Friday, May 30, 2008

In Vacuo

Won't be blogging today. Have to get this data I've just received, analyzed and merged with other data my lab has already acquired/assembled/analyzed for a manuscript I'm in the process of writing. Until later, toodles.

Currently ...

Listening To

Thursday, May 29, 2008

Hey, you got your spaceship in my video ...

... no, you got your video on my space ship! Go to their Multimedia link and select RocketCamTM. There is some neat video in there.

Exiles: The Rocks!

Oh, if Victor Hugo only knew. The ocean floor is teeming with microbial life.
While seafloor microbes have been detected before, this is the first time they have been quantified. Using genetic analysis, Edwards and colleagues found thousands of times more bacteria on the seafloor than in the water above.
... and ...
The scientists also found higher microbial diversity on the rocks compared with other vibrant systems, such as those found at hydrothermal vents.

Even compared with the microbial diversity of farm soil--viewed by many as the richest--diversity on the basalt is statistically equivalent.
Microbial diversity, which is one of my fields of work. The article should prove to be very interesting, and I'll blog on it once I get a chance to read it. Maybe tomorrow.

Rachael Ray is a Terrorist

Which is why Dunkin Donuts pulled an ad featuring her wearing a black and white scarf.
Critics, including conservative commentator Michelle Malkin, complained that the scarf looked similar to the black-and-white checkered kaffiyeh, the traditional Palestinian scarf. Critics who fueled online complaints about the ad in blogs say such scarves have come to symbolize Muslim extremism and terrorism.
Here is a picture of the terrorist herself. What a bunch of damn fools, especially Bill O'Reilly's whore Michelle Malkin. The argument as presented by these fools: Something A "looks similar" to something B, and because something B is bad something A needs to go. Is beyond stupid. It's a friggin scarf for crying out loud. One of my favorite sweaters is a black/white/grey argyle sweater similar to the one seen below ... am I a terrorist? Am I giving a secret nod to Al-Qeada because I wear it?What total nonsense. I'm sure there are several items which Ms. Malkin herself probably reveres which could be linked back to something heinous. Almost sounds like a new game which we could call Six Degrees of Al-Qaeda. Let's try it out once.

1. Rachael Ray wore a black and white scarf in a Dunkin Donuts ad.
2. Some people in Palestine wear black and white scarves too.
3. Some of those people may be terrorists.
4. Some terrorists belong to Al-Qaeda.

So there you have it, we link Rachael Ray to Al-Qaeda in four steps. Now it's time to send her to Guantanamo, but not before she does another spread for FHM.

Wednesday, May 28, 2008

Paper or paper?

China sacks plastic bags. They use over 3 billion of them a day!
The Chinese government is banning production and distribution of the thinnest plastic bags in a bid to curb the white pollution that is taking over the countryside. The bags are also banned from all forms of public transportation and "scenic locations." The move may save as much as 37 million barrels of oil currently used to produce the plastic totes, according to China Trade News. Already, the nation's largest producer of such thin plastic bags, Huaqiang, has shut down its operations.

The effort comes amid growing environmental awareness among the Chinese people and mimics similar efforts in countries like Bangladesh and Ireland as well as the city of San Francisco, though efforts to replicate that ban in other U.S. municipalities have foundered in the face of opposition from plastic manufacturers.
I thought there might be a significant impact on petroleum, and there is ... to the tune of 37 million barrels. And why am I not surprised that US efforts have been curbed by plastic lobbyists. I don't want to see anyone lose their jobs, but surely you can redirect your efforts ... maybe biodegradeable plastics?

Here they come to snuff the rooster ...

... and the rooster is obviously pissed.
COPEMISH, Mich. — An 11-year-old boy has been injured when an eagle attacked him during a walk through the woods in Manistee County, Michigan.

I did it!

I biked into work today. Eight miles in a shade over 30 minutes. It wasn't too bad this morning, saw maybe a couple dozen cars on my ride in. I'm not sure what it's going to look like later this afternoon when I head home around 3:30 - 4:00. There are a couple of places where there is absolutely no shoulder whatsoever, so I have nowhere to go if someone doesn't give me enough room ... well, except down into a ditch. Hopefully drivers will be courteous and give me wide berth. Most of them did this morning, so here's to hoping the afternoon drivers are just as good.

