Thursday, December 31, 2009

Auld Lang Syne

Ok, I'm not really going to wax poetic on the year. It certainly had its ups and downs. Some of the highs were really, really high. Some of the lows were really, really low. All told, I got through another year with my health and sanity relatively intact, and that's got to be a good thing. On a blog note, I'm pretty amazed that I've kept at this for two years fairly consistently. Most of it is utter crap, and useless to everyone, including myself ... but I stuck at it anyways. So I am going to make one resolution for 2010. I'm going to try to add more substance to this blog over the next year. If I can do that, and life cooperates, I'll keep at it in 2011. If I can't be bothered to really utilize this blog to explain and push science, it'll be time to move on.

Anywho ... hope everyone has a great day, and I'll see you all next year!

What gives NewScientist?

So I'm reading an article today and about a minute into reading, the screen goes black. A bright blue box in the middle of the darkened screen tells me I've read 3 articles from NS this month, and if I want the privilege to read up to four more -- free of charge -- I need to register. Yes, I need to give you my email address so you can spam me incessantly, right? Yes, I have an email account I use just for these purposes, but that's besides the point. I stopped using ESPN to catch up on my sports because they started switching their articles to their INsider service (that and they now pipe live video on just about every page you read ... which is annoying because I don't care to watch or listen to Sports Center blurbs when I'm reading an article ... it's like websites with music on the page, they're damn annoying and intrusive). So, NewScientist ... I will not register for access to four more articles a month. Which means, I suppose I should stop visiting your site altogether. Or I will, once you fix the workaround I employed. I just don't allow any java scripts to work from your site, and the blackened screen went away, allowing me to read articles to my hearts content.

Baby want a bottle? A big dirt bottle?

LaMarr Woodley is an idiot. A really big idiot. An idiot that gets paid a lot more money than I do, but an idiot nonetheless.

Listen ya big crybaby ... if your team hadn't laid down for five games in the middle of the season, you laid down for the Cleveland Browns for crying out loud, you wouldn't have to worry about the final game on the Patsies or Bungles schedules. But, ya didn't ... you screwed the pooch and have no one to blame but yourself.

Besides, a team that lost to the Browns will surely strike no fear in the heart of any other NFL team.
Once we get into the playoffs, the Pittsburgh Steelers is a playoff team.
No duh. Like I said ... idiot.
"I think when you say that [teams will lay down], it calls into question the character of the players on their team. And I think all those guys are character football players and competitors," Clark said. "Now if it were last year's [Steelers team], yeah, they probably wouldn't want to play us. But this year's team, I don't think strikes fear in anyone."
Woodley's teammate, Ryan Clark, is not an idiot. Oh, and he thinks Woodley is an idiot too.
"To say Cincinnati doesn't want to face us, that would kind of be a little dumb, being that they beat us twice this season," Clark said. "So I'm sure they have a lot of confidence if they do have to play us."

There is hope!

If this article is correct, by my calculations the Mets should win the World Series in 2014!
The outcome: Foster hit 13 home runs in his first season in New York. He played an abysmal left field, was booed mercilessly, shunned in his own clubhouse and -- even as he went on to spend 3½ more decent seasons with the Mets -- labeled one of the biggest busts in the team's history. By the time the team won the 1986 World Series, he was out of baseball.
So, the Mets sign Jason Bay for the start of the 2010 season. They tank the 2010 season and the following three, and then Viola! World Series Champs!
As we approach 2010, New York Mets history is about to repeat itself.
One can only hope!

Wednesday, December 30, 2009

Forget explosive-laden tighty whities ...

... being the biggest threat to your health when you travel by air. The greatest danger may come from the airport itself!
The newspaper said that 77 percent of the 35 restaurants reviewed at Reagan had at least one "critical" violation. Tasty!
I generally do not eat fast food when I'm traveling. Doesn't matter if I'm traveling by plane or car. There is nothing worse than being a couple of hours into a lengthy travel schedule and getting the Aztec two-step. Explosive diarrhea and/or vomiting at 30,000 feet in close quarters is one of the least appealing things I can imagine.

Of course, the thought does conjure up the notion of a different sort of explosive-laden tighty whities. *shudder*

Can you say ...

... "Mama's boy"? What is this kid going to do if he gets drafted by the NFL, by a team out West? Tell them no, that he's decided he's going to play for the Patriots?

It's good to be a Mets fan ...

... ok, not really.

Interesting articles ...

... in Newsweek. How Dams Influence Local Climate Patterns.
[D]ams increase atmospheric instabilities in the vertical profile of temperature and humidity. Those instabilities arise because the presence of a dam—specifically, the reservoir it creates—increases evaporation and therefore atmospheric moisture. That enhances the amount of convective energy in the air above the reservoir. The end result: more precipitation.
And another environmental article (2009 in review) from the New Scientist, complete with photo caption gold.
This strange bug-eyed salamander is was discovered in the Cordillera del Condor.
Next time I does/do make a discovery, I'll be sure to write just like they does/do.


I'm starting to see more spam rise up on my site. I'm going to hold out putting in some sort of moderation for comments as long as I can, and I hope this is just a blip on the radar that will pass. However, if I need to put in some sort of moderation, I'll try to use the least intrusive method available.

Tuesday, December 29, 2009

Is death a "complication"?

It appears so, at least in this instance.
Then came the Hermanstorfer's Christmas miracle. "Immediately after delivering him, her pulse came back," said Dr. Martin. Martin tells 11 News, when pregnant women have complications, they have been known to recover once the baby is delivered.
Both mother and child survived. I guess the obvious response for the child -- as he is growing up -- to the hyperbolic question "Are you trying to kill me?" (sometimes said in exasperation) by his mom should be "Been there, done that, Mom."

Pretty shocking statistics

Found here.
*In 18 U.S. states, not even one elementary math class is required for certification.

*Some teaching colleges allow admittance as long as students have math skills equal to their future students -- that is, as long as they could pass a 5th grade math test.

*It's possible in some states to pass the teacher certification exam (Praxis) without answering a single math question correctly.

*In Massachusetts, there's a special program to reacquaint teachers with math. The man who runs the program says half of teachers can't answer basic questions involving fractions and has concluded that many elementary teachers are "phobic" about math.

*Teachers seem to be math-averse from the start. College bound seniors headed for elementary education have math SAT scores significantly lower than the national average (483 vs. 515).
Pathetic. No wonder things don't add up properly.

Friday, December 25, 2009

Happy Holidays

Hope everyone enjoys this time where we usually get to slow down for a day, or two, or three ... and appreciate all that most of us already have.

Sunday, December 20, 2009

I dunno ...

