Sunday, April 21, 2013

Science Knowledge/Teaching

So this weekend I volunteered to judge a Chicago High School science fair/competition. The people participating were all mostly affluent it was enjoyable and an interesting experience. What I want to comment on is that state of scientific teaching that it appears these kids have had.

Science is not easy. Most Ph.D. scientists have been studying science for around 12 years before they even receive their Ph.D. There are so many people out there who think that science is easy. That one can just make up scientific theories in their spare time if they are "smart" enough. I don't really believe greatly in intelligence though. Just as in sports you have people with lots of natural talent, I am sure there are people that have lots of natural talent with their mind. However, that doesn't mean that someone who trains can't be at the same level or better. Someone who learns and thinks and takes care of their mind just like an athlete would their muscles and body. So what is scientist then? To start out being a scientist one needs to accumulate knowledge. That is the way it is for everything. Is there a chance that someone will be able to write down a random proof that proves P != NP or some such? ( Maaaaybbbee but in all likelihood that will never ever happen.

So back to the science fair. These kids know nothing about science. Instead what they are taught is that they should try and "Reject their Null hypothesis." It is sad. Scientists don't sit around trying to reject Null Hypotheses. People don't even mention a Null hypothesis in college besides perhaps a statistics course. The lack of scientific thought and knowledge was somewhat appalling. I am not saying it is this way all across Chicago or even all over the US but for an affluent Chicago competition I expected more. I volunteered with FIRST robotics for two years and it was quite impressive. The things kids can program these days and their computer knowledge and skill is advanced. We have only had personal computers for the past ~20 years and people have been doing molecular biology for the past 50.

Myself as an example. I started programming in High School on my own. Eventually by my senior year they had a C++ class for advanced students. Our biology labs however didn't even have a basic electrophoresis setup. Why? This makes no sense to me. Why are we not teaching younger people advanced science techniques or exposing them to advanced science it is the only way they will learn. Instead of having kids drop out of college to start the facebook. They will drop out to start their own biotech company. "Smart" takes time and it seems in science we are all starting a little further behind everyone else. We are not "allowed" to learn about real science until college. I think this is a big issue. I think science needs to be more accessible. Science knowledge needs to be more accessible.

I don't think this is something that can be easily fixed but requires many/all scientists to believe this is something we need.

There are 16 year olds programming video games and websites and robots and they don't even know what DNA is. I think that is a problem.

Friday, April 12, 2013

Transient Voltage Through Photoexcitation of Metals(Iron?) in Water. (Photoelectric effect?) (Photo-Fenton reaction?)

This sounds crazy I know. I thought it was crazy when I saw it but I have tested it so many times and have shown that it actually works.

I stumbled upon this while working with the light activated protein domain from Oat(Avena sativa) LOV2

You put metal electrodes in ordinary tap water  and you see photovoltages. This data is not so precise, I know but I ordered a multimeter I can attach to my computer a few days ago. So once I receive it I can have actual plottable data.

This is very similar to the Original battery except without salt and with light

Basically what is happening in these electrochemical cells is Atoms are being oxidized in one electrode(anode) and reduced in the other(cathode). So electrons from the oxidized electrode flow to the reduced electrode.

So this is what I tried:
All were measured in 300uL of tap water in a polystyrene plate.
I took two pieces of metals and placed them in the liquid not touching, one higher than the other and connected a multimeter to each electrode.

Steel wire, Steel is an Iron alloy, so it is composed mostly of iron but has ~1.5% Manganese and 0.8% Silicon and other trace elements
( )

About 10-20mV from one electrode to the other in tap water. This voltage increases over time about 10 mV every 15 minutes. There is a transient photovoltaic action of about 10mV. Repeatable with delay. I think this is the photo-fenton reaction in which the light is photoexciting  Fe3+ to Fe2+.
( In the photofenton reaction light produces free radicals producing Fe2+ and OH radical. These radicals should react quickly. But why doesn't continuous light keep a stable voltage? Maybe it is something with my setup.
These transients last for about 1-2 seconds and then the voltage starts to return to the normal value even if there is still light in most cases. I don't quite understand the process.

Copper wire, which is composed from as far as I can tell mostly of copper. Maybe not? 
Pretty good acquired the highest voltages from this. >100mV on some occasions.
Stable around 80-100mV.
Electrodes wear out in about 30 minutes

Platinum Electrode
No voltage which was expected as platinum is pretty inert.

Steel and Copper

This is a steel cathode and copper anode.
>400mV and 5uA of current

Light effect transient stays with continuous light. A ~5-10mV decrease is observed after a few seconds of light exposure. However, there is an increase upon long-term light exposure. The voltage was around 500mV after about 5 minutes of light exposure! That's 50-100mV increase from light. crazy! also, upon removal of the light we don't lose much in terms of voltage maybe just a few mV.

