These are all the materials I used/planned to use in class. I'll also put some links below for topics/sites I find interesting. Hope it helps! If you leave comments, I can try to get back to you and direct you to resources.
Happy Coding!

Where to go in order to...

Stuff I wrote for the class (I'm planning on teaching this class again next year, so I may write more worksheets...):


Imaging Exoplanets: Out of this world pictures

   Back in 2008, the image at left was plastered across the front page of many science related publications. For the first time, scientists had directly imaged an exoplanet (a planet which orbits another star) with visible light.
   Exoplanets themselves were nothing new.  In late 2008, 333 exoplanet canidates were known, and 8 of those had been detected using direct imaging. In fact, Fomalhaut b itself, the planet pictured, was actually not truly a new discovery. Since 2004 scientists had been reasonably confident it existed because of the sharp inner edge of the band of dust around the star Formalhaut. The thought was that a large planet (namely Fomalhaut b) was sweeping the material from the inside of the band into itself.


Of mice, men, and microRNAs.

   Although RNA is most famous for acting as an intermediate between DNA and Protein, we've come to understand that RNA's role in the cell goes far further in recent years. Some kinds of RNA, like miRNAs, actually change the balances of proteins made, leading to a wide variety of effects.
  What exactly is a miRNA? miRNAs or microRNAs are tiny segments of RNA. Where most RNA segments are about 1,400 nucleotides long, miRNAs are typically only about 22 nucleotides long. While miRNAs are sometimes written out by themselves on DNA (as in the video above), it's more common to see miRNAs created as a byproduct of the creation of other kinds of RNA. Unlike many other types of RNA, miRNAs don't encode for proteins or assist in their transcription of RNAs to protein. Instead, miRNAs prevent proteins from being made from mRNAs by latching onto them before they can be transcribed. In the past few years, miRNAs have been implicated in certain types of cancer, and been used as biomarkers to help detect and diagnose diseases.
   All of this is very exciting on its own, but more exciting still is a paper recently published in Nature Cell Research which suggests that miRNAs can actually travel from material in the digestive system of an organisms you eat into its bloodstream. Scientists at Nanjing University, China found a certain miRNA from rice, called MIR168a, in the bloodstreams of both humans and mice. By varying the diets of lab mice, they were subsequently able to show that the miRNAs found in mouse blood were being ingested.
   This alone is an important discovery, but the researchers further "hypothesized that [plant miRNAs] may play a role in regulating the functions of mammalian cells and organs". Looking through the known sequences of mouse and human mRNAs, they identified about 50 proteins which MIR168a was likely to interfere with, including LDLRAP1, a gene that codes for a liver protein in both humans and mice. By exposing a certain type of liver cell (HepG2) to increased miRNAs, they determined that "Plant MIR168a...significantly decreased the LDLRAP1 protein level in the recipient HepG2 cells" while LDLRAP1 mRNA levels remained unaffected. In other words, the miRNA was preventing the transcription of the LDLRAP1 mRNA, as expected.
   Why care about this result? It further clouds the waters regarding the role environment plays gene expression, an area of much of interest in biology right now. In addition, if miRNA uptake turns out to be common (or at least easy to induce) in humans then it could lead to whole new classes of oral drugs that target the expression of specific proteins.



   If there's one result worth posting about from this week, it is the now famous (and in some circles infamous) exchange of neutrinos between CERN and OPERA, two European physics laboratories. Neutrinos are pretty cool as is, but what's really of interest here is what the neutrinos (muon-neutrinos, to be exact) appear to be doing on their trip from their creation at CERN to their detection at OPERA. They're arriving ever so slightly early: 60 nanoseconds early to be precise. For reference, quick calculation shows that light only travels 24 meters (just under 80 feet) in that time.
   How fast light travels is actually exactly what's at issue here; the neutrinos seem to be arriving at OPERA before light traveling along the same path would. If it is true this is the most significant find in physics for a century at least. For all practical purposes though, getting a result like this is a really good reason to check your equipment for obvious problems.


What is about to happen.

Starting next week (and possibly this week for practice) you can expect to see two new articles per week (posted on Saturdays?)on current events in science along with some reasons you should care.
As part of my first semester at MIT, I'm taking a Science Journalism class. Part of this class is the creation (and weekly updating) of a blog on science, medicine, technology, and related topics.


