New Code Discovered in DNA? 285
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.'"
So wait (Score:5, Funny)
So my body has built in DRM?!
Re:So wait (Score:4, Funny)
Tom
Re:So wait (Score:2)
Re: (Score:3, Funny)
Re:So wait (Score:2)
Re:So wait (Score:2, Funny)
Yes, and (Score:3, Funny)
Re:Yes, and (Score:5, Funny)
Precisely. (Score:2)
Re:Precisely. (Score:3, Funny)
Re:Precisely. (Score:5, Funny)
Re:So wait (Score:3, Funny)
Re:So wait (Score:5, Funny)
Re:So wait (Score:2)
God: "Pete, put a temporary override on the lawyer auto-filter. Apparently, I'm gonna need a few."
Re:So wait (Score:4, Funny)
I think you mean to say, "Where the hell is God going to find a lawyer?"
Re:So wait (Score:2)
Re:So wait (Score:2)
Unfortunately, if there IS a god out there (the kind that certain people prefer to kill in the name of) he/she/it doesn't seem too interested in keeping certain secrets extremely well-protected. Almost as if allowing humans to go ahead and violate certain aspects of nature, life, mortality...
Some god...
Maybe "god" needs an upgrade or two?
Re:So wait (Score:2)
It's worse than that! (Score:2)
Re:It's worse than that! (Score:2)
Re:So wait (Score:2)
Well, yeah - You don't want just any ol' genetic fragment (such as a virus) coming along and modifying your code... You only want properly authorized DNA from a compatible player to merge with your own. And don't even think about trying any region unlock codes - We all know that leads to nothing but the big "C".
Now, if they find that our DNA has a copyright notice, I'll get a tad worried. But DRM can count as beneficial, just not the kind controlled by an evil megacorp.
Re:So wait (Score:3, Interesting)
No, no, you got it all wrong. Your body is built using the Object Oriented paradigm, by the use of encapsulation/information hiding [wikipedia.org].
Re:So wait (Score:2)
You'd darned well had better hope so.
Re:So wait (Score:4, Funny)
Re:So wait (Score:3, Funny)
Re:So wait (Score:3, Funny)
DNA DRM? (Score:3, Funny)
Does this mean that DNA has DRM?
Midichlorians? (Score:3, Interesting)
Re:Midichlorians? (Score:4, Informative)
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.
Re:Midichlorians? (Score:2, Informative)
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.
Re:Midichlorians? (Score:2)
Re:Midichlorians? (Score:3, Informative)
In plants, chloroplasts have similar characteristics, and *also* so do the plant mitochondr
Re:Midichlorians? (Score:2)
I've heard this before, and it "makes sense"... But just to confirm: Do sperm cells not have mitochondria? Or do their mitochondria not make it into the fetus?
Re:Midichlorians? (Score:3, Interesting)
http://en.wikipedia.org/wiki/Sperm [wikipedia.org]
Re:Midichlorians? (Score:2)
Re:Midichlorians? (Score:2)
Re:Midichlorians? (Score:2)
Genes, introns and nucleosomes (Score:5, Funny)
Re:Genes, introns and nucleosomes (Score:2)
An important reminder (Score:4, Insightful)
Some of this isn't terribly new (Score:4, Interesting)
It turns out there's some vastly complex actions around how genes are actually expressed. Methylization semi-permanently deactivates DNA. Other things control the unfolding of DNA so that they're accessible to be exposed. Much of the "junk dna" is probably not junk, but rather controls gene expression to some degree.
The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cells. This is also a great context to talk about evolution - no sane intelligent designer would make a cell this way. If you think about small changes over billions of years, though, you can see how the warping and twisting of DNA could produce interesting results that are passed down from generation to generation.
Science is rarely boring.
Re:Some of this isn't terribly new (Score:2)
Of course, it could also be that the Designer's intelligence is so far beyond your own as to be beyond your comprehension. Things which humans cannot comprehend are often labeled as illogical. Until we learn to understand them, at which point they become perfectly logical.
Not that I am neccisarily arguing for intelligent design, it's just that our universe is infinitely complex. Deeming something "insanely designed" only points out your limited kno
Re:Some of this isn't terribly new (Score:2)
Ummmm... (Score:2)
DNA is transcribed into mRNA which is then translated by ribosomes in the cytoplasm. DNA is not "turned into" proteins.
Methylization semi-permanently deactivates DNA
Methylation is just one aspect of chromatin structure. It's not semi-permanent, it's dynamic.