I'd be doing somewhat better if I was feeling 100%. Spent part of the day at the beach on Monday and wound up with sunburn on the back of my knees, and then pulled my calf playing softball last night though it was a good night at the plate (3 for 5, 1 HR, 3 RBI) and in the field so I suppose I'll take it.

At any rate, I hope to keep this biking trend going. Not only does it help me reduce my carbon footprint, it allows me to give my wife my car which has better gas mileage than her beast. With gas hitting almost $4/gallon, we need to find a way to save some money ... and this is one of them. Of course, I guess I shouldn't complain. Watching the news this morning as I was eating breakfast ... diesel in England is (in US dollars) almost $9/gallon. Holy crap.

Tuesday, May 27, 2008

But does it come with batteries?

Something to think about when you're planning on buying that used hybrid. The battery might need replacement sooner than you might want.
Hanson says today's Prius batteries are designed to last "the life of the car," which Toyota defines as 180,000 miles.
... and ...
For those unlucky few who have to replace their own batteries, the cost is coming down. On June 1 Honda is slashing the cost of its batteries from $3,400 (excluding installation) to as low as $1,968 on an Insight or as high as $2,440 on an Accord hybrid. Toyota also plans to substantially cut battery prices, which now stand at $3,000 (excluding installation), down from $5,500 on the original Prius.
Installation runs around $900, so the total cost for the Honda will be about $4,500. Not insignificant.

This IS pretty cool

Best. Image. Ever.

My Metropolitans ...

... suck. Which makes Mr. Met sad. I don't like it when Mr. Met is sad.


I blogged a bit back on Le Grand Saut and Michel Fournier who planned on skydiving from 130,000 feet. There seems to have been a bit of a snag.
A French skydiver's hope to set a new free-fall record has been dealt another setback — his ride to the sky left without him.

The helium balloon Michel Fournier, 64, was going to use to soar to the stratosphere detached from the capsule he was going to use to jump from 130,000 feet (40,000 meters).

It happened as the balloon was being inflated on the ground at the airport in North Battleford, Saskatchewan.

The balloon drifted away into the sky without the capsule.

Monday, May 26, 2008

This Memorial Day

Prayer of a Soldier in France

My shoulders ache beneath my pack
(Lie easier, Cross, upon His back).

I march with feet that burn and smart
(Tread, Holy Feet, upon my heart).

Men shout at me who may not speak
(They scourged Thy back and smote Thy cheek).

I may not lift a hand to clear
My eyes of salty drops that sear.

(Then shall my fickle soul forget
Thy agony of Bloody Sweat?)

My rifle hand is stiff and numb
(From Thy pierced palm red rivers come).

Lord, Thou didst suffer more for me
Than all the hosts of land and sea.

So let me render back again
This millionth of Thy gift. Amen.

About Joyce Kilmer (1886 - 1918).
When the United States entered the war, Kilmer went to an officers' training camp, but he soon enlisted as a private in the 7th Regiment of the New York National Guard and later transferred to the 165th Regiment. (He began writing a historical account of his regiment in France, but it was unfinished when he was killed.) Unwilling to take time to undergo officer training, he was proud of his rise to the rank of sergeant. His letters show him to be an earnest and enthusiastic soldier, welcoming new experiences. There is sadness but also acceptance in the declamatory lines of "Rouge Bouquet":

There is on earth no worthier grave
To hold the bodies of the brave
Than this place of pain and pride
Where they nobly fought and nobly died.

His Catholicism and painful wartime experiences combined to produce some of his best verse in "Prayer of a Soldier in France," a poem through which the reader may painfully stagger with Kilmer and Christ along the via dolorosa of World War I:

My shoulders ache beneath my pack
(Lie easier, Cross, upon His back).
I march with feet that burn and smart
(Tread, Holy Feet, upon my heart).
Men shout at me who may not speak
(They scourged Thy back and smote Thy cheek).

Volunteering to take the place of a slain officer during an attack on the hills above the Ourcq, Kilmer went out to scout machine-gun nests. On 30 July 1918, he was found dead with an enemy bullet through his head. For his bravery he was buried beside officers, mentioned in dispatches, and posthumously awarded the Croix de Guerre. He was survived by his wife, Aline (who became a minor poet), and four children.
For all those who have sacrificed their bodies, minds and souls for the ideals of this country, I thank you.

Saturday, May 24, 2008

I thought you'd go to New Mexico ...

