Jump To:
Introduction
Closed-Source Genetics
Open-Source Genetics
Going Public With My Genome
Better Living Through Personal Genomics
DIY Genomic Sequencing for Programmers
My Personal Genomic Results
Further Reading

Single Nucleotide Polymorphism (SNP)

Introduction

It’s been over a year since I signed up with 23andMe and several months now since I downloaded my raw genomic data from them and started seeing what I could learn from it on my own. Although very few services out there will fully sequence your personal genome, by focusing on sequencing an individual’s Single Nucleotide Polymorphisms (SNPs), pronounced “Snips” for short, which are the variables between human genomes, we can focus on what’s of interest in our personal genomic data and get this data relatively cheaply. By comparing the differences in our genes, our genotypes, my wife and I could learn about how they differently express themselves in our lives, our phenotypes, to gain insights about our health risks as well as interesting traits about ourselves that may explain our behaviors and experiences throughout life.

“Time you enjoyed wasting was not wasted.” ~ John Lennon

“Time is the fire in which we burn.” ~ Tolian Soran, Star Trek Generations

The Dilemma

We have a finite amount of time in this life, and we should be mindful of how we spend it. I’ve recently become highly cognizant of the fact that the majority of games are simply Skinner Boxes, tricking players into pushing buttons in return for meaningless rewards. Truly challenging games like Portal and SpaceChem keep you playing because the gameplay is its own reward, while Skinner Box games keep you performing repetitive tasks with virtual rewards. Other games, like Skyrim or Final Fantasy VII, keep you playing because the story and graphics are simply that engaging.

The Original Earth Starbase Was Just Okay

The Redesigned Earth Starbase Looks More Familiar

For the past two years I have played Star Trek Online (STO) casually, probably investing maybe a hundred hours in the game, two weeks of my life out of 104. So the question arises: Is STO time wasted? The game was never challenging, but was it at least entertaining? I think this is a question we should be mindful of with any game in which we choose to invest our time to make sure we aren’t burning it.

This is the uncensored version of my Science Fiction VS Fantasy piece I wrote for the Science Creative Quarterly several years ago. I’ve also written much more extensively on this topic in the past. This is the abbreviated version with 10% more snark:

Fanboy: Hey gang! Did you read The Sword of Shanara? The characters traveled hundreds of miles described in excruciating detail for hundreds of pages, until they reached the ultimate battle between good and evil! Cool huh?

Scientist: Whatever. The characters in Red Planet traveled 48 million miles to Mars, while those in 2001 traveled 369 million miles to Jupiter. Characters in Asimov’s Foundation books travel millions of light-years all over the Milky Way galaxy in routine manner. Isn’t it amazing what people can accomplish when they don’t have to walk everywhere? Thank a scientist for your planes, trains, automobiles, and spaceflight whydontcha.

Fanboy: Yeah, but did you see in The Lord of the Rings when Gandalf fought the Balrog all the way down a really deep hole and then all the way back up to the top of a mountain peak!?!?

Scientist: Big whoop. The adventurers in The Core traveled to the very center of the Earth, fighting technological, natural, and human hazards all the way down and all the way back up to the Earth’s crust again. Characters in Fantastic Voyage and Innerspace fought their way all through the human body in microscopic form.

Fanboy: Ooookay… But did you see all those maps having to do with the Wheel of Time books? It’s a huge continent! Pretty epic, huh?

Tron and Tron Legacy

I attended the Experiments with the Imagination session at Science Online 2011, where we discussed what made good versus bad inclusion of science in fiction. Interesting points were made, such as audience members being able to excuse bad science for kick-ass portrayals of scientists, like in the movie 2012, and a deep concern for how science is portrayed in film because Hollywood blockbusters carry so much cultural influence in America.

There was also an intriguing question about working scientific elucidation into fiction, which stuck in my mind when a member of the audience mentioned how terrible was the film Tron Legacy and was met with lots of head-nodding and murmurs of agreement. I had actually enjoyed Legacy, and, after rewatching it, realized that I was seeing a very different film than the average audience member.