The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cell
Re:Some of this isn't terribly new (Score:3, Interesting)
No one designed the way DNA and genetics work to produce a given biologic result. Evolution naturally selected for certain results without concern for the implementation. In short, DNA/genetics is the ultimate "slop code". It has no clean architecture or consistent rules. Making matters even worse, the code not only defines structures, but it defines how to interpret itself, such that you
Re:An important reminder (Score:2)
And, as I see it, a reminder that we should stop playing with DNA and setting the resulting stuff free as long as we have no fucking clue.
Proff of intellijent design!!!11 (Score:4, Funny)
Re:Proff of intellijent design!!!11 (Score:2)
you are probably correct (Score:2)
The creator(s) are one of:
1) more complicated than us. So they even more likely created by another being than us. by the "intricate things have a creator" theory.
2) more complicated than us as a whole. The creator society as a whole created us.(**)
2) less complicated than us. Our creators used there intelligence, and directed evolution to create us. (***)
3) we are not allowed to think about this according to our religion, sorry.
(**) Similar to how a s
Re:Proff of intellijent design!!!11 (Score:3, Funny)
Come to think of it, a lot of the crappiest programmers I know think they're God -- er, intelligent designers. Anselm would be proud.
Bemopolis
Re:Random error produces error control mechanism? (Score:5, Insightful)
Re:Random error produces error control mechanism? (Score:5, Interesting)
Here is some information [wikipedia.org] about reverse transcriptase error rates. In contrast, here is some [jbc.org] for one of the DNApolymerases. As I recall, in eukaryotes there are three DNA polymerases, and only DNApolyIII has bidirectional proofreading ability (I may be wrong) so only it can scan finished DNA, but all three can scan DNA while it's being built. In contrast, I don't believe there are any enzymes that can scan finished RNA (since it's not, to my knowledge, found double-stranded in anything we've found, and you'd have no way of determining that there was an error) so the best you can hope for is really good DNA->RNA fidelity, and as I said earlier, there's not much evolutionary pressure FOR that in the rest of nature, while there's some evolutionary pressure AGAINST it (because it's expensive) so if it were to exist, it would only exist in things that would benefit from it, those being small RNA viruses that are much less likely to have either the history, the machinery, or the overhead to afford proofreading replication enzymes. Besides which, if their gain (number of viruses produced for each cell infected) is high enough, they A: don't care about individual viral particle loss from bad fidelity, and B: actually benefit from high mutation rate because of its help in evading host response.
whew. that was wordy. sorry.
Too randomly (Score:2)
As in cases of cancer, mutation, and other such things. We want our bodies to adapt, but not necessarily mutate (and I don't mean in the X-men way)
Re:Random error produces error control mechanism? (Score:2)
Re:Random error produces error control mechanism? (Score:2)
Re:Random error produces error control mechanism? (Score:2)
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
You mean like white blood cells?
Re:Random error produces error control mechanism? (Score:5, Insightful)
No, error correction would counter the mutation process. Given that, generally, more mutations are harmful than beneficial, error-correcting genetics would be a short-term benefit in reducing genetic disorders. The downside would come if another species with a higher mutation rate evolves into a more successful form and crowds out the now-obsolete organism with rigid genetics. The overall winners would likely be organisms within some range of error-correction--neither a total free-for-all, nor a very rigid genome. This seems pretty well reflected in real life, unsurprisingly.
Yes, this discovery does not hurt the ID movement at all.
This is also true; no scientific discovery will hurt the ID movement, since it has precisely nothing to do with science...
Re:How the hell does *that* follow? (Score:2)
Now, each generation needs to have some variability. After all, if everyone is identical, then there will be no adaptability. But, they need t
Re:How the hell does *that* follow? (Score:3, Insightful)
Consider the very first round of evolution, the original species over used the enviroment to such an extent that they produced a mass extinction event, terra formed the planet and rendered it suitable for previously disfunctio
software problem (Score:5, Funny)
So apparenlty we are a software problem.
C'mon baby... (Score:5, Funny)
Re:C'mon baby... (Score:5, Funny)
Just don't expect you to maintain it.
Re:software problem (Score:2)
Me, I'm just another steam engine [chronicle.com] trying to contain the pressure.
Evolution proves totally brilliant once again (Score:5, Insightful)
It's not like nucleosomes are anything new though, the real discovery here is that the scientists found a pattern to their binding.
Sadly the times article is filled with a lot of fluff. This isn't really a "second code" nor do I see why it's "hidden".
Evolution, Schmevolution, let's just talk science (Score:3, Insightful)
It's a bit like the way you can embed... (Score:3, Insightful)
Original article (Score:5, Informative)
And in further news, the histones... (Score:3, Funny)
Metadata (Score:5, Insightful)
First DNA virus hackers? (Score:3, Interesting)
Re:First DNA virus hackers? (Score:4, Insightful)
New Code Discovered in DNA (Score:5, Funny)
b-e-s-u-r-e-t-o-d-r-i-n-k-y-o-u-r-o-v-a-l-t-i-n-e
Re:New Code Discovered in DNA (Score:2)
Re:New Code Discovered in DNA (Score:2)
Old "News" (Score:2)
Re:Old "News" (Score:4, Informative)
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.
