Raman spectroscopy has been used to analyze beer before. There’s even a undergraduate exercise that will let a student calculate the percent alcohol in a sample. I want to try it. It’s definitely not just an excuse to try a bunch of different beers.

Raman is like the complement of IR spectroscopy. People are familiar with IR spectroscopy because it is commonly used in organic chemistry classes. Raman is better for aqueous samples than IR (usually) so it makes sense to apply it to beer. This spectrum adapted from Zou et al shows why. The peaks for ethanol are nicely distinguishable above a low background from water.

There are nice hand-held Raman instruments that will give all kind of useful information about a unknown substance. It has been used for things like law enforcement (is that powdered sugar or freebased adrenal glands?) and Department of Defense business. So it’s natural to apply it to beer. It should be possible to amass a big database of beer spectra, annotate it, and mine it for useful information.

But what we need is a cheap instrument that beer enthusiasts can use to take spectra and contribute. A Beer-o-scope or Beercorder. I’m not sure about the name. But as fun as that sounds, I do need to make sure it will work. To the lab!

“The wheels of open-source,” is a plea to not keep reinventing the wheel. It resonated with me because I love reinventing wheels. I’ve been writing code since 1997. My favorite thing about writing code is implementing my own idea and seeing it work. It’s addictive. The fact is that someone else had that idea, implemented it first, then tested it and improved it. Using their code would have huge advantages, but I don’t get the same dopamine rush.

Logic and preference diverge.

I’ve been learning to use BioPython to analyze high throughput sequencing data. I’ve tried k-mer analysis based on an article from 2011, and that sort-of worked. I got an aptamer… but it didn’t bind native protein, only recombinant protein. And it was the most successful candidate that came out of the k-mer analysis.

So: back to the bench, or back to bioinformatics?

Might as well try to get more from the data we have, I thought. The trouble was that… bioinformatics is hard. I could figure out how to do k-mer analysis by trial and error. How about phylogenetic trees? How about a scoring system for sequence similarity? These things have been done carefully and checked for statistical correctness and computational efficiency.

So… it’s time to not reinvent the wheel. It’s time to follow logic.

The Allen Lab acquired an open qPCR instrument about a year ago. We were on the waiting list for a year, but they delivered. It’s about the same size as a conventional thermocycler, but it does more. It has blue LED illumination inside the heated lid and a green light sensor below. The result is that you can track fluorescence as you thermocycle. The key patents on qPCR just expired so I think they are safe from major litigation.

The instrument’s software is open and quite well designed. You connect to it with a USB cable and then use a browser to connect to its internal software. Once it is running, it doesn’t seem to need the PC connection.

It can do conventional real time PCR as well as melt curve analysis. I have been using EvaGreen dye but I suspect that it would work with SyBr Green or Syto9. I’ve read good things about syto9.

My application has been to use qPCR instead of cyclecourse PCR for my students’ aptamer selections. We also used it to verify the DNA on the surface of microparticles. We can go down to about 10,000 molecules (probably limited by cheap plasticware that adsorbs some DNA; lo-bind plastic might lower detection limits further).

I did have to do a hard reset once after a failed update, but for the most part it has been a reliable instrument.

I avoid the news like the plague but I do like zombie stories. I’ve been thinking about why zombie stories are so popular in American culture. Cracked has some funny hypotheses (excitement, free stuff, simple choices, immediate promotion to head honcho). I think all of those are part of it. I also think that zombies are the perfect example of fake news style marketing.

Robert Anton Wilson warned us of how news could be used for marketing. He made up a conspiracy he called the fnords. In the Illuminatus! Trilogy, the word “fnord” is hidden in all sorts of text – news especially. We have been trained not to see the fnords. We ignore them at a basic psychological level so they are essentially invisible. But they make us feel scared and apprehensive. Everything you see and read has fnords hidden all over, especially the news. The only exception is advertising. Advertising is our one relief from the relentless attack. This encourages consumerism.

Zombies are the same thing. They represent all the fake threats that haven’t happened, but that we sense might happen. And these fake threats are really good marketing.

Yesterday, despite my best efforts, I ran into a “news” report about a new and worsening crisis at the Fukushia Diichi power plant. It was garbage. No, the reactor is not falling into the ocean. It’s as stable as ever. Yes, it is still dangerous to go in. Yes, it will be an expensive clean-up. Recent assessments indicate it might be even more expensive than earlier estimates.

So why make stuff up? Why put “Japan declare state of emergency as Fukushima reactor 2 falls into the ocean” as a caption on an image?

Ads. The original fake story has ads plastered all over. How to win the lottery! Photoshopped pics of Emma Watson! You won’t BELIEVE what happens next! Fast relief from all the anxiety we JUST CAUSED! Click! Click and Consume!

I was just struck this morning by the absurdity of a jobs shortage. Isn’t that a crazy idea? There’s just not enough to do? Really? Because I don’t feel like there’s too little to do. In point of fact, I feel like there’s way too much to do and not enough hours in the day to do it all.

I suppose that, economically, a jobs shortage is really a demand issue. When there is not enough consumer demand, we see that as a jobs shortage.

When there are too few jobs, the government can spend money to increase consumer demand. When there are too few jobs, the government can spend without competing with the private sector.

When there are lots of jobs, that means that the private sector needs people. Then it has to compete with the government to get those people. That reminds me of the Eisenhower quote:

This world in arms is not spending money alone. It is spending the sweat of its laborers, the genius of its scientists, the hopes of its children. The cost of one modern heavy bomber is this: a modern brick school in more than 30 cities. It is two electric power plants, each serving a town of 60,000 population. It is two fine, fully equipped hospitals. It is some fifty miles of concrete pavement.

When human labor is scarce, we must choose how to spend it. Schools or bombers? Ships or hospitals? There are only so many people. There are only so many man-hours for labor. It takes a certain number of man hours to do these things. We allocate those hours using an accounting system called dollars, and the premise is scarcity.

But when excess labor is abundant, we don’t have to give up the bomber to build a school. There are “spare” hours going into TV, Facebook, and World of Warcraft. Lest you think I’m joking, WoW users have logged about 50 billion hours of game time. For comparison, we spent about 4 billion hours on the Apollo project (and that’s a generous estimate).

There are spare hours, why are there not spare dollars?

Automation will exaggerate this situation further. The creation of “stuff” will require fewer man-hours (that sounds good). That leaves more spare man hours without a way to translate them into dollars or economic demand (that sounds bad).