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."

Comments

Re:Of course its not junk

[buswolley]

I doubt it. Analogies always fall down.

Re:Of course its not junk

[TekPolitik]

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

[MikShapi]

Not quite. Your analogy appears somewhat broken.

Here's the question - is non-gene DNA /machinery/ or /DATA/?

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

[cnettel]

Genome space is damn cheap, just like disk space. The added tax on each cell to carry bloat is minimal. No matter how much is transcripted, we can analyze the sequences that we do see in the "junk". They are often very repetitive, with some sequences clearly deriving from viruses that integrate into the genome. The added selectional advantage of having the same (possibly now suppressed, but originally pathological) sequence, over and over, should be quite small, and the pattern and frequency of changes seems to indicate that most of these regions do not undergo any directed selection, i.e. mutations that do appear are kept at random, indicating "no value".

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).