... who dies at the age of 32 of a heart attack?

Has to be either a congenital issue, or drug-related.

You Could Have It So Much Better

by: Franz Ferdinand

The last message you sent,
said I looked really down,
that I oughta come over,
and talk about it.
Well ... I wasn't down,
I just wasn't smiling at you, yeah.
As I look at you now it seems,
that you're slapping my back,
as if it's alright,
but its not.

I'm trying to get up,
but you're pushing me down,
oh yeah, you're pushing me down,
so I'll get up on my own.

Now there's some grinning goon,
on my TV screen.
Telling us all that
it's alright ... because
she wears this,
and he said that,
and if you get some of these,
it'll all be alright.

Well I refuse
to be a cynical goon.
Passing the masses
an easy answer.
Because it won't be alright,
Oh no it won't be alright,
it won't be alright,
unless you get up,
come on and get up!

Well I'm just a voice in your earpiece,
telling you no it's not alright.
You know you could have it so much better,
You could have it so much better.
If you tried. If you tried. If you tried.

Get up on your own!

Thursday, December 17, 2009

This is not how you win the war on terror ...

... $4.5 million dollar US military hardware hacked by $26 off-the-shelf software.

Wednesday, December 16, 2009

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.

Friday, December 11, 2009


Small Worlds - a very interesting flash game.

Wednesday, December 09, 2009

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.

Tuesday, December 08, 2009

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.

Monday, December 07, 2009

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.

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.

Saturday, December 05, 2009

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, December 04, 2009

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:

United States

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.

Thursday, December 03, 2009

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!

Have you ever ...

... had one of those days that made you want to scream, and then go home and just go back to bed?

Yah, that's been my week so far.

Wednesday, December 02, 2009

Six weeks?

Read this article over at ESPN: From Hunk to Chunk, and Back Again. Crazy dude decides to gain 90 pounds so he can relate to his clients. I can see where he's coming from, but this is the part that scares me the most.
James says it took about six weeks of training and willpower to finally kick his addiction to junk food and start eating healthy food consistently again.
Yikes! This is what I'm looking forward to as I attempt to lose the 20 pounds I've gained since I stopped running competitively in college.

I should probably start soon ... right after I finish all the Thanksgiving left overs. Nom nom nom.

How microbes can save the world ...

7 ways microbes may solve our energy woes by MSNBC.

I think our best efforts (and greatest impacts) would be by focusing on butanol and methane.

Interesting read ...

... over at Mark Shea's. He reported on a Dick Cheney hullabaloo yesterday as well, and it gets interesting in the comment section. Here is a comment by a reader named Sean O'Kane:
A further problem with Cheney's "tough guy" stance is that when he was a young man he went to great lengths to avoid serving in the armed forces during the Vietnam war. Cheney fully supported the Vietnam war yet he sought 5 deferments to avoid the fighting because he "had other priorities." He was content to let others do the dying & dirty work. I find his "tough" stance to be very hollow and hypocritical.

Unfortunately, his experience was the norm among top Bush adm people. The notable exception was Colin Powell had expressed the most caution about going into Irag. Powell served in Vietnam.
Being President of the United States calls for an individual to wear many hats. He has to make sure the country is safe and secure from threats, has a strong economy, sound social policies, and that the citizens are happy, healthy, and productive. There is a lot more to it, and I know that I'm probably overlooking a great many things but I think that only further supports my point that whoever takes on the position of President has to have a wide range of experiences and knowledge.

Washington D.C. has become a place, at least it seems that way to me, where politics is the fabled perpetual motion machine. It doesn't need anything but itself to run. To hell with economics, to hell with sound military policy, to hell with medical health care experience. All they need to know is how to wiggle out of their fumbles and scandals come election time, and how to bring home the bacon to fund projects which really only impact a few people in their districts but have a nice dollar value on the bottom line.

It also points out to me that the populace is naive at best, stupid more likely, and downright apathetic at worst. Instead of clamoring for individuals experienced in things outside of how to perform the perfect "back stab" or "reach around", we continue to elect people, seemingly for life, who continue to flush this country down the toilet (I'm thinking particularly of people Barney Frank and Chris Dodd). Why didn't Colin Powell run for President? Probably because he didn't want to deal with the backroom crap and negative campaigning, part and parcel of politics. I think that if he could have been allowed to just do the damn job of running the country and not deal with all the whiny pissants who scuttle around the Capital, he could have been convinced to do it.

I guess what this boils down to is that I would prefer someone with actual military experience to run this country. They are, after all, Commander in Chief and a knowledge of what our forces are capable of, how they can be usefully deployed in a way that they are the most effective, not over-extended, or put into a losing situation thanks to politics (notice a trend here with politicians?) would be great. We're not going to get that in this Presidency, we sure as heck didn't get it in the last Presidency (or the one before it). You can think through a situation as much as you like, but sometimes actual experience will prove the most valuable commodity. Right now, I don't see much of that and haven't in a very long time.

Mr. Powell, would you consider running for President?

Ho boy ...

Kerfluffle over PETA ad. Bill Donahue is about as bombastic an individual as you'll ever meet, so I'm sure PETA is thrilled that he's on the case. Mr. Donahue's problem is, he seems to fail to realize that every time he rails against something, he only gives those people more exposure. He fell into this trap with Dr. Pharyngula, he's falling for it here. Let the idiots have their rambling, don't give them their fifteen minutes of fame too.

It's typical PETA crappola, but this really caught my eye:
Krupa issued a statement responding to the Catholic League, saying: "As a practicing Catholic, I am shocked that the Catholic League is speaking out against my PETA ads. I'm doing what the Catholic Church should be doing, working to stop senseless suffering of animals, the most defenseless of God's creation."
Wow. I guess Ms. Krupa doesn't keep up with the times, and seems to overlook the generation-long struggle of the Pro-Life movement. I would not be surprised if Bill Donahue points out the unborn and asks if they're not defenseless too? If he doesn't, he's just a loud idiot.

Besides, given that St. Francis of Assisi (Patron Saint of Animals and the Environment) is such a celebrated figure in Catholic circles, I really find the charge leveled by Ms. Krupa a bit odd.

Tuesday, December 01, 2009

Please God, No!

Dick Cheney in 2012.
"Why would I want to do that?" he replied. "It's been a hell of a tour. I've loved it. I have no aspirations for further office," Cheney said in an interview with Politico.
Yeah, it was hell alright.

Joe Mauer as a Met

Oh that would be sweet. Spring training can't get here soon enough!
The Mets’ plans at catcher are fluid ...
With the exception of Francisco Rodriguez, Johan Santana, and David Wright the status of the entire Met's franchise (including their GM, Manager and Owner) is fluid.

