Monday, September 30, 2013

Climate Change and Miss-represented Data

I will be honest with you. I am what most people might consider a "Climate Change skeptic". Maybe?

Do I believe the Earth is warming. Yes, it appears that the Earth is warming. Will it continue to warm? I don't know. Do I believe it is caused by human beings? Honestly, I couldn't tell you.

Why Climate Science bothers me.

First the graph that I just saw on a website that inspired me to write this:
I added in the lines for clarity. I mean. I do maths and statistics constantly. Please tell me how someone created this "future" prediction and still has a job? 1900 isn't at 0 but is in fact higher than 0, from the looks of it 0.1 to 0.2C higher. So this means that the preindustrial average was also higher than 0? See how easy it is to manipulate with these graphs. Does anything in this graph look like an exponential increase? Yet, the "future" is. So the highest increase in temperature was between ~1980 and ~1995(~ <= 0.4C) according to the graph and then since the late 1990s there has been virtually no increase. If current trends of the past 10+ years continue there will be no more increase in temperature! WTF!!!! From ~1940 to the late 1970s there was a decrease in temperature.

The Earths temperature has fluctuated a shit ton over its history.

This image is from ( from (Hansen, J.E., and Mki. Sato, 2012: Paleoclimate implications for human-made climate change. In Climate Change: Inferences from Paleoclimate and Regional Aspects. A. Berger, F. Mesinger, and D. Šijački, Eds. Springer, 21-48, doi:10.1007/978-3-7091-0973-1_2.)

The first thing you notice is that the temperature has been warmer when humans did not exist. Whoa. The bottom part of the graph is a blowup of the past 800 thousand years. You can see an obvious pattern of warming and cooling. Whoa. The current temperature we are at does not fall outside any of the normal trends. Whoa. We are at one of the coolest times in the history of the Earth! WHOA! Do you notice also that there always appears a rapid increase then exponential decrease in temperature? Hmm.... And we appear to be in one of those increases. These increases appear to occur every 75,000 years to ~100,000 years. Hmm...

So wait but how much is the current temperature changing?

First let's start with how temperature is measured.
Usually not much thought is put into this by people but have you ever wondered how even a daily average temperature is measured? Is it measured in the sun, or the shade or in the ground. Is it measured 1 meter or two meters or 3 meters above the ground? 1 meter. 2 meters, 3 meters under the ground. If the measuring is in the ground how much does precipitation change those measurements. Water has a higher heat capacity than soil so we should assume that wetter years will have different temperatures than warmer years. All of these things change the temperature measured. Is there any consistency in the way temperature is measured around the world? From what I can find the answer is No.  hmm.

Now we are looking at changes of less than 0.5 of a degree C and sometimes on the order of 0.1 of a degree by averaging non-standardized measurements from around the world. I have looked at this data and plotted the data and it does show an increase since the 1800s ( but is that increase important? Is it even caused by humans or is it a natural fluctuation? how reliable is the measurement data?

Ok so let's assume the measurement data is good. Is averaging the data the correct way to view it? The mean is usually a way to view "the central tendency" of a distribution. Is taking a mean of the whole Earth in any way a good measure of the overall climate trends. I don't see how this can be the case in any reasonable way.

If you told your landlord he needed to weather-proof the windows in your bedroom because they are not sealed and temperature is very low in there and he asked you to take the average temperature of the apartment and he would fix it based on that. Obviously, next to the radiator the temperature is going to be much warmer then in the room with the open window. You would probably say that a mean temperature of your apartment has little meaning. Also, simply being in the room for a long enough period of time would fluctuate the temperature.  Earth is similar the amount of heating in cities during winter changes regional temperatures.... ( (PDF Available here because Science should be free)

So how does taking a mean make sense for the whole Earth when an insane number of factors are contributing to fluctuations most of which we don't even know about or consider.

I currently live in Illinois and though Illinois is long and actually in two different temperate zones let's look at a smaller more meaningful "mean".(

What we see immediately is that in single year periods there can be fluctuations on the order of 4-5 degrees F (2-3C). Whoa. That's crazy. What we also see is that the current "high point" in temperature was not the highest ever, it is less than points in the 1920s and is very similar to points as far back as 1850s. Though one might be able to pick out some small warming and cooling trends no one could really say that there is a warming trend that is different from anything seen before or greater than anything seen before. In fact it appears Illinois has been on a cooling trend since the 1930s if you look at the 11-yr moving average.

