Saturday, December 1, 2007

Crazy Judge

Judge suspended for jailing court

A US judge is removed from his post for jailing everyone in court after no-one admitted to owning a ringing phone.

This is hilarious! I really wish I could have been there for that.

Friday, November 30, 2007

The thuggery behind the harmonious facade - International Herald Tribune, Part 2

The thuggery behind the harmonious facade - International Herald Tribune: "Ma: Enough of this. I've heard from the 'relevant departments' that people like us are not allowed to make big bucks. We're just doing enough to make a living. The police: We haven't bothered your business, have we? Ma: Really? Unless I remember it wrong, you guys once talked to my partner and said, 'if we see him dealing with your company, your business will end.' The police: That's because you did something we didn't want you to do. Over the last few years you haven't made any trouble for us, so we haven't made any trouble for you. Ma: Is that so? You asked me to come here today. Isn't this trouble? The police: How can you say this is trouble? We're friends. Isn't it O.K. to have a cup of tea together? Ma: It's a pity we're not sitting here as friends. Enough beating around the bush, let's talk about why I am wanted here today. The police: O.K., are you or are you not planning to go to Beijing soon? Ma: I am. I'm flying there tomorrow. Any problem? The police: You have to go? Ma then insists that he is only going for business, and the police reply that if that's the case, they won't try to stop him. But they warn him, for good measure..."

This article makes me question the ethics of investing in the Chinese market. Another important question it brings up is whether or not the Chinese government will be able to continue to allow business in China to prosper or whether this type of harassment of the populace will lead to serious economic issues. In any case I am uneasy about my investments in emerging markets at this point...

The thuggery behind the harmonious facade - International Herald Tribune

The thuggery behind the harmonious facade - International Herald Tribune: "SHANGHAI: Last October, as Ma Shaofang prepared to travel from the Chinese city of Shenzhen to Beijing to attend a writers' conference, he received a menacing call from the police. Why trouble a businessman who wants to attend a conference? The problem was that as a student hunger strike organizer during the Tiananmen protests in 1989, Ma had a 'dossier' that still trails behind him wherever he goes in China. The Chinese calendar is filled with special dates, 'sensitive moments' whose association with events either historical or current put the authorities on alert and the people on guard. October 2007 happened to be the month of the Communist Party's 17th Congress, a once-in-five years affair whose political significance is such that the capital is locked down, potential 'troublemakers' rounded up and even the airwaves scrubbed with extra vigor by censors whose job it is to see that nothing can sully the image of a serene and clear-sighted leadership. So with that backdrop in mind, the police 'invited' Ma for tea. Ma's account of the meeting, which he recently published, and which was subsequently translated by the University of California at Berkeley's China Digital Times, offers a chilling glimpse of a Chinese reality that few foreigners ever see."

Very interesting article... Definitely a must read.

Thursday, November 29, 2007

Intense Term

I know every college student says it, but this term was intense! Most likely I will say it again next term, and the term after that... Anyhow I have been cramming tons of information to attempt and keep up with my new lab while also trying to stay on top of 3 science based classes. Not an easy task but I love it.

On the computer science front I am currently learning my way around python. Python is a high level scripting language with some pretty cool functionality. My only gripe with it so far is that regular expression handling has to be imported. Granted that there is probably a more elegant way to do the regex stuff I wanted to do, I ended up using about 5 lines of code to go through these files the lab uses for running bioinformatics simulations and pull out relevant data for a new project I am working on. I was not pleased with the relatively confusing commands for dealing with regular expressions either. Other than that I love what I have seen so far in Python. It seems much less confusing to me than Perl.

Thanksgiving was fun. I spent it in Seattle with my girlfriend and her sister's family. Seattle is a fun town and I am definitely adding it to my list of habitable locations.

Thats all for now. It's dead week and I need to get stuff done.

Monday, November 5, 2007

learning perl and feeling nerdy


print(("a","c","e","h","j","k","l","n","o","p","r","s","t","u"," ") [4,13,11,12,14,0,7,8,12,3,2,10,14,9,2,10,6,14,3,0,1,5,2,10]);

#thats how I roll...

Tuesday, October 9, 2007

Emerging market boom

Today I am writing about the booming emerging markets. In the past 5 years or so they have been averaging, as a whole, over 20% gains annually. If you were to invest in the Vanguard Emerging Markets Index fund one year ago you would have already earned 40%.

