To all my biohomies...

[kickaha]

I am aswim in ncRNA, miRNA, snoRNA, transposons, introns, exons, and transgenic events. I know now the beauty of ultra-conserved sequences (and how they kept robust against intron invasion), and deny the junk-DNA orthodoxy.

I also see precisely how my research fits into all of it.

John Mattick said "We should talk."



Yeah, it was a good afternoon. :)

Comments

[franktheavenger.livejournal.com]

....

What?

[kickaha.livejournal.com]

My research in software, being able to extract the abstract relationships between elements of source code, and produce a model of what the system does, how it does it, and *why* it does it?

...could be applied to DNA.

Seriously.

[franktheavenger.livejournal.com]

No way!

....

Of course, I assume this means you have another project. :p

[kickaha.livejournal.com]

This means I have another project.

*sigh*

ObWay:

Way!

Dude.

[badger.livejournal.com]

Cool.

[flinx.livejournal.com]

Rock.

Of course, some of that stuff is in the far, far hard-core structural molecular bio that I dodged back in grad school.

[kickaha.livejournal.com]

What, you think I know what I'm talking about? :D

Why think small?

[ssandv.livejournal.com]

Just analyze the universe as a whole and be done with it already. I want to know the answer. I'm not buying that whole '42' dodge.

Re: Why think small?

[kickaha.livejournal.com]

Well I *do* have that idea for a nice programming model for quantum computing that leverages the superposition of states not just for data, but for type information as well to give a superpositional polymorphism... does that help? :)

Re: Why think small?

[ssandv.livejournal.com]

Heh. If you leverage it in that way don't you get Heisenberged out of one in trying to get the other? Or is there a way to spin it that avoids that? (sorry. well, not really.)

I was thinking more about projective spaces, compression, and entropy, actually. But I'm really more of a classical mathematician at heart, so what do you expect? :)

[herithoth.livejournal.com]

I'm considering a postdoc position that involves micro RNA and I've been trying to read up about various nontranslated RNAs, so we should talk. I've been thinking that retroposable DNA element propagation has a special relationship with the male germline although it may differ depending on which family of DNA elements one is talking about. Approaches like you used in your graduate work could link the structure of a regulatory network and potential purposes of network components. What aspect of RNA regulation are you thinking about?

[kickaha.livejournal.com]

Would it help if I said "all of them"? :)

Basically, the way that my research in software engineering took programming and distilled it down to the basic elements, and all the way those could interact, and then built it back up again, I see treating the processes inside the nucleus as a nice big rich run-time environment. The coding DNA bits produce output. The non-coding DNA bits produce the infrastructure for the coding DNA to work in. My research teases apart the infrastructure-producing code from a mix of that and output-producing code, and tells the user what the infrastructure is, and what it does to facilitate the output code's work.

Well, if you have a basic knowledge of the pieces of what the non-coding DNA produces, and how those pieces interact with one another, you can start to build a larger picture of what the overall infrastructure of the DNA processes are. I'm not looking at *one* aspect, I'm looking at *all* of them. If new interactions are discovered, toss them into the soup of what the tool can look for, and start generating new results. Every time a new relationship is figured out, new avenues of inference open up.