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New Code Discovered in DNA?

Zonk posted more than 7 years ago | from the we-needed-more-than-one dept.

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.'"

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285 comments

So wait (5, Funny)

antifoidulus (807088) | more than 7 years ago | (#15776572)

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?!

Yes, and (2, Funny)

2names (531755) | more than 7 years ago | (#15776608)

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

Re:Yes, and (5, Funny)

n2art2 (945661) | more than 7 years ago | (#15776646)

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

Precisely. (1)

2names (531755) | more than 7 years ago | (#15776664)

It is also why humans pass around so many damn virii. And how much junk mail do YOU get each week? We could go on and on, but I think it is fairly obvious that All Our DNA are Belong to Billy G.

Re:Precisely. (0, Troll)

Anonymous Coward | more than 7 years ago | (#15777008)

Viruses. People who say "virii" look very stupid. Don't look stupid, say "viruses".

Re:Precisely. (3, Funny)

LiLWiP (918943) | more than 7 years ago | (#15777026)

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:So wait (2, Funny)

JudgeFurious (455868) | more than 7 years ago | (#15776614)

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 you merely licensed from him when you agreed to the EULA by leaving the womb.

Re:So wait (4, Funny)

3waygeek (58990) | more than 7 years ago | (#15776834)

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

Re:So wait (1)

IAmTheDave (746256) | more than 7 years ago | (#15776895)

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

God: "Pete, put a temporary override on the lawyer auto-filter. Apparently, I'm gonna need a few."

Re:So wait (4, Funny)

baKanale (830108) | more than 7 years ago | (#15776920)

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?"

In other news (0)

Anonymous Coward | more than 7 years ago | (#15776632)

The RIAA has announced that they are suing the entire human race for violation of their client "God"'s intellectual property.

Re:So wait (1)

DrWho520 (655973) | more than 7 years ago | (#15776678)

Nah, more like private and protected data members. And probably one or five mutex locks.

Re:So wait (0)

Anonymous Coward | more than 7 years ago | (#15777041)

Just let one thing be clear: I will allow no-one to mutex my private members!

Re:So wait (1)

pla (258480) | more than 7 years ago | (#15776908)

So my body has built in DRM?!

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.

DNA DRM? (3, Funny)

shadowknot (853491) | more than 7 years ago | (#15776573)

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?

Protected memory? (-1, Redundant)

Anonymous Coward | more than 7 years ago | (#15776590)

So dna has protected memory?

Midichlorians? (3, Interesting)

digitaldc (879047) | more than 7 years ago | (#15776592)

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

Re:Midichlorians? (1)

UbuntuDupe (970646) | more than 7 years ago | (#15776775)

Windu: Does Anakin Skywalker have enough midichlorians to join the Jedi Council? You're damn right he don't!

Re:Midichlorians? (3, Informative)

syntaxglitch (889367) | more than 7 years ago | (#15776846)

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? (2, Informative)

dan828 (753380) | more than 7 years ago | (#15777044)

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.

An important reminder (4, Insightful)

QuantumFTL (197300) | more than 7 years ago | (#15776609)

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 (3, Interesting)

PIPBoy3000 (619296) | more than 7 years ago | (#15776870)

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.

Intelligent Discovery. (0)

Anonymous Coward | more than 7 years ago | (#15776612)

"The NY Times is reporting that scientists have found a second code in DNA that goes beyond the genes."

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

Re:Intelligent Discovery. (2, Insightful)

HTH NE1 (675604) | more than 7 years ago | (#15776812)

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 [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. (0)

Anonymous Coward | more than 7 years ago | (#15777047)

Just because something might be explicable, doesn't preclude it being of divine origin.

God put a rainbow in the sky to remind man that he would never flood the Earth with water again.

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.

It's not that God works within the laws of physics to accomplish his ends as much as he created those laws in the first place, and it's therefore to be expected that the laws of physics would be amenable to God's intentions.

Proff of intellijent design!!!11 (3, Funny)

Lord_Slepnir (585350) | more than 7 years ago | (#15776616)

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

Random error produces error control mechanism? (0, Flamebait)

geoffrobinson (109879) | more than 7 years ago | (#15776643)

Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

Yes, this discovery does not hurt the ID movement at all.

Re:Random error produces error control mechanism? (4, Insightful)

plalonde2 (527372) | more than 7 years ago | (#15776680)

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.

How the hell does *that* follow? (1, Interesting)

Anonymous Coward | more than 7 years ago | (#15776685)

Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.

Why? Why couldn't DNA evolve error control mechanisms over billions of years? Because you don't want it to?

