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."
Of course its not junk (Score:5, Interesting)
Re: (Score:3, Insightful)
Re:Of course its not junk (Score:5, Funny)
Re:Of course its not junk (Score:4, Funny)
Re:Of course its not junk (Score:4, Funny)
Re:Of course its not junk (Score:4, Funny)
Re: (Score:2, Funny)
Re:Of course its not junk (Score:5, Funny)
Or would that be a car that would only allow other cars to ride in it?
Re: (Score:3, Funny)
Re: (Score:3, Funny)
Re: (Score:2)
Re: (Score:2)
Not if you use the right analogy. Sure, the GP used a pretty poor analogy which fell over before he even hit Submit:
The entire DNA sequence is both data and instruction. Bad analogy right there.
A better analogy might be: "It's what we in IT would call error correction" because if you mess with the so called "junk DNA", it makes it nearly impossible to reliably make copies, just like with CDs....
no wa
Re:Of course its not junk (Score:5, Informative)
Re:Of course its not junk (Score:4, Interesting)
In laymans terms, the "Junk DNA" provides the bootstrap routine and program code of an life form building nano-machine. The "Gene DNA" provides the instructions to the life-form-building-machine on how to make this life form a "human" or "fly" or "bacteria".
Papers such as A minimal gene set for cellular life derived by comparison of complete bacterial genomes [pnas.org] provide some first steps into understanding how all this DNA works together.
And to the grandparent post - I would argue that the "junk DNA" is not the data segment. For decades we've been thinking of the "Gene DNA" as the program when it is in fact the input data, while the "Junk DNA" is the boot loader, operating system and interpreter. But the machine doesn't build stuff and then move on (like a human-built factory) - it replicates itself, subtly altering the replicants to become more specialised along a growth path that will make one new machine produce stuff that will eventually become a femur, while the other new machine starts building stuff that will eventually become a gluteus maximus.
I've heard of a project where a company set out to create a synthetic bacteria based on the minimal possible DNA, which they could then patent, and use as a base for testing genome manipulation or gene therapy or some such nonsense. Not sure if that's fact or fiction though.
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: (Score:2)
Here's the question - is non-gene DNA /machinery/ or /DATA/?
Non-gene DNA is data -- ribosomes and RNA polymerase are the machinery. I like to think of them as compilers. Chemistry is the real computer, ribosomes etc are among the most important programs. Interestingly, they're sophisticated enough to "compile" themselves, I think. There's some level of control in the data itself as to what gets transcribed: promoter and inhibitor sequences, introns and exons all control what gets transcribed, and there's undoubtedly more and higher levels of expression regulation g
Re:Of course its not junk (Score:4, Interesting)
Re: (Score:3, Funny)
But on to my original reason for posting. If some kind of networks are involved in DNA operation, three ideas come to mind: 1) genetic spam 2) denial of DNA service attacks (I think viruses kind of do that in a way. Making them biological black-hat hackers), and 3) if the RIAA even THINKS of suing me for copying DNA, next time I catch the flu, I'm going to cough ALL over their lawyers. DMCA THAT, yoo ho
Re: (Score:3, Interesting)
How about this:
The non-gene DNA is software - i.e. the CODE segment.
The gene DNA is data - the DATA segment - and defines how to build specific molecules.
The cell and its internals are the hardware.
All IO is through chemistry - i.e. concentrations of various molecules.
There are more things scanning DNA than the repair devices aren't there? Could some of these things be interpreters of some sort? If they had the ability to "write" a base pair
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: (Score:2)
Re: (Score:3, Funny)
Re: (Score:3, Funny)
We've known this for a while [xkcd.com].
Re: (Score:2)
Re: (Score:2)
Re: (Score:2)
Messy Speghetti Help (Score:3, Funny)
Re:Messy Speghetti Help (Score:5, Interesting)
Obligatory.. (Score:2)
Imagine a Beowulf cluster of...wait a minute.
My hairbrained idea... (Score:5, Interesting)
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
Re: (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 th
I never read the instructions (Score:3, Interesting)
Re: (Score:2)
They're experts, they're omniscient (Score:2)
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.
They used to say that the pancreas was just there to keep the rest of the guts in place.
They once removed a part of the brain that was obviously useless, and getting in the way of their operation to a vital part... the patient could never again acquire new knowledge after the operation (as in Memento).
So I never believed them when they were saying "junk DNA".
As usual, that was just hubris.
interesting (Score:4, Informative)
The Selfish Genomicist (Score:2)
Hmm... (Score:2)
Well that just proves it once and for all - it's not junk, hence it was designed properly.
Therefore, God exists!
FUCK!
Re:Hmm... (Score:4, Informative)
Re: (Score:2)
Not sure about birds but it might explain flying snakes [flyingsnake.org].
