Sgt. John McCary: Tribute to the fallen.

I was just listening to Wisconsin Public Radio’s To The Best of Our Knowledge, a great podcast/radio show (if you can get it in your area) that takes an hour each week to examine topics from whether Shakespeare is still relevant to high energy physics to something as “simple” as salt.  And they make it astonishingly interesting.  Like to the point where you wonder how you every went without knowing an HOUR’s worth of information about… well… salt.

They have a recent series of hours called “Boots on the Ground: Stories from the war in Iraq.”  The episode I am on is called “Coming Home.”  As yesterday was memorial day, I wanted to share a particularly poignant excerpt of an impassioned email from an Army Sergeant named John McCary as read on that show by its author.

Please take the five minutes to listen to him.

I hope that you will have a much more visceral understanding of why days like yesterday are important to honor, regardless of your particular view of whether we should have stepped foot inside that country to begin with.  It is not a day for honoring politicians or war mongers, but of honoring young men and women that put their safety and comfort aside for the very real need that any country has (like it or not – for the time being) to defend itself or others.  They knowingly put their future and welfare into the imperfect hands of our politicians.  And whether you agree with the decisions of those politicians, that sacrifice of the soldiers, especially those that do not return, can only be described as honorable.

A biologist’s Mother’s Day musical tribute

So I do know that its a bit late for Mother’s Day but I just ran across the most adorable musical tribute to moms and had to post it.  As PZ warns (which is where I found it), this is MASSIVELY chock full of nerd power.  So try not to be too embarrassed when you realize that you really wish you had come up with it.

Setting Your PYTHONPATH environment variable (Linux/Unix/OsX)

Environment variables are lovely little shortcuts that your system uses to give many programs the ability to find certain shared resources easily.  In the *nix environments, these variables are set up for you when you log in to your terminal.  In order to customize these, you will need to modify a little shell script that runs every time you log in. Continue reading

Simple Python FastQ Parser


UPDATED (Sun Feb 19 14:56:28 PST 2012)

High-throughput sequencing (HTS) is rapidly advancing our ability to understand how the genome responds to its environment.  It also presents a challenge to those tasked with analyzing the results.  Massive files can be produced that can overwhelm a modest computer’s store of available memory.  The simplest way around this problem is to only work with a small part of the file at a time.  I have provided an example of a very simple; easy to extend; and stand-alone python parser that returns a single fastQ record at a time to provide memory efficient access to these commonly massive files.  It is also small, simple to understand, and does not depend on other packages.

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Researching a Scientific Topic

A friend of mine recently asked me what types of resources I used to read up on and explore areas of science that I might be studying or planing to delve into with more focus. I remember how she feels. It can be quite daunting to stare at the screen and wonder, “where do I even start?” I hope that this will be a useful starting place for folks that want an idea of how to attack the staggering resources that the internet age has made available. This post is mostly aimed at folks with a mind towards academic literature searching with the purpose of becoming more of an expert on a scientific niche – an undergrad researching a writing assignment or preparing to interview with a lab they want to join for example. However, the process is not limited to this. Continue reading

Baldwin’s “These are not negotiable”

A very dear friend of mine posted an essay by Chuck Baldwin, a politician, pastor, and radio personality titled “These are not negotiable“.  I do not exactly belong to the same school of thought as the essay’s author, so I tried to compose a response to the essay.  I have posted a version of the response below.  I do not intend to make this blog overtly political, but there are examples of how political ideologies can overlap with science in the essay which can be educational.  I invite your thoughts in the comments.  Feel free to contradict me, but as you read please keep in mind that I mean no disrespect and that it is NOT my intent to initiate a flame war. That being said, I must take issue with this essay and wish to highlight for you a few of my problems with it. Continue reading

Huffington Post Claims to have Cure to Cancer

I came across an article in the HuffPo a couple days ago by Kathy Freston whose headline rather blatantly claimed that eating vegetarian diet is in fact a cure for cancer.  Now you may respond by pointing out that whoever penned the headline used a question mark which may indicate that the website is not making a direct assertion. However, upon reading the article, I am forced to conclude that this is a mere act of keeping up appearances. The article is completely credulous and goes so far as offering recipes.

So why am I up set by this? There are two reasons. First,  I feel, along with many other folks on the interwebs (see blog links), that it is important to the collective well being of society for crap science reporting to be called out and dissected in public and as loud as possible. Second, it plain dangerously irresponsible of the HuffPo, and frankly Dr. Campbell as well, to come right up to the brink of recommending to a massive reader base to forgo proven treatments for a bunch of nonsense.  I have yet to address such articles, quite frankly, because I have let this blog lay fallow for quite some time.  I have been busy trying to keep my head above water in my studies and have since all but abandoned the site till now.  This article has woken me back up.  I don’t pretend to claim that my response will cause any change by itself.  To tell you the truth I don’t claim that any impressive number of folks will even read it.  But I feel that it is important for me to at least add one more opportunity for some hapless internet mariner searching for more info on a subject to run into this side of the story.

I am sorry that this one is a bit long…

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