... to get away from your allergies. Guess that holds true only if you're not allergic to Wi-Fi.
A group in Santa Fe says the city is discriminating against them because they say that they're allergic to the wireless Internet signal. And now they want Wi-Fi banned from public buildings.
I dunno ... maybe they're onto something.

Friday, May 23, 2008

President Bush ...

... is obviously a fan of Ashleigh Brilliant. Why, just look at one of Mr. Brilliants famous epigrams.

Cheer up! The worst effects of what we're doing won't be felt until after we're all dead.


Probably, but ...

... what happens when they read about the shirt on my blog?

BTW: Despair dot com rocks.

Fold It!

It's a video game (seriously). I received the following brief in my email today.
Seattle, WA, May 8—Howard Hughes Medical Institute (HHMI) researchers at the University of Washington (UW) working in biochemist David Baker's laboratory launched a free online game called "foldit," in which players compete to design proteins. Scientists can then test the proteins to see if they could make viable candidate compounds for new drugs.

Because protein modeling requires trillions of calculations, over 200,000 volunteers have donated their computers' down-time to performing those calculations in a network, called Rosetta@home, developed by Baker's laboratory. The network uses the Monte Carlo technique to find the best fit for all of the parts of a given protein. The volunteers began to believe that if they could help guide their computers, the solutions could be expedited.

Click on the link to look at and/or play Foldit

Taken from their About Foldit page.
Foldit attempts to predict the structure of a protein by taking advantage of humans' puzzle-solving intuitions and having people play competitively to fold the best proteins.

Introducing the ...

... Telectroscope!

Ooooh. Ahhhh.

Note: It's a work of art.


101 Amazing Earth Facts

Seven Minutes of Terror ...

... no, not the seven, uncomfortable minutes you spend sitting with your parents-in-law when your spouse is getting something out of storage from their house. Rather, I'm talking about the landing of the Phoenix project on Mars this Sunday. A little over half (55%) of Mars missions have ended in disaster, so obviously the people at NASA are a bit on edge.

Well, here is to wishing them the best of luck and a successful mission (which includes the landing).

The Phoenix landing site is targeted for the far Northern plains of the Mars, near the northern polar ice cap. Data from the Mars Odyssey spacecraft indicate large quantities of ice in the area, likely in the form of permafrost, either on the surface or just barely underground.

Phoenix is equipped with a robotic arm that can dig down and scoop up some of that ice and dirt, to look for organic chemical evidence that life once existed there, or even still exists now.

"We are not going to be able to answer the final question of 'is there life on Mars,' " said Smith. "We will take the next important step. We'll find out if there's organic material associated with this ice in the polar regions. Ice is a preserver and if there ever were organics on Mars and they got into that ice they will still be there today."

Thursday, May 22, 2008

I blog because ...

... it makes me feel good.
Self-medication may be the reason the blogosphere has taken off. Scientists (and writers) have long known about the therapeutic benefits of writing about personal experiences, thoughts and feelings. But besides serving as a stress-coping mechanism, expressive writing produces many physiological benefits. Research shows that it improves memory and sleep, boosts immune cell activity and reduces viral load in AIDS patients, and even speeds healing after surgery. A study in the February issue of the Oncologist reports that cancer patients who engaged in expressive writing just before treatment felt markedly better, mentally and physically, as compared with patients who did not.

Currently ...

Grizzly Maze - Nick Jans

Rocks of Ages - Stephen J Gould

Listening To
Narrow Stairs - Death Cab for Cutie

Wednesday, May 21, 2008

Another Metropolitan ...

... to eventually be enshrined in the Baseball Hall of Fame?

Former Mets catcher, Mike Piazza retired today.
But I have to say that my time with the Mets wouldn’t have been the same without the greatest fans in the world. One of the hardest moments of my career, was walking off the field at Shea Stadium and saying goodbye. My relationship with you made my time in New York the happiest of my career and for that, I will always be grateful.
Bold emphasis mine, which means hopefully he'll go into the HoF as a Metropolitan, which will double the total number of Metropolitan representatives in the HoF. Especially since the HoF screwed Mets fans when they slapped an Expos cap on Gary Carter's plaque.

At any rate, thanks for the memories Mike.

