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.'"

Comments

An important reminder

[QuantumFTL]

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.

Evolution proves totally brilliant once again

[realisticradical]

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".

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

[exp(pi*sqrt(163))]

...a Whitespace 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.

Re:Random error produces error control mechanism?

[plalonde2]

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.

Metadata

[Aladrin]

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

Re:First DNA virus hackers?

[plalonde2]

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

Re:New Discovery

[dan dan the dna man]

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.

[HTH NE1]

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 Trust 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:Random error produces error control mechanism?

[syntaxglitch]

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...

God-in-the-Gaps

[ACQ]

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.

Re:God-in-the-Gaps

[Maximilio]

I disagree that the non-theist asserts nothing

Without going into too much detail, you're wrong.

OK, some detailBut if "God exists" were simply an academic question, it would be confined to academia.

It's not an academic question. It's a fundamental assertion regarding the nature of the universe. Theists assert that it was created by God. Non-theists don't. We aren't replacing a logical quantity (GOD) with another quantity. That's something you just don't seem to be able to grasp.

And I think to be a human being, you have to take a position on that, which, incidentally, is why religion has been used so successfully throughout history to control people.

No, I don't. My position is, that being's existence isn't real. I don't have to prove anything. I'm not even asserting anything. I'm simply failing to nod my head in agreement when that fictional being's existence is asserted by someone else. The real world is sitting right there in front of us, and it operates just fine whether you believe in God or not. There are a good number of glurge-y myths, often promulgated by 700-club devotees and others, that assert that atheists live some sort of dark, miserable life and are ruinously unhappy and unsuccessful in life but quite frankly they are a load of bull.

It is a promise that there is morality, redemption, and hope despite a world that allows suffering.

People choose their moral compass first and then twist their beliefs to fit their actions. And, bluntly, suffering is an unfortunate condition but no one's prayer has ever alleviated it in the slightest -- except in their own minds. If you choose to imagine that the Big Sky Fairy will fix things for you, you may be missing out on the opportunity to take action for yourself, and I am pretty sure many people do.

But to live his (or her) life, he has to have some answer. And even if that answer is as simple as despair, it cannot be based entirely on deductive logic, or on scientific facts, because it is going to be subjective, and logic and science are not subjective. It will depend on something akin to faith, or at least on imagination.

I invite you to read the book in my .sig. You can listen to it for free on podiobooks.com if you like. Because that's what it's allllll about.

Evolution, Schmevolution, let's just talk science

[chloroquine]

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 reporting becomes more and more fluffy as time passes. I know that biology and medical writing for the layman is awful and misleading, but I'm not so much aware of how bad writing for the layman is in fields that are not my own: comp sci, physics, maths, and so on. If it is as bad, then we should all go with our pitchforks and torches and demand that the monster be delivered to us so we can fix the problem.

The only way this code was hidden was that we didn't know about it before. It took a whole bunch of yeast work and number crunching to see it.

[OT] I must be new here

[espressojim]

When I read articles about biology, especially molecular biology/genetics, I see lots of interesting "facts" about the field given by various members of the slashdot crowd. I'm not a leader in the field, but I feel knowledgeable enough working in the field to know just how wrong these "facts" are, yet get modded 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:How the hell does *that* follow?

[rtb61]

The biggest driver for evolution is not the slow process of natural selection but natural disasters. A major event will clear an enviroment and create a low competition enviroment allowing more mutations to survive and fill the various vacant ecological niches within that enviroment.

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 disfunctional mutations.

Error correction is required not so much for us reproducing as a collective organism but for the individual cells in our bodies to continue reproducing. You are continuously dying and being reborn every day and you don't want some of your cells evolving and becoming dominant within the eco system of your own body (cancer).