Thursday, April 30, 2009

The stupid, it burns ...

... over at New Scientist. It appears that Debora MacKenzie suffers from a lack of reading comprehension ...
So what are we to make of US Secretary of Agriculture Tom Vilsack saying: "There is no evidence or reports that US swine have been infected with this virus"?
This quote comes directly from Secretary Vilsack's release to the public about the safety of pork for human consumption, Release No. 0137.09. Taken in context, it reads as follows:
"I want to reiterate that U.S. pork is safe. While we in the U.S. are continuing to monitor for new cases of H1N1 flu, the American food supply is safe.

There is no evidence or reports that U.S. swine have been infected with this virus. USDA is reminding its trading partners that U.S. pork and pork products are safe and there is no basis for restricting imports of commercially produced U.S. pork and pork products.

This is not an animal health or food safety issue. This discovery of the H1N1 flu virus is in humans. Any trade restrictions would be inconsistent with World Organization for Animal Health (OIE) guidelines.
Regardless, Secretary Vilsack is correct, as far as I know when he says that there is no link between this current H1N1 virus and American swine. Whether or not it was ever in American swine is irrelevant, because that particular strain (or more likely strains) didn't jump from pigs to humans. If you compare those strains to the current strain causing all these problems, there will no doubt be some major differences which will explain why the former wasn't deadly to humans, and the latter is.

What is even more amusing is one of the comments, obviously made by a PETA member (MarkInColumbus), where he rants incessantly about "Animal Agriculture". It seems that he wants to wipe all animals off the face of the planet because they're evil ... with their belching and farting of methane, their propensity to drink water, and their ability to cause cancer, stroke, heart disease, and diabetes by transfixing their big bovine/swine/ovine gaze upon poor defenseless humans.

Jimminy Christmas!

And damn the animals to hell, why do we need them? I mean, we can just convert fossil fuels into ammonia and use it for fertilization ... I mean that won't hurt the environment none. No sir!

Better to keep your mouth closed and be thought a fool than to open it and remove all doubt.

Words of wisdom MarkInColumbus, words of wisdom.

Oh, and it appears that Debora MacKenzie likes blaming random animals for our viral woes. In 2006 she blamed migratory birds (geese in particular - the damned fowl) for spreading H5N1, and blamed ornithologists for being complict in their denial of the facts. Gee, sounds sort of like a regurgitation of this latest story, no?

ETA: Time has a piece on pigs and H1N1 as well: Don't Blame the Pig.

ETA2: Two hours later and they have not posted my response to MarkInColumbus.

Tuesday, April 28, 2009

Sweet Release

All I need to do is finish the figure legends and then I can get this manuscript out to my collaborator! Within the next couple of weeks this manuscript should be on its way to the journal! w00t!

ETA: Done, and out!

ETA2: A couple of more hours and my ASM poster will be finished, and then it's time to move onto the next manuscript.

What mission?

"It's clear that the mission created confusion and disruption. I apologize and take responsibility for any distress that flight caused," Caldera said in a White House issued paper statement.
Yah uhhh ... exactly what would that mission have been? A photo opportunity? Good Lord.

Monday, April 27, 2009

GenBank Lesson for the Day - Ok, it's a rant

GenBank can sometimes be very usefulless. Ok, maybe not useless*, but a general pain in the toosh. Case in point ...

Our lab is doing some real time PCR to examine the gene densities of denitrification genes in a number of environments. In order to do so you need to make plasmid standards which will allow you to generate a concentration curve based on dilutions of that control plasmid. Then you can take your environmental sample, run the real time PCR on it with that particular primer set and match up the Ct value with your standard. From that, you can figure out how many copies you have in your sample (per mL, per g, per ng DNA ... whatever you choose).

What is important is that your plasmid be what you think it is and not just some amplified product of the correct size which works with the primers but was actually an unrelated gene. How can this happen? Well, the primer set for nirK ... the original manuscript published on that primer set uses amplification conditions starting at 43C and stepping down to 40C. That's not exactly a stringent condition, and so you get a whole mess of crap amplifying. The first time we tried it, we had a product of roughly the correct size but upon sequencing hit some gene encoding an enzyme in Nitrosomonas eutropha, and it wasn't nirK. As a matter of fact, the reverse primer was a 100% match to this particular non-nirK gene. Yah, that sucked.

At any rate, we started over again and got a better band. [If you read the original manuscript they don't even gel visualize their PCR products ... they did southern blots ... and claim that if you concentrate your sample down far enough you'll see a really faint band along with a huge smear. Ok, great ... thanks for that]. So, we did that, got a product, cloned it and shipped it off for sequencing.