Taking that kind of hot performance into consideration my risky side wants to throw my money at it. Here is where my conservative economist side comes into play. I really do not know a lot about emerging markets. What are the average PE ratios of those markets? That is a very relevant question, it would tell you how much the current prices are due to betting on the future and how much of the price rise reflects actual growth of the economies.

In theory I can understand a certain degree of price inflation on the stocks of emerging markets. They are just now coming into the world economy as actual players and they represent the majority of the world's population. China and India for example are both considered emerging markets. Imagine for a second what it would be like if the majority of the billions of people in China and India became what we in the West would consider "middle class" socioeconomically. As a whole they would have an unheard of spending power and who knows how far that could go. It is an exciting idea. It would be kind of like buying into the stock market back in the early 1900's in the US except... bigger...

Here is my theory. It is based on nothing other than the idea that there must be some kind of gravity involved with the price of those stocks. If they are actually price inflated as I fear, they could suffer the same kind of market crash as we did in the late 20's. If one were to invest in the US stock market at the height of the boom in the 20's they would have had to wait over 10 years to make their money back after the crash. Is there a crash coming in the emerging markets? When will it happen? If I put my money into emerging markets today would I be in the negative for the next 10 years?

Another thought. We know there is an imminent rise of a middle class in the emerging markets. How do we know that those markets are going to be the ones that profit the most from that class. With the expansion of globalization eventually anyone will be able to do business easily and cost effectively anywhere in the world. It is already happening. That said what is stopping todays giants from growing into those emerging markets and being the ones who capitalize. Just because a company is based in the states doesn't mean that it is confined there. Case in point look at the popularity of Japanese automobiles in the US. They are probably making more money from the car market in this country than many of the car companies in this country are. What then makes investing in companies located in emerging markets so special?

I know that in the long term investing broadly across emerging markets is a very good idea. However is now the time to do it? Can it keep going up? Eventually it will and people who invest in it now who have 20 or 30 years to wait will probably be very happy about that decision.

I have things to do and I am not going to bother editing this now. More on this topic as I learn more about it. I will be sure to post something when I find out a little more about PE ratios and such. If they are low I am in!

Friday, October 5, 2007

Investing in Volitile markets, Surf's up!

I am going to share an idea I came up with a few weeks ago that has been going well. Here is the background: I am a big fan of investing in stocks, bonds and whatever else. I have been doing it since I was about 12. The thing is though that I am a huge wuss when it comes to the market. When stocks are shooting up I get really excited and throw money into the market. Then when the market falls and I start loosing money I typically panic and pull out. By doing that I tend toward selling on the lows and buying on the highs. I guess some investing is better than none at all. Anyhow I invested in some really secure high yield municipal bonds that provide a slow and steady tax-deferred income stream. That was so boring! I couldn't take it. I am young anyhow so I hear taking more risk at this point in my life is the sensible thing to do. Anyhow I needed to get into a nice risky investment that would still allow me to have enough money to put a down payment on a house when that time comes. The option I came up with: REIT's. They make total sense for my situation and here is why. I want risk and some excitement, REIT's provide that. I want something with high historical returns, REIT's have that as well. I want something that will still give me enough money for a down payment when the time comes. REIT's may be the best option for that. My logic is that if I put my money in something that will track the general trend of the housing market, and say the housing market plummets like so many of us are afraid of, I will lose a bunch of money. The plus side though is that I will not need as much money for a down payment if that happens so I am still OK. Say on the other hand that the stock market as a whole plummets but hosing holds firm. My REIT's will hold to the general trend of the housing market and I will not be hurt as badly by the fall of the stock market as a whole. So as I see it, REIT's although risky are the best option for me and my goals. For what it is worth, that is all for now...

Thursday, September 20, 2007

Progress in the new lab

For the past 2 weeks I have been trying to cram in all the information I can on what is called "Maximum Likelihood". This is a mathematical technique for figuring out, probably among other things, a tree that best represents how a given set of DNA, Protein or whatever is related to each other. From what I gather so far the maximum likelihood method does this by plotting out all the possible trees that could fit the data set and then it computes which tree is the most probable given whatever model parameters you feed in. In other words the maximum likelihood is the highest probably of your data given the best model. A simple example often used is tossing a coin. Say you toss one 100 times and you get 47 heads and 53 tails. Now we have to chose a model. The model is our theory about how the coin flipping works. I will propose 2 and we will see which results in the maximum likelihood. The first model is the "fair coin" model, that you get 1/2 heads and 1/2 tails. Next I will propose a weighted model, say 1/4 heads and 3/4 tails. In the "fair coin" model we get a high likelihood because of the fact that 47/53 is so close to our expected value of 50/50. The second model doesn't seem to be a very good picture of what is really going on, 25/75 is pretty far away from our actual result of 47/53. Thus given the two models I proposed the one that leads to the maximum likelihood given our coin flipping data is the "fair coin" model. That process I just went through is called Model Selection and it is more specifically what I am going to be working on. It is not an exact science and what I gather is that I am going to be working on ways to improve the models used for inferring how much evolution takes place between two sets of data sequences.

