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New Code Discovered in DNA?
anthemaniac writes "The NY Times is reporting that scientists have found a second code in DNA that goes beyond the genes. The code is superimposed genetic information and 'sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself. The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.'"
Abstract and full text PDF. (currently freely available).
Any sufficiently advanced libertarian utopia is indistinguishable from government.
So did we finally discover the Midichlorians that Qui-Gon was rambling about?
No, we already knew about those. They're called mitochondria, they provide the energy that powers the machinery of our cells, and they're descended from independent microscopic life forms that long ago entered a symbiotic relationship with animals.
In plants, chloroplasts fill a similar role.
Ummm, error control mechanisms are EVERYWHERE in biology and are nothing new. Take a look at:
kinetic proofreading
programmed cell death
nucleotide excision repair
base-excision repair
http://en.wikipedia.org/wiki/DNA_repair
I'm sure a real biologist could point out even more points to note. From an evolutionary point of view, an organism that couldn't control its cell growth or repair damaged DNA strands probably wouldn't last that long!
FTA: "Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern."
Honestly, many of us biologists are kind of giggling at how the NYT (and I guess Slashdot) have been hoodwinked by hot headlines. We have known for decades that histones bind DNA and organize it (into nucleosomes), periodically, all along its length. Now, this group has identified some concensus sequences where the nucleosomes are most likely to form. Turns out, yeah, it's what we thought, with the little twist that precise positioning of nucleosomes could help regulate gene expression (also heavily predicted and fully expected). There are new articles about DNA organization weekly. I think the NYT just picked one and labeled it as a "code beyond genetics", which is absurd, since the organization of DNA is controlled ultimately by DNA sequences. Also, if you want to talk about codes beyond genetics, there is a whole field of study called "epigenetics", which is "the study of reversible heritable changes in gene function that occur without a change in the sequence of nuclear DNA".
In plants, chloroplasts fill a similar role.
No, in plants, mitochondria do the same thing as the do in the cells of all other eukaryotes. Chloroplasts convert the energy in sunlight into stored energy. Two very different functions.
To expand on that a little, mitochondria in animals seem very likely to be bacteria that have been engulfed and now form a symbiotic relationship with the cell, since mitochondria have their own DNA (and a slightly different code for converting DNA -> RNA -> protein) and reproduce themselves independently of the cell's nuclear DNA (hence the discussion of 'maternal DNA' since you only get maternal mitochondria.)
In plants, chloroplasts have similar characteristics, and *also* so do the plant mitochondria.
In other words, bacteria have one source of DNA (or RNA...), animals have two DNA repositories, and plants have three.
Nostalgia's not what it used to be.
When I was in graduate school, one of my thesis advisor's friends at Weizmann (not the cited author, but a colleague) was developping HMMs for nucleosome binding prediction. It worked, though not very well at the time. That was about 10 years ago.
This isn't a "new code" of any sort, but rather a pattern of stacking properties in the binding regions. There are other similar physical phenomenon that are well know, but poorly characterized (that is to say, you know it happens and you've a good idea why, but coming up with a model that is strongly predictive is very tricky).
This "discovery" is not that the signature exists, but that we've finally got the statistical sampling good enough to build a computer model of that signature that can be used to predict/identify the sites. Interesting and good work, but a fundamental shift in our understanding of biology it is not.
This is called the argument from personal incredulity, and is a favourite of the IDers. See http://www.millerandlevine.com/km/evol/design2/art icle.html for an excellent example of how this argument fails spectacularly with the nature-evolved wheel, the eubacterial flagellum.
Call me old fashioned, but I like a dump to be as memorable as it is devastating - Bender