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.'"

So wait

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?!

Re:So wait

That means farking is a DMCA violation. Hmm...

Tom

Re:So wait

No it's not because you're creating a new compilation with another member. ;) Now cloning however...

Yes, and

I'll bet it is controlled by an Active Directory installation.

Re:Yes, and

Is that why we have to crash once a day, and it takes 6-8 hours to reboot?

Re:Precisely.

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?

Re:Precisely.

Nah, they just run the other os in a virtual machine.

Re:So wait

Exactly and these guys are getting themselves into a world of litigation by trying to break it. My client, known to many of you as GOD ALMIGHTY has retained the services of my firm to protect his substantial investment in your genetic code which I may add

Re:So wait

Yeah, right. Where in heaven is God going to find a lawyer?

Re:So wait

Yeah, right. Where in heaven is God going to find a lawyer?

I think you mean to say, "Where the hell is God going to find a lawyer?"

Re:So wait

So my body has built in DRM?!

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

That's not a surprise. For years, I've been friendly enough to offer sharing my genetic code with any number of buxom, nubile females. I was told the code was "incompatible" and often never even got to the I/O phase.

Re:So wait

So, you never got past the Handshake phase?

Re:So wait

My cells factor very large primes, therefore I am

DNA DRM?

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.

Does this mean that DNA has DRM?

Midichlorians?

So did we finally discover the Midichlorians [wikipedia.org] that Qui-Gon was rambling about?

Re:Midichlorians?

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.

Re:Midichlorians?

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 -> R

Re:Midichlorians?

It gets destroyed by the egg cell:

http://en.wikipedia.org/wiki/Sperm [wikipedia.org]

Genes, introns and nucleosomes

Personally, I think it's God's version of Sudoku.

An important reminder

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.

Some of this isn't terribly new

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.

Proff of intellijent design!!!11

Only Go^H^Han intelligent designer could have implemented DNA with private and protected data. This sort of thing just can't randomly 'evolve'.

Re:Proff of intellijent design!!!11

Only a crappy programmer would fill essential code with this kind of cruft. No wonder it takes the hardware decades to split off daughter processes.

Come to think of it, a lot of the crappiest programmers I know think they're God -- er, intelligent desi

Re:Random error produces error control mechanism?

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.

Re:Random error produces error control mechanism?

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 [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.

Re:Random error produces error control mechanism?

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...

software problem

Any software problem can be solved by adding another layer of indirection.
So apparenlty we are a software problem.

C'mon baby...

I have a lot of good code, ready for re-use!

Re:C'mon baby...

And like any good programmer, you're willing to share the source for free.

Just don't expect you to maintain it.

Evolution proves totally brilliant once again

I'm always thuroughly impressed by the ability of cells to use lots of simple mechanisims to achieve complex results.

It's not like nucleosomes are anything new though, the real discovery here is that the scientists found a pattern to their binding.

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.

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

I also found the NYTimes article painful to read. At first I thought they were running a piece on the histone code, something that has been discussed for years now, not this more recent discovery of a system of arranging nucleosomes. Science writing and

It's a bit like the way you can embed...

...a Whitespace [dur.ac.uk] program inside a C++ program. The Whitespace program coexists with the C++ program because of the "wiggle room" (to borrow a phrase from the article) that the C++ grammar givess you.

Original article

Abstract [nature.com] and full text PDF [nature.com]. (currently freely available).

And in further news, the histones...

have been discovered to be eighty units long and oriented face down, nine edge first.

Metadata

I find it interesting that god/evolution/the great green arkleseizure/FSM/whatever invented metadata LONG before we did. Not surprising, just interesting.

First DNA virus hackers?

When am I going to see my first wetware virus that uses an "escalation of privileges" type attack?

Re:First DNA virus hackers?

Think of cancer as a fandango on core followed by a DOS/fork bomb.

New Code Discovered in DNA

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

Duh!!

Everybody knows there's a hidden code in our DNA... Leonardo DaVinci put it there!

For large values of second

This isn't a second code. The second code is the binding sites for proteins that activate and inhibit gene expression. Then there are a number of other codes already known that affect replication or expression in various ways.

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

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.

Argument from Personal Incredulity

This is called the argument from personal incredulity [wikipedia.org], and is a favourite of the IDers. See http://www.millerandlevine.com/km/evol/design2/art icle.html [millerandlevine.com] for an excellent example of how this argument fails spectacularly with the nature-evolved wheel, the eu

A new "twist" in an OLD OLD story...

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

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

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!"

Organic Software

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.

Re:New Discovery

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..

Re:Intelligent Discovery.

Man! How long did it take evolution to figure that one out?

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 Trus [acm.org]

Re:Old "News"

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.