Tuesday, May 20, 2008

Primum Non Nocere - Part III

Was reading Laelaps recently and came across the following entry entitled Paleontological Profiles : Robert Bakker. It's a good read, at least from my perspective, and an excellent interview conducted by Mr. Brian Switek. Personally, I know I grew up loving dinosaurs, my favorite exhibit "Of All Time" being the dinosaur exhibit in the American Museum of Natural History in New York City. Heck, I fell in love with the place the minute I saw their T. rex on display. I still look at their virtual tours from time to time.

At any rate, the interview seemed to be standard-fare except for the very end when Dr. Bakker dropped what could only be described as a bombshell for most of the ScienceBlogger audience. This part of the interview went as follows:
[Switek] Finally, as someone who works with the "bones of contention" and the fossil record, what do you think about the current controversy surrounding evolution in the United States? How can we do a better job of communicating science to the public?

[Bakker] We dino-scientists have a great responsibility: our subject matter attracts kids better than any other, except rocket-science. What's the greatest enemy of science education in the U.S.?

Militant Creationism?

No way. It's the loud, strident, elitist anti-creationists. The likes of Richard Dawkins and his colleagues.

These shrill uber-Darwinists come across as insultingly dismissive of any and all religious traditions. If you're not an atheist, then you must be illiterate or stupid and, possibly, a danger to yourself and others.

As many commentators have noted, in televised debates, these Darwinists seem devoid of joy or humor, except a haughty delight in looking down their noses. Dawkinsian screeds are sermons to the choir; the message pleases only those already convinced. Dawkins wins no converts from the majority of U.S. parents who still honor a Biblical tradition. Hitchcock is a far better model. He had his battles with skepticism. He did worry that the discovery of Deep Time would upset the good people of his congregation. But Hitchcock could view three thousand years of scriptural tradition and see much of value - and much concordance with Jurassic geology.
Shit storm ensued. While a few agreed with his comments, a whole heck of a lot did not.

Mr. Switek, in response to the hullabaloo, wrote back to Dr. Bakker and received a reply which he recently posted.

Personally, I commend Dr. Bakker. I think he's done a good job summarizing everything I think is wrong with how the vocal minority go about the defense of science. Once again, there were a few who definitely were not happy (Though, in this blog entry PZ Myers goes after both the original interview, approximately a month after it occurred, and the latest reply). Yet again, his readership froths at the mouth. This gem here by Etha Williams is one of my favorites.
Well, what other option is available for a theistic scientist? Either you have to distort reality and logic (creationists) or just compartmentalize and ignore reality and logic when thinking about religion (Bakker, Ken Miller, etc). Or you could just stop wasting mental energy trying to defend indefensible notions....
I like the false dichotomy she puts forth. Either you fully accept the truth and become an atheist, with the implication that you can then become a good scientist, or you're faced with two options. You can either ignore logic if you're a creationist, or you can compartmentalize. Either way, I believe the implication is there that theists really don't make good scientists. Her comment wasn't the first along that line in the comment section of that blog entry, and it certainly wasn't the last.

Religion As A Litmus Test?

Etha Williams boneheaded comments are typical of what you see in the commentary section of Pharyngula. She's even been bestowed an award by PZ Myers for her "excellent commentary" on his blog entries (which I think is more of an indictment of his blog than it is a testament). I don't know if I should be relieved that a lot of these comments seem to be made by people who don't have advanced degrees in the sciences (which appears to include the excitable Ms. Williams), or if that should concern me. At least under these circumstances we can attribute them to ignorance and the indiscretions of youth. However I do believe these reactionary diatribes do not bode well for future discussion between scientists and the laity. If this is what is to be expected, I'd say it's an alarming trend. It is also exactly this sort of "militant atheism" which Dr. Bakker was talking about. Nevermind that Dr. Bakker has probably done more for the advancement of science than Etha Williams and her ilk have done, or may ever do. The fact that he dared criticize them, and the fact that he's Christian, was enough to set off a series of shotgun blasts in the direction of religion in general. There were few criticisms of Dr. Bakker, there were more criticisms of religion in general. How the two must be inextricably intertwined is beyond me.

Nevermind the fact that since science never sets out to prove the existence (or non-existence) of a God or gods, one has to wonder exactly who is defending indefensible positions. Religion is a matter of faith. If you don't have that faith you're probably at a minimum an agnostic, or an atheist. If you do have that faith, you're probably at a minimum a deist, or more likely a theist. That faith however, is pretty much inconsequential when it comes to the proper practice of science. I believe Stephen J. Gould's Nonoverlapping Magesteria is in effect. For those wishing to get their heads out of their asses on these matters, I would recommend the National Academy of Sciences 1999 publication entitled Science and Creationism.