Good riddance to bad rubbish

Cop killer dead.

Before I was against the death penalty, I was for it. There are instances, like this one and others* that force me to reconsider that stance. I think it's no surprise that they didn't bring this piece of crud in alive, but the point is ... he should never have been out on the street to begin with. I also believe that there is no way Huckabee will run for President now in 2012. These sorts of things tend to haunt people for their entire lives. I know the families of these four police officers will have to live with it, so it's not as if Huckabee will suffer alone through all of this. Besides, he still has his television show ... those families don't have their sons and daughters, moms and dads, brothers and sisters.

*Jessica Lunsford is another one that comes to mind. While that scum died in jail, every breath he took was an insult to humanity.

Monday, November 30, 2009

NASA finds Martians

Martians exist(ed). They're also (well, were) bacteria.
Close examination suggested that about 25 percent of the crystal structures were chemically consistent with being formed from bacteria.

"We feel vindicated. We’ve shown the alternate explanation is absolutely incorrect, leading us back to our original position that these structures are formed by bacteria on Mars," Dr Mackay said.

Dennis Bazylinski, an astrobiologist from the University of Nevada who peer-reviewed the findings, said: "Until now I was on the fence but this paper has really thrown out the non-biological explanation."
So at some point, there was life on Mars. The question one must ask now is ... is it still there?

What I learned when I was in Pittsburgh ...

Note: I'm a bit late with this one. Had it 80% of the way written and then forgot about it.

Other than learning that GPS systems are stupid and suck and should never be used, I did learn a few interesting things. I'll relate them here in this post. Some will be rants, some will hopefully be useful bits of information for other people as well (or at the very least drum up a bit of discussion).

1. The American Society of Agronomy is losing members. Hemorrhaging might be the more appropriate word. The society has lost approximately a third of the membership over the last decade, and the trend still points downwards. This is part of the reason that ASA is planning a restructuring which will be coming to a vote probably some time in November.

2. The Cherry Quadzilla at Church Brew Works was awesome. It also only comes in 750ml bottles, so you'll want to take a cab (which we did). Also, bring a camera ... it's a very interesting pub. The chicken pot pie was also really good. As were the perogies.

3. When you are arranging the poster sessions, and you map out where the posters are going to be, discuss the lighting situation with the people at the Convention Center. There was at least one section that after the sun went down and cut out all of the natural light, was in the dark. It was dark enough to hinder reading posters from afar. The rest of the hall was just fine, but at least 40 poster boards were placed underneath an overhang that had absolutely no lighting. That means that approximately 120 people (40 boards over 3 days) had to put up with those cruddy conditions. Unacceptable. I find it hard to believe that after realizing people were sitting in the dark on Monday evening, that something could not have been done to redirect the posters to a better lit area ... which would have required moving some poster boards maybe 40 to 50 feet away. A sign pointing in the direction would have sufficed. The meeting was filled with Ph.D.'s ... if they couldn't handle a redirection of poster boards, they had no job being there anyways.

4. If you plan a business meeting for the 30 minutes before a poster session you are hosting, make sure the business meeting doesn't start with a 45 minute presentation on restructuring. Some of us really had to get to the poster session because we were, you know ... presenting.

5. Metagenomics fraught with pitfalls. I know metagenomics, especially deep 16S sequencing, has taken the microbial ecology world by storm. A whole lot of people have been swept up in the frenzy, including yours truly. Now, I can be a worry wort, and after attending a session where people talked about various metagenomic projects, I just had to go up and ask a question. What about the chimeric sequences? I have a long-ish blog entry on chimeric sequences (which I really need to get out onto the site, it's still a draft), so I won't go into too great a depth on them now, but they're PCR artifacts which can increase your microbial diversity artificially. As pyrosequencing reads get longer, the chances of getting artifacts are probably increasing as well. Any amplification based system is going to have this problem.

So how do you avoid it? Well, I had hoped the people at this session, who have done metagenomic sequencing now for a few years, would have the answers.

None of them did. They figured (rightly, I might add) that the rates would be about the same for these approaches as they would with regular sequencing schemes, but it doesn't help with how to deal with them. Let's do the math.

If you have a 6% chimeric sequence rate (a reasonable value I believe), then you'll have to throw out 6 sequences for every 100 you do. If you have a 200,000 read metagenomic project that's 12,000 sequences you have to throw out. Problem is, how do you find them? Chimera_Check and Bellerophon, the two major programs on the net that do chimera checks, are really hands on programs. You have to really check the results. That's impossible (I won't say near impossible because who is going to read a quarter of a million chimera check reports, other than no one). So what we're seeing is ... no viable (and reliable) way (that I can see) to check metagenomic projects for chimeras. That sucks.


Who the heck is going to wear this thing?


Sounds like a creepy children's video game turned cartoon.

Interesting article from Newsweek

On how America's economic woes could impact our standing in the world.

Friday, November 27, 2009

Today I am an Auburn fan ...

... I'd love to see the BCS blow up with Alabama losing to Auburn and then turning around in the SEC Championship and beating Florida. I'll also dream that Nebraska whoops it up on Texass in the Big XII Championship too, but I'll take what I can.

Currently after the 1st QTR, Auburn is beating Alabama 14-0.

ETA: 14-7 in the 2nd QTR.

Currently ...

PlayingThe World Ends With You. An awesome RPG for the Nintendo DS.

Listening To

WTF people ...

... does everyone try to get a paper published before Christmas? I got requests for two more manuscript reviews today. It brings my monthly total to 4, only one of which I've completed.

I know what I'm doing today. Reviewing your damn papers!

Thursday, November 26, 2009

Tuesday, November 24, 2009

Tuesday Funny

When science is abused ...

The United Kingdom provides us with a lovely example.
Britain has built the world's biggest DNA database without proper political debate and police routinely arrest people just to get their DNA profiles onto the system, the genetics watchdog said in a report on Tuesday.
Good going PoPo.

What would Hell be like?

I imagine it'd be like this.
Rom Houben was misdiagnosed as being in a vegetative state after a car crash left him totally paralyzed.

But, in actuality, he was trapped in his own body the whole time with no way of letting friends and family know he could hear every word they were saying.

The 46-year-old, who can now tap out computerized messages and read books on a device above his hospital bed, has revealed: "I screamed, but there was nothing to hear.

"All that time I literally dreamed of a better life. Frustration is too small a word to describe what I felt," he said. "I shall never forget the day when they discovered what was truly wrong with me — it was my second birth. I want to read, talk with my friends via the computer and enjoy life now people know I am not dead."