Ok well that's Illinois. What about places that are heavily polluted, lots of CO2 and greenhouse gases. Maybe it would be more apparent there. I know people will say, that's not how Climate Science works, the CO2 emission will diffuse into the atmosphere and over the Earth and I agree. But let's just do this for arguments sake.
I always hear Los Angeles is awfully polluted so let's look at Los Angeles. The temperature record is located here ( I picked Jan and June at random to have two different seasons.

We see similar things in LA that we saw in Illinois. Changes in average temperature can be on the order of 4-5F(2-3C)  between years. However, we do see a temperature increase between 1980 - 2000 in both Jan and June. In June it seems that from 2000-Present the average temperature has dropped back down. The current June average was 59.5 F. If we discount that the average was 59.4 in 1999 this is the lowest temperature since 1976! Obviously, one cannot use individual yearly averages to conclude anything about trends. Either way the temperature fluctuations do not look in any way anomalous as compared to other times. Except that they look anomalously lower than 1980-2000. The Mean temperature for June between 1930 and 1940 is 62.4F and between 1961 and 1971 is 61.9 and between 2003 and 2013 is 62.5F. So is there a change? Are averages really the best way to look at this change? Hmm....

What about CO2? Let's look at the history of the Earth and the correlation of CO2 and temperature variation. This data is from the Vostok ice cores modified from Wikipedia. (original data can be found here

Ok so let's compare high levels of CO2 to high temperature. You don't need me to fourier transform this data to see the repeatable phenomenon. Just glancing at the data it looks like there is a trend but does high CO2 mean high temperature? The data is different in that current time is at the left at 0 thousands of yrs.

What we see is that both high and low temperatures correspond to high CO2 levels and both high and low temperatures correspond to low CO2 levels. Hmmm. There appears to be a trend that high temperatures are reached after an immediate jump in CO2 levels but high CO2 levels do not mean there are high temperatures. Further, the temperature appears to equilibrate back to lower temperatures after the initial jump in CO2 levels even when CO2 levels are still high. This usually happens in 10-25 thousand years. haha. Way outside our current models.

What we can see is that CO2 and temperature increase every ~75,000 years or so and then decrease again and the current CO2 and warming cycle appears to be on time. High fluctuations in CO2 levels appear to follow a pattern over the history of the Earth that doesn't seem to be deviated much by current patterns. The current increase in CO2 started ~25 thousand years ago!!! Is it conclusive that humans are the cause of the increase in CO2? Hmmm.

Current CO2 levels are currently higher(~395ppm) than they have ever been estimated from Vostok Ice cores. But so were preindustrial Vostok Ice Core CO2 levels at ~295ppm(PDF here because Science should be free).

In the history of the Earth CO2 levels have been much much higher than current measurements. Are humans contributing to the current highest CO2 levels in the past 400,000 years? It is hard to say. Is it just a coincidence that we have high CO2 levels and the CO2 levels have been increasing for the past 25,000 years? Is it just a coincidence that preindustrial CO2 levels were also measured to be higher than anything in the past 400,000 years? Hmm...

More NASA graphs:

In the 1920s temperature anomalies were higher than every year until about the year 2000. In fact from 1930 to the late 1980s there was a downward trend in temperature...
From 1992-1993 there was a greater than 0.5C drop in temperature and many more equal or more in previous and future years. In 2012 there was an ~1.2 C increase. But from 1921 to 1922 there was a ~1C drop. So wait. What you are saying is that next year there could be no anomaly as compared to this year!!!! (


The Arctic a place constantly mentioned as a test case for global warming.

The 100 year trend is 0.06C/decade increase and the past 65 year trend(1935-2000) in the Arctic is a -0.07C/decade decrease trend...(yes, that minus is correct). Hmm... Was the temperature increase from 1985-2000 really a trend or just an anomaly/part of normal fluctuations? Is the Arctic melting more than it was in the 1930 and 1940s? The temperature is less than it was in the 1930s to 1940s.


What does all this data say to you? Can you honestly look at this data and graphs and not be skeptical?

Does it appear that there is an increase in "average" temperature in some parts of the world? Sure, but what does that even mean(pun intended)? How can you average the temperature of the USA, much less the whole world? What is the standard deviation for these means? There IS NONE! Because we only have one Earth. Most data without replicates would receive an F in a high school Science lab.

Does this warming seem man made? If you look at the data it seems we are in a natural climatological cycle. Maybe not though.

I hate this whole "consensus science". Science was made so that consensus would not matter. So that data would matter and accurate and truthful representation of data would matter.

