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Human Genome More Like a Functional Network
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."
Its what we in the programming field would call the Data Segment.
They need to hire some Perl and 60's-style-COBOL programmers who know how to read tangled code ;-)
Table-ized A.I.
It's somewhat funny - I remember having this exact discussion with my genetics professor. I was a chem major who is now a developer.
... but perhaps I've just looked at too much dissassembler. I will feel a little vinticated if this is proven.
It seems to me that DNA/RNA is "machine code" and data which runs on the laws of nature. It's a layer removed from silicon design, more akin to a self-modifying FPGA.
In other words we're so far only looked at the boot code and associated data. The "program" is what we were calling junk.
And it makes sense - if you think of the program as a massive recursion network which builds common parts (stem cells) and then organizes and specializes.
I know that's a simple bastardization
I said no... but I missed and it came out yes.
After assembling something, if there are any parts left over I simply declare them to be extra junk. With scientists declaring the same thing about DNA they can't identify, I guess the old saw is true, great minds do think alike.
Sigs are too short to say anything truly profound so read the above post instead.
I don't think evolution would be very kind to unneeded material.
There's really almost no selection pressure against extra DNA sequences, particularly ones with no associated promoter. One of the proofs of this is the fact that the human genome is comprised more of endogenous retroviruses than actual functional sequences.
I never have frustrations, the reason is, to wit:
If at first I don't succeed, I quit!
These scientists have probably been looking at cells running in the debugger...
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.
Intellectual Property is a monopolistic, selfish, and defective concept. It is "tyranny over the mind of man"
I walk down the street and see 100s of people who appear to be predominantly junk DNA.
No one thinks that flight just popped into existence. There are all sorts of useful traits prior to actual full flight that the earliest flyers would have developed: heck, things like feathers pretty clearly evolved long before flight was even remotely possible, and likely for very different reasons than flight. As for the thing itself, there are lots of different adaptions and traits on the way to flight that are all useful: things like decreased weight for sprinting across the ground, and of course brief gliding from tree to tree without actually being able to fly.
I've always suspected that "junk DNA" was the key to micro-evolution and speciation. I read an article once about how bacteria that could not metabolize lactose were cultured in a lactose-rich liquid. After about 60 generations, some bacteria that could metabolize lactose appeared. It turns out, they had non-functional genes for metabolizing lactose in their junk DNA, and somehow those genes were re-activated.
He who lights his taper at mine, receives light without darkening me.
Why it was called junk before you'd ask? Because our definition of what is useful wasnt all that accurate.. just looking at so called open reading frames and declaring everything else to be junk does not work. There is also the problem with insertions in a gene sequence that are either not or alternatively used. There are plenty of sequences that are never translated (no proteins are made of it) BUT without them we would be missing a big chunk of regulators etc. 'Recent' findings like ribozymes, IRES elemtens, attenuation elements etc. are all not translated into a protein yet serve a very specific function. Some of this 'junk' also serves as a insulator / separator between various sequences. We may never be able to map every nucleotide to some function but declaring it junk from the get go was just looking to be proven wrong. Just look up NCBI and look for some good reviews on this topic ;)
"No junk DNA would seem to indicate more of an overall design to the system, no?"
Not really. Exactly how and why DNA keeps or discards various sequences, coding or not, is not something on which design or no design rests: it's a matter of the particulars of how DNA works (and it doesn't, actually, work the quite same way in every creature, which complicates matters even more: some creatures have much more robust ways of catching error than others, for instance).
It's also worth noting that the term "junkDNA" is a bit of a misnomer, and any good discussion of the term in biology generally notes it as such: it's possible that your 110 class basically just, well, sucked. If you do a PubMed search, you'll find this discussion goes back way farther than 97: biologists were noting that even apparently non-coding DNA had usefulness for mapping out genomes even back in the 70s.
Why would we evolve to lose the appendix? Evolution doesn't work that way. It's not causing people to die, so it's gonna stay there. The only way evolution would get rid of it is if people mutated to have no appendix and they were somehow better able to reproduce. Human society being how it is, there isn't much that's gonna make you unable to reproduce. That's probably part of the reason we have so many genetic diseases now - they can be treated, so they don't kill you, so they get passed on.
Being one of the 0.1% of /.ers that believe God created mankind, (and that we have been in slow genetic decline ever since),
I thought when this 'Junk DNA' was mentioned many years ago that given time, that opinion will be reversed.
Thus there was an advantage to ID biologist who would have the opinion, 'cells are an incredible biological computer with beautiful design, this is great fun reverse engineering it all, and there won't be Junk DNA because that goes against God creating life, so lets keep looking for its purpose'
flame away
46137
"junk DNA" reminds me of the mysterious "dark matter", or "god" or whatever words we use to name something we know nothing about and don't understand, to give them some sort of magical status. It would probably be better to call it "unknown DNA", or "DNA Incognita", or even why not "Here be Dragons", to better remind us of how ancient maps were conceived (answer : it took ages to "publicly" discover all continents and isles).
One thing I'm sure is that Nature doesn't waste resources, only Humans do, so each yet unknown thing has certainely a very good reason to be there.