His misdiagnosis was discovered by neurological expert, Dr. Steven Laureys, who fears there may be similar cases all over the world.
I read this story and I think of the Metallica song One. I truly cannot imagine being trapped for 23 years ... 23 YEARS ... without being able to communicate at all. I'm surprised the guy isn't totally insane at this point, and to think that other people might be in a similar condition? WTF!

Monday, November 23, 2009

Microbial coolness

Video of nematode-eating fungi.

Video courtesy of Tom Loynachan, Professor of Agronomy (and Microbiology) at Iowa State University. All of the videos (accessible via the second link) are informative and worthy of a view.

Woe is me

After a four day weekend (self imposed), I have a backlog of manuscript peer reviews that need to be done today. The first one is obviously from authors who have English as a possibly fourth or fifth language. When you find over ten grammatical and typographical errors in the abstract alone (150 words max) you know you're in for a long slog. It's an interesting subject though, so I'll push all the way through rather than fight the urge to triage it.

Don't drink the water ...

... interesting study, gross findings.
COLUMBUS, Ohio (AP) - Intrepid Ohio State University researchers have learned students don't just party in a campus lake during rituals before the annual Michigan game. They also potty there. Thousands of students will jump into Ohio State's Mirror Lake Thursday night, ahead of Saturday's football game between the Buckeyes and Wolverines.

Before, during and after last year's big swim, the College of Earth Sciences monitored the water quality.

Postdoctoral research associate Steve Goldsmith said the lake's temperature went up 3 degrees throughout the night, and the ammonia level surged.

He said body heat could explain the warmer water, but the ammonia likely means one thing: urine.

Goldsmith advises students to have fun, just not open their mouths.
Bold emphasis mine.

Tuesday, November 17, 2009

Monster Rancher With DNA!

There was a PS/PS2 line of games that I thoroughly enjoyed playing. The series was called "Monster Rancher". The concept was that you inserted a CD or DVD into your system, and then based on some sort of algorithm, the game would make a "monster". Different CD's and DVD's produced different monsters.

Now, a company is launching a line of perfumes based on a celebrities genetic code.
Verdun makes clear that the recipes are secret formulas based on the genetic coding for mitochondrial DNA, or mtDNA, which exists outside the nucleus of every cell and is passed down genetically only from the mother's side. There are a limited number of variations in mtDNA, and millions of people share the same variation. So if the fragrance called "Blue Suede" is based on Elvis Presley's genetic code, it could also be based on the code for Elvis Weisenheimer who lives down at the end of the street.
Yep, sounds like they'll take some sort of pattern from the DNA, run it through an algorithm and then the result will be used to formulate a perfume.

Big whoop.

Be on your best behavior

I know it stinks to go through life having a target on your back, but when you know you have one, and you don't take it seriously, you open yourself up to legitimizing the attacks that you know could possibly come.

Case in point.
But animal producing farms, including CVFF, realize they have become targets for groups like MFA, which promotes a strict vegetarian diet.

The president of the American Association of Swine Veterinarians, Dr. Butch Baker, who also watched the MFA video, says it is upsetting to see animal rights organizations try to destroy America’s farmers.

“They (MFA) would like to put all those people (farmers) out of business and out of work," Baker told Fox News. "I have no patience for anyone who abuses animals or no tolerance and I don’t think anyone should, but these films ... really are an attack on the rural lifestyle of America.

"People in rural communities depend on farms and farming for their livelihood. If you let an extremist group run the industry that’s just as bad as letting the people who didn't care about the animals at all run the industry,” he said.
Dr. Butch Baker just doesn't freaking get it. The tape obviously shows people who don't care about the animals, handling them. It's also obvious that CVFF did not, at least at that facility, have proper procedures in place to ensure that such abuse did not happen. I am very sympathetic to the plight of the farmer. I think rural America is a necessity for the continued success of our country, and I want to do everything to ensure that farmers have profitable farming systems.

It is said that an ounce of prevention is worth a pound of cure. Some upfront training in proper animal husbandry for these employees, and an effective oversight system would have saved the industry from getting this black eye. So, instead of trying to demonize MFA, fix the damn problem with CVFF and get back to business.


Monday, November 16, 2009


I know some people feel that the United States needs to do everything it can to restore itself in the eyes of other nations, but ... we shouldn't drop ourselves below our peer status.

There is no need to bow to other world leaders. Just shake their hands with a nice, firm handshake, and look them square in the goddamn eyes. How hard is that?

STI's on rise in US

CDC reports that sexually transmitted cases are increasing.
The CDC's latest study on STDs found:

* 1.2 million cases of chlamydia were reported in 2008, up from 1.1 million in 2007.

* Nearly 337,000 cases of gonorrhea were reported.

* Adolescent girls 15 to 19 years had the most chlamydia and gonorrhea cases of any age group at 409,531.

* Blacks, who represent 12 percent of the U.S. population, accounted for about 71 percent of reported gonorrhea cases and almost half of all chlamydia and syphilis cases in 2008.

* Black women 15 to 19 had the highest rates of chlamydia and gonorrhea.

* 13,500 syphilis cases were reported in 2008, an almost 18 percent increase from 2007.

* 63 percent of syphilis cases were among men who have sex with men.

* Syphilis rates among women increased 36 percent from 2007 to 2008.
It shouldn't be this hard folks. You have several options to decrease your chances of acquiring a sexually transmitted disease. First, you can abstain. No sex means no sexually transmitted diseases. If that's not for you, you can find yourself a monogamous relationship with a person who likewise has no STI's (sexually transmitted infection). Third, you can practice safe sex, which means wearing condoms. Of course, condoms may* reduce, but won't eliminate your risk of acquiring HSV or HPV, the two STI's which are carried by large portions of the sexually active population. You'll need to consider that when deciding to have sex.

*Depends on where your partner is infected with HSV or HPV.

Saturday, November 14, 2009

Well one thing is certain ...

... Oklahoma will go bowling this season. They romped Texass A&M. Next is Tortilla Tech, then OSWho? in Stoolwater.

Friday, November 13, 2009

I am so glad ...

... I'm not traveling for the holidays. At least not anywhere outside of driving distance.

What to do?

So my dream has always been to get a widescreen, high definition television (somewhere around 42" minimum) for my living room. I wanted to get it set up with surround sound, extra speakers for placement through the house, and connect it to a computer which would serve as a media platform. I could use it to stream NetFlix movies, play my music collection (well over 120 GB at this point), and record television shows. I'd also have it connected to my Wii and PS2. Well, just recently NetFlix announced that the PS3 can now stream movies. The PS3 also can play music. The only thing I don't think it will do is record television shows, which I guess isn't much of a loss since I don't get anything but local television. The benefit of getting a PS3 then is the array of videogames. Killzone 2 and Borderlands look awesome, and I'm a huge fan of the Unreal Tournament series. It'd also be cheaper than buying a computer with the capabilities I'd need. The only problem is having something at home for word processing and the like ... but I can always bring home my work laptop for that.

