Speaking of inhumane treatment ...

... sounds like this guys son should get a little. Then again, perhaps the dad is the real dummy for putting his 13 year old son on his phone plan without taking the proper precautions (like only allowing the phone to dial home and 911).

Growing up ...

... I had fond memories of attending the circus. I've been to the Ringling Bros. a couple of times as a child. However, where there is smoke, there is fire. I do not, any longer, view these shows as humane.

Article ...

... in Scientific American.

Bugs Inside.

Linkage

Small Worlds - a very interesting flash game.

Currently ...

PlayingDead Space: Extraction is a cool on-rails FPS for the Wii. It's the first time I've ever played an on-rails game, and while it took a bit of getting used to, I've become a bit fond of it. It certainly helps that EA put a ton of extras into this game, not to mention that it's fleshed out with a great story and voice acting. Definitely my game of 2009. Thanks EA!

Listening ToThe Veils are an alt rock band that has been around for a bit, but I found this album mentioned in a "Best of 2009" list somewhere on the internets. It's definitely a great album and worth a listen. They have a video or two on Youtube.

There are very few things I want for Christmas

But to see the Patsies implode ... that would be on the top of my list.

Surprise, surprise ...

... wasted stimulus funds.

Senators John McCain, R-Ariz., and Tom Coburn, R-Okla., held a news conference Tuesday in which they released a report criticizing 100 projects paid for by the stimulus package that they claim wasted $7 billion.

How much agricultural (and medical) research could $7 billion fund? Alone, that money could fund the place I work at (given current funding) for over a millenium. Just imagine what we could do with double the budget (which would only fund us for a handful of centuries).

Oh, and here is my non-FOXNews link to the same issue. ;)

I can't believe ...

... I had not read this short story (PDF, 4 pages) until last night.

He did not remember when he began to regard the heap of books on his desk with boredom and dread, or when he grew angry at writers for writing them. He did not remember when everything began to remind him of something else.

This is what he remembered. Heat. A baseball field. Yellow grass, the whirr of insects, himself leaning against a tree as the boys of the neighborhood gather for a pickup game.

Sorry, I can't make spinning class today ...

... I just won the Nobel Prize. How cool would that be? Well, very cool.

Reading that story, it's obvious that Carol won the prize with work she did as a graduate student.

The holiday season

This is typically the time of year that most/some/a few of us think back over the last 300+ days and reflect on how cruddy/great/boring they were. I'm not going to bore anyone with my own musings, other than to say that I think I'm in a much better position than a lot of people, and for that I should be thankful -- and I am. Therefore, I'm going to shameless plug a favorite charity of mine, in the hopes that if you're looking to spread some holiday cheer, you might consider them.

CFCA the Christian Foundation for Children and Aging. Why? This reason, if for no other.

CFCA assigns the highest reasonable amount of available resources to the direct benefit of sponsored members. In 2008, CFCA’s total contributions and revenues exceeded $103.9 million, a record level. A total of $93.6 million was disbursed in direct assistance to our projects for the benefit of the children, youth and aging persons we serve.

That's a pretty good return on your dollar. I receive several letters a year from Alex, the child I've been sponsoring, and I've gotten to see him grow up and thrive thanks to this foundation.

Chimera! (Part 1)

NOTE: I've been sitting on this for quite awhile, and while I wanted to add to it, i figure I may as well post this now, and then followup at a later date. I think it can hold up on its own for the purposes of discussing the problem. So I'll call this post "Part 1" for now.

To the left is the mythical creature known as the chimera. Though, to be honest, do you know how hard it is to find an actual drawing of what the mythical chimera was described as? It was a fire-breathing creature with the body of a lion, with a tail ending with a snake's head. On top of that a goat head sprouts up from the middle of the back. Weird creature, eh? And you wouldn't think that's too terribly hard to draw, but that's not typically how artists do it. I dunno, artistic license and all that jazz, eh? But anyways, that's a bit of an aside, as I don't really intend to hearken back to my geeky AD&D-playing teenage years to talk about mythical creatures. Rather, I want to talk about the phenomenon that gene jockeys who do microbial community analysis face when doing 16S rDNA gene sequence analysis. Yes, I'm talking about that chimera.

It's a problem, and depending on who you read, it's a very BIG problem at that. I'm going to cite a couple of papers to illustrate. The first is by Kevin Ashelford et al. who titled a 2005 AEM article: At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies. Quoting from their abstract (this article should be in the public domain by now, so I'll link to it down below):

A new method for detecting chimeras and other anomalies within 16S rRNA sequence records is presented. Using this method, we screened 1,399 sequences from 19 phyla, as defined by the Ribosomal Database Project, release 9, update 22, and found 5.0% to harbor substantial errors. Of these, 64.3% were obvious chimeras, 14.3% were unidentified sequencing errors, and 21.4% were highly degenerate.

Translation: Our sequence databases (which start with GenBank) are a mess.

Then there is this study by Hugenholtz and Huber from 2003 in IJSEM entitled: Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. Quoting their abstract (I believe this is also a freely accessible article) they state:

A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing phylogenetically novel non-existent organisms, are routinely being overlooked in molecular phylogenetic surveys despite a general awareness of PCR-generated artefacts amongst researchers.

Now, this article was written a little over 6 years ago, but it continues to be a problem. These sequences are still in the databases and will no doubt remain there in perpetuity. So yah, we're stuck with the mistakes and total messes that people have submitted in the past. What needs to stop happening is adding to the problem in the future. That doesn't seem to be happening though. In 2006 Ashelford published again in AEM that recent large library submissions contained high percentages of chimeric sequences.

