Human Genome More Like a Functional Network 304
bshell writes "An article in science blog says we may have to rethink how genes work. So called "junk DNA" actually appears to be functional. What's more it works in a mysterious way involving multiple overlaps that seems to be connected in some sort of network." From the article:
"The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.
The new data indicates the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Nature paper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered."
Re:Of course its not junk (Score:3, Insightful)
junk genes was a junk idea (Score:2, Insightful)
Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. So, 90% of genes aren't "junk" after all. To anyone who does know something about the aforementioned topics, duh!
First, evolution would weed that sort of thing out in a hurry. Two organisms with genes that achieve the exact same thing, but one has a more efficient encoding? No contest! And, yes, such is possible. DNA isn't some mystical "super" language. It can't violate basic principles. There surely are many many ways to encode the same thing.
Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.
Third, why this obsession with zeroing in on a magic gene that causes X? Do they think the language of DNA is context free? Defects could indeed be expected to have no context, but for the rest-- which genes determine a person's blood type? Eye color? Skin color? Going about that task by trying to find the magic gene for something like that is like a person who never learned to read trying to figure out the plot of a book by trying to recognize patterns of letters.
They used to think the Romans were just "lucky" with their aqueducts. Found it hard to believe the Romans really could carefully and correctly engineer such massive projects.
Re:Of course its not junk (Score:5, Insightful)
Its what we in the programming field would call the Data Segment.
Overlapping, independent sequences? It's quite obviously spaghetti code.
Re:Of course its not junk (Score:5, Insightful)
Here's the question - is non-gene DNA
If it's the latter, junk DNA would be conceptually closer to filesystem metadata (and maybe even "free diskspace" in as far as introns etc. go) than the OS.
I fail to see how it bootstraps anything. A DNA molecule does not to my best knowledge start proliferating on its own when put on agar. Cellular facilities are required. True, you build said cell facilities from data stored in genes, but still I can't find any underlying principle shared by the bootloader, OS or whatever interpreter on my computer and my non-gene-coding DNA.
FWIW, I'm a coder, a unix sysadmin and a (somewhat late-aged) biochem undergrad student, so feel free to dive as deep as you like into a technical comparison. I've been playing with comparison models of my own for a while (all of which have the annoying habit of breaking at one point or another) and am intrigued to hear more ideas on this.
Re:error correction (Score:5, Insightful)
We have this huge disk, and most of it is malware or free space. The results in RTFA are interesting, but the general idea that we can measure the frequency of changes and statistically determine whether evolution is working on a specific sequence, should still be sound, so if they are indeed used, it is probably in a far less sequence-sensitive context (sometimes overall folds, sometimes just stochastic effects from the whole pool of junk transcripts affecting the balance in the nucleus).
Re:ID's advantage of evolution (Score:3, Insightful)
Re:Hmm... (Score:2, Insightful)
Other key differences are that with evolution and science in general can observe what has happened and make predictions; that's a pretty powerful and convincing tool. If you read creationist literature, you'll find attacks on evolution and the research; the vast majority of the creationists don't do actual research; they'll go out to win converts and preach to the choir.
Just see Ars Technica's recently posted photo series about the creation museum; you'll see evolution and creation diametrically opposed with evolution always on the receiving end of the kicks - and meaningless fluff about gay marriage, school prayer and abortion that plays the heartstrings of the audience. It's in the interest of the founders to turn it into a black-and-white issue and make the visitors feel good because they've chosen the "right" side (or bad because they haven't). Ever seen a biology book that has several paragraphs littered through it about abuse of children by the clergy and the consequences of the Crusades? Yeah, that's just as irrelevant.
Do keep in mind that the "was there a creator" position is not compromised by this; whatever happened before Planck time, we know nothing of. Whatever happened afterwards, we can at least observe. Because it's not right to skip the question at that god; namely, where'd he come from? And where'd the previous one come from? And so on; adding god to the equation doesn't actually make us wiser, which is why he's left out. No. If it wasn't there, I wouldn't be thinking about it, would I?
Re:My hairbrained idea... (Score:3, Insightful)
One of the more interesting examples of such metaphor is brain research, in which every IT advance has been put forth as the model that would finally allow us to fully model brain function.