What to do?

Thursday, November 12, 2009

Down from above

Whether Mount Pinatubo
Or the threat of God's love
There'll always be something that's raining
Down from above.

by: Moxy Früvous


No, not the California Highway Patrol*. I'm talking about Combined Heat and Power. Mike at the Big Stick blogged an entry about nuclear power, to which I replied:
I think there are current applications such as combined heat and power that will serve us immediate benefits. Oak Ridge National Laboratories recently put out a report where they state in their executive summary:
Combined Heat and Power (CHP) solutions represent a proven and effective near-term energy option to help the United States enhance energy efficiency, ensure environmental quality, promote economic growth, and foster a robust energy infrastructure.
It’s also hugely underutilized.
I was quoting from the ORNL document entitled COMBINED HEAT AND POWER: Effective Energy Solutions for a Sustainable Future which can be found here (PDF, 38 pages).

If you go through the document, you'll come to page 35 and the section What Fuels Does CHP Use? The beauty of these systems is that they're open-ended. Just about anything that can be burned can be utilized for CHP. You can run it on natural gas, but you can also run it off of land-fill gases, rubber and plastics, and better yet ... biomass. We have tons of biomass, especially excess wood. This is an issue that Secretary of Agriculture Tom Vilsack addressed early on after his appointment.

Right now the US Forestry service is hampered from doing anything but primarily fighting fires. That is not their only mission, but it is the one which they are straddled with. Part of the problem is, there is little money to clean up wood residue in forests, which serve as great kindling for future fires. Since it is so good for kindling, it would also be a great source of energy for CHP. Get enough CHP plants and the government could license forested areas to those companies to harvest all that woody biomass. That would decrease the potential for future fires, would provide an additional source of funding for the US Forestry service (to research how to effectively and efficiently provide CHP plants with sustainable woody biomass), and would cut down on the expense to the average citizen. Forest fires increase insurance rates, divert tax money from other programs to fund fire fighting, and probably increase taxes to ensure that they money in future years will exist to fight those fires. To me, it seems like a total win-win situation.

We need to let our Senators and Representatives know that we know of an excellent energy source, that is environmentally friendly, that will give us a huge degree of energy independence, and that can be put online almost immediately ... if they move us in the proper direction. Send them a link to this document as well.

*I don't own a pair of Estrada sunglasses.

Wednesday, November 11, 2009

A Nation's Strength

by: Walt Whitman

Not gold, but only man can make
A people great and strong;
Men who, for truth and honor's sake,
Stand fast and suffer long.

Brave men who work while others sleep,
Who dare while others fly --
They build a nation's pillars deep
And lift them to the sky.


1. Adopt a Microbe (linked to this last year around this time, it's been updated).
2. Cell Size and Scale

Monday, November 09, 2009

Work? What's work?

I did it. I went and bought Guitar Hero. For some reason I also bought a microphone. Those "game nights" my family has once a month are going to get pretty ugly now ... karaoke has never been my strong suit, and I doubt anyone in my family can sing either.

When your dogs howl ... it's because I'm playing GH. Sorry.

Sooners Go Boom ... Errr

What a disappointing year. It's hard to get upset with the Huskers though ... they're a classy fan base and program.

TeleNav still sucks ... and so does Mapquest

I have had GPS horrors before. Returning home from Pittsburgh was no exception. However, before there was the "return home", there was the "getting to" which also was eventful.

So, as my title says: In addition to TeleNav sucking, Mapquest sucks too. I suppose I'm just a glutton for punishment but printing out directions is the last thing I put on my agenda when I'm traveling. I did manage, Saturday evening, to print directions TO Pittsburgh, but I never did print the return directions. At any rate, Mapquest got me most of the way to Pittsburgh without incident, though it certainly didn't like sending me the most direct way (and I specifically tried to get it to do so). It also didn't know (or failed to inform me) that the exit I needed to take when I got to the city, was under construction, so I had to handle a detour. For those who have not visited Pittsburgh, I don't think there is a single straight avenue in the entire downtown area, and Penn Avenue seems to wrap around half the city. So let's just say that I got to see Duquesne University at 7 PM at night. Problem is, Duquesne University was nowhere where I needed to be. Fortunately, TeleNav actually helped me out of that predicament, after 45 minutes of wandering aimlessly through every backstreet in Pittsburgh known to man. So much for making good time. My bad.

Fortunately, the meeting went mostly according to plan with minimal angst. Wish my traveling had been so simple.

Then it was time to return home ... at 6 PM in the evening (yet another story*). I paid my parking bill, climbed into the company van, and went topside. Turned on my Blackberry, clicked over to TeleNav and started it up. Only to be told that the signal was too weak and I needed to move to an "open area". So essentially ... I needed to leave the city before I could use the GPS system ... that I needed to work properly so that I could leave the city in the first place. Jimminy.

So I hop on some street and it takes me to a highway, which of course at 6PM is loaded with rush hour traffic. So things start moving at a crawl. Still nothing from the GPS, signal is too weak, so I keep traveling. Eventually get to a fairly open area, pull off the highway (because I'm not programming this thing in rush hour traffic) and set up the stupid GPS. Turn it on and receive directions to HEAD BACK THE WAY I JUST CAME! Figures. So I start heading back the way I came, get told to get onto another highway, under heavy construction of course, and then exit shortly thereafter. It sends me down a road, has me DO A U-TURN, and get BACK ON THE HIGHWAY I had just been on. Sure enough, a few minutes later it's telling me to get back off the exit I had just gotten off of to turn the GPS on and get directions. Of course, TeleNav is calling it "Exit 5A" and the sign is calling it "Exit 67". At this point I'm damning every TeleNav employee to hell.

So I turn the damn thing off, keeping heading out on that highway (because it's obviously taking me out of the city) and see a sign for the airport, and I head towards it. Funnily enough, it's the road I need to take for a large portion of my trip.

Blind Luck: 1
TeleNav: 0

Of course, that wasn't my only trouble with TeleNav on the trip. The other fun part was when I had about three miles before a turn-off and TeleNav lost connection with its server and was down for 45 minutes (which means it wasn't giving me directions). If it had not been for a friend and Google Maps on their computer, I may not be here writing this. That was also oodles of fun.