When I figure this out to a fuller extent I will be sure to write a more accurate entry on the subject. If you are really interested in it though check out the wikipedia page on Maximum likelihood at also you could check out the wiki on model selection at

Take care and have a great day!
-हवे अ ग्रेट दय!

Monday, August 27, 2007

Leaf Cutter Colony

Cool picture of the ant colony courtesy of Jack Niedbala.

Monday, August 20, 2007


Confrontation is difficult for me. I will do it but I really dislike it. I realized since I took on a new job a little more than a week ago that I have too much on my plate. To top it off the new job really was not progressing me toward my goals of grad school. I need to get as much research in as possible.

I am doing pretty well in research. Currently I am working in a lab that deals with metal-halogen biomaterials. We study critters that have metal deposits in the parts of their bodies that are used frequently and generally prone to wear. It is interesting research and I am able to get very involved. I have already suggested a means for the binding of said metals that will definitely have to be looked into more because it is more or less a shot in the dark. I am also still trying to get into the Thornton lab, which looks like a likely possibility now.

The picture to the right is one taken by my friend Jack Niedbala. It is of the leaf cutter ants at work right here in our very own lab. They are very fun to watch.

If you are interested you can check out the website for the lab I am currently working in. I am actually in the process of building that website as well.

Wednesday, May 2, 2007

Exciting possibilities

I found out today that I have a shot at getting into Joe Thornton's lab. If it works out I would probably be working on phylogenetic reconstruction of ancestral gene sequences. It seems really interesting and it could turn into a really valuable experience for me; possibly even a foot in the door to get into one of the more exciting grad schools I hope to go to one day. In any case I practiced reaching out to someone who is a leader in the field of computational biology which is exactly what I need to keep doing to succeed.

Monday, April 30, 2007

Donate your excess computing power: Distributed Computing

I started fighting to find a cure for cancer, Alzheimer's and ALS; I haven't even finished my bachelor's degree. To do this I participated in a distributed computing project through Stanford called Folding @Home, All I had to do was install their software which downloads protein folding problems and uses my computer's excesses processing power to solve them. I even get a cool GUI that shows me the protein while it is being folded in real time (note the picture on the left). They also have a site that explains the importance of the molecule that your computer is working on. I personally think that this whole thing is really cool and I am very excited to be participating in this. I hope others will share my enthusiasm and contribute to the cause as well, if not with Stanford's program then another one. At the end of this article is a wiki link that has some more examples of distributed computing problems and links to get involved.
Finding out how a protein folds is very important in determining its function and how it is able to react with other molecules. This information in turn can be used to explore possible cures or treatments for currently incurable ailments. I take pride that I can do my part in helping researchers study the properties of proteins. I am a huge fan of distributed computing and what it can do. To learn more about what distributed computing is or for links to more distributed computing projects check out

Monday, April 2, 2007

Yum, Sushi

I just got back from an incredible spring break in Boston and New York. In case you were wondering the picture to the left is me at the Boston aquarium. I am not really about to eat the poor little star fish.

I really need to stop asking people about what they do in life. I am one of those people who really listens and absorbs things. I am often fascinated by what is going on at the forefront of science and each time I hear about what project someone is working on for graduate work in whatever field I get sucked in. Next thing I know I start to plan out how exactly I am going to switch my majors yet again and take up whatever this new and exciting field is that I have just heard about.

Luckily for me and my school financiers I have realised this about myself. While I was in Boston I checked out the labs of my Girlfriend's sister and brother-in-law at MIT where they are both working on Graduate degrees. I was first introduced to Sal's (the Brother-in-law) lab. He is working on nano-scale coatings. May sound boring to the lay person but the applications for his work and his lab equipment were very cool. Next I visited Andréa's (the Sister) lab. She is working on nuclear Fusion as a possible alternative energy source. Through nuclear Fusion, one day we could all get the power we need from sea water. On top of how cool that idea is, her lab basically looked like a NASA rocket control room. It was very hard for me not to start thinking about my future as a physicist. Just to make sure that I still like what I do though I visited a lab at MIT that works on Genomics and Proteomics. They are doing things like searching for possible means of controlling HIV that do not enable the HIV to simply work up a resistance to the drugs. I must say, despite how cool Andréa and Sal's labs were I am still very much in love with Bioinformatics. The idea of coming up with a cure for cancer or aids is really appealing to me.