Teleological Argument (Score:3, Insightful)
The whole "junk" DNA thing always bothered me (Score:3, Insightful)
I guess this bugs me so much because I see the problems caused by an ignorance of the facts every day. "Hey, quit standing around! Let's git'r'done!" Yeah, charge into a situation like a bull in a china shop. Hey, asshole! There's a reason why we didn't want you to go through that wall, the cat-5 was back there! Wow, a new hire that I just found out about this morning? Why yes, we have no computer for him, we told you there's a reason why we have to be informed of hires once a position is announced.
Re:junk genes was a junk idea (Score:3, Insightful)
I think your understanding is a little naive... There *are* magic genes that do X. There are also pseudo-random sequences that we have found a use for, and there are, further, sequences we carry around that are malicious, or do exactly nothing. But we carry all these genes around anyway, because the cost of doing so is negligible, and the chance for quick modification is beneficial in a population crisis. To get an idea of the tasks geneticists face, familiarize yourself with the Brainfuck [muppetlabs.com] programming language (which is hilarious) and an uncommented sample program [sange.fi].
Now, imagine that -- over the course of MANY, MANY years -- we have evolved a usable Office Suite, circulating it on media with little or no error correction. There are no versions -- If yours doesn't do what you need, you toss it out and get a copy from somewhere else, or you try to randomly merge a friend's copy with your own using a little utility inside the software. The source code is over 8GB, and nobody knows what everything does. No individual programmer or team, at this point, can change much of anything because the chances of screwing up badly outweigh the benefits of any expected improvement -- but we are trying to gain the understanding to work with it. Exacerbating the problem, random copy errors exist, and have become functional and necessary, in every remaining copy of the program. People do research to try and find out how feature "X" works, but at some point, the code accepts a memory address from user input and jumps to it. Now, we have to find out where the input came from, and track down the code that created it.
Certainly, there will be parts of the program that do only one very specific thing, and there will be parts of the code that behave differently depending on state. There will be parts of the program that do nothing, and there will be parts that are seemingly random but just happen to contain instructions that do something useful under certain circumstances, or can serve as / generate useful input in others. There will be sequences with stable output, and those that vary wildly on input. Just because someone is looking for feature "X" doesn't mean that they will find it, or that it won't be an emergent property of the system -- some code written into memory by random-looking source scattered throughout the program. But it also doesn't mean there are no encapsulated features to be found.
At the stage we're in, we look for highly correlated output from the system, or at least easily-measured output, and try to track down any parts of the code that seem to affect it. Sometimes, there will be a clearly delineated subroutine, or portions of the output will occur literally in the code. Sometimes, the feature we seek will be a side effect of otherwise unrelated code, or the result of an error in code that originally did something else (and otherwise still would, except for the error). But you can't assert "There is no magic gene." any more than a geneticist can blindly assert that there is.
Re:ID's advantage of evolution (Score:3, Insightful)
Weird. If you ask me, what's truly amazing about nature is the mind boggling complexity and variation that has grown out of beautifully simple principles such as natural selection. If you ask me, that's *way* cooler and more impressive than some god-thing running the show for kicks. After all, a fractal, to the naked eye, looks unbelievably complex... and it's expressed with a simple formula. The same is true of something like Conway's Game of Life. Simple rules generating remarkably complex behaviours. To me, that seems like a far better answer to Occam's Razor...
Another misleading "junk DNA" article (Score:2, Insightful)
The only thing worse than these poorly-written articles are the inane comments they generate.
The biologists who actually study DNA have known the following for a long damn time. Any "science" writer who gets them wrong should be sent back to writing obituaries and wedding announcements.
Most DNA in multicellular organisms does not code for proteins. Some non-coding DNA performs other functions. Lots and lots of non-coding DNA has no function at all. None. It's not "data", it's not "metadata", it's not structural or anything. There are very long stretches of DNA that you can alter radically or even delete and it makes no difference to the organism at all.
I'm just a layman and my technical knowledge on this subject is just about nil, so don't take my word for it. Go read what a Biochemistry Professor at UToronto (Larry Moran) says here [blogspot.com] or here [blogspot.com] or what another biologist (T. Ryan Gregory) says here [blogspot.com].
Biology is insanely complex and messy, especially compared to computer science. Here's a hint for all the programmers, database admins, sysadmins, and other bright and talented professionals who feel moved to speculate about DNA and similar subjects: If the viability of your idea depends on the assumption that the actual researchers are too dim or ill-informed to make the connection, it's either a bad idea or it was done years ago.