Seems to me a mechanism to make the genes encoded into DNA more stable and reproduceable would produce enormous benefits to an organisms ability to rapidly and accurately reproduce and thus would have enormous evolutionary pressure behind it.

Re:How the hell does *that* follow? (1)

geoffrobinson (109879) | more than 7 years ago | (#15776723)

Well, it seems like you are saying that if organisms are more prone to blind Darwinian processes that would make organisms less prone for survival. And putting the brakes on mutations and changes which are at the heart of the Darwinian mechanism would make an organism more prone to for survival.

So if Darwinian processes produce the survival of the fittest, the first thing those processes have to do is protect an organism from random mutation and error.

I'll go with that and agree with you.

Re:How the hell does *that* follow? (1)

The Only Druid (587299) | more than 7 years ago | (#15776787)

You seem to misunderstand how "error correction" benefits a creature. In order for evolution to work, you need natural selection, i.e. a pool of creatures (generation-n) who have slightly variable features due to mutation, which is then reduced by natural selection factors (e.g. predation, limited resources, etc.). The survivors then reproduce (generation n+1).

Now, each generation needs to have some variability. After all, if everyone is identical, then there will be no adaptability. But, they need to have a much more significant sameness, i.e. lack of variability. After all, they need to be able to breed (among other interrelationships). Moreover, like all course-corrections, it's always better to move in small steps instead of big leaps (at least, almost always).

Error correction in genetic material would help curtail big leaps, while making small steps more viable (by reducing the number of critical mutations that kill the individual).

Of course, every now and then, environmental pressures would mean that lower error correction might be beneficial - consider the near-extinction of the Cheetah's ancestor to apparently fewer than 50 individuals - because you need a larger population of genetic variation. Such situations would result in some species having more or less "correction" built in. Species that never had such a bottle-neck would be expected to have more error-correction, most likely.

Reproducing accurately and rapidly (0)

Anonymous Coward | more than 7 years ago | (#15776902)

If you assume error-correcting DNA allows more accurate and rapid reproduction because cell division can be faster and offspring are more likely to be viable (I think those are probably pretty safe assumptions - at least on the single-cell organism level), I'd venture to assert that even a small advantage in reproductive rates would utterly outweigh any lost advantages from any loss of potential genetic variability.

In other words, having the potential for large evolutionary leaps isn't much help in outcompeting a similar organism that can outbreed you.

Post to piss off conservatives (0, Offtopic)

aussersterne (212916) | more than 7 years ago | (#15776724)

Evolution! Natural Selection! Darwin! Condoms! Abortion! Diplomacy! Secularism! Science! France! Hollywood! Palestine! Environmentalism! Global warming! Nudity!

Hahahahahahaha!

Re:Random error produces error control mechanism? (1)

Darkman, Walkin Dude (707389) | more than 7 years ago | (#15776781)

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? (1, Informative)

Anonymous Coward | more than 7 years ago | (#15776859)

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 [wikipedia.org]

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!

Re:Random error produces error control mechanism? (5, Insightful)

syntaxglitch (889367) | more than 7 years ago | (#15776960)

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...

Re:Proff of intellijent design!!!11 (0)

Anonymous Coward | more than 7 years ago | (#15776759)

Don't be so sure. I'm sure Da Vinci must have had a hand in it somewhere.:-)

Re:Proff of intellijent design!!!11 (1)

kesuki (321456) | more than 7 years ago | (#15776811)

if humanity is your definition of 'intelligent design' then you've got a way to evolve yet. seriously god should have quit at the garden. animals? what was he thinking.

Re:Proff of intellijent design!!!11 (1)

wateriestfire (962915) | more than 7 years ago | (#15776850)

for one would everyone stop calling it mechanisms, it is really processes. Now under the processes it seems reasonable that the system, which is the entire body structure, including cognitive thought would access these parts in a way that will maintain the system. By this logic it is easy to beleive that because of the entire system's need for such a crutial element that that element would create itself when the system is pushed far enough. ---- In Chaos there is Order

you are probably correct (1)

GodWasAnAlien (206300) | more than 7 years ago | (#15776890)

But, then we must of course examine our creator/creators.

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 single person cannot build a jumbo jet, but thousands of people can.
(***) Note that we can create machines that can make calculations faster than any human. Note also that we can use software evolution to create efficient algorithms.

software problem (4, Funny)

hey (83763) | more than 7 years ago | (#15776629)

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

Re:software problem (1)

PMuse (320639) | more than 7 years ago | (#15776916)

You are adaptively self-programming software running on adaptively self-replicating hardware. TFA is more of a hardware issue.

