Unreal

If anyone ever doubts that the Internet can truly be a powerful democratizing force in the world, where the average person can say something and have it matter, check this out.

I started this blog last week. I've never blogged anywhere before, and a search for my name on Google isn't going to bring up any significant hits to me (except now for this post I'm about to talk about!). In other words, I'm not a "big voice" on the Internet.

A few days ago, I posted my third blog post ever to this free Blogger account. I wrote about how I liked David Weinberger's book Everything is Miscellaneous, and made an observation about how the themes he develops tie into what I work with, namely the human genome. Nothing big, maybe a little insightful (I thought it was neat, anyway). I wasn't really writing "for" anyone... this blog is just a place I can write some of my own thoughts down, and if that might be useful or interesting to someone somewhere, then all the better.

Today I'm sifting through my newsfeeds, and I see that David Weinberger has linked to my post on the main page of his book's website.

Think about that for just a second.

Thanks to the infrastructure that has been built up surrounding the Internet (Google indexing, Technorati blog indexing, folksonomic tagging, etc.), the words that I wrote were found and read by the author of the book I was talking about. This isn't a top-down organization, either: there aren't professional indexers, catalogers, and abstractors out there reading and organizing everything that gets published online. This is truly bottom-up organization, growing organically out of the miscellaneous pile of information we're growing online: the content, the usage patterns, the metadata—everything. Nobody needs to see that "Ah, Christopher Maier has published a post on "Everything Is Miscellaneous." We need to properly file his post in the "Everything is Miscellaneous" bin (or was it the "genomics" bin, or...)". Furthermore, very few people, in the grand scheme of things, are going to particularly care that I've done such a thing. However, for the people that would care about it and are looking for something about Everything Is Miscellaneous, or genomes or whatever else I talk about, this infrastructure presents it to them, as if by magic.

It is difficult, if not downright impossible, to see kind of thing happening prior to the advent of the Internet. And it's really exciting to see where this will ultimately lead.

The Genome Is Miscellaneous

Hopefully by now you have read David Weinberger's Everything Is Miscellaneous: The Power of the New Digital Disorder. It's quite an interesting and absorbing read, one of those books that makes you look at the world just a bit differently. I seem to be doing that an awful lot lately, finding unexpected applications of Weinberger's thesis all over the place. The latest? The human genome!

The ENCODE Project just published its findings from a detailed investigation of 1% of the human genome, and it looks like it's waaaaaaaaaay more complex and interesting than we thought. There's the main article (DOI: 10.1038/nature05874) in the current issue of the journal Nature, and a whole slew of additional articles in this month's Genome Research. I've been working through Gerstein, et al.'s What is a gene, post-ENCODE? History and updated definition (DOI: 10.1101/gr.6339607) for a very absorbing look at how our notion of a "gene" has changed dramatically in the years since Mendel and his peas, and where our understanding of "gene" stands in light of this exciting new data from ENCODE.

It looks like the genome, far from being a nicely organized library of genetic building blocks, is a messy snarl of bits of coding DNA, all mixed up together in a pile. There is of course some physical structure to it all, but it seems pretty well jumbled up; the parts of a gene don't even need to be on the same chromosome. It reminded me of Weinberger's big miscellaneous pile, into which all our information goes, waiting to be organized by users and searchers according to their needs and desires. In the Miscellaneous Genome, the users and searchers are the complex regulatory networks of the cell, which seek out and assemble the bits they need to create the machinery and processes of life. They know how to read the genomic metadata that we are trying to grasp; once we can read the metadata, we'll be able to sift through the Miscellaneous Genome with ease.

Go read the book; go read the articles. Good stuff.