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.

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

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....

Why I think that pondering the existence or non-existence of God is a waste of time

I usually describe my religious views as "strong apatheist", which means that I think it doesn't matter whether God exists or not, and I think I can prove that it doesn't matter.

This post is meant to explain and defend that position (my first comment below is a much more concise defense than the post itself, you could save yourself a lot of time by skipping this post and just reading that comment instead).

This post is also partly meant to elicit defensive responses from Christians (particularly those who are not some kind of universalist), so if you fall into that category, and if you've thought more carefully about this topic than I have, please leave a rebuttal in the comments.

It was originally written as a reply to a post on Facebook, so please excuse the scars it retains from its origin.