Is the Earth going to warm 1.5C in the next 50 years? I don't know. It might. Though I might bet against it. Especially since there has been no significant change in the past 10+ years. Does anyone know? They don't. The Earth is N=1. Something constantly taught against making generalization about in statistics. In all honesty this is the first time anyone has ever experienced what we are experiencing on this planet. We really don't know what will happen.

That being said. I don't own a car, I walk and take public transport everywhere and I recycle as much as possible. I am not for pollution or creating trash. However, I am against trashy statements being made(pun intended again).

Science is not zealotry it should be questioned and we should be critical of it.

The Earth is very complex and at this point in time uncomprehendible and unpredictable. Yet, people are telling us that they can predict what will happen in the next 100 years with a 95% confidence level (whatever that means). A 95% confidence interval is only as good as the data and models. If I predict that tomorrow will be 80F because it has been 80F for the past 3 days I would have a 95% confidence interval. But we all know that is bad. That is not the way temperature or climate works. Especially in Chicago, jk jk lol. This data is very missleading because there is only 1 Earth. It does not even make sense to use it that terminology because they are based off models not real life!!!
Currently there is a prediction of between 2C and 5C+ change in temperature. That is a 3C range between the models. The current temperature increase since preindustrial levels has been on the order of 1C. So the error is currently 3 times greater than any change we have even measured yet. I just don't understand how the global mean temperature could be ~ the same for the past 10+ years and no model created shows little or no increase in temperature? I just don't understand it.

(read here for more info on the graphic

Is the data saying what the media is saying and do we know enough to actually make a 95% confidence level actual mean anything? I think not but maybe I am just a deranged person who is viewing all this data completely wrong. I never said I was a climate scientist just a skeptic.

I wish I could talk to a climatologist and ask them about this data.

Fuck the consensus let's dance.

Thursday, September 26, 2013

Molecular Dynamics Sonification and Music Hack Day Chicago

I went to Music Hack Day Chicago this weekend ( It was the first time I ever went to a Hackathon but was looking forward to spending 30-40 hours coding out something cool. Of course these hacks were supposed to have something to do with music and I decided upon programming a mechanism to sonify data from Molecular Dynamics simulations.

I recently received a grant from the national supercomputing center for computer time on Stampede at UTexas, currently ranked the sixth fastest super computer in the world ( I have been running some equilibrium molecular dynamics simulations of proteins to understand conformational change pathways and basically figure out how proteins work the way they do. The amount data from these simulations is huge and complex and it is very multi-dimensional because not only are you looking at how each atom in the protein is moving in 3-dimensions but you are also looking at the physical forces that control this.

Normally one uses a variety of analysis software and also watches the simulations to try and observe obvious changes. As you can imagine simultaneously trying to understand any portion of this data is a crazy task visually so I set out to to use more senses. I wanted to sonify the data and play it back while watching the visual part of the simulation. Harnessing our auditory ability to pick out unique sounds.

So I created a layered musical arrangement that allows someone to listen for more subtle conformational changes while watching video of the simulation. This is different then most any other form of data sonification that I have found because it uses easily recognizable musical instruments whereas most data sonification just uses frequency shifted sine waves.

It surprisingly work really well and is really cool to experience. Code for demoing it is available here (

The sounds that one can hear in the video:

The piano key in the beginning represents the radius of gyration of the protein as it becomes higher in pitch the radius of gyration is becoming larger, as it becomes lower the radius of gyration is smaller. The radius of gyration is a measure of movement away from a center of mass, so basically if the protein is expanding or shrinking (

The beeps represent the RMSD of each residue as compared to frame 1 of the simulation. As the RMSD from the starting structure become higher the pitch becomes higher. Each beep is for each residue and they are performed in order. RMSD is basically how far each residue moved from it's initial position in relation to the protein(i.e. minus translation motion) (

To determine where a residue is located listen for secondary structure cues.

The percentage secondary structure as calculated by dssp is the background sounds.
This is an explaination of secondary structure (

A violin is played for the first quarter of the protein and represents the amount of structure in the whole protein, a combination of alpha helix, beta sheet and turn. It becomes higher in pitch as the number goes up and lower as it goes down.
The second quarter of the protein's background sound is Monks making an ohhh noise(according to MIDI tables) it is a representative of the percentage alpha helix. It becomes higher in pitch as the number goes up and lower as it goes down.
For the third quarter of the protein the background sound is a guitar it is a representative of the percentage beta sheet. It becomes higher in pitch as the number goes up and lower as it goes down.
The final quarter is a Sci-Fi noise (called so by MIDI tables), it represents percentage coil. It becomes higher in pitch as the number goes up and lower as it goes down.
So for instance if you hear a group of high pitch beeps during the violin you know they are in the first quarter of the protein.

