Tuesday, June 21, 2016

Can compassion ever be powerful enough to stop terrorists?

Our country and our world keep experiencing devastating and seemingly senseless acts of mass violence. Some of the violence is committed by people who are clearly mentally ill. But a shocking amount of mass violence is committed by rational people who know exactly what they are doing. My ideological heroes, like L.L. Zamenhof, Amon Hennacy, and Leo Tolstoy, were strong proponents of non-violence, even to the point of pacifism.

In my life as a middle class American (that is: incredibly wealthy compared to the world-wide norm), I've never really experienced the threat of violence, so perhaps I'm a little rosy-eyed and unrealistically idealistic. But it seems to me that our strongest weapon against violence is, and will always be, compassion.


Here's a poem that kind of addresses these issues. I wrote it after reading the article “Young Lives, Lost in the Fog of War” by Rod Nordland in the Sept. 15 2012 New York Times.

I'd be remiss if I didn't also credit the inspiration of the Flaming Lips, and their performance at the Oklahoma City Zoo, and Bart Budwig for a line I stole from one of his songs.

Monday, June 20, 2016

Code Release: Circle the aardvark in the back of the pickup truck

A while ago I made a game called: Circle the aardvark in the back of the pickup truck. Now, by popular demand (or just because I felt like it...), I've posted the code and resources for public download. I think there's a lot of potential for using the core mechanic (circling things) for other games for touch devices. I intend to do a series of posts explaining some of the important or innovative aspects of the code.

In the meantime, the code can be found here.

Topics I hope to cover are:
Discrete random distributions
How to know when a circle (n-gon) is closed
How to know which objects are inside a closed circle.
Global timer control
High scores tracking with php and an sqlite database

Sunday, June 12, 2016

Assembling the Mentha Longifolia genome

A group of researchers, including myself, recently made a draft genome assembly for Mentha longifolia. The publication for which is currently under review. This post is my notes for my part of that effort. Basically that means that this is my lab notebook for part of the summer of 2014. It's pretty disorganized and may or may not be useful to anyone ever....


Long story short:
I was trying to figure out how to integrate PacBio reads with Illumina reads.
In the end, I used ECtools to correct the PacBio reads, and then used PBJelly to merge the PacBio reads with an assembly generated from the Illumina reads. It is my understanding that there may be better options for PacBio error correction today, but at the time ECtools seemed to be the best.

Read on for the juicy details....

Saturday, June 11, 2016

Musings on the meaning of meaning and the pursuit of happiness

This afternoon I intended to write a post about the phrase "be compassionate", which I think is the essence of morality. The intended title for the post was "Be compassionate: Morality in simplest terms".

It just so happened that my extremely thoughtful cousin wrote something about the meaning of "true happiness" on his Facebook wall, which prompted me to respond with the following 1000 word essay, which is kind of related to what was on my mind this morning.

So... this isn't quite the post I was meaning to write today, if you're looking for an in-depth analysis of the phrase "be compassionate" you'll have to wait for another week. If you're really into moral/existential meta-philosophy, this post may yet be worth reading for you. If you're a Christian (particularly one who isn't some kind of universalist) and have thought about these things more carefully than I have, leave a comment.