Tuesday, August 21, 2012

On the teaching of genetics

Rosemary J. Redfield wrote an article on the teaching of genetics that resonated with me. Apparently the standard theory for teaching genetics is a sort of reprise of the history of genetics - you start with Mendel and dominant and recessive genes, move on to genes being on chromosomes, and slowly get on, if you're lucky, by the end of the course, to the molecular analysis of genes. The theory behind it is that the students will stand in Mendel's shoes and ask, "Well, why are some genes dominant", which will be answered by the next phase of the course, which will prompt more questions, to be answered by the following unit, and so on.

The problem is, that strategy doesn't work.

(Close-Up) Erratic Black Hole Regulates Inside Quasar (NASA, Chandra, 03/25/09)It reminds me of astronomy classes both in high school and college. Now, astronomy is an awesome and fascinating subject. Go pick up any popular science magazine with an article on astronomy and just check out the language that they use: "Quasar". "Black Hole". "Dark Energy". "Strange Planet". It's like the whole subject was created just to appeal to teenagers. There is a podcast dedicated to astronomy called AstronomyCast that goes over a lot of this stuff, and my eleven-year-old son cannot go to sleep at night without listening to at least a few episodes.

But I hope that the interest isn't torn out of him in high school. If his courses are anything like mine, they will discuss: Stonehenge. Galileo. How, if you stay up night after night, you can see the position of the planets change slightly in relation to the stars. How an optical telescope works.

“Students know what the cool stuff is.”
This isn't the cool stuff. Students know what the cool stuff is. If they don't listen to AstronomyCast, they've probably seen episodes of Nova, or at the very least, played a videogame in which black holes or wormholes play an integral part.

Genetics is just the same. Engage the student's interest by hitting them with the cool stuff first. Don't try to emulate the thinking of Mendel, because the instruments and techniques we use today are so much more powerful than Mendel ever dreamed of, and students know that, and often know what the techniques are. Redfield suggests starting with personal genomics, which seems like a good plan. Students, who know that they have a unique genetic makeup, should be interested in knowing what that makeup is, or at least how to find out. This would lead directly to the ethical questions surrounding that knowledge, and the course is off and running. Redfield is on to something.

Saturday, August 18, 2012

DNA as storage mechanism

It seems some East Coast researchers are pushing the envelope in storing information in DNA. They encoded a book, roughly 5 megabits of data, into oligonucleotides, which were "synthesized by ink-jet printed, high-fidelity DNA microchips" which I don't fully understand but I presume means "made into a glob of DNA". The authors then sequenced the DNA and recovered all the data, with 10 incorrect bits. DNA
The innate four bases (A,G,C,T) of DNA seem to lend themselves to some interesting storage techniques. The authors used simple redundancy for their storage - A and C both represented 0, G and T were 1, which was apparently a departure from earlier attempts which encoded each pair of bits into a single base. This made it easier to construct more robust sequences. I wonder if additional error-handling could have been done by placing checksum bases at intervals along the strand? Two bases would provide a range of 16 possible checksum values which seems it would handle a nice string of bits.

The book that was encoded had 50,000 words and eleven pictures. With an average code space of 40 bits per word, the text should have taken a tiny fraction of the total space, with the images providing the majority. Suppose that all ten bit errors were in one picture? It would be interesting to know how tightly compressed the images were. With a high compression factor, some of the bit errors might be substantial, but small changes to the compression might make a large difference in the visibility of any bit errors.

The authors say that DNA storage is dense, stable, and energy-efficient, but prohibitively expensive and slow to read and write compared to more standard storage. It will be fun to see how this technology evolves!