Sunday, September 11, 2011

Magnetic Tweezers

So I thought I'd just write down what I'm working on for the average person who's curious. I work on an instrument called a magnetic tweezer. We use magnetic tweezers to study biophysics. We can take a single strand of DNA and bond a magnetic bead to one end of the DNA and a glass slide to the other. Since the bead is paramagnetic, we can stretch a single strand of DNA when we bring a magnet close by. By changing the distance of the external magnet we can change the force on the DNA, and thus we can do force spectroscopy (a fancy word for measuring DNA length as a function of force). Within the Saleh Lab where I work, there are a few main topics of research using magnetic tweezers: ion-DNA interactions, DNA-DNA interactions, and protein-DNA interactions.

I work on protein-DNA interactions. Specifically, I am interested in a class of proteins called helicases. These proteins unzip genes and are therefore the subject of many biology-related pickup lines. Perhaps even more interesting is that they are involved in replication and all sorts of biological functions. You have trillions and trillions of helicase molecules in your body. Helicases are the bulldozer at the front of the replication machinery. We have classified a bunch of different types of helicases, but we don't yet understand how helicases move. We know that they burn ATP, but do they take single base-pair step for each ATP consumed? Or do they take steps of multiple base-pairs? Right now we don't know, and I hope to use magnetic tweezers to measure the step-size of helicase molecules.

There are numerous technical challenges standing in the way of answering fundamental questions about how helicases move along DNA. First of all, we can't actually see the DNA or the helicase. All we can see is the magnetic bead and use that bead as a probe to deduce the position of the protein. We typically use a hairpin of DNA, whereby each base-pair that is unzipped results in the magnetic bead moving towards the magnets by about 0.6 nanometers per base-pair unzipped. To put that in perspective: that's very small!

Measuring helicase steps are further complicated by the fact that the magnetic beads are undergoing Brownian motion from being bumped around by the surrounding water molecules. So when we see the bead move, we never really know for sure if it was because the helicase unzipped a single base-pair or if the water molecules bumped the bead and stretched the DNA a bit. The only way to get around the thermal noise is to take lots of measurements and average out the noise. So that's the reason I have been playing with a high-speed camera a lot lately. Oh, and everything is cooler in sloooowww moootttiiiooonnnn.

I'm trying to make the best of your tax-payer dollars, but if you have any questions or comments I'd be happy to hear them.

Thursday, July 14, 2011


What is the future of bitcoins? In the short term, I see one major opportunity: point-of-sale terminals. In the medium term, I see one major potential problem: deflation. In the long term, I believe that some sort of hybrid Bitcoin system will take hold that allows for variable inflation rates.

What is Bitcoin? You can download a Bitcoin program at This program creates a digital wallet for you with a balance of 0.00 BC (bitcoins). To fill up your wallet you can do one of 2 things. You can either buy bitcoins from someone in exchange for some good or other currency, or you can mine your own bitcoins. Don't bother trying to mine though if you don't have at least a high end graphics card, it's not worth the electricity costs. I personally have mined around $0.50 equivalent in bitcoins over the course of a few weeks. Not much, but for me it's about the idea not so much the money.

One immediate opportunity that I see and would love to get involved with is a point-of-sale (POS) terminal. Veriphone makes POS terminals, and these can apparently be programmed in C/C++. Unfortunately, you have to be accredited to be officially allowed to make applications for them, and I'm too cheap to do that so I can't. These terminals could be set up to process Bitcoins through custom-made smart-cards loaded with a private key. A smart card costs less than $1USD, so this should be feasible. I imagine that stores could request their Veriphone terminals to be loaded with a Bitcoin program. Alternatively, someone could make their own POS terminal to process Bitcoin transactions. If I was a store owner, I think that I would like to have a physical device that sits on my counter and accepts Bitcoin cards. I don't like the idea of using a computer or smartphone to process a transaction, which is unfortunately the only way to do things right now. The hardware should be physically there, but again that's just my opinion. A bitcoin POS terminal doesn't currently exist, so it's a great opportunity for someone!

Deflation? Well, there are only ever going to be around 21 million bitcoins in existence because the mining that myself and others are doing is becoming more and more difficult. Some people have argued that this could lead to a deflationary spiral, where hoarders hold their bitcoins hoping that they will gain value, and as a result nobody buys anything until eventually nobody is using the currency anymore. It's difficult to say for sure whether or not this will happen, but I do see it as a major threat. A bigger threat I see to Bitcoins is more fundamental.

To me, the idea that anyone can mine the currency into existence (and secure everyone else's transactions Bitcoins the process) isn't necessarily the only way for a cryptocurrency to exist. The way US dollars are created is that the Federal Reserve buys US Treasury Bonds on the free market. In other words, they create a dollar by backing it with a promise to pay it back with 5% interest per year. That is not currently the case with Bitcoins. There is no free-market buying of securities to ensure the long-term stability of Bitcoins. On the one hand, this means that Bitcoins are completely decentralized, which is attractive to many. On the other hand, the inability to dynamically grow and shrink the money supply is a serious limitation to the potential upside. I believe that Bitcoin would be much more effective if it could expand the money supply quickly (or contract if need be). Since Bitcoin cannot expand/contract the money supply dynamically in response to pressures and can only grow at an arbitrary predetermined rate, it is missing a key piece of the recipe for success.

I predict that a future cryptocurrency will allow for dynamic inflation rates to be set by users in a peer-to-peer network. If a user or group sets the inflation rate too high, they will eventually go belly-up. If the inflation rate is too low, that person or organization will get out-competed by more aggressive growers. It's actually very similar to what is happening now, just without a bunch of bankers and politicians determining the correct rates and bailing out their "too-big-to-fail" friends. It could be a nice future, one where 40% of the economy is not based on the financial sector, but is instead based on real things.

I think that this is an exciting time to be witnessing these thought experiments in finance turn into multi-million dollar ideas.

At this time, the value of all the Bitcoins in existence is: $95.4 Million USD

Wednesday, July 13, 2011

Airport Scanners

There is some controversy about full-body airport scanners. The two concerns fall into categories of privacy and public health. I will focus on the health effects. There are 2 types of scanners, X-ray and microwave. Since I did my MSc in nanotechnology with a focus optics, I can't help but think about these 2 different sources in terms of their physical effects on human tissue.

On the one hand, a single x-ray photon can ionize an individual atom, (rip an electron off). When ionized particles are created inside cells, they can create oxygen radicals and other nasty charged particles, which can cause cancerous mutations. At very low doses, x-rays have no measurable effect since the body can clean up most mutations, but at high doses or consistent medium doses, they can cause cancer (see Fukushima for details). The airport x-ray scanners are not routinely tested by an independent body, and we therefore have to accept the claim of the manufacturers that the doses are not harmful. I for one do not, and neither do a large number of UCSF Professors:

As for microwave scanners, these emit lower wavelength radiation. The wavelength is so low that an individual photon can only heat up a large molecule, not ionize it. This means that I would feel perfectly comfortable standing in front of a microwave beam. Well, not perfectly comfortable but at least I wouldn't have to be worried about cancer:

So if I get stopped at the airport and pulled aside for an x-ray scan I'll say no, microwave scan: go ahead. What about you?