Living in Simmons

My sketching is still awful, but at least I'm getting the hang of cleaning it up in gimp... More after the jump.

The Hough Transform: New and Improved!

  Ok, well it's still not better than a kerneled transform, but I am getting pretty pictures without the use of any trig! To sum up what I'm doing, I'm trying to use python's lambda expressions to generate a function in Cartesian space from the given points. Then I want to run BFGS over that function to find local maxima. By multiplying r = x_0 cos( theta ) + y_0 sin( theta ) through by r and rewriting as x^2 + y^2 = x_0 x + y_0 y , it's easy enough to see that the hough transform of a given point is actually a circle with one point at the origin and centered at \left( \frac{x_0}{2},\frac{y_0}{2}\right).
  This has the nice property that it's easy to calculate the distance between a given line ( point in hough space ) and the nearest point on the circle as a single square root.


An awful haiku.

Deathcube, what great mass!
Rubber over the solid heart
of a neutron star.


A quick sketch from last night's "Welcome to Simmons" talk

Done in the corner of some scrap paper. I've played around with some post editing in Gimp. Best part was the "Fire Alarm Prevention/ Popcorn Cooking 101" bit. Wish I could have sketched that instead, but I was out of paper space.


A Native Google Talk Client for Linux(Sort of)

I've been using Google Talk more frequently as of late, but upon investigation, I was disappointed to learn that Google hasn't released a Linux client for Google Talk. I did, however, notice a reference to a "native" (whatever that's supposed to mean) ChromeOS client. Since I knew that ChromeOS is running Linux under the hood, I decided to check it out. Amazingly, despite wads of yellow tape warning me that it would wreak havoc on my computer and slay my firstborn, it seems to work seamlessly as a Linux client for Talk in Ubuntu 11.04! Video chatting between two semi-native clients doesn't always work, and using both the client and, say, gmail chat at the same time has it's rough edges, but it's fine.


Thoughts on Child Protection Legislation in Ireland

[BBC] via [Boing Boing]
I'm not going to summarize the article above. That's been done enough. Just read it, poke around the issue for a while, then come back and read what I have to say.


Off to MIT

I thought for a long time about what I was going to say here to show that I wasn't scared. In the end, that would be a lie. I am scared, scared out of my mind.
At least I'm excited.


On Regression to the Mean.

   It's been almost a full year and a half since I wrote On Grades. On that time, I've come a lot further than I imagined possible then. I managed to patch up my mediocre grades and scored 5s on all 6 APs I took that march. I won the State Siemens Award for Oregon (Dad - if you ever read this, thank you for believing in me when I didn't believe in myself). Somehow, my sub-par GPA didn't keep me out of MIT, a school which I'd already given up all hope of attending (I still catch myself once or twice a week wondering if there's been some mistake, or I applied to the wrong MIT somehow, or if I'm just downright bonkers. It's been more than a half year since I was accepted.).
   There are some bit of the On Grades pessimism that still apply. I am still living in a very small pond, and I am about to be thrown into an ocean. I am certain that at MIT I will not be in the to 10% as I am here. I probably won't even measure up to the average student. I still lack diligence. I lack experience, and I'm too used to running into tests and quizzes unprepared, counting on my logic and intuition to get me good scores. That will not, cannot, work here.
   Most of all, I'm afraid of how I might react when I'm faced with a challenge that will take more intelligence than I possess to overcome, while surrounded by people who may very well see obvious solutions. I'm afraid of being thrown into an environment where so much of my self identity will be so common place, because to at least some degree, I rely on that to drive me.
   I have hope. I was easily out gunned by some people at SUMaC last year, and it just made me work harder. What I have considered my identity has changed in the past, and as it does I generally become more comfortable. Perhaps being in an environment where I'm no longer near the top of the pack will give me an opportunity to find an identity that's more healthily linked to my academics. Despite my fears, I really can only look forward to being surrounded by people who share the same sorts of enthusiasms as myself.
  I have one more week left here, and then it is time to fly away from this little valley behind for the time being. Despite my constant complaining, I'm going to miss everything about it.


An open letter to Google.