I swear, I'm never going to use that damn GPS function ever again. I even went so far as to complain to our purchasing agent to buy some damn road atlases and put them in our vehicles.

*I love when your boss comes to you at 4:30 on a Friday, says he won't be going and that you're going to give his poster. Problem is, his poster session is 7 hours after you planned on checking out of your hotel and start your trek home. It's also half a dozen hours after any remotely interesting talk in your area was going occur, leaving you to sit there bored out of your skull the entire time. Oh, and when you call the hotel to extend your stay a day ... they're booked solid. Lovely. The icing on the cake comes when a whole three people in the two hour span show up at the poster to talk with you.

Sunday, November 08, 2009

Currently ...

Listening To

Well take me, take me back to your bed
I love you so much that it hurts my head
Say I don't mind you under my skin
I'll let the bad parts in, the bad parts in
When we were made we were set apart
Life is a test and I get bad marks
Now some saint got the job of writing down my sins
The storm is coming, the storm is coming in

Apple - Whiskey Tango Foxtrot!

New iTunes songs are set at $1.29 a song now? That's a thirty freaking percent increase! When did this happen? Screw that, I'm going back to buying actual CD's ... the prices are now comparable, and I'll actually get liner notes now ... and I can rip them onto iTunes for free.

You suck Apple.

ETA: I guess I'm late to the party. Apple did this back in April. It still sucks though.

Thursday, November 05, 2009

So ...

... I'm back from Pittsburgh, and while I have several rants about my experiences there (from more GPS issues, to poster sessions, to business meetings, etc etc) ... I want to clarify my exasperation about Comic Sans font.

On Monday, I judged several 15 minute oral presentations from graduate students. We had a list of criteria they wanted us to judge on, and one of them was presentation. I will readily admit, I took off a point for poor font choice (too small, wrong color, wrong style). I know I've talked about this before, but I'll say it again:

1. If you choose an 8 point font for your slides, it's going to be too small.
2. If you have a white background, and you use lemon yellow font, it's going to be invisible.
3. If you use a serif font for your text, you're going to cause your audience to tune you out to read it.
4. If you write entire paragraphs, you're going to cause your audience to tune you out to read it.
5. Bullet points are for points, not paragraphs.

Ok, for #3. Studies have shown that serif fonts draw a readers eye. If you WANT someone to read something, make it a serif font. For slide titles, that's great ... you want them to know what you're talking about, so a visual cue at the top will immediately clue them in. Of course, make the one or two words at the top RELEVANT. However, the bulk of the text on the slide is FOR YOU, NOT THEM. They should be listening to you, not reading your slides. The text on the slide is mostly to jog your memory so you can then engage the audience. So if you make your text a serif font, and serif font catches people's eyes ... by using it, you're going to lose your audience. So, don't use it.

More than one of the students did use serif fonts in the text of their slide (and oddly enough used sans serif fonts for their slide titles) so they lost a point (1 out of 100 isn't going to kill anyone so don't accuse me of being draconian -- plus I explained it to them!). Plus, I told them to stick to professional fonts (Times New Roman, Arial, Courier, etc). So it royally chapped my behind when I got into the talks of people who SHOULD KNOW BETTER ... there were a ton of talks with bulleted paragraphs, horribly mismatched slide background and font colors, and COMIC SANS FONT! Great way to set an example to the societies future!

You know what, if I ever find myself in charge of an ASA division (or the society itself), I'm going to suggest standards for oral presentations.

PS: The student talks were all great, and on my score cards all scored quite high. Kudos to them!

Tuesday, November 03, 2009

If I see ...

... one more presentation at ASA done in Comic Sans font, I'm going to scream.

Friday, October 30, 2009

ASA-SSSA-CSSA Annual Meeting

It's that time of year again. Time to get ready to attend the American Society of Agronomy meeting which this year will be held in nice, warm, sunny ... Pittsburgh. I didn't attend the meeting last year, which was held in conjunction with the Geological Society of America in Houston, so I figured I'd catch up with collaborators and friends at this years meeting. I've also been tapped to judge some student oral and poster presentations, which isn't so bad as I've been really trying to increase my visibility within the society lately anyways. Even though I doubt I'll get an answer in the affirmative I'll ask the following question anyways ... anyone else going to ASA?

As for me, I've already got at least one activity planned ... drinking at Church Brew Works. The Cherry Quadzilla sounds interesting.

Peer-to-Peer Networking Software

You would think that Congress' IT department has a way of ensuring that PtP software wouldn't work. Guess not.
The committee's review of investigations became available on file-sharing networks because of a junior staff member's use of the software while working from home, Lofgren and Bonner said in a statement issued Thursday night. The staffer was fired, a congressional aide said.

The committee "is taking all appropriate steps to deal with this issue," they said, noting that neither the committee nor the House's information systems were breached in any way.

"Peer-to-peer" technology has previously caused inadvertent breaches of sensitive financial, defense-related and personal data from government and commercial networks, and it is prohibited on House networks.
I am assuming the reason for having the files accessible from a PtP network was so they could be transferred from offices in the House, to this employees home. I guess they never heard of staying late at work, or (probably equally as forbidden, but easier to get away with, and somewhat safer) putting everything on a USB drive and taking it home that way.

Not surprised this person lost their job ... and they should have.

Thursday, October 29, 2009

If you find me out of pocket ...

... I'm in England booking my death.
We are really pleased to be able to offer you some new Registration services.

You can now make your appointment to register a birth or a death using our online booking system, or by calling (01243) 642122.
h/t: The New Scientist

Wednesday, October 28, 2009

Nautical Disaster

by: The Tragically Hip

I had this dream where I relished
The fray and the screaming that filled my head all day
It was as though I'd been spit here, settled in, into the pocket,
Of a lighthouse on some rocky socket,
Off the coast of France, Dear.

One afternoon, four thousand men died in the water here,
Five hundred more were thrashing madly as parasites might in your blood.
Now I was in lifeboat designed for ten, and ten and only,
Anything that systematic would get you hated.
It's not a deal, nor a test, nor a love of something fated.
The selection was quick, the crew was picked in order,
And those left in the water were kicked off our pant leg,
And we headed for home.

Then the dream ends when the phone rings,
You're doing alright, he said it's out there,
Most days and nights, when only a fool would complain.
Anyway "Susan" if you like our conversations as faint a sound in my memory,
As those fingernails scratching on my hull.

Never thought this song would mirror aspects of my life, but that's what you get sometimes.


And completely heartbreaking.

