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."

Exactly.

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!

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.

Spam

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.

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.

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.

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!

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

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

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!

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.

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.

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.