Tuesday, July 10, 2007

Crazy Sheep DNA Project Progress

Heading off on the first vacation in a long, long time, so this blog and my email and Anglo-Saxon Aloud will be on hiatus for a little while, and I won't be able to fill Beowulf Aloud orders for a while (though you might want to order anyway, as I am going to have to raise the price for the next print run as soon as this one sells out). I had thought to bring the computer with me, "for emergencies," and my beloved wife quickly brought me down to earth: "You are the Chair of an ENGLISH department!" she said. "What POSSIBLE emergency could happen that couldn't wait until you get back?" I did not have an answer.

So I'm goin' fishin'. But I wanted to give a little progress report on the Crazy Sheep DNA Project. Like many ideas that sound good from an outsider's point of view, the science is turning out to be both harder and more interesting than I had realized. Today my research partner, Amanda Shorette, and I had a good meeting in which we realized how each of our areas of research will feed into the other, and how all are interdependent. We came up with the chart below, and I'll explain how we're tackling each problem so that others who are doing complex interdisciplinary research can steal ideas.

We begin with the historical research, which tells us what questions are most worth asking. Thus I am training Amanda in paleography (she's right now gotten a pretty good grip on writing basic scripts and is now moving to uncials) and she is reading the introduction to Ker's Catalogue and scanning through Gneuss's Handlist. This work tells us about manuscript distributions and what particular problems might be solved by knowing the relationships of the sheep that gave up their skins.

Then we move on to the physical research. We need to find a non-destructive method of testing; otherwise, libraries won't let us near them. We believe we have a patentable testing kit that could be manufactured very cheaply and distributed to thousands of libraries and researchers, but getting it right requires work in microscopy as well as engineering (conveniently, I'm married to a brilliant engineer; I recommend this approach to all researchers). We have to figure out the thickness of the parchment or vellum, its physical structure, and where we are likely to get the most DNA. Then we prototype the extraction kit and hope somebody gives us money to manufacture them.

The next level, which I've labeled "Chemical," but which should really be called "Chemical/Biological," is where Amanda is teaching me. She is learning well enough to teach the processes by which DNA is extracted from material (using Proteinase K, for example, which breaks down all the protein, leaving the DNA behind), identified (using gel electropheresis) and amplified (using polymerase chain reaction). This is all the wet lab work that we'll practice in the fall under the supervision of my previous co-author, Professor of Biology (and diamondback terrapin expert) Barbara Brennessel.

Then there is an additional Chemical/Biological step that is more on the biological side: we need to figure out the best way to characterize the information we get, whether in terms of complete sequences, or microsatellites, or single nucleotide polymorphisms, or other aspects of DNA. Amanda knows about these, but she needs to teach me.

Then we have to learn how to take the next step, to go from the chemical/biological to the bioinformatic: how to we get our amplified DNA into sequences of base pairs such as TTCSGATTACA, etc.? I don't know, and Amanda is just learning.

But when we do that, my work with Prof. of Computer Science Mike Gousie begins. We will be designing a database with a visual interface to hold all of the information that will, we hope, pour in from libraries and researchers all over the world once we get the whole prototype project running. For a mock-up of the interface (which has been re-designed and much improved thanks to input from Tiruncula, see this post).

Then, and here is where the magic happens, the results from the database feed back to help answer the original historical questions and help us pose new and interesting questions.

So that's the status of the Sheep DNA project right now. Most of the "work" is happening in our heads, as we teach ourselves what we have to do. But I've learned from hard experience that the most important work you do may be the planning that occurs before you ever set foot in the lab, and so my desire to monkey around with PCR must be frustrated for a few more months. But in the end, we hope to end up with some very solid foundations for the research: and maybe a patent or two. Any patent attorneys out there who want to help, given that the value of this particular patent would probably approach zero in financial terms but would be a good contribution to human knowledge (do you think I have to mention that zero-money part when I talk to the college attorney?).


Jason Fisher said...

Jurassic Park meets The Name of the Rose, maybe? What a mind-blowing idea this is. Insanely interdisciplinary (I mean “insanely” in a good way, of course :), and as you say, very likely to open up completely new avenues of research.

Good luck and do keep us posted. In the meantime, enjoy your vacation!

John Cowan said...

If the value of the patent is zero, why do you want a patent? They cost real money (US$50,000 to file, and that's just for the U.S.) and don't do anything for the advancement of knowledge.

Instead, publish any novel and useful techniques in the open literature, so that anyone else attempting to patent your techniques will not be able to.

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