But what do we have instead? We have Creationists claiming that evolution is a farce, and instead of science claiming that evolution really doesn't have anything to say about the Bible, we have a few loud and vocal members of the community (who happen to be atheists) saying that people who adhere to religion are stupid. So much for addressing the actual issue head on folks! To make matters even better, some go so far as to say that religion should be eliminated. And then we wonder why Creationists have essentially waged war on evolution specifically, and on science in general? It's because some members of the scientific community developed verbal diarrhea and their vacuous clones ran off at the mouth as well.

Not only is this indicative of the lost opportunities that science has had to discuss matters with non-scientists, it is also a lost opportunity for those who have come under criticism to reassess their approach. Instead of taking Dr. Bakker's comments under consideration, they were summarily dismissed and the man was attacked instead. What a waste, what a shame. If members of the scientific community can't be expected to keep a level head in the face of opposition (whether that be data, ideas or opinions) who can we expect to keep a level head?

Monday, May 19, 2008

Peel-N-Stick ...

... Solar Panels.
On the residential front, Lumeta plans what the company calls Solar S Tiles. These tiles, which will cost on average between $25,000 and $35,000 for a total system, are made to look like tiles found on concrete and clay roofs. Government subsidies will cover about one-third of the cost, according to Lumeta.

Bacterial Farts - Part Deux

In the comments section of previous blog entry of the same name, Blake asked:
Fantastic! The GM article points me in the direction of the next question on my mind, i.e. to what extent can this technique replace current consumption. It looks like a significant source already; could it become a primary source, largely or even completely replacing diminishing mined reserves?
Answer: It would depend on what you mean by "primary source". According to the EPA's Landfill Methane Outreach Program (LMOP), a total of 445 landfill programs were active in 2007. They generated 11 billion kilowatt-hours of electricity per year. They also delivered 236 million cubic feet/day of usable gas for direct consumpion (I'm assuming mostly for heating and cooking). According to the DOE, in 2001 the United States consumed 1,140 billion kWh (kilowatt hours) of electricity. One can only assume that energy consumption has increased over the last half a decade. If we take those numbers however at face value, it appears that landfill gas (LFG) currently supplies ~1% of the electricity for US consumption. What is also important to know is that the number of facilities collecting LFG is set to double in the near future. So in the immediate future, ~2% of our electricity will be provided by methane (natural gas) produced by landfills. I'd consider that substantial. I also doubt that that accounts for every major landfill in the country. Also, according to PowerScoreCard, ~40% of LFG is produced by landfills which don't fall under EPA guidelines given their small size. If the proper infrastructure was put in place at all landfills (currently, large landfills must flare (burn) the methane so the wells have already been drilled), I would think that it might be possible to see LFG account for between 5% (reasonably) and ~10% (best case scenario) of our electricity. We might not think of, under those circumstances, calling LFG a "primary source" but it'd definitely be a significant source.

That's not even considering methane produced by anaerobic digestion from municipal waste projects.

According to the California Energy Commission, anaerobic digestion from their cows could result in ~1.25 kWh per cow per day. If I'm doing my math right: At average kWh/year usage rates (10,000 kWh/year/family), California's cows (all 1.2 million of them) would be able to provide electricity to ~55,000 families/homes. (For reference: In 2004, there were ~96 million cattle and calves in the United States.) If you take the swine numbers from California (~0.33 kWh per pig per day) and apply them to North Carolina (which is home to over 10 million swine) you'd be able to provide electricity to ~120,000 homes a year (~3% of North Carolina homes). And we haven't even touched on anaerobic digestion from municipal waste ... and with over 300 million individuals, there is a lot of waste which is generated. Whether the non-fecal waste would be best suited to be sent to a landfill, or used as a feedstock for direct anaerobic digestion would need to be determined (it may have already, but I'd need to look).

Couple these with solar and nuclear, as well as (where applicable) geothermal and wind, and I'd say we could drop dramatically our need to use fossil-fuels for heat and power purposes.