The sequences came back today and I began analysis. So the first thing I did was blastn (BLAST against the nucleotide database) our data against GenBank. They came up, fortunately, to "nirK sequences" ... but they were all from uncultured isolates. Knowing the mess we had previously gone through I wasn't satisfied with that. There are a lot of things out there in the GenBank database which are not what they say they are (it's a non-curated database after all) so I wasn't taking that for an answer. So, I did a blastx (translate our DNA sequence to protein sequence and BLAST against the protein database) and came up with NirK, once again all from uncultured organisms. If it's uncultured, how did they get protein from it? Well, 99.9999% of the time they didn't ... it's just a translation of the nucleotide data and it hasn't been verified. Therefore there is no guarantee that the protein is what it is since the database is not curated. For example, if you submit a sequence that you claim is nirK, then the protein translation is NirK, even if the gene you accidentally cloned is fucK (for the sake of argument**, and an eventual pun). And from that point on, everyone who accidentally clones fucK thinks they have nirK, but they don't. Leaving them fucK'd. Add to this the fact that they'll submit their fucK'd sequences as nirK and you see how this can eventually snowball out of control.

And don't think that can't happen because it has happened before ... the first complete microbial genome ever sequenced, H. influenzae claims to have two lactoferrin binding protein operons. Problem is, it actually doesn't ... one of those operons encodes for a pair of transferrin binding proteins, it was just mis-annotated ... and will be forever. How many other sequences were subsequently mislabeled based on that GenBank comparison?

So just because GenBank told me at this point that I had nirK, I was not satisfied. What you need to do at this point is do a blastx but under the "Choose Search Set", select "SWISSPROT protein sequences (swissprot)" as opposed to the "Non-redundant protein sequences (nr)" most of which we now know are not really protein sequences but are rather unverified translations from nucleotide sequences (and there are distinct differences between the two). Why SWISSPROT? According to their website:
UniProtKB/Swiss-Prot; a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.)
It's a manually curated database of actual protein sequences. So while you won't get a large number of results, the results you get will have been verified many times over.

Fortunately for us, SWISSPROT informed us that our sequence did indeed match a curated NirK protein (from A. faecalis). Yay us!

So, a final word of caution. GenBank can prove to be very useful, but only if you take your results with a grain of salt ... and you're conscious of what the data is telling you. Knowing how to best frame your question so you can get solid results is also a very important skill when utilizing GenBank.

*It's a highly useful repository, but it's got some major flaws which can cause some big headaches if people aren't aware of them.

**As far as I know, fucK which encodes fuculose kinase and nirK which encodes a nitrite reductase do not share any sequence similarity so having this occur is infinitesimally slight.

Sunday, April 26, 2009

The NFL Draft

NY Jets Logo
So the Jets drafted Mark Sanchez in the 1st round (trading away essentially no one of note) and then picked up Shonn Greene in the 3rd round. They're set for at least the next year or so with Thomas Jones at RB*, but I wonder if this means we'll see a two back setup like the one that the Carolina Panthers employ. I also wonder what this means for Leon Washington.

*Of course now I'm reading that he's not exactly happy with his contract situation.

On a side note, Oliver Perez (SP for the NY Mets) sucks. We paid how much for this guy this offseason? I'd like to note that we could have had Derek Lowe for about the same price, and Lowe is currently 2-1 with a 3.10 ERA while Perez is currently 1-1 with a 8.50 ERA. Oh, and Jerry Manuel says the Mets pitching must improve. Yah well, Jerry ... that's like saying a bunch of illiterate individuals better start reading more proficiently. They can't do it better until they start doing it in the first place! Aside from Santana, the Mets have NO. STARTING. PITCHING.

Friday, April 24, 2009

Currently ...

Listening To

Thursday, April 23, 2009


Oh man, I've got to stop laughing ... it hurts!

h/t PsD.

Come on guys ...

... it's a little bit of paperwork/legwork and wasting taking time to fill it out/do it would be worth it in the long run. It'd also save you from being publicly embarrassed, ya?
Vander Linden said the investigators know that several years ago an entire freezer full of biological samples broke down and all the samples had to be safely destroyed. But a complete inventory of what was in the freezer was not done before the samples were destroyed. Vander Linden said there's a "strong possibility" the vials were in that freezer and destroyed, but that isn't known for sure.
Where I work, we need to keep a complete inventory of what microbial isolates we have on hand*. As species/strains enter and/or leave the lab, the list needs to be updated. It's a bit of a pain in the toosh ... especially when we're talking about having to keep track of things even as simple/safe as E. coli K-12, but it's better than the alternative ... losing a sample and having it hit the news.

*I can't believe that I'm going to give kudo's to Microsoft but ... MS Access comes in really handy with this. It also helps in our chemical, plasmid, and primer inventories as well.

Wednesday, April 22, 2009


Who in their right mind, when submitting the 16S rDNA gene sequence for a type strain, submits a sequence riddled with N*'s? It's a type strain for crying out loud ... you can't make sure you've got a clean sequence? I mean, WTF folks ... combined, a new forward and reverse read would cost you $7. You lazy sons of motherless goats.


*According to IUPAC nomenclature, N stands for aNy nucleotide, which certainly doesn't narrow the field for that position.

Tuesday, April 21, 2009

A Tale of Two Brothers

Once upon a time two brothers who lived on adjoining farms fell into conflict.

It was the first serious rift in 40 years of farming side by side, sharing machinery, and trading labor and goods as needed without a hitch.

Then the long collaboration fell apart. It began with a small misunderstanding and it grew into a major difference, and finally it exploded into an exchange of bitter words followed by weeks of silence.