What are you looking at in that picture? You're looking at the remains of a baby albatross, which starved because it was fed plastic which its parents had picked up from the ocean thinking it was food. From the site:
These photographs of albatross chicks were made just a few weeks ago on Midway Atoll, a tiny stretch of sand and coral near the middle of the North Pacific. The nesting babies are fed bellies-full of plastic by their parents, who soar out over the vast polluted ocean collecting what looks to them like food to bring back to their young. On this diet of human trash, every year tens of thousands of albatross chicks die on Midway from starvation, toxicity, and choking.
Pathetic. We are starving these birds through our own actions, and we'll wind up being the poorer for it. If things like this don't make you think long and hard about how we treat this planet ... I don't know what's wrong with you.

h/t: bioephemera

ETA: CBC News article on an upcoming manuscript documenting this tragedy.

ETA: A Scientific American article on the story. This one comes complete with a video of albatross chick necroscopies. And this article does (weakly) pay homage to Samuel Taylor Coleridge's epic poem.

Tuesday, October 27, 2009

Currently ...

WiiWare title

Listening To
You know what to do, you know what I did
Since you know everything just clue me in
I am such a wreck, I am such a mess
I know what I know, why don't you fill in the rest

I will bring you down, I will make it bad
While you're feelin' proud, why don't you help me

I'm spinning 'round, I will make you ill
Since I'm so broken down, why don't you fix me

Such a shame that I wouldn't know by now
Your revelations
Let me in I don't want to live without
Your revelations

SciBlog NFL challenge - Week Seven

Won a three-way tiebreaker to keep the trophy again this week.

Ohhh, shiny.

Monday, October 26, 2009

I guess Jesus Christ is ...

... a Penn State fan?
"At first glance, you don't necessarily think that's what it looks like, but when you look at it more, it does look like a cross," Berns told "That's the reason I didn't purchase it."
Eh? So it doesn't look like a cross when you actually look at it, but it does look like a cross when you look at it thinking it might be a cross?

Give me a break. It's a stupid school spirit t-shirt!

To be honest, at first I thought the article might be about someone being offended at the "White Out" comment and thinking it was causing some racial issues ... I looked at the shirt and didn't even think "cross" until I clicked on the link and started reading (and yes, that means I didn't read the caption underneath the image on the FOXNews front page, and I didn't get the "Crossing the Line" pun either).

Come on people, find something to really find offense over.

Sunday, October 25, 2009

I hate the Phillies ...

... and this certainly doesn't make me think any better of them. Obviously, their fans are idiots. The last few seconds make the video a total laugh riot.

H/T: Bugs and Cranks.

Friday, October 23, 2009

The Drop Off

by: The Tragically Hip

There’s no swimming past the drop-off,
or feeling sorry for ourselves.
Ya don’t go swimming past the drop-off,
or else.

Personal stakes will get raised and get raised til your story gets compelling.
If you lacked the sense or were willfully dense is forever in the telling.
The surface is green and the dark interweaves in a lonely iridescence,
It’s terribly deep and the cold is complete and it only lacks your presence and nothing else ...

... nothing else ...

... no one else.

Thursday, October 22, 2009

The Last Recluse

by: The Tragically Hip

You rode out of view
As far as I knew it was you
Who broke my heart from the start
Made me work and work so hard
To get where I am
To where I'd let you do it all again

Who are you? Who are you?
What do I do without you?

Who are you The Last Recluse?

Wednesday, October 21, 2009

It's only after Oklahoma drops three games ...

... in it's first six that they get some media lovin. Of course, I'm not going to complain, and it's an interesting point. However Oklahoma should have won all three of those games, and if we did, we'd be right there for the BCS Championship. Problem is, our offensive line stinks and is undisciplined. If they could keep their blocking assignments and their composure, Bradford would have two functional arms and OU would most likely be 6-0.

Interesting little ...

... article over at the New Scientist. Six diseases you never knew you could catch. Where I work, we're looking at something which could potentially be #7 on that list.

Tuesday, October 20, 2009

Week Six Is Mine!

After my tie-breaking win of Week 1, followed by four decent but lackluster runs in the pool, I thoroughly dominated this week in the SciBlogs Football Challenge. Nine wins peeps! This week pulls me within two correct picks of the overall league lead as well. Of course, Prof-like Substance marred my celebration with the talk of flying junk, but I'll take the win regardless.

Once again, the trophy is mine bitches.

Monday, October 19, 2009

If You See Her, Say Hello

by: Bob Dylan

If you see her, say hello, she might be in tangier
She left here last early spring, is livin' there, I hear
Say for me that I'm all right though things get kind of slow
She might think that I've forgotten her, don't tell her it isn't so.

We had a falling-out, like lovers often will
And to think of how she left that night, it still brings me a chill
And though our separation, it pierced me to the heart
She still lives inside of me, we've never been apart.

If you get close to her, kiss her once for me
I always have respected her for busting out and gettin' free
Oh, whatever makes her happy, I won't stand in the way
Though the bitter taste still lingers on from the night I tried to make her stay.

I see a lot of people as I make the rounds
And I hear her name here and there as I go from town to town
And I've never gotten used to it, I've just learned to turn it off
Either I'm too sensitive or else I'm gettin' soft.

Sundown, yellow moon, I replay the past
I know every scene by heart, they all went by so fast
If she's passin' back this way, I'm not that hard to find
Tell her she can look me up if she's got the time.

Thursday, October 15, 2009

I'm sorry but ...

... anyone who runs a business dedicated to investigating the "mysteries of science and physic phenomenon." does not make them science-buffs. It makes them loopy.

So loopy that one of their children is believed dead because a tin-foil balloon (oh, there's some irony for you in that if you want to dig deep enough) he was supposedly seen crawling into, crash lands about fifty miles away.

Ten to one this was all a publicity stunt.
Although Richard Heene said he had no specialized training, they had a computer tracking system in their car and a special motorcycle. Mayumi Heene, often called "ninja" by the family, was in charge of equipment and drove the storm-mobile. She also filmed storms while her husband rode his motorcycle into the storm to launch rockets to measure magnetic forces.

You know what ...

... I really like reading review articles. I don't like writing them though.

The last remaining loose strands of my graduate school ...

... days have been tied. Received word recently that a manuscript I was co-first-author (is there really such a thing?) on has been accepted. It was the last major aspect of my dissertation, and it involved some slick bioinformatics work and some even slicker expression assays that added a good chunk (if I do say so myself) to the existing knowledge about the regulon I was studying. This work was to form the bulk of my final manuscript, but got held up by various issues. By then I was knee deep into my post-doc and the demands of writing those papers superseded IMO any obligation I had to work on my graduate school manuscripts. It led to a semi-scoop on part of the system (which meant I didn't get to name the gene we identified a function for), even though I eventually got that published on its own anyways. This was supposed to be the grand finale, but was handed over to another person in the lab for additional work and stood that way for awhile. Almost five years after I walked out the door of graduate school, it's been published.