Just for you all I will throw in a picture I took of NYC at night while I was there. Enjoy...

Friday, March 16, 2007

An inconvenient truth for Fox, Forbes and whoever else I missed

I am writing this in regard to the headlines I have seen on Fox and Forbes this past week that went something along the lines of "An Inconvenient Truth for Al Gore". The spin here is ridiculous. Below are some key points.
  • Scientists weren't trying to debunk all of what Gore stated in his movie "An Inconvenient Truth" they were saying that he threw in some exaggeration.
  • The medieval warming period in the 1600's which was as warm as it is now was due to natural fluctuations. Scientists agree on the fact that the current warming trend is due to us.
  • It is scary to consider that us human beings have the power to bring about something as major as a global warming trend.
  • Scientists do not know how long it will last or if it will "naturally" reverse. We are talking about something totally different than a natural flux, we are talking about a man made issue.
  • The article I read on Forbes didn't mention a single thing about the CO2 levels in the atmosphere which was one of the biggest arguments Gore made in his movie.

OK so I know this isn't the best put together piece. I don't have time to make this pretty. I just wanted to get my opinion out there. The media needs to pay attention to what it says and the effects that it causes. When I read the headline I just thought to myself "Wow, there must be conclusive scientific evidence negating what Gore said. Whew, what a relief!". In reality when I read the paper on Forbes it said, to paraphrase, that scientists are in agreement that this current global warming trend is due to us. I wonder how many people skimmed that headline or even the first few paragraphs of the article and thought what I thought without bothering to read further.

Wednesday, March 14, 2007

Wahoo its almost time for finals!!

OK so I don't really get that excited over finals. It is definitely a time to pause and reflect on how far I have come in my schooling and how far I still have to go. It is hard to believe I have already been in college for nearly 3 years. I have the majority of a General Science major completed and I have a Chemistry minor under my belt. Also as of this year I have taken on another major, Computer Science. I am getting used to college which is a very good thing considering I have slightly under a decade left to go. Yes, I am shooting for a PhD, probably in Bio-informatics.

You must be thinking, wow this guy loves school. Well, yes and no. I really like learning about things I am interested in. I love the college atmosphere. I absolutely hate doing assignments and required classes that I do not want to do. The only thing that keeps me going through those classes is the fact that they are needed to take the ones that I really want to take.

I really like Bio-informatics. I took up computer science after completing a biology course because I was introduced to Bio-informatics. However I went into the CIS (computer and information science) field knowing that it would be a good 2 years of prerequisite courses before I was eligible to get into my first class in Bio-informatics. I am almost one year into that goal now and the harder year lies ahead. I am not shooting blindly though. I study bio-informatics on my own and I volunteer in bio-informatics labs at the university when I can. It is really a fascinating field.

I guess I will quickly write about what exactly it was that got me hooked on bio-informatics in the first place. I was in my 3rd term of the "Foundations of Biology" sequence which is one of the two possible lower division required sequences for Bio and pre-med students at the University of Oregon where I go to school. Going into that class I was a pre-med student as so many of us science related students are at the U of O. We had an open project to study the genetic sequence of HIV from a large population of HIV positive patients with varying rates of CD4 decline. We got the information from a paper written by Markham et all circa the early 90's. Pictured to the right is the image of the protein on the HIV molecule that we had genetic sequences for with a color coded conservation score from the study's participants who had a fast rate of CD4 cell decline. Circled is the molecule that I theorized was partially responsible for the fast rate of decline because it is highly conserved in the patients with quick rates of decline and it is very lightly conserved, if at all, in patients with a slower rate of CD4 decline. It was such an exciting thing to find that I instantly fell in love with the field of bio-informatics which studies problems exactly like this one.

I could keep blogging on but I need to get ready for class now. More from me later on this and other topics.

Saturday, March 3, 2007

Owch... my finger.

Last night I closed my finger in the car door. It hurts quite a bit and typing is pretty dificult. I will post something more substantial when I can type again.