Me, I'm just another steam engine [chronicle.com] trying to contain the pressure.

Cue the "irreducibly complex" creationists... (0)

Anonymous Coward | more than 7 years ago | (#15776638)

What an arrogant, presumptuous argument.

"I can't figure out how this could evolve, so God must therefore be precluded from creating a universe in which living creatures evolve."

As if God is limited to what one human can or cannot understand...

Evolution proves totally brilliant once again (5, Insightful)

realisticradical (969181) | more than 7 years ago | (#15776639)

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".

Re:Evolution proves totally brilliant once again (0)

Anonymous Coward | more than 7 years ago | (#15776773)

While you're correct, given that the comments here are overwhelmingly devoted to yet another round of scientifically illiterate ranting about creationism, the DMCA and stem cells, if anything it would seem that the NYT didn't dumb down the issue nearly enough.

Don't worry (-1, Troll)

ArchieBunker (132337) | more than 7 years ago | (#15776651)

Bush will veto research soon enough so we don't go messing around with god's work.

Re:Don't worry (-1, Offtopic)

Anonymous Coward | more than 7 years ago | (#15776763)

a score 2 troll?

Re:Don't worry (0)

Anonymous Coward | more than 7 years ago | (#15777020)

Secretary: Mr. President, it's God on the red phone.
Bush: Make him hold.
*ten minutes later*
Bush: Yeah?
God: Sorry to interrupt. I just wanted to call and ask if you could stop killing innocent people.
Bush: F&"! You!
God: C'mon, it's not nice to kill innocent people and provoke wars around the world. Could you at least back up a bit?
Bush: *hangs up the phone*

You don't mess with higher powers. Bush is above law, above God and you should not speak against him. (Or you end up in some distant resort and learn some new hobbies like waterboarding.)

It's a bit like the way you can embed... (2, Insightful)

exp(pi*sqrt(163)) (613870) | more than 7 years ago | (#15776656)

...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.

And in further news, the histones... (2, Funny)

dpbsmith (263124) | more than 7 years ago | (#15776672)

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

Metadata (4, Insightful)

Aladrin (926209) | more than 7 years ago | (#15776693)

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

Breaking News!! (1, Funny)

Anonymous Coward | more than 7 years ago | (#15776710)

Hidden message deciphered in nucleosomes: WE ARE SORRY FOR THE INCONVENIENCE.

How exciting can it be? (1)

butterwise (862336) | more than 7 years ago | (#15776712)

FTFA: "I think it's really interesting," said Bradley Bernstein, a biologist at Massachusetts General Hospital.

If this guy is so pumped, shouldn't we all?

New Discovery (0)

Phillip2 (203612) | more than 7 years ago | (#15776713)

NYTimes is reporting a new discovery. However, because neither their journalists couldn't be bothered to understand or imaginatively report the discovery, they have instead decided to simplify it to the point that it appears to be exactly the same as something that biologists. It's hoped that in future, reporting will improve. This could revolutionise newspapers to the point where they are actually useful.

Phil

Re:New Discovery (3, Insightful)

dan dan the dna man (461768) | more than 7 years ago | (#15776771)

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:New Discovery (1)

Phillip2 (203612) | more than 7 years ago | (#15776999)

Pah.

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

First DNA virus hackers? (2, Interesting)

farker haiku (883529) | more than 7 years ago | (#15776731)

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

Re:First DNA virus hackers? (0)

Anonymous Coward | more than 7 years ago | (#15776779)

There already is one, it's called Cancer. That's when cells start making proteins they're not supposed to and go haywire.

Nicely coded. (1)

Fuzzums (250400) | more than 7 years ago | (#15776745)

"...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."

Personally I think some of these genes are not declared as 'public', but rather 'protected' or 'internal'.

The most important question... (0, Troll)

creimer (824291) | more than 7 years ago | (#15776752)

Can you program your DNA with PHP?

Re:The most important question... (0)

Anonymous Coward | more than 7 years ago | (#15776891)

I can't believe this is modded Troll!
Who could possibly find this post offensive?

Survival of the Fitness to Print (0, Troll)

Doc Ruby (173196) | more than 7 years ago | (#15776762)

Geneticists have already found a "second code" in DNA, called methylation [wikipedia.org]. And that NYTimes article also reduces the basebair redundancy to "wiggle room".

The underlying research, published in Nature magazine [nature.com], is extremely interesting and valuable, no doubt valid. The NYTimes coverage is oversimplified into wrongness out of reporter ignorance, and an insult to both readers and scientists.

