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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.
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.
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...
I walk down the street and see 100s of people who appear to be predominantly junk DNA.
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 ;)
Whenever I read something like this, I get a reminder how poor is biologists' comprehension of Computer Science, Information Theory, and languages.
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.
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
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...
Only to idiots, are orders laws.
-- Henning von Tresckow