Re: (Score:2, Insightful)
Evolution doesn't "come up" with anything. The idea is that those with whatever advantage they have survive can breed, and the rest doesn't.
It's mindboggling to see what a computer is capable of if you had no previous looks at what the program did, or what the hardware does.
Its just code that's there for debugging purposes (Score:4, Funny)
Re:Its just code that's there for debugging purpos (Score:2)
sneaky (Score:4, Funny)
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.
Re: (Score:2)
And it is NOT obvious that parts of DNA that don't code for anything useful would be weeded out: there are any number of mechanisms by which this would be prevented, and actually very little incentive TO weed anything out in any case.
Re:junk genes was a junk idea (Score:5, Interesting)
Whenever I read a post like this, I get a reminder how poor is most techies' comprehension of biology, and more specifically, what biologists do.
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.
Okay, why do we care? Because finding the genes (note my use of the plural there) that influence certain traits is the first step toward understanding the overall processes that create them. Obviously this is most critical in the area of genetic disease, although it's interesting for everything else too. We've known for decades that most traits, including diseases, aren't controlled by a single "magic gene." What statistical geneticists try to do is find locations on the genome which have a strong relationship to the trait of interest. And we know perfectly well that there will be a whole bunch of these locations for most traits, and that some of them may represent genes and some may represent something else. The purpose is basically to give the wet-lab biologists something to zero in on.
Second, two of the examples you chose -- blood type and eye color -- are really terrible ones for your argument, because genetically speaking they're very simple traits (two or three loci each, IIRC) and, at least in the case of blood type, we know exactly where they are in the genome. Eye color I'm not sure about, and skin color is a little more complicated, but not a whole lot more so.
Please do not confuse the pop-sci "scientists seek gene for X" writeups with what really goes on in the world of genetic research. It has exactly as much to do with real science as TV portrayals of hackers have to do with real computing.
Re: (Score:3, Funny)
Whenever I read a post like this, I get a reminder how poor is most techies' comprehension of biology, and more specifically, what biologists do.
Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages. And I am a Computer Scientist who worked heavily in genetic research.
Re:junk genes was a junk idea (Score:4, Interesting)
Be careful here--you might just show your own ignorance. "Biologists" is a very broad term that covers a vast array of topics. Sure, ecology might not require much knowledge of computers and information theory, but such things are required reading for fields like molecular biology or modern genetics.
Not necessarily. Sure, that may be the case for single-celled organisms that rapidly reproduce, whose selective forces dictate sheer metabolic efficiency, but for multi-cellular organisms, like mammals, there's good reasons to believe that that simply isn't true.
Evolution isn't like a programmer. It isn't some transcendental force guiding a species to some aesthetically "perfect" design. The result of natural selection frequently isn't the "best" solution but rather whatever happens to work. In fact, many times adaptations based upon the selective pressures of the present are, in time, ultimately maladaptive for the species. A classic example of this is the trait for the disease sickle-cell anemia in humans which originally served to offer slight resistance to malaria but otherwise causes health problems and even death.
A more efficient genome doesn't necessarily mean greater fitness. Consider the following example. For a large multi-cellular organism, which do you think has more reproductive/survival significance: (1) a mutation that deletes a few bases of non-coding DNA OR (2) a mutation that brightens a metabolically-wasteful, colorful marking that attracts mates?
OR that they are mostly random. The current model of DNA/genetics states that most of the DNA in the human genome is non-coding, not (significantly) subject to evolution. As such, it gets shuffled around (i.e. randomized) during cross-over events and mutations. That being the case, one wouldn't expect it to be very redundant or compress very well.
In short, because that's what's easiest. A holistic approach to genomics research like you're describing is not currently technologically, academically or economically feasible for a myriad of reasons. The science just is not there yet.
As an aside, I suspect we'll start to see a more integrated approach to genomics once the relatively low-hanging fruit of the one-gene --> one-protein research lines are throughly covered. However, I wouldn't expect such things to happen in our lifetimes given the difficulty of that aforementioned task and the sheer profitability of more conventional approaches. But what do I know? I'm "just a biologist." =P
-Grym
Re: (Score:3, Interesting)
Exactly, and it's a popular misconception that evolution is always about the "best" and anything that is 1% "better" is going to dominate. Which simply isn't true, or our appendix would have vanished long ago. The fact is that appendicitis isn't enough of a problem to select against it strongly. The appendix just doesn't help, so the genes to maintain it aren't selected for either, resulting in the sl
Evidence for an old idea (Score:2, Interesting)
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 say ;)
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!
Actually, generally no and genome sizes can very a lot. There are a great many thing
Re: (Score:2)
Re: (Score:2)
Good luck! Let us know how it goes!
Re: (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 l
Junk DNA (Score:4, Funny)
Re: (Score:2)
Next on the list (Score:2)
I'm guessing a lot of the "human genome" is *airborne*.