The protein is HIV protease is a dimer(i.e. composed of two of the same protein). This means the sonification of the first half will be one half and the second half will be the other. Being a dimer doesn't mean that the conformational changes are symmetric either so the two halves can sound different.

Listen to the sounds a see if you can identify where in the protein the conformational changes are occurring. 

What one can tell is that the high pitched beeps are in the beginning and end also the middle of each half.The beginning and end of proteins, the termini are often very flexible and so change alot but are often not related to protein function. However, the high beeps in the middle(residues 40-60) are the flaps of the HIV protease that open up to allow substrate binding and cleavage and allow the virus to be active. It is pretty cool that this works!

Saturday, September 7, 2013

Scientific American

So this week has been crazy. Two articles were published online that were widely read and accessed based on the Chromochord. One in Scientific American by Nona Griffin that Karen Ingram did some cool artwork for!

The other was by the awesome Katie Drummond at The Verge . She was super cool and so much fun to do the article with. 

I will be honest. All the the attention was fun. It was cool to interact with new people and I even was able to interact with Zoe Keating ( my favorite musician! She wants to do a duet with me! hah. If only I could actually play good music on The Chromochord.

I think my main goal from the press was to try and leverage it in some way to acquire more press and to make connections that I can use now or in the future. Partly to try and fund this Indiegogo Campaign I have been working on with Francisco Castillo Trigueros the composer. I probably emailed every major news organization but no one picked it up . It was fun while it lasted but now I need to continue moving forward. My 5 minutes of press are up.

I do think it was good though. It was inspiring. Inspired me to fix some software bugs in the Chromochord. Inspired me to work on new projects and Inspired me to keep doing what I am doing because it really is a productive path. I am excited to see how far my mind can take me! Just need to keep thinking of new ideas and how to implement and keep working to implement them.

Monday, September 2, 2013

Is Being a Scientist Cool?

Sorry, Roger Tsien, you're my boy but you look like a huge nerd.

You walk into most academic institutions and go and meet the Scientists and they look like huge nerds. Now there is nothing wrong with looking like a huge nerd. People should feel like they can be themselves and people should not be judge by what they wear and how they look. Let's be honest here though if you met these people would they inspire you to be a Scientist?

What do people aspire to? Well obviously positions in which they will make lots of money but besides that people aspire to things that look cool and sound cool despite what the actual work consists of. Why do so many people want to work for all the Facespaces and Googles? Sure, there is pay and benefits and such but I am sure a job at Yahoo or Zipcar pays similarly. It is because of status.

In the late 90s and early 2000s I worked at Motorola as an engineer and programmer for the iDEN cell phone network. I wasn't paid an overly large sum of money about $30k but I wouldn't have left there if some company came and offered me $50k to do web development. I didn't want to do anything but work for Motorola. My cool ID badge and RSA secureID card and access to cell phone systems. For a technology nerd I was living the dream. A job with a really famous technology company giving me access to important data and control over cell phone networks. It was awesome.

So why would people rather work for Facespace with their job description revolve around trying to make people click ads rather than work in academic Science and Technology doing something so much "cooler".

Why isn't being a Scientist cool? I mean, being an Astronaut is barely cool these days. A couple thousand applicants for the last Astronaut application cycle? Survivor receives more applications than that!

Iron Man the movie has started to bring some coolness back into Science and Technology. The other day I was at the Grocery store and I heard a kid say that he wanted to be Iron Man. Hopefully because he wanted to invent cool things and not just because he wanted to beat people up but you take what you can get.

I dare you to show me a picture of a Scientist that would make someone in high school or younger think "Wow, that person is cool I really want to be like him or her". Why do we pay footballers and rap stars so much money? Because everyone wants to be them. They look cool, they act cool and they live what seems like a fun life. Their tweets are entertaining and funny, they are enjoyable people.

Is it just the life of the Scientist to be absorbed so much in their work and their head that they don't really care how they are perceived by other people?

I mean everyone loves people like Neil deGrasse Tyson but does anybody really aspire to be him and wear a suit everyday and act pretentious?

Is it our job as Scientists to make Science cool, Accessible, and seem like it is a fun job?

I don't know.

I am in no way endorsing that I am cool and other Scientists are not at least not outright but why do most of us seem so boring? TV shows and movies portray Scientists as ugly and nerdy and boring. Well except Iron Man. Are they portraying Scientists the wrong way or is that the way we all really look and act?