~20mV per 10 minutes decrease in  voltage that is based solely on the copper. i.e. Switching out the copper brings the voltage back up.

In a solution of table salt(Sodium Chloride, Dextrose, Potassium Iodide, Calcium silicate)
The current increases to between 10-20uA.
I also see transient current increases in response to light.

This solution decreases what I assume is the destruction of one of the electrodes to about 5mV / 20 minutes, which means the electrode has a half-life of about 1 day if the destruction is mostly linear.

Steel and Aluminum Silicon
There is a light effect but surprisingly unlike the other light effects this one takes a bit of time before it will work again. Usually when I shine light I see the transient and then it starts to decay and it decays in a few seconds. After it is decayed I shine again and it works to the same magnitude. In this one if I try the same the second time there is much less amplitude in the transient.

Steel and Aluminum foil
~200mV 1uA
I see a nice 10mV change upon light which is alot more stable than in all the other cases. Under continuous light I see a somewhat stable value. However, I think the aluminum is being rapidly oxidized from the increases in Fe2+ so the voltage starts to decay pretty fast. A very small change in the current upon photoillumination.

Using filters I narrowed down the light wavelength that causes the effect to somewhere between 300 and 450 nm.
It seems like this is some form of the photo Fenton reactionor maybe a Photoelectric effect. I don't know much about this type of photochemistry.
Iron can be photoexcited between those wavelengths.

I know this data is not that exciting at the moment but it was interesting to understand the properties of these metals and see crazy photochemistry. Even in just tap water. Who knew that you could generate voltage and current like this!

I need to scale it up and I want to build a light that works by using rain and the sun! Much cheaper than a solar panel! Can connect in series and it works great but low current. Which means I need a decent electrolyte.

Or what about a piezo-electric light that works by rain?

More studies on electrochemistry coming. I just need to learn more about it.

Friday, April 5, 2013

The Good About Science

I think often  people express all the bad about science.
I am guilty of it also. Lack of funding. Hard to find a job. Discrimination. All the politics. Hard to publish. Blah blah blah. But what about the good in science. We don't often hear people talking about that.

I love science, I love it. I mean if you read my blog you know this because I spend much of my free time doing weird and random science experiments or engineering or programming projects. The past few days I have been working on some really cool projects, building and developing DIY lab equipment, programming machine learning stuff, optimizing my 3D printer and other extra special projects I will write about soon. It is so much fun, it is so beautiful.

I love science and building stuff it is my heart and soul. I love learning and thinking and contemplating. These things challenge me in such a way that I constantly have motivation to learn more and try harder.

Problems. That is what inspires me. How do I solve this problem? How can I gain/provide more insight on this topic? I constantly think about these things.

Ideas. That is what inspires me. Nothing makes me more excited than a new idea that is complicated enough to challenge me and requires me to learn and gain new skills or combine skills in a new way in order to bring the idea to reality.

Some people do science or do engineering. It is different for me. I am a scientist and an engineer. Someone once asked me what I would do if I was last person left on Earth and I said "I would go to work and do research and it would be nice because no one else would be around." Now I am developing my own personal lab/work space at home so I guess I could just stay home and work. 

I am not one of those people who can sit around and do nothing all day or watch TV. I have so many things I want to study or work on or accomplish or fix or develop or discover.

Science shows me the beautiful parts of the world. It allows my life to be exciting without even leaving my chair. Science and engineering and knowledge have given me the ability to discover amazing things and see beauty without traveling to far away places.

Yeah it has been hard work and yeah it sucks sometimes but I won't give it up, I can't give it up.

Thursday, April 4, 2013

Machine Learning and Perl

----EDIT TO POST----
To the people who find this post by an internet search I suggest you give up on machine learning in Perl and learn to do it in Python. That's what I did.

Yep, that's correct. I started to do some basic machine learning programming in Perl.

See I had this large dataset that I generated and wanted to understand it better. We were working with someone who was using RandomForest modeling and I wanted to have a better grasp of that so I decided to program a Decision Tree learning program to take a general dataset and map it to a binary effect. I chose a binary effect because non-binary effects are much harder to do especially on a small dataset like mine with ~75 values.

Basically what the program I wrote does is take the whole dataset and calculate binomial probabilities for a given feature value to predict the outcome. This has led me down many streams of inquiry.

How to bin features?
Been thinking of using k-means clustering.

How/If to calculate feature entropy?
I have been having trouble with Information Gain Entropy because some features I use have lots of possible values. Information gain entropy biases to features with fewer values. I could iterate over all possible mutual information values but that could possibly become very problematic with datasets with many features. But probably not.