New Code Discovered in DNA (5, Funny)

Anne_Nonymous (313852) | more than 7 years ago | (#15776785)

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

Re:New Code Discovered in DNA (0)

Anonymous Coward | more than 7 years ago | (#15776900)

ahaahaahaahaa

OOPS, encapsulation (1)

vasanth (908280) | more than 7 years ago | (#15776813)

wow we have discoved that genes use encapsulatio now.. OOPS is the way to go... no wonder it cant access private members of other classes erm.... genes..

I don't know much about DNA... (0)

Anonymous Coward | more than 7 years ago | (#15776817)

...but is this anything like the Hot Coffee mod?

Contact? (1)

soxos (614545) | more than 7 years ago | (#15776838)

If you put the new code together correctly will it form the plans for a dimensional portal?

Old "News" (1)

DrKyle (818035) | more than 7 years ago | (#15776866)

The placement of histones on DNA is something I learned about 10 years ago in my genetics textbooks. This is merely a slight addition to our current knowledge of which sequences histones are likely to bind.

Even better idea... (1)

Chabil Ha' (875116) | more than 7 years ago | (#15776873)

"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... (1)

DrKyle (818035) | more than 7 years ago | (#15776984)

The short answer is this: "selfish" DNA like transposons invade a genome, they replicate and produce many copies, some preferentially insert near genes. These transposons over time degenerate but their ability to create mutations, including using their own proteins to control expression of some genes leads to diversity = better ability to cope to environmental pressures. This leads to a better capacity for evolution than waiting for single base mutations from cosmic radiation and the like. When a transposon has gone from genomic invader to a productive member of the gene pool it is said to be domesticated. Over long periods of time (hundreds of millions of years) a lot of the copies of the transposons, which are not necessary, and therefore not selected for, are allowed to mutate, degenerate and appear to be "junk".

Nobel (1)

Glog (303500) | more than 7 years ago | (#15776877)

From TFA: A histone of peas and cows differs in just 2 of its 102 amino acid units.

Mmmm, a histone of peas... Seriously, let me be the first to say: I smell a Nobel prize for this one.

DNA code read backwards ! (0, Interesting)

Anonymous Coward | more than 7 years ago | (#15776892)

As if superimposing two codes into the same gene (the way the article describes) was not enough, DNA has extra surprises for us. There are genes that code one protein when read normally and another different protein when read backwards. And that's not all. Some genes code for a different second protein when read using different frames (starting points). And yet other genes code for another new protein when the complementary strand is read !

Our view on life mechanisms was so simplistic at the beginning of our scientific quest for origins. That's why we ended up accepting a theory that postulates mutations as the generator of genetic information ! Knowledge advances incrementally but our mind is so unprepaired and suspicious to the real answer: We've been created ! In an wonderful way...

Just beginning to understand (1)

PineHall (206441) | more than 7 years ago | (#15776937)

I find it fascinating how cells are amazingly complex, and yet are able to reproduce of themselves. It is like there is a whole world found in a cell, and it is able to transfer all this needed information accurately to the next generation. I think we are just beginning to understand cells and there is a lot more complexity to be discovered.

For large values of second (2, Interesting)

iabervon (1971) | more than 7 years ago | (#15776946)

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.

Epigenetics is the future (0)

Anonymous Coward | more than 7 years ago | (#15776954)

Those cold, dead sequences of DNA that everyone has been sequencing are only the starting point, not the endgame that some were promising. Those dead letters do not exist like that in living cells. Everything is epigenetic. It is in the runtime. It exists in the living, breathing cells, and not in the literal dead sequences. These histone manifolds are just one piece of the puzzle along with chromatin remodeling and DNA methylation that have been discovered and yet-to-be discovered. Many systems control the runtime expression of genomes, build endogenous stem cell lines and sex cells, and control the growth from embryos to adults. The methylation mysteries started showing up in clones, when nothing in the raw DNA sequence could explain what was different in the cloned adults. Turns out the imprinting (which gene gets expressed - mom or dads? Or even both!) is not stored in the DNA, but in the DNA's methylation patterns. And this pattern can be inherited. Will turn out to be one of many mechanisms.

To heck with the code... (1)

kybred (795293) | more than 7 years ago | (#15776978)

What we need to find are the comments!

      if (replication_count < MAX_REP_COUNT){
              childcell = new Cell;
              replication_count++; // FIXME: should check for overflow here!
      }

God-in-the-Gaps (5, Insightful)

ACQ (966887) | more than 7 years ago | (#15777000)

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.

A new "twist" in an OLD OLD story... (5, Informative)

posterlogo (943853) | more than 7 years ago | (#15777003)

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".

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