One morning there was a knock on John's door. He opened it to find a man with a carpenter's toolbox. "I'm looking for a few days' work", he said. "Perhaps you would have a few small jobs here and there I could help with? Could I help you?"

"Yes," said the older brother. "I do have a job for you. Look across the creek at that farm. That's my neighbor; in fact, it's my younger brother. "

"Last week there was a meadow between us and he took his bulldozer to the river levee and now there is a creek between us. Well, he may have done this to spite me, but I'll go him one better. See that pile of lumber by the barn? I want you to build me a fence - - an 8-foot fence -- so I won't need to see his place or his face anymore."

The carpenter said, "I think I understand the situation. Show me the nails and the post-hole digger and I'll be able to do a job that pleases you."

The older brother had to go to town, so he helped the carpenter get the materials ready and then he was off for the day. The carpenter worked hard all that day measuring, sawing, nailing. About sunset when the farmer returned, the carpenter had just finished his job. The farmer's eyes opened wide, his jaw dropped. There was no fence there at all. It was a bridge -- a bridge stretching from one side of the creek to the other! A fine piece of work handrails and all -- and the neighbor, his younger brother, was coming across, his hand outstretched. "You are quite a fellow to build this bridge after all I've said and done."

The two brothers stood at each end of the bridge, and then they met in the middle, taking each other's hand. They turned to see the carpenter hoist his toolbox on his shoulder.

"No, wait! Stay a few days. I've a lot of other projects for you," said the older brother.

"I'd love to stay on," the carpenter said, "but, I have many more bridges to build."

-Over The Hills and Everywhere by Manly Wade Wellman, from the book Who Fears the Devil

Monday, April 20, 2009

Oh, by the way ...

... if you plan on donating any money to a humane society this year, don't give it to the HSUS (Humane Society of the United States). The "humane society" tag in their name is a total fabrication.

Humane Society of the United States
Despite the words “humane society” on its letterhead, the Humane Society of the United States (HSUS) is not affiliated with your local animal shelter. Despite the omnipresent dogs and cats in its fundraising materials, it’s not an organization that runs spay/neuter programs or takes in stray, neglected, and abused pets. And despite the common image of animal protection agencies as cash-strapped organizations dedicated to animal welfare, HSUS has become the wealthiest animal rights organization on earth.

Manuscript Homestretch

Got the office door closed, playing some Mighty Mighty Bosstones (currently Someday I Suppose off of their Don't Know How To Party album), and configuring the dozen or so phylogenetic trees I'm including as Supplementary Material for my manuscript (over 500 OTUs will do that to you). Once that is done, its off for a final reading of the manuscript to find typos, clean up the other figures, and catch any minor errors that I may have passed over previously. Then, it's off to the collaborators for their review prior to submission.

And then, I get to turn right around and work on the next manuscript. Whee!

So, no more blogging for today (and probably tomorrow).

Carbon Dioxide a Deadly Gas?

The answer to that question is: Yes.

Which is why the EPA was right in making the call that they did when they said that greenhouse gases, which includes carbon dioxide, pose significant hazards to humans.
The scientific analysis also confirms that climate change impacts human health in several ways. Findings from a recent EPA study titled “Assessment of the Impacts of Global Change on Regional U.S. Air Quality: A Synthesis of Climate Change Impacts on Ground-Level Ozone,” for example, suggest that climate change may lead to higher concentrations of ground-level ozone, a harmful pollutant. Additional impacts of climate change include, but are not limited to:

* increased drought;
* more heavy downpours and flooding;
* more frequent and intense heat waves and wildfires;
* greater sea level rise;
* more intense storms; and
* harm to water resources, agriculture, wildlife and ecosystems.
Bold emphasis mine, and here is Exhibit A.
In a "Perspective" published in the journal Science, Peter Brewer and Edward Peltzer combine published data on rising levels of carbon dioxide and declining levels of oxygen in the ocean in a set of new and thermodynamically rigorous calculations. They show that increases in carbon dioxide can make marine animals more susceptible to low concentrations of oxygen, and thus exacerbate the effects of low-oxygen "dead zones" in the ocean.
Carbon dioxide can pose more than the direct health hazard to humans, as you can see above. Those dead zones, mostly located near the coasts also will translate into reduced food supplies. I don't know about anyone else but ... I'd like to be able to continue to eat in the future.

Sunday, April 19, 2009

Angling drives evolution in bass

Cool article over at Scientific American on fishing.
A new, 20-year study, led by University of Illinois at Urbana–Champaign ecologist David Philipp, "provides the first direct experimental evidence that vulnerability to angling is a heritable trait," the authors wrote.
So how'd they figure this out?
With the help of anglers, Philipp and his colleagues tagged and released largemouth bass in a state park pond in central Illinois beginning in the mid-1970s. Many fish were caught time and again, they found—up to 16 times in a single year. The researchers drained the pond in the 1980s and discovered that 200 of about 1,700 fish had never been hooked.
From there they did ...
From this stock, they have since bred the separate groups of "low-vulnerability" and "high-vulnerability" bass, and through three generations the offspring have stayed true to their parents' susceptibility—or aversion—to getting caught.
Pretty cool. So what does this mean?
"This type of selection experiment, which we propose has been going on in all bass lakes since the inception of angling, has the potential to alter, perhaps quite significantly, the behavior and even the life history of individual fish in those populations," the study said.
What form does the impact take?
Female largemouths swim away from their eggs after laying them; it is the male that guards them for their first month of life. The aggressive males are best at protecting their fry from predators—but they also may strike more readily at lures in their territories, making them more vulnerable to being caught.

