxpayer funded and given the NIH's and Harvard's push toward open access that the authors didn't choose a more accessible journal for such a groundbreaking piece of work.
Actually, fractals generate arbitrarily complex structures with very simple rules (e.g. the Mandelbrot Set - take a complex number, square it, add the original number, repeat.) That's pretty much exactly the kind of structure you'd expect an evolutionary process to come up with. If I may say so myself.
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I would guess that the development of this sort of fractal packing was a watershed moment in the development of eukaryotic life, but the process itself can be logically seen as an extension of existing processes. Most bacteria, which lack a nucleus, arrange their DNA in a simple circle.
This has advantages: the entire genome is always accessible for transcription and replication, there aren't telomeres to deal with, and it requires less maintenance. There are disadvantages: if every gene is accessible to the cytoplasm, you have actively keep the 99% you aren't currently using shut off, which is why bacteria use the operon system, and a big circular strand floating around is liable to tie itself in an awful knot. Bacteria have the equipment to fix small topologically issues in their genome, but overall, bacterial genomes are limited in their potential size. Some more complex bacteria have found a partial solution: they draw folds of their circular genome around proteins, to make a single circle more manageable as a group of pinched off loops. So you can see that there's an intermediate stage between "circle" and "our DNA has Hausdorff dimension 3."
Of course, if you're going to head down the road of DNA folding, you would really benefit from a plan. The beauty of fractals, and a reason they are found so often in the natural world, is that very complex behavior can come from the repeated iteration of very simple rules. Your cells don't need to understand Hilbert curves; all they need is a protein complex that grabs a strand of DNA, then puts a short, specific sequence of folds in it. As that happens along the entire strand, you make a space filling curve that would impress a mathematician.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
It seems to me that Benoit Mandelbrot's discovery of fractal math is at least as important as Buckminster Fuller's obsession with geodesics. If Fuller got "Bucky Balls," I think fractal globules really ought to be called Benoit Balls.
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To which premise do you refer? That it is carried out by the passing of genetic information to offspring, or that it is driven by competitively succesful adaption? I'm not sure of any other premises, and while the first seems undeniable (the 'how') the second is more questionable (the 'why'). I'm a bit hesitant that we even have the first clue why, and are barking up the wrong tree entirely. The sheer marvel and scale of the extrodinarily diverse forms that life takes needs a damn good 'why', 'natural selection' just passes the buck to the invisible hand of mother nature. It's not a petty question as to why evolution happens, indeed most of the answers explored so far have given us great insight into all life on Earth. So without invoking omnipotent beings (which evolution doesn't even speak of anyway) or pointlessly bickering could I politely enquire what premise troubles you?