Saturday, January 26, 2008

Scientists create synthetic genomes: Don't jump to conclusions

Scientists have created the first entirely synthesized bacteria genome . I like looking for connections in things, whether it be in literature, science, math, or music. This news article heavily connects with yesterday's post about zeros and ones. The impression that first jumps to mind when reading this story is that "Oh my God, we'll be genetically engineering a master race any day now". The fact of the matter is, writing assembly code is a lot different than writing in Java, the programming language I'm using, these days. To create higher structure than just a single cell will require a massive amount of research as well as engineering. I don't know the direction it will take, but from analogies to computers, I imagine they will need subroutines, to take common pieces of DNA and use them in different ways. DNA has developed by duplicating the same sections and then evolving subtle changes which confer a reproductive advantage. Decades of work, maybe more, is needed for this research to reach its pinnacle.

Still, this is an amazing achievement. Too much C02 in the atmosphere, create a bacteria to process it. The ability to engineer bacteria to suit our needs could open up whole new worlds to us, and greatly increase the standard of living for all humanity in the next century.

Friday, January 25, 2008

When I look up at the sky, all I see is 0s and 1s

Andrew Bird sings in his song Masterfade, "When you look up at the sky, all you see are zeros, all you see are zeros, and ones. My previous post reminded me of this line, as well as a number of other things. As a computer scientist (code monkey, really), I am very capable of seeing things as zeros and ones. To a lay person, the idea that complex structure is dictated by DNA is difficult to grasp, but not to someone who majored in computer science.

Every piece of software is composed entirely of zeros and ones. Every message you send over the internet, every pixel displayed on your monitor. Starting with and gates and or gates (or nand gates), you can design a processor which works entirely on zeros and ones, something you do in freshmen or sophomore year of college. You then write computer programs in hexadecimal, which is a condensed representation of binary. You have larger structure, assembly, to make it easier to use. If you considered DNA to be the zeros and ones, take the proteins to be assembly code. You can then write a compiler to write more complicated programs in a simple format. The C compiler takes C code and converts it to assembly. You can look at this as kind of like building organs.

Obviously this isn't a perfect analogy, but it is one which makes the whole process seem a lot simpler. If we could create this complex structure in a matter of less than a century, imagine what could happen over a billion years. One more parallel I'll draw is this. Regardless of what you have, man, fish, insect, fungus, bacteria, you have the same basic DNA. The same is true of Java, C++, python, perl. Despite the vast differences, the underlying structure is completely the same.

Thursday, January 24, 2008

A Simple Evolution Primer

The Bad Astronomer posted this excellent video about evolution. It reminds me of the line from Sneakers ,

The world isn't run by weapons anymore, or energy, or money. It's run by little ones and zeroes, little bits of data. It's all just electrons."

To a computer scientist, this is gospel. And yes, I pronounced Primer to rhyme with dimmer.

Sunday, January 20, 2008

50 most loathsome people of 2007

I know it's a bit late to be posting links for end of the year stuff, but I had meant to post this a few weeks ago when I read it. It covers politicans, both democrats and republicans, athletes, celebrities, fictional characters, historical figures, and even you!

50 most loathsome people of 2007

Wednesday, January 16, 2008

Mike Huckabee, Crazier than Ron Paul

Pharyngula posted today a story about Huckabee, where Huckabee wants to amend the constitution to be the Bible . The Constitution was specifically written to be independent of religions, and Huckabee wants to change it to be based on his Bible. To be fair, that only excludes Jews, Muslims, Catholics, Buddhists, Hindus, the non-religious, northern Baptists, so it won't really effect anything.

Thursday, January 10, 2008

Awesome Video

It's often difficult to imagine the sheer size and immensity of the stars compared to the planets. This minute long video goes from the smallest worlds to the largest stars, and the contrast is made stark. It was a fabulous spent minute, although it took quite a bit longer for me to constantly stop to look up various stars on Wikipedia.

Planets and Stars in scale

Wednesday, January 9, 2008

Arabic Lessons

A fabulous article in the New York Times about learning to speak Arabic. I know a little bit about Arabic from my linguistics classes, but never really caught on to how hard it was. Additionally, it is a widely spoken language that has been around for hundreds of years and over a geographically and ethnically diverse region, so there are many dialects. It is probably similar to learning to "Chinese", since there are a bunch of different languages spoken in China, and that's languages, not dialects. A particularly fascinating passage is linked below.