Most times of the year male and female fish are caught in equal numbers. But during spawning season, males are caught the most. And hanging on to a caught male for longer than a few moments during nesting season could spell death by predation for the fry.

"Anglers may be negatively impacting the populations without knowing it," Philipp says.

Saturday, April 18, 2009

That whacky South Pole!

Seems that the Antarctic ice is actually increasing in parts of the continent.
Extensive melting of Antarctic ice sheets would be required to raise sea levels substantially, and ice is melting in parts of west Antarctica. The destabilisation of the Wilkins ice shelf generated international headlines this month.

However, the picture is very different in east Antarctica, which includes the territory claimed by Australia.

East Antarctica is four times the size of west Antarctica and parts of it are cooling. The Scientific Committee on Antarctic Research report prepared for last week's meeting of Antarctic Treaty nations in Washington noted the South Pole had shown "significant cooling in recent decades".
... and ...
Ice core drilling in the fast ice off Australia's Davis Station in East Antarctica by the Antarctic Climate and Ecosystems Co-Operative Research Centre shows that last year, the ice had a maximum thickness of 1.89m, its densest in 10 years. The average thickness of the ice at Davis since the 1950s is 1.67m.

A paper to be published soon by the British Antarctic Survey in the journal Geophysical Research Letters is expected to confirm that over the past 30 years, the area of sea ice around the continent has expanded.
I'll see if I can link that paper when it comes out.

A must read ...

... by Bill Whittle of Eject! Eject! Eject.

... a dream becomes a goal once you make a viable plan and stick to it ...

Quid Pro Quo

Lately I've noticed that a few people have listed me in their blog links section. For that I'm most appreciative, and I'd certainly like to reciprocate. So ... if you've linked me and you're not listed in my Quid Pro Quo section, by all means shoot me off an email (or comment to this blog entry) and I'll rectify the situation. Once again, thanks!

Nom nom nom!

This weekend I decided to stay up late watching bad sci-fi movies, sleep in late with the dogs, and then treat myself to a nice thick sub at the local deli. That's the other half of my corned beef, pastrami, swiss on honey wheat sub. Finished off with a couple of dill slices, lettuce, tomatos, peppers and deli mustard. Wash it all down with a diet Mt. Dew (have to watch my figure ya know) and today is starting off rather well. Now I can work guilt free on a Saturday.

Friday, April 17, 2009

Oh jimminy ...

... trying to watch the movie Dark Star (Netflix rules!) but it's completely horrible. I don't know how it managed to get such a good rating.

I will say this though, if you manage to get through the first few minutes, you'll see the inspiration for the Bishop "knife trick" from Alien.

Don't give me any of that intelligent life crap, just give me something I can blow up!

Linkage ...

... to some web-based resources I've had to use lately.

Libshuff (Sequence Library Comparison) - To determine whether or not your various DNA (in my case microbial) libraries are statistically similar or not. It's hosted by UGA.

DNADIST - In order to use the web-based program above, you need a DNA distance matrix file. It's a part of the Phylip package. There is an online resource for this though hosted by the Pasteur Institute (which is what is linked above).

Or, if you don't want to use libshuff like I am, you can use UniFrac.

Thursday, April 16, 2009

Is it a bad thing ...

... if I know the MCS sequence of pCR4-TOPO by heart?

Manually sorting through over a dozen 96 well plates of sequencing is a pain in the toosh. I'm dreading what's going to happen when I need to submit all of this to GenBank. Fortunately for me, it's mostly a descriptive study of a site, so I can probably get away with submitting it as an aligned environmental set!

Get off it ...

Read this article on MSNBC and had to laugh. They just don't get it.
The frugality of ... millions of other Americans who still have their good jobs feed back on the economy, holding down growth and encouraging other worried workers to trim their spending — causing the whole vicious cycle to run another lap.
Oh, so because I'm not in the currently dire situation of losing my job I'm causing the economy to stay tanked because I don't spend my money like a fiend? Piss off. Who knows how long any of us have at any job really. Of course I have a bit more to worry about than the average individual since I'm coming up for tenure soon.
Economists say many still-flush consumers are handcuffed by psychological traps that cause them to tighten their purse strings even though economic hardship is not their reality.
Sorry, it's not a trap, it's what I call "common sense" and "living within your means". A lot of people thought they had nothing to fear prior to this whole collapse, and look at them. Things take unexpected turns. I'd hardly call it a trap to think that an unexpected turn can happen to me even though I haven't been hit yet. So, I cut down a bit more here and there. It's not that I've ever really been free with my wallet ... except when I first got out of college and wasted money on a 3DO system (what a friggin mess that was). I shop for clothes at Old Navy and Kohl's, not Abercrombie. I don't buy brand name food. I mean, I doubt the chicken I can buy from Wal-Mart is worse off than buying Purdue. And I avoid fads ... which is why I still don't have a Wii or PS3 (though I'm dying for one). So, now that I'm smart with money ... you know, I actually liked buying shares in my IRA at this reduced price ... I'm to blame for the economy staying in the doldrums?