Is it possible to generalize machine learning?
Kind of but not really. There are so many caveats with every machine learning technique. It cracks me up. I will spend time thinking about about why something shouldn't work only to read about it and find out that it shouldn't work or that there is a bias in the method.

So I wrote a basic machine learning program in Perl that takes binary effects and tries to predict them using the features and states of features that you give it. I used it for trying to find any information as to how or why mutations I made to a protein did what they did. It didn't tell me much besides the fact that many characteristics of each residue determine it's effect on function. Surprisingly BLOSUM62 scores are a really good measure of the effect of a mutation on a proteins function.

The code is a total kludge but I like Perl because of hashes. You can put anything in a hash and do anything with a hash. Very nice. However, the way Perl handles array values vs array references is not very nice.

The code will take a training set of data and find the best predictors for your binary effect it will then attempt to predict data in your prediction set. It will compare the top 3 best predictors for each datapoint to come up with a prediction. It will tell you how often you predicted correctly. Mutual information code is in there but it doesn't use it because my data doesn't have enough points to make mutual information useful.

Decision Tree Code

0-6 on Post Doc emails (1 response)
I think I will blame it on sequestration.

Tuesday, April 2, 2013

Solidoodle 3 Review! My first 3D printer.

Yep, that's correct I purchased a 3D printer. The Solidoodle 3.
I was in the market for a 3D printer because I had saved up a little bit of money and wanted one that was built and tested and under $1000 and I knew I would receive it in less than 2 months or so. I was thinking about the Robo3D they had a kickstarter campaign and were priced about $650 but they really failed to post any videos of a finished product and the quality of the prints. I decided on the Solidoodle 3 which had a delivery time of 6-8 weeks at the time, it has since changed to 8-10 weeks. I will be honest, their customer service is shit. I purchased the printer at $799 and a few spools of ABS filament and the total came out to about ~$950 with shipping. I received one email from them when I purchased it and that went to my spam folder so I didn't even notice it till after I emailed them asking what was going on. Then I received an email that it shipped 7 weeks later. I emailed them in the interim, actually a few days before it shipped to ask on the status and the person who emailed me back said, "Delivery time is 8-10 weeks." If they can't/don't even check to see when a customers item will be shipped that just spent almost $1000, that is pretty shitty. On top of that. The printer came with no instructions. Their website makes really no mention of using Linux and Solidoodle 3 besides to install some software that they don't even provide updated config files or parameters for. Actually, I couldn't make it work initially and posted on the Solidoodle Google Group asking about it. After, I figured out how to make it work and posted what I did someone form the company asked me for the config file I used! haha. Seriously? You don't even know how to make your own printers work?

3D printers are not ready for the average non-technically inclined person to use. I imagine most other printers in a similar price range are the same way. From what I see and read it appears that printers in the $2000+ price category are somewhat more beginner friendly and non-technical.
Technically documentation is extremely lacking and up-to-date tutorials and guides are also. The Solidoodle is decent piece of hardware but it needs so much more to make it even remotely a good investment.

As for printing.
Nothing sticks to the bed unless it is huge. That is a problem because huge things tend not to print well due to lack of temperature control and the bed only heating to ~80C when they say on their website that it should go to >100C. They admitted on Solidoodle Google Group that they were just too lazy to change this on the website. 

Well I am sure I will have much fun with this thing printing off stuff for my projects. However, I don't think 3D printing is ready for the general public commercial market just yet unless one is willing to pay > $2000.

My first successful print. Pint glass for scale obviously.

I have created a Beginner's Tutorial if you have a Solidoodle 3 and it can be found here:

Monday, April 1, 2013


So many cool things I have been working on lately. I have been spending so much time doing experiments and learning and coding that my writing has not been catching up. Hopefully I will have some free time this week when I am not obsessively thinking and working on a project.

Still no Post Doc. A few people have offered me jobs here at the University of Chicago. One of my Professor friends Tao Pan is top of the list. We will see. I just don't see why/how people don't reply. I mean seriously. It is very weird how these people treat other human beings when not long ago they were in the same position. Weird. I wish I could vent more about it but I guess I don't really care enough to. Too many cool things I am working on.

Been testing my memory every morning without fail. It is very difficult to try and figure out memory techniques. I can't tell if my memory is improving much. Strangely (why do adverbs seem so weird?), I can remember 10 digits by looking at them for less than 5 seconds by chunking them into 3s and a single (111 111 111 1). But 11 numbers is significantly more difficult for my mind. I have been trying to figure out a simple way to overcome this without resorting to extension mnemonic devices. Difficult for the time being.

I have drastically reduced my drinking and my mind has been working better than it has for the past 5 years. I don't even have enough time and energy to keep up with all the ideas and learning I want to do.

Hopefully, new fun experiments/ideas will be posted soon.