Monthly Archives: August 2009

New generation of drugs, and the next things for TBU

Occasionally, I get asked what I do. Here’s a little introduction to the kind of technology I’m working with. Aptamers are short bits of DNA that bind to whatever target of interest you might be interested in. Why is that useful?

Here’s one good reason, from a TED talk by Kary Mullis. He won the Nobel prize for inventing PCR. Now he is making aptamers that act like the tape on a big note on a bacterium’s back that say “EAT ME” to the immune system.

I’m going to take the Big Upshot in a new direction. From here on out, I’ll be doing my best to make posts relevant to current and future medical students and biomedical graduate students. We’re going to talk about the periphery of a scientific education that might otherwise get missed.


Smart Dogs

There have been a few articles recently about the finding that dogs are about as smart as two-year-old, human children. They have a similar level of vocabulary and mathematical ability, and they can deliberately deceive – something that children only learn to do later. So that’s where dogs stand today.


Here’s a question I have been considering for a while: how long would it take to selectively breed dogs with human level intelligence? I’m not considering transgenic dogs or gene-splicing. Genetic mapping for mate selection is OK. What are we talking about, here? I imagine it would be a logarithmic curve: quick at first as we collected all the smart genes in one dog, then slow as we wait for mutation to produce a breakthrough.

But if we don’t look for anything but intelligence – that is, let the breed characteristics fall where they may – how close could we get and how fast?

Let’s say we have a pool big enough to get to human level intelligence in 200 years. That’s probably quite optimistic – about 100 generations. What are the ethical implications? Moral implications? Did we just create a creature with a soul? Was that morally right or wrong? Are we morally obligated to do this, if it is possible?



MATLab and Biology

I made a bold prediction today. I predicted that Biology, as a discipline, would adopt MATLab as its computing environment. That may have been overstating things, but still, here’s why I think so:


1. Marketing: There are plenty of development environments out there. I’m looking at this from the perspective of a non-programmer. And non-programmers think in terms of “what program do I have to buy to do this?”

Anybody can code in a text editor in C and compile with a free compiler. But it’s not a complete development environment with a box, a price tag, and a user-friendly GUI. Biologists won’t use it. In terms of a packaged development environment, there’s MS Visual Studio, Mathematica, MATLab, Maple, Mathcad and some Open Source projects like SAGE.

2. Function Library. I’ve played with all of those but Maple. In terms of large, pre-made scientific funciton libraries, Mathematica and MATLab come out ahead. And they have a similar learning curve.

3. Math. Mathematica definitely has its advantages. But I don’t think that biologists think in terms of solving boundary value problems symbolically. They think more in terms of Finite Element simulations. Discrete math. That leans toward MATLab.

4. Social network. I suspect that the biologists will turn to their biochemist, chemist and engineer friends for adivce on computing, and they will hear MATLab overwhelmingly. I doubt they will go to
the physicists and mathematicians, where they might hear more about Mathematica.

OK, so MATLab’s the way of the future… what can you do with MATLab?

You can do everything that Excel does (including much nicer graphing options). Plus you can analyze images, spectra, or any other data. Most importantly, when you’ve gone to all that trouble, you can apply it as a loop to other inputs.

Take this for instance. Say you have a fluorescence image of cells. You go to all the trouble of figuring out three data values from that image. Maybe you measure cell count, average cell area, average cell fluorescence brightness. The trouble is that you probably have 100 images. Or you would like to in order to have a publishable result. That will take forever. If you “train” your PC to do that with MATLab, you can just run the program on a whole directory of images and have it spit the results out as an Excel file (if you insist on using Excel). Or a nice graph (it will look better if MATLab makes it).Or you can make a little GUI for your friends. I worked out how to do that in about 3 hours. Next time, 15 minutes.

Quantification is the future, and it is now.


Future Energy and 10 Dollar Gasoline

I’ve been thinking a lot about energy lately. I just drove to Austin, and I spent $700 on gasoline at about $2.75 per gallon. The word in the blogosphere is that oil production peaked in 2005, and if that’s true, it will play mad hobb with our economic recovery.

So let’s say for a minute that it is true. I took 5 days to get from Seattle to Austin with a huge truck pulling a small car. At $10 per gallon I could go home for about $2500 (just in gas) if I go the same way. Or, if I drive my car, which is far more reasonable, it will be about the same price (if the car makes it). Is that a realistic scenario? Well, if Saudia Arabia really has peaked, then it might be reasonable that we could see $10 per gallon in 2012.

I’ve mentioned it before. In the US we love cars. We won’t tolerate $10 per gallon (interstate trucking will have to be subsidized, or there will be serious problems with moving food around). We will start up alternative fossil fuel liquification and we will convert vehicles to natural gas… delaying the problem, not fixing it.

Nuclear will play a big role. Nuclear powered fuel reforming can bring prices back down… if we can decide what to do with the waste…

None of this answers the climate change question.

The politics of the above are just too messy. A Greenpeace person talked to me the other day. I had nothing positive to say, really. Greenpeace is polishing the deck chairs on the titanic. Whales? The whales will be fine. Wind energy? That’s great. If we have a miracle, maybe it can offset 20% of our fossil fuel problems. What we need is nukes, and we need the no-compromise ninnies to get out of the way.

Meanwhile I’ll be working on Alzheimer’s Disease. When there’s a real crisis, people will get out of the way. When gas is $10 per gallon, we’ll see action. Maybe we’ll see if I want to look into nuclear career options at that point.