The other issue is energy consumption. According to an article by Salon, vampiric energy consumption results in ~5 to 8% of our energy consumption per year. That is obscene. So not only do we need to look for (and apply) alternative energy sources, we need to be mindful of electrical usage, and insist on new appliances/devices being energy friendly. If we do this, I can honestly say that I can envision non-fossil fuel sources making up the major portion of our electrical supply by the time the next generation is faced with this issue.

The questions now are: Are we willing to pony up for the changes in infrastructure? Can we be innovative enough to cut those costs? Can we come up with even better technologies to make these processes more efficient?

Saturday, May 17, 2008

Planet Earth

Just rented Planet Earth, the BBC Documentary, from Netflix. The version Netflix sent me has David Attenborough as narrator.

Watched the first episode From Pole to Pole with the wife last night, and I've got to say, it looks like it's going to be a great series. I'm impressed with the photography, which was done in part with a heligimbal. With this camera, they were able to take shots from over 1.5 km (almost a mile) away, which is damn impressive ... especially when you see the shots. I might be extremely late to this party, but if you haven't seen this series yet ... I'd highly recommend it.

Friday, May 16, 2008

Primum Non Nocere - Part II

Was reading my copy of Microbe, which is put out by The American Society of Microbiology (ASM), yesterday and came across this article by Bernard Dixon. It's entitled "Questionable Experiments" and leads off as follows:
Imagine that you understand little or nothing about microorganisms, genetic modification, toxins in the natural world, or the biological control of plant pests. Now consider the following. A scientist tells you that he has been breeding venomous scorpion spiders in his laboratory. He’s also been cultivating some extremely infectious microbes, and he plans to alter them genetically so that they produce the same potent poison as the scorpion. The poison is called a neurotoxin because it attacks nerve cells, causing paralysis and death. The scientist now plans to produce astronomical numbers of his mutant microbes and release them in the countryside.
A lot of lay people would freak out. The reason being, they're not trained in the practices and principles which guide scientific research. They don't know about the safeguards which are put into place, and while they might be told about them, they can't relate to them. Sometimes they can't judge between what is safe practice and what they should be rightly leery of. It also doesn't help that with just about any scientific finding, there are going to be people who object to it. Unfortunately, a vocal few are of the "conspiracy theory" type and they will do their best to convince people that such research endeavors are dangerous, impractical, and will ... if allowed to continue ... tear at the very fabric of society, killing children, ruining crops, allowing millions to starve, etc etc.

In fact, the exact opposite will most likely be the result.

People can be naive, and if something is presented to them in a coherent and cogent form, they'll take it at face value. It's the first impression, and it takes a lot of effort to persuade someone that that impression was wrong. Which is why it's important that the scientist be there to give that first impression. If a "conspiracy theorist" (e.g., an anti-vaccine type) gets there ... woe be to science. Getting the fear out of that lay individual will be a nearly impossible task. I imagine there are a lot of reasons for that, but by and large it's rather simple, people don't want to consider the fact that they've been duped. If they admit that for one idea, they have to consider it for others. Sometimes it's just too hard to accept. This is why people fall for scams, and when they finally figure it out, rarely go for help. It's bad enough that they've been duped, they don't want to let others know about it too.

So, after they've adopted that first impression, they're probably not going to come to you (the scientist) for clarification. Especially after they've been warned that you're the source for current and/or future potential problems.

What can be done? Well, I think a lot can be done. Scientists need to be active in the community, they need to be active on the internet. Putting a face to a name is essential for proper and effective communication. Touch base with people who might be considered "customers". For example, if you work with swine pathogens, are you talking to the National Pork Producers Council? Are you speaking with local swine producers? It's not enough to be holed up in the lab thinking that your ideas will help advance science and eventually help people. You need to let people know what you're doing, and how it might eventually impact their lives for the better. In my experiences, while most people may not understand the principles behind molecular biology and/or microbiology (or any other science they're not trained in), they can understand the story the research tells. As long as the storyteller (i.e., the scientist) takes the time to explain it. Unfortunately, this is seen as a burden (for reasons which are unknown to me, since 99% of the scientists I know love to talk about themselves, and as an extension ... their research, if you give them an opening).

What is the current face of science? From my vantage point, at least in the biological realm, it's dominated by people who, while brilliant, are not necessarily in-tune with the rest of society. They take antagonistic approaches (ala P.Z. Myers and Dawkins) to beliefs held dear by the majority (e.g., religion for example), which is going to automatically result in that portion of society tuning them out. Where is the connection between these scientists, in their ivory towers, and everyone else? I don't see it.