  Here we are, only a little more than a week after I've deleted my facebook, and I can't help but feel the temptation to go back and stop the process. Only my lingering anger, and the time I invested in getting my data out are keeping me from doing it.
  At the heart of why I'm writing this (still pointless) apostrophe to you. At stake here is your cleanup of Google+ accounts with false names. I wish there was some sort of official statement I could link to instead of that article, but I can't find one. Basically, those users who either have used pseudonyms on Google+, or have multiple Google accounts, seem to be at risk of being locked out of (in some cases at least, though accounts vary) the rest of their Google account. I admit, this is especially disturbing to me because I technically fall into both categories (if you're from Google, please read on as I explain why I believe this is a technicality.).


3D Scanning, the Bowyer-Watson Algorithm, and Real Time (maybe) Delaunay triangulation.

  Wasn't that a mouthful! I'm taking another look at my 3D scanner. I really haven't talked about this scanner very much on this blog, so I've posted a video of it I made earlier this fall as part of my MIT application above. I'll move a good deal of the content from that portion of my application onto this blog over time, so long as it doesn't become too obsolete.


Why I'm leaving: An open letter to facebook

Dear facebook,
A few years ago, in a fit of rebellious teenage rage, I joined facebook. I knew my parents didn't want me to have an account. I knew "all" my friends already did. I wanted to fit in.
 Since then the idea of social networking has grown on me; I've come to know and love my facebook profile and it's not an easy decision to leave. What's triggered my decision to jump ship is simple: you won't give me my contact data back. I wanted some numbers to put on my phone and some gmail addresses. Your APIs wouldn't give them to me.


Fear my pixelated magic!

I got bored with my header, and decided to make a new one. Made with GIMP (From scratch!), uploaded to Dropbox, done. I wish I'd been able to give my ninja alter ego a slightly better left foot, but overall I'm happy with how it turned out.
I've also changed titles and dates over to a visually-consistent font with the font-family command. At the moment, this won't show up on firefox because my font files are hosted on dropbox and firefox won't show externally loaded fonts. I'll be tinkering around with this a little more.

Up, Up and Away

   It's over. The last launch has happened roughly on schedule (somewhat surprisingly, given the weather), and Atlantis is in orbit. The shuttle is something I grew up with. I had shuttle shaped toys throughout childhood. A picture of an old discovery launch taken by my mom hung on my wall until very recently. The shuttle is a symbol of what humanity can do when we work together towards a higher goal in the same way the ISS is. I can only hope  the event we've seen is, ultimately, a step forward, not a step back. I'm all for commercialization of space flight, but I hope that we're not sacrificing our capability to put humans into space for nothing. Here's to a safe final flight for Atlantis.



Said Conrad Cornelius O'Donald O'Dell,
My very young friend who is learning to spell,
"The A is for Ape. And the B is for Bear.
The C is for Camel. The H is for Hare.
The M is for Mouse. And the R is for Rat.
I know all the twenty-six letters like that...
... through to Z is for Zebra. I know them all well.
So now I know everything anyone knows
From beginning to end. From the start to the close.
Because Z is as far as the alphabet goes."

How to liberate your phone book from facebook

This is a quickly written, hacky script for personal use. For the time being, this script will only work on 99 friends at a time (Amusingly, facebook thinks there are 100 on the first page, but you're welcome to count. There are 99. Buggy programming FTW!). I'm playing with a workaround, but don't hold your breath. In the meantime, you can do the following to take your friend's phone numbers back into your own care:


Coding music...

When I'm planning, I play Mozart or similar. When I'm coding, it's Techno and Electronica all the way (The Frozen Synapse soundtrack is good too, by the way...), for debugging, Amiina. Some days, I have a feeling I'd put my keyboard through a window any other way...


Cellular Turing Machines(Physics Simulation)

If everything works as planned, we've go our creature all the way manufactured, popped out, everything. It's sitting in the environment, ready to rock and roll. Now what?


I only wish you could dream.

May God us keep From Single vision & Newtons sleep.
—William Blake
   Science is amazing. Think about it, take a look around, and hopefully you'll see what I mean. Heck, don't take a look around. Stare straight at these words on this screen, and realize how incredible it is that we can control electrons to such a degree we can make them take these words from my screen onto yours. It's something almost laughably absurd, it's absolutely ludicrous, but it's reality, the reality we live in because of the generations of scientists who first messed around with amber and cat fur. We owe our modern standard of life to the generations that sought not just to live in, but also to understand the universe and to the people who wrenched every drop out of our collective knowledge and back into the bucket of tools we have to confront and observe the natural world.