My Biotech Life

On a sunny afternoon in July of 2008, I decided to join other residents of Tang Hall to a building barbecue. This seemed like a great opportunity to get some free food and meet some interesting people. But it was far more than that. It was probably the most marking moment of my stay as a visiting graduate student at MIT.

Before I get into that moment let me take a couple steps back.

All of my higher education was done in Portugal, except for that stint in Cambridge, MA. I’m a biological engineer by academic training and, as some of you may know, engineering degrees can be quite demanding. I’m not mentioning this to make it seem like I’ve done anything extraordinary, it’s just a reality that I’ve experienced. Challenging courses, demanding professors and an underlying sense of ineptitude are all parts of the puzzle. Or so I thought.

Back to the barbecue. I grab a cheeseburger, a bottle of water, and take a seat on the grass. There are about 20 or so graduate students sitting around in the sun enjoying their free food. I take a seat near two guys that are beginning to have a conversation. Keep in mind that I’m just sitting near them, not necessarily joining them.

As I enjoy my burger, I can’t help but listen in on their conversation. One of the guys is Asian, possibly Chinese. The other is Eastern European, I’m guessing Russian or Ukrainian. They briefly introduce themselves, one a physicist and the other an aeronautical engineer, respectively. They chat for a while about their ongoing graduate projects and at this point I’ve phased out while I enjoy my food. Only until out of the blue, one of them says something that regains my attention. The engineer tells the physicist that he’s thinking about designing and building a folding bicycle that can fly. I almost spray out the water I was drinking. He follows up by asking what the physicist thinks about this. My immediate thought: “Haha! You’re mad!”.

And then it hit me. The Chinese physicist contemplates the idea and begins a structured conversation about this idea. He doesn’t consider it outlandish and does not impulsively react like he’s talking to a buffoon. He actually goes on to discuss this topic in more detail. So here, this is the marking moment. This is where I realize how close-minded I was regarding education and exploring ideas. This is where I realize how constrained my academic training had been until then. This is where I realize that extraordinary things could only come to exist by virtue of extraordinary ideas. This is where I genuinely realize that the box is meant to be stepped out of.

The two fellows discuss the implications and requirements of building a utility bicycle that could be used by everyone. Discussion about wings that could fold up when flying is not required or possible, about materials that could be used, limitations in air space, and much more. I — I just sit there in wonderment as they approach this idea from various angles and give it a good scientific and rationale run down.

While the conclusion of their mutual thought piece ended up ascertaining that it would be impractical to use such a bicycle, their approach to this result was definitely something that I had not been ready for. I felt like a fool to have quickly brushed off the idea without putting it through the rigours of scientific thought.

I’ve kept that brief conversation in my mind ever since.

As I previously mentioned, my academic training was in-depth but quite rigid in format. In most cases, having far-fetched ideas would render the same reaction I had that sunny afternoon, from my colleagues and/or my professors. Unfortunate, I know. This is certainly not the case at all universities in Portugal, but it was pretty much my experience.

Nonetheless, I believe that amazing things are discovered or invented where there is space and openness to explore seemingly outlandish ideas. MIT looks like one of those places.

If you’re curious, man-powered flying bicycles do exist. However, they are indeed impractical and wouldn’t be viable for your daily commute.

It’s saturday night again and while baby is sleeping and I’m not in the mood for coding or reading, I decided to finish up these graphics and share. So, here is a set of 9 differently coloured test tubes I recently created. The zip file has all 9 colourful transparent background PNGs. Let me know what you think and feel free to make suggestions for my next pixel pushing endeavours.

And here you can download the zip file containing all 9 images. Enjoy!

It’s been a while since I’ve posted anything here. I blame it on Twitter (or just laziness). Anyhow, I stopped coding a bit this Saturday night and decided to fool around with some graphics tools. I wanted a new wallpaper for my shiny new macbook pro retina display and couldn’t find anything I liked so I decided to make something myself.

So here is the result: 5 different coloured variations of a DNA themed wallpaper. They’re hosted at my alternate website-to-be – bioinformati.co (more on that later…)

Check them out here (files are quite large):

I hope you enjoy them. I’ll try get back to this blogging thing soon… I’ll try. Meanwhile, enjoy the wallpapers and let me know what you think. Here, or on twitter @rvidal

Over the last few months I’ve been spending more and more time with R. Not only R but also Bioconductor packages which allow me to easily work with the massive data contained within the microarrays I’m currently looking at.

As this is my first post about R, statistics and Bioconductor, I won’t go over the various things I believe should change within the R/Bioconductor community. I’d rather just take this opportunity to show my appreciation for such a cool and powerful tool, or should I say, set of tools.

From simple statistics to amazingly complex visualizations, I’ve slowly grown to fall in love with R. Well, I love and hate R. But I’ll keep things positive for now.

Where my biggest interest falls is in the interface between data and art. Visualizing data in interesting and new ways that allow us to extract new or better understanding from said information. This is what I hope I’m moving towards as I spend many and long hours coding R and attempting to find patterns in my scores of biological data.

Another side effect from spending so much time sifting through data sets is seeing data everywhere. It’s as if everything can be re-analyzed or further processed to produce new and interesting results.

