Tuesday, May 28, 2013


Haven't posted in a bit lately. I have a bunch of stuff that is half-finished/almost finished that I will post on soon. Mostly I have been working on developing Molecular Biology Lab Equipment. And trying to have crazy ideas.

I started playing Chess again which is fun but it is definitely a time sink. I really enjoy Chess though because it is a "fair" game. Most strategy based games out there in the world involve some sort of randomness. Chess is about focus, creativity, knowledge and skill. There is currently no chess perfect game and there most likely never will be, meaning there is no clear cut way to win. There is obvious strategy that one should take into account but for those strategies there are always caveats. Never lose your Queen unless it is traded for the opponents Queen, well unless you are sacrificing it for alot of materials or well unless you are going to win the game or maybe you will be acquiring another Queen through pawn promotion. I have been playing chess for a while now and as I age I become better because I am less likely to attempt some crazy shenanigans. Instead opting for the progressive and slow attrition battle waiting for the opponent to make a mistake and then captializing on it. Maybe that also relates to my life and how I have calmed down a bunch and am much less crazy.

I also have been working lots on my thesis. Writing at least a few hours a day. It is not due until August 2nd but it needs to be mostly done before my thesis defense which will be around the beginning of July. Then I graduate.

Haven't found a Post-Doc yet and I don't even know if I want one. I am trying really hard to start up some sort of business thing so I can just do Science and Engineering on my own. I have so many ideas and projects that I want to work on. I just hope something can succeed.

Will be in Boone, NC this weekend visit friends and then I fly out to the Gordon Research Conference on Synthetic Biology for 5 days, which should be fun. Maybe someone there will be interested in hiring me for a Post-Doc.

Wednesday, May 15, 2013


This is a topic that has interested me for a long time. Metacognition basically means to think about the way you think. Aside, from some philosophical reason, why would one want to do that? Well I view myself as a sort of athlete of the mind. I am constantly trying to improve my brain function and creativity even if I happen to drink a little too much Scotch every once in a while.

There are a couple of areas I actively try and foster in order to improve my "intelligence".



This is probably the most difficult one to improve and is seems to be directly related to Knowledge and Memory but there are a few things that I have learned I can do to improve my own creativity.

Experience new ideas or new knowledge is a big one. When something new enters my brain and I begin to amalgamate it with the rest of my knowledge new and interesting connections and ideas pop up. This however is not really related to new experiences. New experience tend to make people cultured and have new points of view but traveling and visiting new places or meeting new people has never really enhanced my creativity in any way. Every once in a while I might see a painting that can give me interesting ideas but this is so few that to me it is not a productive method.

Take time to think of new things. I always can tell when I am stuck in a rut it probably means I am not taking enough time to think. I have set a reminder in my calendar on my computer to take at least 5 minutes everyday and drop everything I am doing and spend that 5 minutes only trying to think of new and interesting things. It is amazing how much this works.

Creativity seems to feed off of creativity. Talking to other creative people and seeing other creative projects or ideas feeds me. Some of my best ideas happen after sitting through a bunch of interesting scientific talks in a day.

Streamline your life. When I don't need to think about problems or dinner or food or money or whatever I can spend all my time thinking of interesting problems. I like familiarity. Do you think about how to put on your clothes? or think while eating? Probably not. Once this autonomous system takes over the mind can live outside the body. The more things in my life that are familiar and similar the easier it is to spend lots of time thinking and attempting to solve problems or come up with creative ideas. I can't stress how important this aspect is. People might think I am weird because I want to use the same spoon, cup, bowl, sit in the same seat and walk the same path. But what they don't know is that this familiarity allows me to do everything autonomously and I can spend that time thinking.


I think so many people give up on knowledge at an early time in their life. They figure that they learn enough with the job or that they know enough so they don't need to learn. Knowledge, to me, is intimately linked with creativity.

Learn. I spend so much of my time learning. When I am walking alone I try and listen/watch lectures or podcasts. I constantly try and teach myself new subjects. This takes alot of dedication but it allows me to have an idea and then apply the idea and make it real. Ideas stay ideas too much because people don't know how to apply them or are not willing to learn enough to apply them.

Do. Doing things is what builds those conceptual connections in my brain. When I am programming or building electronics or doing a science experiment I build the conceptual connections of things I only understood in passing. Someone can tell me how NMR works but if they can't sit down and run a spectra or work with a spectrometer then the knowledge is only theoretically useful, which is ok in some cases but for me it is less useful in most cases.


I think this is the most difficult to improve. Some people appear to have an inclination to memorize things easier maybe through their upbringing or practice but memory really takes practice.