--
Toro
This is hardly 'news'.. (Score:4, Interesting)
ID's advantage of evolution (Score:2, Interesting)
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 f
Re: (Score:3, Insightful)
Re: (Score:3, Interesting)
For me, its an Occam's Razor thing.
If I find a pencil on the sidewalk, the most obvious thing is someone dropped it.
I see life, and am at awe of its complexity. I have to conclude something designed it. Jehovah - Yahweh - the name as I understand it is Hebrew meaning "to cause to be". The name of God. Fair enough.
My problem is finding God. I mean God. Not religion.
Religion is Man's doing. Even if it was done in the best of intentions. The Church has killed some fine scienti
Re: (Score:2)
Based on what I've read in the Bible, I'd believe God implemented religion, specifically Judaism/Christianity. However I'd have to agree with you that, like always, Mankind has thoroughly mucked up God's handiwork.
Re: (Score:2)
Teleological Argument (Score:3, Insightful)
Re: (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 someth
junk DNA (Score:2, Interesting)
One thing I'm sure is that Nature doesn't waste resources, only Humans do, so each
Do we even have the *full* genome mapped? (Score:2)
Re: (Score:3, Interesting)
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
Jesus, bring on the Intelligent Design wakos! (Score:2)
Patent wrench? (Score:2)
Ah, yes... (Score:2)
"This creature has no recognizable central nervous system - no heart, lungs, kidneys, liver or even a simple brain that I can find. Maybe if I WERE an Engineer I could make sense of all of.......this..."
If McCoy couldn't envision a connection between data networks and the human genome, what does that say about - Wait...he was an actor, right? Not a real doctor in the future...?
Roddenberry has some explaining
Ban GMO Grops Immediately (Score:2)
If this research is right, it would be naive to assume it only appli
Cells run on Unix not Windows (Score:2)
The only thing that gives me huge pleasure in this (sorry) is that I find Richard Dawkins overbearing, overclaiming, and pompous. It's nice to know that his approach to
Re: (Score:2)
so are individual genes still real? (Score:2)
Great, so now we have junk RNA (Score:2)
In reality, it only shifts the issue: we now have tons of RNA with no apparent function. That RNA is in the exact same situation that junk DNA was - in essence, we now have a junk RNA question. If that RNA tur
Some of this is not so new. (Score:2)
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.
this is familiar to anyone who's studied GA (Score:3, Interesting)
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):
Re:error correction (Score:5, Informative)
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.
Re: (Score:2)
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:error correction (Score:5, Interesting)
There's really almost no selection pressure [wikipedia.org] 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 [wikipedia.org].
A promoter is a marker in the DNA strand. The protein "machine" (a transcription factor [wikipedia.org]) 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 [wikipedia.org] 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 [wikipedia.org] is one of these retroviruses that has infected our DNA. So when we look at the entire human genome [genome.gov], 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...
Re: (Score:2)
Re: (Score:2)
Anything, of course, is possible -- until we can simulate the system and take an exact inventory of the code and everything it produces. If there actually are endogenous retroviruses integrated into our genome, then their being functional requires some type of promoter. They could even bring their own transcription factors along with them. You could imagine that, in order to get the "original" transcription factor produced it would have to bring it along from the original cell, or inherit it in breast mi
Re: (Score:2)
We've got pwned in a CoreWar.
... ebola...?) that deterministically causes exactly such an error, we could die very quickly (and in horrible way, falling apart, fast
On the serious note, does it mean we are trap wired ? An error in positioning could activate viral DNA and start "insider" infection, anywhere in the tissue. If there was an chemical agent (i.e. a bacterial toxin or another virus, e.g.
Re: (Score:2)
Re: (Score:2)
Re:error correction (Score:4, Interesting)
Re: (Score:2)
Wouldn't that be cool? Like, you know how when we're under stress, we feel *almost* sick -- totally drained and useless, but not in any way that would keep us from doing what we need to survive? What if our bodies are actively searching for genes to reactivate (somatically), and some of those changes can be made semi-permanent through changes in the balance or design of certain transcription factors, or even fully permanent by modifying the genes themselves in meiosis?
It would seem that this particular t
Re: (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
Re: (Score:2)
Re: (Score:2)
Re: (Score:2)
You have to take into account the energetics of the system. Extra (x) = Extra energy (E).
We, who live in the petroleum age, take energy for granted, but when you have to get energy by murdering other animals and eating them, energy comes at a premium. Therefore, things that burn a boatload of energy have to "perform" (i.e. be really useful to genetic transmission) to become dominant features over time. So, the peacock tail is a huge expenditure of energy growing it and
Re: (Score:3, Informative)
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
Re: (Score:2, Interesting)
Re: (Score:2)
Re: (Score:2)
Re: (Score:2)
Re: (Score:2)
Re: (Score:2)
This is what I found: The article [scienceblog.com] and its source [ucsd.edu].