Simple things like waiting at the bus stop lead me to think that it would be interesting to see how efficient the buses are or if their routes could be improved. Looking at the seating in the cafeteria makes me consider the many possible optimizations in table/chair positioning, etc.

I know that this is not necessarily due to R or data but rather more interest in mathematics and statistics. However, the fact that I live and breathe R, statistics and data sets has been making the cogs move…

Accessing the web from a smartphone is great but feels confined.

For roughly 10 days, while on Christmas holidays, I was limited (sort of) to my smartphone for email and web access. This is all good and fine for things that have specific apps such as Twitter, Facebook and other popular websites. However, the web is far more than a collection of apps. Not to say that apps are not great, it’s just that the lack of screen real-estate, access to flash (for video) and other technologies leave me wanting more. It just feels like something is missing…

Keep in mind I’m talking about mobile access and I’m aware that tablet computers such as the iPad or the Galaxy Tab would probably be much more pleasant to use while away from a “real” computer/laptop.

For example, many times a day someone will tweet or post a link to some cool new site or video. I’ll see the link, click it and then see that either Youtube does not yet have that video available for mobile or the given site is not properly formatted for mobile devices and takes a long time.
If the site is interesting not only for it’s content but also it’s design, many times half of that awesomeness is lost while on a mobile.

So what ends up happening is that I bookmark the site or the tweet (favorites) and check them all when I get back to my home computer.

I know it’s not supposed to be the same to navigate the web on a computer and a mobile device but with the massive push that has been put forward to get content mobile-ready, I was expecting that things would be less limiting. It looks like there is still quite a bit of work ahead and I’ll be here clicking and bookmarking “for later” as things progress…

Warning: I’m going to get a little meta here. Not a usual thing for me but here it goes, nonetheless.

One of these weekends, I was trolling around the interwebs and came across a post by someone with a hypothetical (far-fetched) question along the lines of: “What would you do if you suddenly discovered that you could not die?”

Quite immediately the silly and equally far-fetched comments/answers started coming in. Some would do such things as walk into volcanoes, leap from buildings/planes and perform other generally mortal activities. However, others took a more cautious route by stating that they would not tell anyone for fear of scientific probing or media exposure. The answers said quite a bit about each commenter’s personalities, to say the least.

However, what I found most interesting were the follow-up questions to the original question. Some quite entertaining and others rather important, given the hypothetical situation.

• “If I jumped from a building, would I get injured at all? If so, would I recover from my injuries or remain injured for eternity?”
• “Although immortal, can I feel pain?”
• “How did I discover that I could not die?”
• “Do I grow old despite not dying?”

My inquisitive nature finds the questions to the original question far more enticing than the immediate comments made without further interrogation. They [the following questions] open up far more hypothetical answers to the original question. The necessity of specifics to provide a correct and conclusive answer to a question is so ingrained in my thought process that it sometimes leads an answer to be delayed until all scenarios are covered. Rambling a bit more, the answers to the various questions asked after the original question would further define my answer and therefore lead to a more specific hypothetical answer.

In short, if you had to answer the question above, would you answer as is or attempt to find out more about the hypothetical situation before answering?

I guess the easiest (and probably lamest) answer is “It depends.”

I have a special interest in most things that sit at the interface of art and science. Be it, graphic design through data visualizations, fancy portraits of your DNA or just geeky hand-made jewelery, it’s all good in my books.

A couple (6?!) months ago I was contacted by Alexandra Pajak, a graduate student from the University of Georgia, with an interesting project. She told me that she was working an album based on the genome of the HIV virus called Sounds of HIV. It immediately caught my attention and I said I’d love to give it a listen.

Sounds of HIV is a musical translation of the genetic code of HIV, the Human Immunodeficiency Virus. Every segment of the virus is assigned musical pitches that correspond to the segment’s scientific properties. In this way, the sounds reflect the true nature of the virus. When listening from beginning to end, the listener hears the entire genome of HIV.

So how does one listen to DNA, RNA or proteins you ask? It’s somewhat explained by Alexandra’s notes:

DNA-based music is music in which the natural chemical properties of DNA is translated into music. In English, the nucleotides adenine, cytosine, thymine, and guanine are abbreviated with the letters a, c, t, and g, respectively. Since A, C, and G are also musical pitches in the Western melodic scale, these pitches were assigned to the matching nucleotides. To form two perfect fifths (C-G and D-A), “D” was arbitrarily assigned to musically represent thymine. The notes of the A minor scale have been assigned to the amino acids based on their level of attraction to water.

On Sounds of HIV, depending on the track, nucleotides and/or amino acids “play” as music. Tracks 1 and 10 are based on the first and last nucleotides of the DNA chain. Tracks 2-9 “play” the proteins and sometimes the nucleotides on top of the proteins.

I’ve listened to the full album and have found it to be a bit strange at times but was mostly expecting the music to very different as it is in fact driven by genetic information which most probably didn’t evolve based on it’s audible features!
You can listen to excerpts at Amazon and if you like what you hear, be sure to buy a copy as a part of the proceeds from the sale of this album will go to the Emory Vaccine Center which does extensive AIDS research.