Practice is really important. I practice memorizing things. I train my memory. Learning how to use ones memory efficiently and beneficially is what makes someone better at "memorizing" than other people. A really good book on the subject is Moonwalking with Einstein by Josh Foer. The book is about training to compete in the World Memory Championships and how memory is more of a learned skill than it is an inherent talent. I wrote a simple Perl script that I run through a couple times each morning, it gives me a number of random digits of my choosing and 15 seconds to memorize them and then it asks me for them. This works pretty much only my short-term memory but I have seen the benefits in my long-term memory. I am up to 13 numbers in 15 seconds and have been stuck on 14 for a bit now. My goal is 15 number in 15 seconds. I also have this neat app on my Android phone Memory Trainer it has a bunch of different "games" that train image recognition, spatial memory and a bunch of stuff. It is pretty cool. I never however understood the N-back game I think it doesn't work correctly. Also, it is not that difficult of a program. After a few months using it one can complete the highest level as a "Memory Master" but you can go back and choose targetted workouts on the games that give you the hardest time. Really nice way to "waste" time besides something like Angry Birds(do people still play that?).

Experience is very important in memory. What does the number "8" feel like to you? To me 8 is a good number it is my birthdate (Feb. 8th) and also is related to my birthname (Josiah became King when he was 8 years old). I can feel the number 8. I also like powers of 2 because they are based on the binary digit system, like 256, 512, 1024, 2048, &c. The more you experience numbers or objects the more you are familiar with it and the easier it is to remember. Experience also allows one to learn what works best for them. Maybe associating smells or people or shapes works best for you. Try it out and see what happens.

I really wish I knew about metacongnition earlier in life or that I was taught how to think in school I am sure I would be much better at processing and synthesizing information.

Saturday, May 11, 2013

The Chromochord: A Bioelectronic Musical Instrument

So I have not been posting much lately because I have basically dropped most projects I am working on to finish up my new version of the Chromochord. If you don't know what the Chromochord is Here is a good description of the original version. On top of building it I have been working hard with Francisco Castillo Trigueros a great composer to make music for it.

The Chromochord projects goal is to create some form of two way communication with nanotechnology and allowing that interaction to create a stimulus that can be experienced in the non-nano world.
I think photoactive proteins are really cool and I work with them. They are perfect for this because we can interact with them using light and they can respond quantum mechanically by changing their light absorbance.
Light-Oxygen-Voltage domains use a flavin-mononucleotide(FMN) chromophore that when reduced(gain of an electron) because of photoexcitation change their absorbance drastically around 450 nm and the protein undergoes a conformational change. They are nano light driven machines!

 Protein Model of a LOV Domain Undergoing Conformation Change

For my Ph.D. research I engineered plant proteins(the second LOV domain of Avena sativa (Oat) phototropin 1) and expressed and purified them using a transgenic bacterial system. The engineered proteins respond to light differently due to difference in amino acid sequence. Data on the engineered variants can be found in this Scientific article here. Many of the mutations centered around the FMN chromophore to modify the electrostatic environment and sterics which helps govern that metastable light excited state.

You can interact with a model of the protein in 3D here: http://www.rcsb.org/pdb/explore/jmol.do?structureId=2V0U&bionumber=1

I chose to use sound as the way the proteins interact with the non-nano world (human beings, &c.). This protein does not actually generate sound. We are sonifying its response to our interaction with it. I don't think people have chances to experience the nano-world and this was a chance to bring it smack-dab to their ears.

Music was generated by measuring the proteins response to light and using that to modulate a base set of notes. So what you do is shine light on the protein to sort of strum it quantum mechanically. You measure it's response to this strumming spectrophotometrically and then you press a key to play a note whose pitch is modulated by the protein.

These interactions have also been used to manipulate custom musical phrases written by Francisco in a self-playing version of the Chromochord. He also integrated protein's thermodynamic unfolding and aggregation was integrated into the music.

 A LOV Protein's Response to Light as measured by UV-Visible Light Absorbance

So basically the way the Chromochord works is that we have the device measure the absorbance of the LOV protein in each well of a plate(What a microplate looks like). Because the proteins response is governed by thermodynamics we have some unpredictability, we don't know exactly how the solution of protein in the well will respond but we have a good idea. As time goes on a percentage of the proteins can degrade or aggregate and cannot interact with light anymore. This is dependent on each engineered variant. This also changes the response.  

The first version of the Chromochord was built on top of a UV-Visible light absorbance based plate reader. As you can see below the Chromochord was of significant size and weight. As you can see it was meant to be played live with music and lights controlled through buttons. I wrote software to interact with the plate reader and interfaced it with an arduino and a custom version of ttymidi I wrote. Layers could be built up with sooperlooper. It is kind of cool. The musical layering idea was inspired by Zoe Keating.