Even better idea... (Score:2)
"The discovery, if confirmed, could open new insights into the higher order control of the genes."
Perhaps this may provide additional information as to the usefullness of the supposed "junk DNA [wikipedia.org]" that fills the human g-nome.
answer from my PhD thesis... (Score:2)
Nobel (Score:2)
Mmmm, a histone of peas... Seriously, let me be the first to say: I smell a Nobel prize for this one.
Re:Nobel (Score:2)
That was my first thought after reading the article!
But, at the speed at which Nobel winners are chosen probably 10-20 years will pass before they are so honored. Assuming, of course, that the research is proven correct.
Duh!! (Score:3, Funny)
Everybody knows there's a hidden code in our DNA... Leonardo DaVinci put it there!
Just beginning to understand (Score:2)
For large values of second (Score:3, Interesting)
This is way down on the list of discoveries of patterns in DNA, and it's really more a storage medium property than a code. This is more like sector markings on a hard drive platter than anything to do with data or filesystems. It's important, but because it will tell us where DNA is likely to get damaged, but these sequences are not functional components of the actual use of DNA.
God-in-the-Gaps (Score:5, Insightful)
Argument from Personal Incredulity (Score:3, Informative)
A new "twist" in an OLD OLD story... (Score:5, Informative)
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" [wikipedia.org], which is "the study of reversible heritable changes in gene function that occur without a change in the sequence of nuclear DNA".
junk press, junk science (Score:4, Interesting)
The existence of nucleosomes is well known. It is not a secondary dna, simply a packing/folding mechanism for DNA, and it may have a role in regulating gene expression.
http://en.wikipedia.org/wiki/Nucleosome [wikipedia.org]
The paper itself is as bad as the press reporting it. Slashdot is hardly the avenue to discuss the fine points of a research, but here is something to chew on: note how the authors claim that they predict 54% of nuclesomes ... yet a little later note how by random chance this so called "prediction" would yield a 39% accuracy anyhow. I guess that 54% accuracy is a whole lot less impressive.
Behind the mumbo-jumbo, p-values, Komolgorov-Smirnoff tests, Boltman partition functions, etc all they do it match a set of 146 bp (start,end) intervals to another one. They are very-very skilled at hiding the simplicity of what they do behind a whole lot of fancy plots and words.
Nature should be ashamed of themselves ... the literature on this subject goes back many decades, besides doing more experimental work none of this is new, novel or even interesting. I also expect a significant backslash from people that are far more knowledgeble than I am in the matter.
New code found (Score:4, Funny)
#!/usr/bin/perl -ane
One scientist looked at the other, and said "This explains everything!"
Re:New code found (Score:2)
Hmmm... (Score:2)
Organic Software (Score:3, Interesting)
[OT] I must be new here (Score:3, Insightful)
What scares me are all the articles about topics that I'm not an expert in, where I can't judge the veracity of comments. I've realized that if you guys are so terribly wrong here, that you're probably not believeable anywhere else, either.
Not that this news to anyone. It just depresses me everytime I see this type of story come up.
*sigh*
Re:New Discovery (Score:4, Insightful)
The headline however, is unnecessarily sensationalist..
Re:New Discovery (Score:2)
I can't be bothered to read Nature and Science these days. The damn articles are so long and hard to read. I mean, have you any idea at all how busy I am? How am I supposed to do any science if I spend all my days reading papers.
Phil
Re:Intelligent Discovery. (Score:3, Insightful)
What time is it?
(Did you meant figure out how to do it, or figure out how it does it?)
I'm anticipating the time when we realize that life and evolution is an example of Reflections on Trusting Trust [acm.org] and thus that the origin of some aspects of DNA and life may be unknowable, and yet explicable, and thus not be of divine origin.
Re:Intelligent Discovery. (Score:2)
Yes, we can explain exactly why it appears there using elementary physics and predict exactly where it will appear at any given time of day based on the position of the sun in the sky.
But that doesn't diminish its divine origin.
The problem with this silly statement is that it would mean that there were no rainbows before the flood, and that the laws of physics were changed to enable rainbows to appear.
Re:Intelligent Discovery. (Score:2)
Yeah, right - were a quarter million people killed [wikipedia.org] by their own imaginations? There are floods even with the fricking rainbows. Read a newer book.
Epigenetics (Score:2)
Re:Don't worry (Score:2)
Re:DNA code read backwards ! (Score:2, Funny)