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…

Diving into R and swimming in data

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…

10 days of mobile web

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.”

The questions to the hypothetical question

• I finished my thesis, I presented my thesis, I concluded my Master’s degree. Good grade, Happy dance.
• I took my (32!!) driving lessons, I passed the written tests, however I did not conclude my driving exam (more on this, later).
• We made a decision, a difficult decision. Time will tell.
• We celebrated our 1 year wedding anniversary. Champagne for all!
• We moved to Canada. First Toronto for a while, now Kingston.
• I switched to Mac. My 6 year old laptop may rest in peace.
• I’m now a Ph.D. student in Squire Lab at Queen’s University.

There were some good (great!) and bad (really bad!) moments since last August, but no need to go further into detail here.

OK, done that, let’s get back to semi-regular blog posts of awesome science stuff.

It’s been a while…

Synthetic biology is great, I really like everything about it. I truly do. I had the privilege of meeting and seeing the work of some of the pioneers in this exciting new approach to genetic engineering last year at MIT.
I must emphasize something about these bioengineers. They are extremely smart, hard working, innovative and, did I say it? smart biological engineers!

So what is it that ticks me off about some of the synthetic biology related articles? It’s not the “Frankenstein” remarks, it’s not the bioterrorism worries and it’s not even the JC Venter veneration!
Nope, it’s the constant comparison between synthetic biology now and computer science in the mid-80′s.

This comparison just brings along a whole truck load of babble that I think is incorrect. Mentioning that synthetic biology makes engineering biology so easy you can do it in your garage as if putting together a new lego set. Stating that people are sequencing their own genomes in their closet as if it were something like baking a cake in your microwave.

These stories are either incomplete or incorrect. You choose. I think that the average reader is going to misinterpret these articles. It’s quite notorious by looking at the comments made on the online news articles.

No doubt that synthetic biology makes engineering biology easier but it’s not something you’ll be doing in your garage/kitchen/bedroom closet. At least not legally, or with much success. Besides, the people that seem to be championing such efforts are mostly graduate students in fields related to biological sciences, not your regular Make magazine reader or science buff.

I’m not against the DIYBio movement. I just don’t think it should be synonymous with “garage synthetic biology”, because it’s not. They have a ton of really interesting projects that I believe would make more sense to put effort into.

So yeah, let’s not get ahead of ourselves.

In summary: Synthetic biology is great awesome! But unlike Obama, it’s not your new bicylce.

[Photo: Alexander van Dijk]

Synthetic Biology is not your new bicylce