The first version is not really portable. But I did bring it to Berlin and demo it at Humboldt University of Berlin. There is a problem with timescale also. The Chromochord uses the physical chemical state of the protein to determine sound played but most plate readers use a beam splitter and/or motors to move the plate through a single light source. It takes seconds(5 s or more) to measure a whole plate at the fastest. I even looked online in purchasing a faster plate reader and no company sells one! Yikes. So that means if I wanted the Chromochord to have more realistic interactions with the world I would need to build my own plate reader. Initially I planned on making it able to read a whole plate but decided that the Chomochord probably wouldn't use a whole plates worth of protein in it so after talking with Francisco I decided on 12 wells.

The new Chromochord I built is based on a single wavelength measurement, which can easily be modified do more than one. Most modern plate readers use a bright white light and filters to generate a number of wavelengths. An easy way to give the Chromochord multiple wavelengths would be to use an RGB LED. Currently, it uses an ~460 nm blue LED as that is the wavelength I am most interested in. The current amount of time it takes to measure and filter on 12 wells is <350 ms (almost all of that is software filtering)!!!

What the Chromochord is now composed of:
24 LEDs: 12 for Excitation of the Protein and 12 for spectroscopic measurement
12 Light Dependent Resistors (LDRs)
1 Arduino Due
Assorted wires and resistors

The LEDs were high intensity Blue LEDs. I used Blue because the protein is both excited and absorbs at around 450 nm. I needed them to generate a significant amount of light in the milliseconds they were flashed on and off so I went for some high intensity ones. I have not measured the lumen output for the flash of light.

If I change anything it will be the LDRs they aren't bad but I think they are the reason I have so many problems gaining stable measurements. I purchased them because originally I was thinking of doing all 96 wells and at $5 a pop for a phototransistor, that's alot of money.

I chose the Arduino Due because it has a 12 bit ADC, which probably wasn't even enough but I had tough luck finding a 12 channel > 12bit ADC that I could soder and using one ADC per LDR I was just too lazy for. I actually thought the 12 bit wouldn't be too bad and it wasn't. I probably could have also used some hardware filters to give my measurement more resolution as my readings were only using a fraction of the actual spectrum.

Here is a link to the Arduino code: Chromocode
The code filters the measurement data, creates baselines and all other sorts of stuff. Then it prints the readings to the Serial port which can be read by any program. We were using Max/MSP. But like with the original Chromochord, one can always route the data to ttymidi on Linux.

I will make another post on the Artistic Installation we did and also post the Max code.

This second version is much faster but cannot be directly played as is. Instead a score is written as 1s and 0s of course and used to control the photoexcitation of the proteins. It allows for much more complicated music to be played.

Here are pictures of the new Chromochord:

The Box

The Guts

Inside the Box

The Chromochord running

Visualizing the Wells and generating the sound using Max

The Chromochord Running

The Audio and Video Chromochord Installation

Thursday, May 2, 2013

What would you give a leg for?

So on my walk home from work I pass by a local bar. The other day I saw one of my friends was bartending and the bar was pretty empty so I decided to stop in for a quick beer and say hi. After a few minutes an older gentlemen came in and sat down next to me and started to chat. I am usually not really into talking to strangers but I was in a open mood. As sports was on the TV we were chatting about them and the conversation came to concussions and Amercian Football and how the players are suing the NFL and the implications of this situation. Are they being paid "X" Dollars(which is way more than your average person) to receive concussions. Is it their job? Are Amercian Football players just entertainers and their job is to hurt and be hurt like Ultimate Fighting? (I know there are college kids who are paying the price of injury without any recompense but lets leave that out of this discussion for now)

We then started talking about if us or someone would turn down hundreds of thousands of dollars if they were told they would receive a few concussions. Sadly, in this world money buys us so much. Not just comfortability but opportunities. The question came to would him or I give up a leg for $1 million. I told him it was a very difficult question for me because $1 million would allow me to pursue my dream of being able to do research and engineering on my own. It would basically fulfill my dream. I don't need a leg to do science or engineering. I have invested so much in my mind. He was a little abashed by my response even though I tried to explain it wasn't out of greed. It was a tough question for me.

Afterward I started thinking about what I would actually give up for my goals and to accomplish the things I want. It sucks that people give up their dreams and passions. It sucks that people don't have something in their life that they would give up a leg for. Or maybe I am just really naive that I would consider it.

I learned long ago that we can't accomplish everything we want in the world. The whole keep your dreams alive is fake and stupid. But with effort and perseverance we can create beautiful things or do beautiful things. Maybe not what we were dreaming of but still beautiful and moving.

If someone told me I would have to give up my leg or I couldn't do science or engineering ever again. I wouldn't even hesitate.

Chromochord UChicago Video

The Arts/Science Initiative that is giving the Chromochord development some funding has created a video of me and Francisco.


The project is coming along splendidly. I finished building the new Chromochord and it is badassssss. Been working on developing music with Francisco. We should have something cool for when we do a demo next Wednesday.