Currently ...

Listening To

Wednesday, April 15, 2009

NUTS! and (*#@&#@!

Yesterday I was pleased with myself. I had finally wrapped up work on my Introduction, to the point that I merged it with the rest of the manuscript, saved it up and went home for the evening. When I got into work early this morning, I attempted to open it up.


Whiskey! TANGO! FOXTROT!!!

We had a power surge last night, about the time I was wrapping things up, and I guess it fried the two files I had open. The two files? My Introduction file and my new Manuscript file. I still have my M&M and R&D seperate (THANKFULLY!) but my Introduction is gone. Forever. Fortunately I have most of the essentials memorized, but it means having to rewrite it. Mother----er!

And yes, I tried to recover the files. I spent 4 hours doing that, to no avail. It's probably easier for me at this point to just rewrite the damn thing.



Lock up these idiots for the rest of their lives.
A mother and her teenage son are kidnapped. The kidnappers place a cell phone in the car of the boy's father so they can communicate their ransom demands. The son is burned with a blowtorch. The mother implores the father to pay the ransom.

A terrifying scenario, but one that the FBI and police say was all orchestrated by the mother to get some fast cash from her ex-husband.

The mother, Alejandra Arriaza, her boyfriend, Angel Ponce, and his nephew, Joel Boza, were charged Tuesday with federal kidnapping counts. If convicted, they could be sentenced to life in prison.

According to an FBI affidavit, all three have admitted their roles in the phony kidnapping.
This lady is a total tool. She kidnapped and tortured her own child!

Tuesday, April 14, 2009

I agree as well ...

... when I say that I think President Obama handled the hostage situation off the coast of Somali correctly. Not that I'm going to kid myself by thinking that he cares what I think about him. At any rate, I think our Navy did a great job. One shot, one kill. They're not the sort of people you want to screw with, especially when you're a strung-out teenager sitting in a friggin boat. As for Gates, got to agree with the article there as well. My only beef is ... I don't think he did enough trimming of the military budget. There are still some bloated carcasses sitting in that thing.

Sign me up ...

... for the Coalition of the Sane. I never have, and I never will ... tweet.

From a recent Sprint commercial.233,000 people just Twittered on Twitter. 26% of you viewing this have no idea what that means.

Notice what the twits are twittering. "me!" Heh. Is Sprint characterizing twits? Some people, including yours truly, think so. Not that I don't think blogs aren't self-indulgent, I just think they're more able to share ideas. Then again, I've never been on Twitter ... is the exchange of ideas as applicable to that platform? At a limit of 140 characters (IIRC) I can't believe it is.

Oh, and then there is this ... Twitter can harm a developing childs "moral compass".
"If things are happening too fast, you may not ever fully experience emotions about other people's psychological states and that would have implications for your morality," said researcher Mary Helen Immordino-Yang.
We're already in a state of constant information overload, Twitter (and other social networking sites) add another layer of noise to our daily lives. Oh, and for the record, I don't Facebook or MySpace either.

Bioethanol ... a drain on water resources?

Article in Science Daily.
The scientists made a new estimate of bioethanol's impact on the water supply using detailed irrigation data from 41 states. They found that bioethanol's water requirements can be as high as 861 billion gallons of water from the corn field to the fuel pump in 2007. And a gallon of ethanol may require up to over 2,100 gallons of water from farm to fuel pump, depending on the regional irrigation practice in growing corn.
If you look at the map, part of the area that is farmed for corn sits on top of the Ogallala Aquifer. Unfortunately, it's a water resource that feeds the nation, and it's beginning to fail. Back in 2007 the non-profit Environmental Defense issued a report on bioethanol and its impact on the Ogallala Aquifer. In the report titled Potential Impacts of Biofuels Expansion on Natural Resources: A Case Study On The Ogallala Aquifer Region (PDF, 18 pages) they state:
In the areas of highest Ogallala Aquifer depletion, new corn ethanol plants currently under construction or planned will increase the region’s ethanol production capacity by 900%. The area currently hosts only five ethanol plants with combined production of 71.5 million gallons per year, but another nine plants, with 639 million gallons per year capacity, are currently under construction. This dramatic expansion of ethanol production has substantial implications for already strained water and grassland resources in the Ogallala Aquifer region.

Water demands associated with individual ethanol plants—due both to ethanol processing and growing corn feedstock—are not exceptionally higher than demands from other industrial or agricultural users, but the construction of new ethanol plants in areas of existing water stress will exacerbate conflicts if water is already scarce. Water demands from new ethanol plants in areas of Ogallala Aquifer depletion may reach 2.6 billion gallons per year for corn-to-fuel processing alone, and between 59 and 120 billion gallons per year for increased water demand if there are local increases in irrigated corn production.
Now, look at those numbers and consider this ... if the above report (at the very top) is true, and water estimates may be 3 times as high as previously considered ... we're talking up to an additional 360 billion gallons of water per year drained out of that aquifer.