Votez ecolo : Chiez dans l'urne !
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).
crashfrog, you may have to correct me, but here's a start...
/bin/perl and that's how it knows to start copying off DNA code. (While on the subject, just because it has #! /bin/perl doesn't mean it will get executed, and even after it's been executed it might get a SIGKILL.) Promoters are not just found in DNA, but read on wikipedia for more on that.
There's really almost no selection pressure against extra DNA sequences,
This refers to the process in evolution where an organism fails to reproduce due to having a disadvantage that the other critters in the species don't have. So if a pig that has useless DNA sequences tacked on in its genome has a statistically lower chance of having piglets, there's pressure against those useless DNA sequences.
crashfrog is saying that for a reason he explains (below) extra DNA isn't going to have any effect on the organism's chances of reproducing.
particularly ones with no associated promoter.
A promoter is a marker in the DNA strand. The protein "machine" (a transcription factor) that gets the "data" off the DNA and into the cell's outside chemistry has a "socket" that matches the "plug" formed by the specific pairs of the "promoter" marker. It's like the transcription factor searches for #!
One of the proofs of this is the fact that the human genome is comprised more of endogenous retroviruses than actual functional sequences.
I'm not sure if I can do this last sentence piece by piece, so here goes...
An endogeneous retrovirus is a kind of virus that infects DNA. So when the cell splits, the virus gets copied along with it. For instance, some scientists think Multiple Sclerosis is one of these retroviruses that has infected our DNA. So when we look at the entire human genome, all the pairs in the whole DNA sequence, and we look at where all the promoters are, it seems (according to current theory -- we may learn more about this!) at a first glance there are some pretty long stretches with no promoters. That is to say, they are either empty sectors on the disk, or some of them look like retrovirus DNA code.
How'd I do at explaining that? Like I said, crashfrog should probably amend my explanation...
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!
If they hadn't suspected it, multiple groups around the world wouldn't have worked on this thing for such a long time. It's one thing to have a theory, another to prove it, despite what creationists may sayFirst, 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!
Actually, generally no and genome sizes can very a lot. There are a great many things that can complicate this. But you do see effects like this in cases like viruses that have limited space to pack DNA in the virus capsid. Not only do these viruses not have junk DNA, but even use some compression like techniques.
Second, ever tried compressing a DNA sequence? They don't compress very well! Meaning, they don't have much redundancy.
I think you are thinking of the coding regions. Redundancy is a notable feature of many non-coding regions.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.
I think you've chosen very poor examples to illustrate you're point. Those are all features controlled by a very small number of genes or a single gene. In other context though, this could be an important way of thinking. For example, cell machinery matters too. Kinda like software vs hardware.To match your analogy, if you can't read you have no hope of understanding the plot. First you have to figure out how to read. You might be able to figure out words from patterns of letters though. You have to start somewhere.
The magic gene thing is a matter of hoping for a solution that is actually simple and viable. If it's one gene, a single drug has a good chance of working. There are many diseases that actually work this way, so why wouldn't you look for a simple answer first. Things that involve lots of genes, like cancers, haven't had much success.
Yes, and yes.
Anyway, it made sense to focus on the almost-understood parts first since the mapping techniques were very limited (but far more efficient each year) and the task so massively huge it would have been stupid not to limit the first steps to a better understanding of the most easy purpose of the DNA, which is protein encoding.
Fully understand the DNA will take decades, if not centuries, and maybe someday scientists could be sure some parts of the DNA are actually useless, but that "90% junk" looks like that thing about the neurons maybe not being the only kind of cells participating in the intelligence.
Just remember that scientist are human, they are trying hard to understand the unknown, but that doesn't prevent them to make mistakes or false assumptions, quite the contrary.
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?
You found your belief in God on what is known as the Teleological Argument. There are a number of formal reasons why this argument is a poor one. The wiki link I've given you is a good place to start learning why it's not good, and Richard Dawkins' The Blind Watchmaker" has a fairly exhaustive treatment.
I'm sure it wasn't a responsible scientist who popularized the term, it was probably a science writer. But it's just a variation on the pointy-haired boss credo "Anything I don't understand is therefore easy" morphed into "Anything I don't understand is therefore unimportant or unnecessary." It's like that other popular fact, "we only use 10% of our brains!" No, we only know what 10% of it is doing.
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.
Kwisatz Haderach
Sell the spice to CHOAM
This Mahdi took Shaddam's Throne
Machine simulation of genetic/evolutionary algorithms often produces so-called "junk" which when analysed further, this frequently proves to be tied to the function of the overall organism in mysterious ways. I'm sure that leading GA researcher John Koza made this observation in early papers, but it's something that anyone playing with genetic algorithms will encounter sooner or later.
I couldn't find the quote I was looking for, but only this broad statement from Genetic Programming: Biologically Inspired Computation that Creatively Solves Non-Trivial Problems, Koza (1998):
you had me at #!
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 or here or what another biologist (T. Ryan Gregory) says here.
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.
I'm a Christian, and what annoys me about Christian creationists is according to "true Christianity" belief in creationism isn't necessary to be a Christian. All you need to do is follow Jesus.
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.