Re:error correction (Score:3, Insightful)
Someone could say the creation part of the bible was figurative/symbolic, whether that someone is wrong or right on that, he/she could still be a Christian.
So why the big fuss over something that IMO shouldn't be that important? Why not focus on what Jesus said, did and commanded (e.g. Jesus said: love one another as I have loved you - by this shall all men know that you are my disciples - that you have love for one another).
The way I see it, most christians are even ignorant about their own religion. It's not just ignorance of science.
You don't need proof of evolution to give those creationists trouble. All you need to prove is how far certain stars are, and how fast the speed of light is, and the behaviour of stuff like Cepheids. There have been creationists that try to explain all that by saying the speed of light has decayed through the ages, but when you examine their "evidence" it starts to fall apart.
OK so _maybe_ the "creation 6000 years ago" is one of those miracles - just like Jesus turning water into wine (at that wedding in Cana)- the wine was excellent wine - and so I suggest the wine had the necessary "history" (fermentation, aging etc).
But then even if the "billions of years history" is created, I argue the "created history" is very likely to be consistent and perfect enough for everyone to learn a lot from and appreciate.
Re:ID's advantage of evolution (Score:2, Insightful)
First, why exclude the newest Abrahamic religion, Islam? Second, granted I'm not a real expert on Bible, but it does seem to speak out against churches, and it also doesn't seem to prescribe any religious hierarchy. The verses about churches are:
God that made the world and all things therein, seeing that he is Lord of heaven and earth, dwelleth not in temples made with hands; ~ Acts 17:24
Howbeit the most High dwelleth not in temples made with hands; ~ Acts 7:48
These are the most straightforward ones, but there are some more that implicitly say the same.
Mankind has thoroughly mucked up God's handiwork.
So, does that mean an omnipotent, omniscient being failed? That's an interesting conclusion for a believer. But let's recap his approach:
1. wait about 10 billion years to create Earth in the outskirts of an unexceptional galaxy that is one of billions, orbiting one of its about 200 billion stars;
2. wait about 1 billion years to get to abiogenesis;
3. wait about 4 billion years more to get to a particular primate species with large brains;
4. let them live short (20 years on average), pain-filled lives for hundreds of thousands of years until they stumble upon agriculture and writing and establish a civilization;
5. wait a couple of thousand years more and pick some desert tribes in the Middle East as the chosen people, give some very imprecise or false information, order some genocides;
6. create a great mess on Earth by sending your son (which is also yourself) to die (mimicking many earlier myths about godmen), supposedly to start over and re-brand yourself as more caring, less jealous diety (also, blame everything on your creation);
7. prove to the primitive people you're the authentic creator of the universe by doing some magic tricks like killing pigs, curing women from menstruations, raising the dead and exorcising "daemons";
8. forget to leave any contemporary evidence and die, forgetting your earlier promises of what you would do (end wars, unite mankind);
9. wait for years and reveal the last part of the story to a man who hasn't ever met you so he writes it down;
10. about 40 years after your death (whatever "death" means to an immortal being) make a guy possibly named Mark write down your feats conjuring food and vandalizing trees, with pretending to have been your disciple, even though he'd have to be exceptionally old then for an era in which the average lifespan was short (making rational people later conclude that this is just made up, or based on an oral tradition, or both; not very credible in any case);
13. have more texts written, some of them more than a hundred years after your supposed death;
12. watch your chosen tribes call you a false messiah because you didn't fulfill the prophecies you gave earlier;
13. see how stupid Gnostics misunderstand everything, pagans call your new followers Atheists, and how Mithrianism almost prevails over your new religion;
14. have Constantine I help out;
15. forget to send the memo about monotheism to very large portions of humanity for more than a thousand years;
16. the council of Nicaea officially recognizes that your son is the same as you, even though you forgot to write it down in the texts; it also discards some writings that you didn't inspire well enough;
17. see your religion spread through the tribes of barbarians wrecking Western Roman Empire;
18. by the way, your religion is already split into the Eastern Orthodox cult and the Roman Catholic cult;
19. some Arab plagiarizes most of your earlier texts and pretends that an angel told him to; do nothing about it, dividing the humanity even further;
19. have your followers destroy Constantinople, ending the last of Roman Empire;
20. establish a complete hegemony of your religion over the illiterate masses, mostly benefiting just the clergy and the monarc