In a way it is pretty liberating. Thank goodness it's now over!

Bashing the Republicans ...

... may still be a favorite pastime, but it doesn't seem to be selling these days.Picture taken a couple of days ago at my local B&N. Yes, that is a hardcover book selling for $3.99.

Boomer Sooner!

Boomer Sooner
Beat Texas!

Wednesday, October 14, 2009

Requiescat In Pace, Lou

Captain Lou Albano, dead at age 76.

If you are considering ...

... adopting a pet, strongly consider one with a black coat. They get overlooked all too often.
"I would say at least 80 percent of our dog kennel is black 98 percent of the time," says Katherine Christenson of Georgia’s Atlanta Humane Society. "People always take the blond dogs first; it’s horrible."
The two dogs I actively rescued (one through a site, the other through the pound), have dark coats. They're wonderful puppies.

You'd really like to think that ...

... educators are smart. Obviously not the case in Troy, NY. An Eagle Scout was suspended for 4 weeks of class because he had a 2 inch pocket knife locked in his car. Yes, a 2 INCH. POCKET. KNIFE. Yes, IN. HIS. CAR.


Way to try to ruin this kids life before it's really begun.
[The] U.S. Military Academy says the missed school days could pose a big problem when it reviews his application.
Hopefully not!

Currently ...

Listening To

Tuesday, October 13, 2009

The shart that could've ended the world ...

... radioactive rabbit poop. Fortunately it's all been cleaned up, so no end of the world scenarios will arise from these bowel movements.

If you are an anti-vaxxer ...

... your stupidity can lead to further instances like this poor girl. Infection with H1N1, complications, pneumonia, further complications. And then I read this ...
About a third of U.S. parents oppose the H1N1 vaccine, despite government efforts to encourage it, according to an Associated Press-GfK released last week.
You're GOT to be kidding me. These are the lives of your children you're gambling with folks!

Monday, October 12, 2009

Real concerns: Like rain.

Will world end in 2012? Article discussing the belief that the Mayan calendar predicts the end of the world at the end of 2012.
The inscription describes something that is supposed to occur in 2012 involving Bolon Yokte, a mysterious Mayan god associated with both war and creation.
But here is the money quote (bold emphasis mine):
"If I went to some Mayan-speaking communities and asked people what is going to happen in 2012, they wouldn't have any idea," said Jose Huchim, a Yucatan Mayan archaeologist. "That the world is going to end? They wouldn't believe you. We have real concerns these days, like rain."
Damn skippy. This is what I can't understand about the "end of days" folks. If I recall correctly, and I most certainly do (so don't tell me I don't), Jesus said (in Matthew 24:36, RSV): "But of that day and hour no one knows, not even the angels of heaven, nor the Son, but the Father only." I don't know how much clearer that can be. No one knows, and frankly no one should care! Yes, live your life as if you may not have a tomorrow ... because you might not. It's solid advice. But live it not out of fear of some impending doom, live it because it's worth enjoying it! You get one life, make the most of it!

Friday, October 09, 2009

Binge Drinking

I remember the situation pretty well. School had not even been in session for a week. It was my freshman year, I had been on campus for two weeks. I had arrived a week early for Cross Country walk-on tryouts. Having made the cut, I was invited to a pre-season party being thrown by some of the upper classmen. Usually the XC and T&F teams would throw a big party before the season started, declare a "dry season" for the team, and then throw another huge party at the end of the season. This was the big one before everything started in earnest.

I didn't drink in high school. None of my friends did, so I didn't either. Never really gave it much thought, but here, in college ... I was an adult, so it was fine. Nevermind that I had ZERO tolerance, and had no idea how much I could be effected by even a little alcohol. I had met new people, they were cool, the booze was flowing ... so I was drinking. Playing quarters with an o-lineman from the football team was my first mistake, doesn't matter if I was technically winning or not. After about an hour of that, I moved onto another drinking game. It was fun, people were laughing ... good times really. That is until on a bet I had to drink an entire pitcher of beer. I did it, but promptly filled it back up with vomit. That was it ... I was escorted outside of the house, placed against the fence and spent ... what people would tell me the following day ... several hours throwing up all over myself. Eventually they placed me in a chair on the front lawn, where people walked by and laughed at the sight.

I woke up hours later inside the house, on the couch with someone standing guard over me ... to see if I wouldn't die in the night. Some of them were worried about not being able to compete because they would likely all get expelled. When it looked like the worst had passed, and I was going to live ... they kicked me out of the house and made me take the bus home to the dorms. Yes, I was still covered in vomit. Hours later, they were at my door informing me that today was Sunday and it was time for our usual 2 hour run. I managed to survive it ... sort of. Every 15 minutes they'd stop for water. I'd take a sip, throw it all up, and off we'd go run some more. This pattern went on at least another 8 times.

I "earned" a lot of respect from them that day. Not shirking my responsibilities and taking it all like a man and finishing the run, even though I probably had barely escaped with my life the evening prior. People thought that was cool. They said I had a brass set of cahones. Now I realize it was just sheer stupidity. I can tell you however that, from that point forward (all throughout college) I couldn't even SMELL beer without getting nauseous. Nowadays I can tolerate a drink now and again, but I can't drink more than one usually without my stomach going sour on me. It's probably a small price to pay for my life.

So why mention this at all? Because I wish that a program like this had been in place when I was an undergrad.
While studies report that more than 80 percent of college students drink alcohol, the latest statistics reveal that nearly half indulge in binge-drinking, generally defined as downing five or more drinks in about two hours for men and four or more drinks for women.
Those numbers are woefully high, and down right scary. Hopefully such programs will cut down on those numbers and make college a safer and more enjoyable experience for everyone.

For reals?

Obama wins Nobel Peace Prize.
"This is probably an encouragement for him to act. Let's see if he perseveres. Let's give him time to act," Walesa said.
Translation: We want the US out of Afghanistan and Iraq, so hopefully this Peace Prize serves as peer-pressure to achieve that aim.

Is that a bit too cynical? That this prize would be used as a political tool?

ETA: Fixed link, hope people liked seeing the bluetooth adapter I'm getting for my Blackberry!

Thursday, October 08, 2009

Question for those ...

... who watched the Yankees/Twins game last night. How many times did they show Kate Hudson?

Currently ...

Listening To
A bit of a depressing album by The Antlers, but one of the best I've heard all year. You've really got to listen to it from Prologue to Epilogue. The title of the album -- Hospice -- pretty much tells you what you're in for.