Biotech Project: The DNA Sonata

Let me start by addressing the elephant in the room: can you nominally have a blog on “biotech integration” and never talk about biotechnology? Alright, you got me. The answer is no, you can’t. I have been delaying this first foray because, well, biology is hard. Not “hard” in the sense of the hard sciences (where you have lots of maths, theorems, and clean data); physics falls into that category and it is all rather easy. No, I mean “hard” in the sense of quite difficult because everything is fuzzy and moving about a lot. “I think you will find it is a bit more complicated than that, actually”. That sort of thing. It is annoying.

But look, you have to start somewhere. And where better to start than with some advice from everybody’s favourite biologist, Nobel-prize-winning physicist Richard Feynman:

Study hard what interests you the most in the most undisciplined, irreverent and original manner possible.

Richard Feynman

As anyone who knows me will tell you, I am certainly undisciplined and irreverent, so I take this to be a good omen.

The DNA Sonata

So here it is then, my most ambitious project to date. I am going to give you my perspective on what DNA is all about. The goal is to end up with a great crash course on DNA. We want to get up the learning curve as quickly as possible, ideally without alienating ourselves from the molecular biology community at large. That being said, I will never promise to not annoy biologists. I see progress going something like this:

Irreverent Claim 1: It is Just Information

One of the reasons I find the study of biology so interesting is that it is basically a mechanism for life to understand itself. Somehow we have these strange molecules in our cells that have allowed us to evolve to the point where we could discover them and then give them names like “DNA”. Everyone knows what DNA is, more or less, and they all love it. It has even made its way into common sporting parlance – “we don’t quit, its not in our DNA”. It has passed the (ahem) acid test for cultural relevance. But what does that actually mean, “its not in our DNA”? I think it means “we are incapable of acting that way because that behaviour is not hard-written into our behaviour”. So most people have an idea that DNA contains instructions and data, in other words – information.

Information is a fundamental concept, arguably more fundamental than physics in some ways. It is therefore cool. Humanity has invented many ways of creating, moving, and reading information over our relatively short history. Probably our best invention has been binary code, simply because it allowed us to pass our information to computers. Computers operate at GHz speeds, the typical human would be lucky to live for 3 Gs (that’s three billion seconds). That means that if a computer works on a problem for ten seconds it has really been at it for the equivalent of three lifetimes – imagine what you could get done with that amount of time!

That being said, if it weren’t for our fascination with digital computers we might not care too much about binary. Imagine if we invent (or discover?) some more advanced type of computer in the future. We might scrap binary altogether. “It was just a phase” we will say. It could be the new semaphore: great if you are interested in naval history or pirates (watch this space for a future post on why pirates are cool) but not something that underpins much of the economy.

How Nature Handles Information

Imagine you are Mother Nature. You think it would be great for life to pass on genetic information about itself. If you could crack that problem it might be possible for life to evolve into a dramatic variety of forms. That sounds pretty interesting. Firstly, whatever you use to hold information is going to have to really small otherwise all your little lifeforms will be unable to carry it around. But it also needs to have some degree of complexity (available entropy) so that it can change enough to hold different states (informational capacity). Okay so it is starting to sound like I might need a molecule here. Well it would have to be a stable molecule or all my data is going to get corrupted too easily. But not too stable because then I couldn’t get some other “machine” to come in and read the information; my information wouldn’t be accessible. If I can imagine such a molecule then I also have to make sure that I can make it out of chemical building blocks that are abundant. I want the proliferation of life to be break-neck, not bottle-necked.

DNA, with its double-helix structure, solves all these problems. For your investment in a handful of super-abundant chemical elements, you get a molecule with a tough sugar backbone and a gooey informationally-rich centre. Information is encoded in the four DNA bases: adenine (A), cytosine (C), guanine (G), and thymine (T). Want to read out that information? No problem, just peel open the double helix a bit (using an enzyme) and start reading off your bases (also using an enzyme – okay so you need enzymes too, we will get to that another time). Oh and remember to close your helix as you go.

Irreverent Humans

Interestingly, not only has Mother Nature worked out her own way of reading, copying, and writing DNA-based information, but we humans have taken a crack at it too. We can read through Sanger sequencing, we can copy information using PCR, we can edit using rDNA, and can even write DNA from scratch through phosphoramidite chemistry. These technologies are not even that new; the most recent invention, PCR, has been around for forty years. But as a species we aren’t satisfied to sit on our laurels, are we? We continue to push advances in each of these areas, often to the point of pushing ethical boundaries, in our quest to “engineer nature”.

Maybe we are just irreverent.