Tag Archives: DNA

Daily Roundup: Not Exactly Junk

It’s never been “junk” DNA. I seem to remember reading about this years ago, but it’s only made the news in a major way now, for some reason. Researchers working on the ENCODE project, which was begun to catalog all the pieces of the human genome — everything besides the genes themselves — have confirmed that about 80% of human DNA is regulatory in nature. That is, those bits of DNA don’t directly code for proteins that the body needs or uses.

As this Wired article puts it:

There are transcription factors, proteins that link these pieces together, orchestrating gene activity from moment to moment, and basic rules for that orchestration. There are also multiple layers of so-called epigenetic information, describing how the activity of genes is modulated, and how that varies in different types of cells.

And the proportion of these rules and regulatory elements to the actual genes themselves is quite stunning:

“Every gene is surrounded by an ocean of regulatory elements. They’re everywhere. There are only 25,000 genes, and probably more than 1 million regulatory elements,” said Job Dekker…

That’s a 40 to 1 ratio right there.

This information is crucial, because it’s often not enough to know simply which genes are expressed and which aren’t. Of course, the gene expression is often only the first step in a long process that results in a symptom or disease or hormone expression. But knowing only where the gene is and whether it’s turned on or off is akin to seeing only whether a a light switch has been thrown or not. You aren’t able to see the internal wiring or to control when and how that switch is thrown.

Hopefully, ENCODE will soon be able to give us glimpses of that wiring.


Daily Roundup: DNA as Storage Device

(Late to the party, or what? Unfortunately, my day job every now and then interrupts my fantasy of becoming a science writer.)

Amid the building excitement around quantum computing, storage and transmission, researchers at Baltimore and Boston have managed to encode an entire book (on — what else? — biology) into DNA. As Nature News puts it, it’s the largest piece of non-biological information ever encoded in a biological molecule like DNA.

The concept isn’t difficult to comprehend, although the execution is delicate, for obvious reasons. The team decided to treat the information as digital bits of ones and zeros, and encoded every character of the textbook (and, note, this includes images and a JavaScript function as well)  into its ASCII representative. Then, they decided on a biological-binary mapping scheme: A(denine) and C(ytosine) would map to 0’s, and G(uanine) and T(hymine) would map to 1’s. The DNA strands would then be synthesized from scratch. To read the information back again, the researchers first multiplied the DNA using PCR or polymerase chain reaction, which ensured that data would be preserved with very few flaws. Then they sequenced the DNA — “reading” it back to determine the sequence of bases — and then decoded it back to 0’s and 1’s and then to characters.

There’s a remarkable graph in their abstract here that places their work in context, when it comes to information density.

Screenshot from the online paper. Copyright George M. Church, Yuan Gao, Sriram Kosuri and http://www.sciencemag.org.

We see that the information density of DNA is a few magnitudes higher than the next most efficient method of encoding information. This is also a good place to point out that DNA itself has evolved to be incredibly high fidelity: it must be capable of preserving information about an entire organism through its lifespan, so storing information in it is very stable indeed. In fact, in this experiment, the researchers recovered their data with only 10 bit errors in 5.27 million — which gives us an error rate of about 0.0002%.

Of course, this isn’t going to be immediately useful for anything we need in our daily lives. The sequencing and coding will take equipment that is far too specialized at the moment, and will take too long for it to be viable as, say, an alternative to an external hard drive. But think of long-term storage. Any highly sensitive, crucial information of international import could be stored long term, in very little space. Or, if you’d like to think futuristically, it could be part of a planetary colonizing ship’s cargo centuries into the future. All of humanity’s data, in one place!

One interesting thing to note is that DIY genetic tools have been around on the fringe of home grown labs for a couple of years now, and have definitely been coming into their own in the biohacking community. I wrote about genetic hackers previously, and a little web surfing has come up with a couple of articles — published in both Wired and Nature, interestingly enough — that highlight this growing community. If anyone’s going to come up with a way to create nano biobots that you can program through a simple desktop tool, inject into your body, and then wait for repairs or enhancements to be made… it would be the biohackers.