Defining a large library as one containing 100 or more sequences of 1,200 bases or greater, we screened 25 of the 28 libraries and found that all but three contained substantial anomalies. Overall, 543 anomalous sequences were found. The average anomaly content per clone library was 9.0%, 4% higher than that previously estimated for the public repository overall. In addition, 90.8% of anomalies had characteristic chimeric patterns, a rise of 25.4% over that found previously. One library alone was found to contain 54 chimeras, representing 45.8% of its content. These figures far exceed previous estimates of artifacts within public repositories and further highlight the urgent need for all researchers to adequately screen their libraries prior to submission.

In this article they talk about a program called Mallard which they use for chimera detection. As a matter of fact, there are a number of programs that can be used to identify 16S rDNA gene chimeras. Two of the most well-known programs are Chimera_Check and Bellerophon. Bellerophon is, of course, the mythical Greek who slew the chimera. All these programs work well, and they do what they are intended to do, under the proper conditions. I add that caveat because as most people who use these know, the conditions are important.

For instance, Chimera Check and Bellerophon are champs at chimera detection when looking at full length 16S rDNA gene sequence. That means that your sequences should be roughly in the 1,500 basepair ballpark. So when you want to analyze sequences in the 300 to 600 base pair size range, those sequences will likely get thrown out by those programs. Chimera Check goes so far as to flat out state that sequences less than 400 base pairs in size may not be reliably analyzed, so it's definitely a case of "buyer beware". So, if you are someone who likes to look at a couple of variable regions (and there is good reason to narrow down your focus, which I hopefully will get to in another blog entry) you're going to have to find another way to check for chimeric sequences.

References
Ashelford, K., Chuzhanova, N., Fry, J., Jones, A., & Weightman, A. (2005). At Least 1 in 20 16S rRNA Sequence Records Currently Held in Public Repositories Is Estimated To Contain Substantial Anomalies Applied and Environmental Microbiology, 71 (12), 7724-7736 DOI: 10.1128/AEM.71.12.7724-7736.2005 (PDF, 13 pages).

Hugenholtz and Huber. Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases. 2003. IJSEM. 53: 289-93. (PDF, 5 pages).

Ashelford et al. New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras. 2006. AEM. 72(9): 5734-41. (PDF, 8 pages)

Biometric fraud

Wow, that's a lot of work and money to slip past immigration.

Local media reports said Ms Lin had undergone surgery to swap the fingerprints from her right and left hands.

Skin patches on her thumbs and index fingers were removed and then re-grafted on to the matching digits of the opposite hand.

The job cost her, allegedly, $15,000. Of course, she went and got caught again.

As a friend pointed out to me ...

... it's quite possible that the last three Heisman winners will all lose their game which immediately proceeds the award. That is, of course, if Colt McCoy wins, and I'm hoping that after Saturdays dreadful performance (Texass had no business winning that game with the way they managed the last 10 seconds) he doesn't.

Last Goodbye

by: Jeff Buckley

This is our last goodbye,
I hate to feel the love between us die,
but it's over.
Just hear this and then I'll go.
You gave me more to live for,
More than you'll ever know.

This is our last embrace.
Must I dream and always see your face?
Why can't we overcome this wall?
Well, maybe it's just because I didn't know you at all.

Kiss me, please kiss me.
But kiss me out of desire, babe, and not consolation.
You know it makes me so angry 'cause I know that in time,
I'll only make you cry, this is our last goodbye.

Did you say "No, this can't happen to me,"
and did you rush to the phone to call?
Was there a voice unkind in the back of your mind?
Saying maybe you didn't know him at all,
You didn't know him at all, oh, you didn't know.

Well, the bells out in the church tower chime,
burning clues into this heart of mine.
Thinking so hard on her soft eyes and the memories,
offer signs that it's over ... it's over.

Friday Funny

Courtesy of Golf Digest. Their January 2010 issue headlined with: Top 10 Tips Obama Can Take From Tiger. Oh we could have a field day with this one!

Oh, not to mention that that cover is a PSD. Either that or I failed to realize Tiger Woods had the legs and left arm of a white dude.

World Cup

Looks like the United States has a very favorable draw for the World Cup:

England
United States
Algeria
Slovenia

The US could wind up 1st or easily 2nd in this group.

Hey Reid ...

... if we wanted you to do stand-up comedy, I'm sure Nevada would not have elected you into office. Then again, with any luck you won't be around after the next election cycle anyways.

PS: What the &%#! does Tiger Woods have to do with Afghanistan and Health Care Reform anyways? Idiot.

Uhhh ...

... I don't think I qualify as "young" any longer. I don't have children. I have as many degrees as I do fingers on one of my hands. So what gives?

Anger is more likely among the young, those with children at home, and the less educated, a new study finds.

It was only a matter of time ...

... before some twit did this.

Home Owner Associations

Can suck it. I'll never live in a development that has one. In this particular case (linked to) it's simple, just write a provision that says Medal of Honor recipients can have a vertical flag pole limited to 21 feet in height. End of story, you stupid asshats.

Yah, yah, yah ... there are benefits to living in a development with HOA's, I know. But they can also be invasive as all get out, and the fact that a group of asshat neighbors with potential axes to grind can slap a lien on your house? To hell with that!