Once that water is gone, it's gone. You can't replenish that aquifer any other way that by rainfall, and that's just not going to happen.

Monday, April 13, 2009


The cost of hiring a coach.
New Kentucky hoops coach John Calipari's eight-year, $31.65-million deal is the richest in college basketball.
Ok, well ... Kentucky is a basketball school ... so what?
College football coaches should feel the blessings, too. There's a good chance Calipari's deal will push the salaries of college football coaches even higher. Why? Football is a much bigger revenue-producer on college campuses than basketball, so it stands to reason the football coach almost always will be higher paid.
You know, I was an athlete in college. I didn't partake in any of the popular sports ... I ran Cross-Country, and both Indoor and Outdoor Track and Field. I was good, enough to be on scholarship, and unlike our popular teams, we were actually successful (I captained and led our team to a Division I Conference championship in XC my senior year). So, while I know about the tough work that goes into being a student athlete, I am dead set against athletes receiving pay for their athletic prowess. Why? Because only basketball and football players will benefit, and that doesn't seem fair to the rest of the athletic program. Of course, that comes tougher to defend when the colleges milk these athletes and bestow multi-million dollar packages to their coaches.

Things have gotten out of hand, just like they have in every other corner of the country. I just hope things don't blow up like I feel they're going to though.

Sunday, April 12, 2009

Be more concerned with your character than with your reputation. Your character is what you really are, while your reputation is merely what others think you are. - John Wooden

Wednesday, April 08, 2009

Man's best friend? Riiigghhhtttt

I'm home sick today and trying to get something, anything, done today (other than watching the soaps). So I'm at the kitchen table with the laptop and other peer reviewed manuscripts spread out, trying to write ... and I have Max, my faithful Norwegian Elkhound mix at my feet. My two other dogs are elsewhere in the house, chewing on rawhide. So, to show Max I appreciate his company, I hand him a treat. What does he do? He runs off with it.

Gee, thanks for nothing buddy.

It's definitely spring ...

... know how I can tell? My sinuses clog, my teeth ache, my eyes water, and my throat gets scratchy. Oh, and I wind up swallowing about a gallon of mucus a day. Yah, spring is here, and I feel like poop. So here I am, at home, trying to mend by drinking lots of tea and getting high on Theraflu. Oh yah, and trying to write.

Tuesday, April 07, 2009

Building trees ...

... for my upcoming manuscript. Not enough room in the paper itself (already have 4 tables and 6 figures) so they're going in as Supplemental Material, but that doesn't make it any easier ... seeing as I have over 600 OTUs in my study.

One thing that's nice about Geneious though, you can color coordinate the branches, which is a nice feature when you want to highlight particular clades (which I want to do).

Currently ...

Listening To
Step right up, gather round
Greatest salesman in town
Selling something seldom sold
Step up, step up, step up behold
Dead mice for sale, they're going fast
Like hell...Last dead mouse now don't be shy
There's never been a better time to buy

Last dead mouse but I'll get more
I'm a businessman and an entrepreneur
Folks say I'm nuts, they can say what they please
You've got to be crazy with prices like these
No overhead so I can keep down the cost
I make my own hours 'cause I'm my own boss
I believe in my product, I love what I sell
Last dead mouse well that's why I yell

Step right up, ladies and gents
Last dead mouse costs fifty cents
It's a steal at any price
Going once, going once, going once, going twice
Half a buck, last in stock
Be the first one on your block
No need to walk, no need to feed
Satisfaction guaranteed

Nice and easy now, nice and easy now, nice and easy now
Last dead mouse.

- Last Dead Mouse, Mighty Mighty Bosstones

Scientia Pro Publica - The New Blog Carnival

GrrlScientist has put together a new blog carnival, titled Scientia Pro Publica, Science for the People. Yours truly managed to snag a spot on the carnival with this post, with the admonishment that I should write some damn longer articles. NOTED!

If you'd like to contribute to this carnival, and I strongly suggest that you consider it (heck, if they published my swill, surely you all can do better) it, you can use the submission form located here. The next carnival is slated to be published on April 20th.

Monday, April 06, 2009

Woo hoo!

The Metropolitans bullpen successfully held and saved a game! Granted, it's only the first game of the season, but hey ... they could have started the season 0-1.

Biochar: Carbon Mitigation from the Ground Up

ResearchBlogging.orgWas doing one of my weekly Scopus searches for new articles and came across the following review (PDF, 4 pages) on biochar, and it seems rather timely given that I've highlighted this topic recently. The title of this blog is taken from the title of the article, and it talks about the terra preta soils of the Amazon.

The soils are proof of concept that burying biochar (biomass-derived charcoal) in the soils will both: increase soil productivity/fertility; and trap carbon for long periods of time in the soil. Quoting the work of Christoph Steiner, one of the leading experts in the area of biochar, the article relates that: ... charcoal-mediated enhancement of soil caused a 280-400% increase in plant uptake of nitrogen, an element essential for crop production.

