I’ve been running blast for ~73-74 hours (Daylight Savings Time kinda messes that up), and so far I have a 1.1 Gb table of output… and it’s not done.

On the bright side, I wrote a successful and useful Perl script after having not coded in Perl in 5 months.  And it was my first ever serious experience in Perl.  Oh, and I remember how to use bash now! Google and the O’Reilly Pocket Reference I picked up have helped considerably.  That and the Grad Students who know the small tricks that make life easy.

Things I’ve noticed:
1) Bioinformatics is all about Open Source software and things that people can use without much experience, if any.  But every piece of software I’ve had to use has extremely obfuscated User Guides, Tutorials, and Instructions.
2) There’s no rhyme or reason for anything as far as software or scripting language choice.  I could write everything in Python… except no one in the lab knows Python.  But even our Postdoc, who is a CS/Bioinformatics person exclusively, doesn’t know Perl and uses Google to figure out things he hasn’t seen before.  He’s never actually learned Perl, and neither has anyone else in the lab. Hell, I could use Javascript (if I knew it), because we don’t use any of the scripting language to work between software/applications.
3) I prefer this type of work to most things I’ve ever done.  Yeah, I’m being thrown out into the wild without knowing where I’m going, but that’s what I like (I think).  It actually feels like MY project, not someone else’s that I’m doing the grunt work for.  That’s refreshing, and very cool.

As far as the project… The BLAST I’m running right now is not actually going to be a part of that project (for the moment, anyways).  The project I’m working on has switched from Protein Family ID to building a Phylogenetic Tree with our Genomes after comparing them to references.  From there protein families might come back in.  But I’m waiting on that data anyways, so until then…

I’m having a BLAST.  Oh yeah, I went there.

If you’re interested in what I’m doing, you can go to archaea.ucdavis.edu (if it’s working).  It has a pretty general overview of the work, and even though it’s being run by the lab that my lab is collaborating with, it’s kinda cool to see it all visualized and whatnot.




December 21, 2009

The video attached to this article is just as amazing as The Hubble Ultra Deep Field.

Or if you care to only watch the video:

The Beginning of The End?

December 21, 2009

One can only hope.  I’m referring to Chiropractic and other pseudoscientific “medical” practices: Homeopathy, naturopathy, etc.  A journal article was recently published by three chiropractors and one Ph.D. in Physical Education , in which they essentially invalidated the practice of chiropractic.  The question is will anyone hear about it, notice, or even care?  I surely hope someone publicizes this.

The article has the effect of relegating chiropractic to doing the same as physical therapy, when used for lower back pain, and of being completely useless when it comes to any other medical condition.  Thus, with osteopaths and physical therapists, chiropractors have no place in modern medical practice.  Here is the key quote, taken from the blog Science-Based Medicine:

“There is a significant lack of evidence in the literature to fulfill Hill’s criteria of causation as regards chiropractic subluxation. No supportive evidence is found for the chiropractic subluxation being associated with any disease process or of creating suboptimal health conditions requiring intervention. Regardless of popular appeal this leaves the subluxation construct in the realm of unsupported speculation. This lack of supportive evidence suggests the subluxation construct has no valid clinical applicability. [emphasis added]”

The blog Science-Based Medicine goes into more detail about the theory of subluxations and how they are used in modern chiropractic practice.  I won’t go into that here, as it’s rather unnecessary, I feel.  To put it simply and generally, subluxations, which exist only in chiropractic medicine, are thought to be the cause of all medical problems, from acne to asthma and from headaches to liver failure.  These subluxations are thought to be caused by misalignments of the spine which impede the nerves, causing these problems.  The chiropractor believes that by adjusting the spine, these subluxations, and thus the medical condition, goes away.  Anyone with a basic understanding of physiology or even medicine knows that this isn’t the case.  There are causes that go beyond the neurological , and in most cases there are few correlations or causations with the neurological.  Beyond that, neck and spine manipulation can be dangerous.  But that’s not the point of this blog entry.

The point of this blog entry is that hopefully this is the beginning of the end for pseudoscientific medicine.  If this article gets the proper recognition and attention, the preying on people’s ignorance of medicine can hopefully stop.  Am I saying that all chiropractors are bad? No.  I’m not even saying that chiropractors should stop practicing.  Chiropractors have their place, and that place should be recognized.  But it should also be recognized that subluxations are not scientifically founded, and are not recognized by medicine in any form.  It should be recognized that a chiropractor is not able to fix or cure anything beyond back pain.  And hopefully once this is recognized, Naturopathy, homeopathy, Chinese medicine, and other pseudoscientific claims will hopefully be recognized as being the same as chiropractic, and will go away as well.