Slashdot Mirror
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.'"
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 my body has built in DRM?!
Monstar L
Does this mean that DNA has DRM?
So did we finally discover the Midichlorians that Qui-Gon was rambling about?
He who knows best knows how little he knows. - Thomas Jefferson
Personally, I think it's God's version of Sudoku.
Intron: the portion of DNA which expresses nothing useful.
I think this kind of thing is an important reminder to all humans how much we really have to learn about this crazy but wonderful world we live in.
Only Go^H^Han intelligent designer could have implemented DNA with private and protected data. This sort of thing just can't randomly 'evolve'.
Any software problem can be solved by adding another layer of indirection.
So apparenlty we are a software problem.
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".
Is that why we have to crash once a day, and it takes 6-8 hours to reboot?
Self proclaimed wannabe geek. You know how it is. Most of us who read this stuff probably fit in that category.
Abstract and full text PDF. (currently freely available).
Any sufficiently advanced libertarian utopia is indistinguishable from government.
Pardon? Your statement is nothing but a bald assertion. Error control mechanisms run in no way against the evolutionary grain. It's easy to imagine that an organism with a little error correction will be more fit in its niches than an organism without. Changing too rapidly, or too randomly, is as dangerous to an organism as not adapting fast enough.
I find it interesting that god/evolution/the great green arkleseizure/FSM/whatever invented metadata LONG before we did. Not surprising, just interesting.
"If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
I have a lot of good code, ready for re-use!
This issue is a bit more complicated than you think.
Think of cancer as a fandango on core followed by a DOS/fork bomb.
I'm not entirely sure this is a problem. We have a heirachy of media that cascades, simplifying down at each stage. In this case we normally have something like Nature article (for the practicing biologist) -> Nature News and Views (for the lazy people who read Nature but can't be arsed to read the article) -> New Scientist article/comment (for the interested layman) -> traditional news media (the proletariat). At each stage something is lost. I don't expect the public to care about a prediction method for the sequences involved in higher ordering of chromatin structure, but the fact they might find out that DNA does more than just 'make genes' I think is a relevant point.
The headline however, is unnecessarily sensationalist..
I don't read your sig, why do you read mine?
New Code Discovered in DNA
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
Over ten years ago, the hot new field in biology was "gene expression". We already knew about DNA, but there was a lot of "junk DNA" that seemed weird, as well as lots of questions around when and how DNA was actually turned into working proteins.
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.
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
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...
In response to a small percentage of posts, I can't help but make this comment: As usual, when there's a new scientific discovery that proves nature is more "complex" (a totally subjective word in and of itself) than we once thought, there's a surge of morons shoving the word "god" in where the words "I personally have no explanation" should be used instead.
Currently theta testing the prototype "Event Horizon" server-scaled desktop box with a 50 Gigameg of Ram.
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".
I am just waiting for the new book due out soon.... Men are Linux, Women are OSX... I guess that the gay and lesbian population are different versions of windows?
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
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.
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.
Case in point: the HIV virus. It's an RNA virus. Most enzymes cells use for replicating DNA (called DNA polymerases) have a proofreading skill: if they detect that what they're reading is incorrect they'll rip it out and try again. Most RNA polymerases lack proofreading skill (because it's expensive: it takes a lot of energy, and RNA is, in the grand scheme of things, considered throwaway material, a transition from the data storage system to the actual machinery.) So, the viruses that rely on RNA as their data storage have a much higher rate of mutation. The result is that they have a vastly higher rate of nonviable viral particles, and a small number of extremely viable particles, which have found, by chance, better ways of evading host immune response. It's a main reason that HIV is so difficult to treat or cure.
Here is some information about reverse transcriptase error rates. In contrast, here is some 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.
Nostalgia's not what it used to be.
Nah, they just run the other os in a virtual machine.
With much fear, surprise, and surprise for some of the scientists, they began to read the new code... it began:
......
#!/usr/bin/perl -ane
One scientist looked at the other, and said "This explains everything!"
For every problem, there is at least one solution that is simple, neat, and wrong.
I find this akin to a computer trying to reverse engineer itself. For instance: I am a software program (mind) that is running on organic hardware (body). Whatever designed me probably coded me in Jah++, I can compile Jah++ natively, but I don't really know what any of it means - because I only understand binary. Is it even possible to understand how we are coded? I mean we can see that there is input and it is n characters long, and it affects the eyeballs. But can we really fully understand why? Why were we coded this way in the first place, and how are we able to understand what little bit we can? Finding comments and metadata etc. in our DNA should come as no surprise to anyone here. We have crudely reproduced the most basic inner workings of animal deduction in modern PCs. We didn't invent the PC, we observed and deduced things that occur naturally. PCs are built the same way we are, foreground processes (listening, watching, reading, consciousness) running on top of background processes (breathing, blood circulation, subconsciousness) inside of a case that cools and provides structure. There are input and output devices, microphone, camera, scanner, printer, speaker, etc. We are the creator's computers. We are a part of a grand design for a self contained network of evolving machinery. As far as our computers go, we are building the dinosaurs and hard shelled organisms, slowly we will evolve into making organic computers that are made out of the same stuff we are and can reason - way beyond AI, I am talking about proper intelligence being built into an organism. Arms being recreated, lungs being grown for implants, brains being repaired after car accidents. It is not a far fetched sci-fi scenario. We are able to interface brain to computer right now. Give us time and we will have a Data, we will not know the difference between man and machine. Just my observations. I could be wrong.
-Scottux