So how did the terra preta come about? There are competing theories:
Anna Roosevelt, a professor of anthropology at the University of Illinois at Chicago, believes terra preta was created accidentally through the accumulation of garbage. The dark soil, she says, is full of human cultural traces such as house foundations, hearths, cemeteries, food remains, and artifacts, along with charcoal. In contrast, Erickson says he’s sure the Amazonian peoples knew exactly what they were doing when they developed this rich soil. As evidence, he says, "All humans produce and toss out garbage, but the terra preta phenomenon is limited to a few world regions."
As I've mentioned before though, not all biochar is identical, and this article highlights some research pointing out this fact:
However, not all biochar performs the same. The importance of biochar’s variable chemical composition was illustrated in studies by Goro Uehara, a professor of soil science at the University of Hawaii, who grew plants both with and without biochar made from macadamia nutshells. He says, "As we added more [biochar], the plants got sicker and sicker." Uehara’s colleague, University of Hawaii extension specialist Jonathan Deenik, says that when they repeated the experiment with a more highly carbonized version of the nutshell biochar, which contained lower levels of volatile compounds, "preliminary results in a greenhouse study showed that low-volatility [biochar] supplemented with fertilizer outperformed fertilizer alone by 60%, in a statistically significant difference." This research was presented at the October 2008 annual meeting of the Soil Science Society of America.
From my particular vantage point, some biochars will act as a chelator (e.g., activated carbon) and pull essential nutrients (e.g., calcium, zinc, copper, iron) out of the soil, making them unavailable for plants and microbes.

However, in terms of storage capabilities, what does biochar bring to the table?
The calculations for potential carbon storage can be estimated downward from the amount of atmospheric carbon that photosynthesis removes from the air each year; using figures from the Intergovernmental Panel on Climate Change, Amonette estimates that number at 61.5 billion metric tons. He says the best estimates are presented in four scenarios for carbon storage calculated by the nonprofit International Biochar Initiative (IBI), a consortium of scientists and others who advocate for research/development and commercialization of biochar technology. The IBI’s "moderate" scenario assumed that 2.1% of the annual total photosynthesized carbon would be available for conversion to biochar containing 40% of the carbon in the original biomass, and that incorporating this charcoal in the soil would remove half a billion metric tons of carbon from the atmosphere annually. Because the heat and chemical energy released during pyrolysis could replace energy derived from fossil fuels, the IBI calculates the total benefit would be equivalent to removing about 1.2 billion metric tons of carbon from the atmosphere each year. That would offset 29% of today’s net rise in atmospheric carbon, which is estimated at 4.1 billion metric tons, according to the Energy Information Administration.
Pretty significant, eh?

An additional beauty to biochar is that it technically doesn't take a sophisticated setup to produce it:
Among other projects, the students made their own biochar in a 55-gallon drum and found that positioning the drum horizontally produced the best burn.
But biochar alone cannot solve our problems ... we need to better use our existing resources, and recycle!
As a carbon mitigation strategy, most biochar advocates believe biochar should be made only from plant waste, not from trees or plants grown on plantations. "The charcoal should not come from cutting down the rainforest and growing eucalyptus," says Amonette.
Now, all we need to do is get cracking and get into long-term field studies.

Tenenbaum, D.J. (2009). Biochar: Carbon mitigation from the ground up. Environmental Health Perspectives, 117 (2): A70-A73.

Interesting title of New Scientist article ...

Bug eats electricity, farts biogas. Doubt they got the idea from my "Bacterial Farts" series from awhile back ... or did they?


Pro-jihadist held captive by jihadists.
"She believed the Taliban were legitimate in resisting armed forces in that country, she believed she could interview these people because she could give them fair hearing and I believe they turned on her," Rees said.

"And after all this, she's depending on the support of the same governments she spoke out against."
"I need somebody to help me," Qaahar pleaded on the most recent video. "My government — the Canadian government, the Pakistan government — I want to go home."
The question is ... if Canada does actually manage to get her released, will she go back to her anti-Canadian ways?

This actually is not an argument to not seek her release, but rather is an argument for continuing to seek her release. Canada (and the United States) are governments founded upon (amongst other things) the principle of freedom of speech. As much as this woman is ungrateful for her country (until her life is in mortal danger) her country should not forsake its ethical duty to protect her. Regardless of whether or not she decides to be grateful to her country if they manage to save her, the Canadian government has an ethical/moral duty to save her. Now we'll see if her jihadist friends let her go.


Recently, I've had a few friends, and a few more acquaintances, hit me up as friends on Facebook. Problem is, I don't have a Facebook page ... and I didn't plan on ever getting one either. So, does Facebook actually keep track of these requests, so if I ever on a whim decided to get a Facebook page 10 years down the road ... I'd start out with a bevy of friends?

It's odd. I also don't know why, all of a sudden, I'm such a popular fellow. All of these individuals are people I knew back in my college days, so maybe something is going on that I'm not aware of ... though why none of them have bothered to contact me directly, is beyond me.

Saturday, April 04, 2009

Colony Collapse Disorder Revisited

Article in Scientific American.


Isle Royale

Ever since I visited this island in the middle of Lake Superior when I was a kid, I've loved the story of the constant struggle between the islands populations of moose and wolves.

