Junk DNA Is Watching You
I note Leon has linked to a story about the IBM research into repeated bits of
the human genome. Coincidentally, I've got that very paper on my desk as it's in
a field that I'm working on. But I'd like to tell you about a lecture I heard
from a professor from UQ on the issue of what all this 'Junk DNA' is really used
for. If I could remember names, or technical details, I'd use them, but for now
you'll just have to cope with my limited memory.
A quick revision for you non-biologists: DNA is transcribed and translated inside the cell to produce proteins, which then go out of the nucleus and do their work in the body. The shape of the protein, as it folds up in three dimensions as it's being created, is what gives the protein its particular abilities - it binds to the three-dimensional shape of whatever it's supposed to work on. There's a fairly direct mapping between the DNA and the protein which it produces it, so it's relatively easy to find the bits of DNA that 'code for' a particular protein. These are called 'coding regions', and the 'non-coding regions' are where this 'junk DNA' lies.
Firstly, junk DNA is not restricted to humans. Anything past prokaryotic stage - anything complex enough to have a cell wall and a nucleus to contain its DNA - has junk DNA. The more 'complex' (in an arbitrary, non-technical sense) the organism, the more of this 'junk DNA'; the actual number of proteins that the DNA codes for stays roughly the same (in fact, some viruses express more proteins than our DNA does). And the most interesting thing is that large tracts of the non-coding regions are still transcribed perfectly across generations, which implies that there's a lot of positive pressure for them to be there. More mutation occurs in coding regions than some of these non-coding regions!
This Professor's hypothesis is that the 'junk DNA' codes for proteins (or even RNA - roughly, single-stranded DNA) that stay inside the nucleus and regulate when various proteins are made, and possibly even how it's folded. This would explain a lot of what we don't know about protein production, which is mostly in the are of why the body produces some particular protein at some times and not others. They do have evidence to show that RNA within the nucleus affects and regulates protein production. Research continues, as far as I know.
It's like observing a machine from the other side of the internet. You have the source code but it's not in any language you understand, and you're trying to deduce what parts of the code do. You can map what inputs and outputs it has, and from those you can pick up what bits of code might produce those messages. But the memory management stuff? The swapping? The disk IO routines? Even the process management code is never physically represented by a single packet sent from the machine. So you write off all that code as 'junk code' and don't worry about trying to understand it.
Stupid, eh?
One final challenge that the Professor offered, which I think is worthy of the
minds of Open Source: Try to come up with a way of encoding a picture such that
the picture contains the instructions to build itself, and the machinery to
execute those instructions, at any scale, and is still a recognisable picture
(i.e. simple quines don't count - it has to look like something.)
posted at: 07:37 | path: /tech | permanent link to this entry
The CanberraNet idea
I had a very nice afternoon drinking beer and eating at Das Kleinhaus (as long as
I've used the correct gender - I don't know) on Saturday with Rainer, Chris and
Matthew from Kororaa with brief appearances
of a very tired Pascal. (We shared a brief complaint about how non-Canberrans,
Sydneysiders especially, feel a need to disparage Canberra, then both dismiss any
attempt at rebuttal with disdain and get all defensive about their native city as
if no person in their right mind could question the urge to live in Sydney.
Thank you, Hypocrisy Central.)
We talked about the idea of a wireless mesh network in Canberra; specifically, a network that existed separately to the internet (which avoids many of the legal problems that you get embroiled in if you look like an ISP). My concept here is that this mesh would duplicate many features of the internet; it would have its own IP range (possibly using IPv6), DNS TLD, and enthusiastic contributors could provide search engines, web pages, VOIP, Jabber, and so forth. Because the same basic structure and technology that powers the internet would be used in the mesh, it would be covered by the same laws: which means that publishing unauthorised copyrighted material is illegal but the network is not held responsible for enforcing that.
I know there's been a similar proposal hanging around here (and elsewhere) for years. I don't know the specifics, and to my mind it gets hung up on the whole "how do I know what people are using my internet connection" problem that's implied when you talk about making the mesh join the internet. I think there are deeper technical issues such as routing and address spaces and such that also need to be solved in that case. This is why I think that any successful mesh needs to have its aim solely as providing an extra backbone for data transfer on its own network that's completely independent of the internet. But this in itself is not a compelling reason to anyone individually to set it up.
There are two problems here: having useful content available to actually make it
interesting, and having a way for end users to find that content. Again, these
problems have been solved on the internet - we now have lots of people putting
all sorts of interesting stuff there, and search engines go around and find out
what's there and index it for easy finding later. The real problem is content;
and to complicate it is the issue of why put anything on the mesh if you're not
going to put it on the internet (and, vice versa, why put anything on the mesh
that's already on the internet). There may be some things, like live video and
audio or high-quality voice chat, that can be done better in the mesh than
through the internet - but why reinvent the wheel?
posted at: 07:15 | path: /tech/ideas | permanent link to this entry
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