Proce55ing Source Code
Credit: Niels Heidenreich

In his book On Writing Stephen King argued that to be a good writer, you must be able to “Kill your darlings,” where, for the sake of keeping the prose moving, you must cut out the non-essential parts, no matter how well-written:

Mostly when I think of pacing, I go back to Elmore Leonard, who explained it so perfectly by saying he just left out the boring parts. This suggest cutting to speed the pace, and that’s what most of us end up having to do (kill your darlings, kill your darlings, even when it breaks your egocentric little scribbler’s heart, kill your darlings)…I got a scribbled comment that changed the way I rewrote my fiction once and forever. Jotted below the machine-generated signature of the editor was this mot: “Not bad, but PUFFY. You need to revise for length. Formula: 2nd Draft = 1st Draft – 10%. Good luck.”

Writing code is much like writing prose, but I think it’s even harder to cut your most beautiful ideas from a computer program. In software design, we have to research heavily and go through hours of trial and error to produce some of our solutions. It’s one thing to slash several paragraphs of prose crafted in a hour of brilliant inspiration, it’s quite another to throw away an inventive solution and the wisdom that came with it.

Mxplx Prezi Screenshot

At Science Online 2011 I was introduced to the Prezi Presentation Paradigm by Stacy Baker of Extreme Biology. After getting past a surprisingly mild learning curve, I was able to produce the following presentation mixing a Prezi presentation with desktop video capture:

Keeping in mind this is not the best example of a Prezi demo, you can step through and play with the Mxplx Prezi itself below (alternately, you can browse popular Prezis here). Don’t confine yourself to just click through the presentation, as you can click-and-drag, double-click, and zoom as well:

Corrosion Mapping, Hotspots Highlighted
(Not an Actual Report Image)

One application I had the honor of working with in my time with the Coast Guard was a Corrosion Mapping tool used by Engineers to track the wear and tear on aircraft parts over their lifetime. Using an Active X control, users would bring up a TIF of an aircraft part, and then click on grid coordinates laid over it to identify places where corrosion was noted. These X and Y coordinates were then saved to the database, where they could be tallied in reports, with the number of occurrences of corrosion highlighted to identify weak points in the parts. It looked something like the image above.

I recently tried to reproduce this functionality with JavaScript for an application where researchers would mark incidents of contamination on a building floor plan in order to determine the radius of the area that would need to be sterilized. Here are three JavaScript variations on this theme of plotting coordinates on a grid.

Social Networking Results for #scio11 Hash Tag on Twitter
(Click to Enlarge)

The above image is just one graph of the many tweets related to the Science Online 2011 Unconference. I generated the above graph using the open-source free software NodeXL, a Microsoft Excel plugin that harvests social networking data from common online sources and provides a variety of mean for analyzing it. In the following post, I’ll provide a brief overview of social network mapping with NodeXL using data harvested from Facebook and Science Online 2011 tweets and provide directions for making your own social network maps, where you can explore and manipulate the data to find your own insights.

The Memetic Ecosystem Within Mxplx

I’m a big reader, and a lot of what I read inspires the posts for ideonexus. I love it when I find a brilliant insight in a text and can slap it down as a blockquote or relate it to other citations I’ve come across in the past. I’m tickled by brilliant ideas, and I love the communal exercise of building on old ideas and mashups from them.

A frustration I’ve experienced often over the years is remembering a brilliant insight from Carl Sagan, Richard Feynman, or some other author that would make an excellent complement for my current blog post, but having no idea which book in which it appeared. Even if I know the book, it can take an hour of thumbing through the pages to locate the passage I need (often because the text isn’t worded the way I remember it). And what about all those brilliant passages I’ve long forgotten?

These are the reasons I’ve written mxplx, an online tool to aide in the practice of active reading, research, and citation management.

Will Code JAVA for Food
(Even with Eclipse)
Credit: cismet_geeks

A newly-minted graduate in software development recently wrote me after finding my resume online, seeking career advice on how to succeed in the IT professional world. These were my personal thoughts; maybe other readers will have additional insights to add in the comments section:

Dedicate yourself to lifelong learning.

Don’t be afraid to research while you’re on the job. You are a professional, a technical expert, and must keep up with the literature and latest developments in your field. Search engines and forums will provide the most practical and nuanced advice, while organizations like the IEEE and ACM provide the academic sustenance. Remember what Adlai Stevenson said, “I reserve the absolute right to be smarter today than I was yesterday.”

Work with people who are smarter than you.