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.