For anyone who knows only European languages, to wade into Arabic is to discover an endlessly strange and yet oddly ordered lexical universe. Some words have definitions that go on for pages and seem to encompass all possible meanings; others are outlandishly precise. Paging through the dictionary one night, I found a word that means “to cut off the upper end of an okra.” There are lovely verbs like sara, “to set out at night”; comical ones like tabaadawa, “to pose as a Bedouin”; and simply bizarre ones like dabiba, “to abound in lizards.” Dabiba (presumably applied to towns or regions) is medieval, but I wouldn’t put it past Dr. Zawahri to revive it.

Tuesday, January 8, 2008


I discovered a few weeks ago that Cosmos , the groundbreaking, inspirational series by Carl Sagan was going to air on the Science Channel, in HD, on Tuesday nights. Of course, I don't get this channel, so I had to call and upgrade my cable. Yes, that's great this series is. I've read the book several times, and seen several of the episodes, but never had a chance to watch the whole series. I urge everyone who has this channel, or knows someone who does, to watch it.

Monday, January 7, 2008

Nietzsche Family Circus

One of the comics I have linked is the amazing Nietzsche Family Circus. Pairing quotes from the philosopher with the comic about children frequently produces hysterical results. Check it out, here is the one it just produced .

Friday, January 4, 2008


I've always hated ice cream novelties. I like ice cream cones, ice cream sundaes, ice cream bars, various nutty iced cream concoctions, those Flintstones push pops, and all of that. It's the term. There is NOTHING novel about "ice cream novelties". The term is patently ridiculous. For a long time, that was enough. I hated the term, people wouldn't stop using it, and no one was on my side.

It turns out though, that I have history on my side. In 1277, the Franciscan order condemned Roger Bacon to prison because of "suspected novelties". The term is someone obtuse and for those who don't understand 13th century church speak, I'm sure it means he was suspected of propagating the term "novelty".

Thursday, January 3, 2008

Demanding Logic in Politics

There isn't much I can demand from todays politicians. All I ask is that they have a logical position on important issues. For example, fertility clinics create (conceive) an embryo. They freeze it, and eventually dispose of it. According to President Bush, this is all well and good. When a scientist attempts to use one of these already conceived embryos which would otherwise be thrown out, this poses a moral quandary? If we as a society are going to decide that a fertilized embryo constitutes a life, then what the fertility clinics are doing should be outlawed. If it is ok for fertility clinics to create these embryos, then stem cell research should be acceptable.

Another example, along the same lines. If a woman is pregnant and wants to have an abortion, it is better to offer incentives to keep the child. A poor woman will need a lot of money and support to raise a child, and if the government is mandating her actions, logically they should have to contribute. Instead of worrying about banning abortion, we should offer plentiful birth control, and when unwanted pregnancies do occur, offer all the support we can to the mothers and families so that abortion is not the better option.

Tuesday, January 1, 2008

Creationism in Linguistics?

Over at the Language Log, there is a post about this insane book, I kid you not, The Origin of Speeches: Intelligent Design in Language (Paperback) . Now, I must say, centuries of linguists haven't been able to trace language relationships back more than several thousand years. Proto Indo-European seems to have been spoken between 5,000 and 9,000 years ago, although those error bars could extend back farther into time.

You might ask, "Why is that a problem?", to which I would have to explain that the thesis appears to be that in the garden of Eden, we all spoke the same language, and that languages diverged due to the tower of Babel. We have no estimates for the time when PIE merged with Hebrew, but it would certainly have been more than 10,000 years ago. However, the Creationists put the date of the garden of Eden much more recently than that.

Let me cite some reviews, "Origin of Speeches is a great way to learn about language, any language. You also learn alot about history and how academic fads or theories, like Darwinism can obscure important and accessible information." Ignoring the obvious misunderstanding of what constitutes a "theory", this reviewer refers to Darwinism (by which they mean evolutionary biology and related fields) as an "academic fad". When I write my first book, I'll make sure to have my mother be the first one to review to.

I may have to find this book at a library (since I won't be purchasing it) and carefully examine all of the arguments.