However, a recent examination of the islands wolves reveals some problems. They are suffering from backbone malformation problems due to the decades long inbreeding of the tiny colony.
Scientists had long watched for problems from inbreeding, such as poor survival rates for pups. Instead, the first solid evidence surfaced when Jannikke Raikkonen of the Swedish Museum of National History, an expert in wolf anatomy, visited Isle Royale several years ago to examine the project's bone collection.

She identified malformed vertebrae in all wolf remains found the previous dozen years. Such abnormalities show up in just 1 percent of observed populations that are not inbred.
The question now is ... do they introduce outside wolves to "save" the colony?
Historically, biologists have taken a hands-off posture as wolf and moose numbers have risen and fallen, preferring to let nature take its course even if it meant extinction of one or both species. But strong arguments could be made for intervening as well, project leaders now say.
So what are some of the things to consider pro/con in this situation?
The question involves competing scientific and ethical values, Vucetich said.

Opponents of intervention believe humans should not tinker with wilderness systems. Even if Isle Royale's wolves die out, their loss would provide information that could save endangered species elsewhere.

Other would counter that attempting to save the wolves also could yield valuable data, while sparing individual animals from painful bone deformities.

"We have an incomplete understanding of genetic rescue — when and how and why it works," Vucetich said. "Even so, it may be an important conservation tool as more population species become rare."
What do others think?

It's that time again ...

... to dream the big dreams, and my big dreams I mean the dream that your team can actually win the World Series.

This is an especially important time when your particular team has choked the past two years.

That's whats so special about baseball ... for at least a month or so you can happily dream.

Thursday, April 02, 2009

Math for chicks!

So chicks can do arithmetic after all, eh?
Solo chicks typically rush over to join the largest group of their companions in the neighborhood.
Not only that, but ...
For the toughest set of tests, each chick watched as a researcher first hid objects behind each of two screens. Then the tester let the chick see some of the objects being moved from behind one screen to the other. To go to the screen with the larger number, the chick had to keep track of addition and subtraction.

About 75 percent of the time, chicks did it right.
Not bad for a chick!


Went to pre-order the new Tragically Hip album, We Are The Same, coming out in less than a week. Went through checkout and then found out the the minimum shipping charge for my $14.99 CD was $8.43. Uh, I don't think so.

Sadly disappointed. I guess I'll buy the darn CD from Amazon, Walmart or somewhere I won't get gouged for simply getting it to me.

Two articles on carbon ...

... the first is on biochar.
Its high carbon content and porous nature can help soil retain water, nutrients, protect soil microbes and ultimately increase crop yields while acting as natural carbon sink - sequestering CO2 and locking it into the ground.
I'm particularly excited about biochar because it's a focus of my research. We're in the process of looking at how biochar effects microbial communities (density, diversity, specific populations, etc). One thing to consider is that most biochars (there are multiple ways to make biochar and change it's physical properties) have a negative charge, and as such will act as a chelator and "mop up" cations (positively charged ions). While this will be a good thing from a remediation standpoint, if there are normal levels of say copper in the soil, this can reduce them to the point where it may detrimentally effect microbial populations. So we're in the process of looking into it.

The second is on carbon capture.
To find out exactly how the carbon dioxide is stored in natural gas fields, an international team of researchers - led by the University of Manchester - uniquely combined two specialised techniques. They measured the ratios of the stable isotopes of carbon dioxide and noble gases like helium and neon in nine gas fields in North America, China and Europe. These gas fields were naturally filled with carbon dioxide thousands or millions of years ago.

They found that underground water is the major carbon dioxide sink in these gas fields and has been for millions of years.
So what does this mean?
Professor Chris Ballentine of the University of Manchester, the project director, said: "The universities of Manchester and Toronto are international leaders in different aspects of gas tracing. By combining our expertise we have been able to invent a new way of looking at carbon dioxide fields. This new approach will also be essential for monitoring and tracing where carbon dioxide captured from coal-fired power stations goes when we inject it underground – this is critical for future safety verification."
IOW, the carbon dioxide that we capture in this manner may truly sit there for millions of years, and we can now feel relatively certain about it.

Wednesday, April 01, 2009

Continuing manuscript madness ...

... so not a lot of blogging today. However, I will take this time to complain about individuals who do not proof-read their manuscripts. My lab is currently working on a project looking at the denitrification pathway in various agricultural settings. So we're doing a combination of Real Time PCR (to look at gene copy density) and DNA analysis (RFLP and sequencing) to try to tease out some relationships. Well, there are several steps in the process, and all of them (save the final step) involve at least two enzymes. So we have a lot of analysis to perform.

Well, for the RFLP (restriction fragment length polymorphism) work we need PCR products which are long enough to be worthwhile to restriction digest. As you can guess, the "universal" primers we use aren't really universal, so it's a mixed bag. Add to this the fact that one of the primers we ordered IS WRONG and kept giving us erroneous results (about 300bp shorter than what it should have been). Turns out, the primer I ordered was based on a manuscript where the authors tacked on two 3' T's to the end of the primer (without an explanation) while citing the original paper. Figuring I had the correct primer sequence (should be identical in both papers, natch), I ordered it and didn't check it against the original. Doh!

At any rate, that drama consumed part of my day yesterday and I hope to close my office door, open up my manuscript word document, and spend a majority of today writing ... because tomorrow is filled with meetings.