A lot of work needs to be done to bring good scientific discussion to the dinner table. Unfortunately, I think it's a skill which isn't taught to scientists, and in this, the Age of Instant Information (Some of Which may not be True), it is a skill which is very much in demand. If we don't fill in the blanks for people, someone else will ... and it may not be filled the way we want it to be, or the way it needs to be.

Thursday, May 15, 2008

Much to my support scientists horror ...

... I'll be spending my day working in the lab. So, no more posts for today. Enjoy the wallpaper instead.

What the floc?

ResearchBlogging.orgIf you ever deal with wastewater, you'll notice that there are small bits of particulate matter floating in it. I'm not going to go into the gory details of what a portion of that matter is because I think your imagination can do a pretty good job of figuring it out on its own.

However, a substantial portion of this matter is bacterial in nature. Some bacteria are free-floating, in that they don't adhere to other bacteria and exist in the environment independently. Others aren't so happy doing things that way, and they form films and flocculants to keep their communities together.

One such example is Comamonas badia. He's the little guy with the "tail" (referred to as a flagellum) on the left. The manuscript cited in this post characterizes this organism, specifically the strain IAM 14839, which was isolated from activated sludge in Japan. Activated sludge is the biological material found in wastewater treatment facilities. It's biomass, and is used in the treatment of raw sewage.

This paper is fairly straightforward. They isolated the organism from a floc and did some basic biochemical studies. First, they Gram-stained it, and demonstrated it is Gram-negative. It was catalase and oxidase positive.

The authors then did fatty acid analysis, which is one way to "fingerprint" bacteria. They also did 16S analysis, which is another way to "fingerprint" bacteria, and this placed the organism in with the genus Comamonas. However, this is the only known strain of Comamonas which can form floc (we've recently isolated similar strains in our laboratory).

So, what?

There may be practical purposes for wanting to use floc-forming Comamonas strains in wastewater treatment. For example, Nitrosomonas species do not like growing in a free-floating (planktonic) form. They would much rather grow adhered to something, anything. This is why Nitrosomonas cultures are typically grown on fine sand or some other surface. It might be possible to use floc-forming Comamonas strains as a platform for culturing specific Nitrosomonas strains for use in wastewater treatment.

BTW: If you're curious as to what a flocculant culture looks like, here is one to the left. This is a culture which does contain both Nitrosomonas and Comamonas. How the two interact with each other is not currently known, but we're in the process of figuring that out.

Tago, Y., Yokota, A. (2004). Comamonas badia sp. nov., a floc-forming bacterium isolated from activated sludge. Journal of General and Applied Microbiology, 50(5), 243-248. Click here for PDF of article.

Wednesday, May 14, 2008

Bacterial Farts

New Scientist Bloggers write about how we should be more worried about methane than we should be about carbon dioxide.

From the blog:
Methane is a potent greenhouse gas, warming the planet 25 times more, molecule-for-molecule, than CO2. It doesn't last as long in the atmosphere, which tempers its kick, but it's still enough to give you nightmares.

As Fred Pearce has reported, thawing Arctic permafrost could give off massive amounts of methane, which would warm the planet. Permafrost is basically frozen mud, and when it thaws, microbes start chewing it up, emitting both methane and CO2, the amounts depending on the temperature, how wet it is, and other factors.
If you want to track methane levels, you can click here on the NOAA link. To choose methane, under "Gas" select CH4.

Methane is produced by methanogens (methano - methane, gen - birth/generate), bacteria which generate methane as a metabolic byproduct. They're found in nature where there isn't much air (i.e., anaerobic conditions) and different types produce methane from different sources. Some use carbon dioxide to produce methane, others use longer chain carbon sources.

These are the same bugs used in anaerobic digestion to make methane that, when cleaned up, can be used as natural gas ... so they're definitely useful and can be used for practical applications.

Have I mentioned lately that I hate ...

... netspeak? My skin crawls everytime I see LOL, ROFL, LMAO and TTFN. I mean, who the hell says "ta ta for now" anyways? It's even easier to write "Bye". No? Jimminy Christmas.

And don't even get me started on lolspeak and lolcats. These two things alone are reason enough to want to eliminate every feline on planet Earth.

Catholic Church says ...

... believing in extraterrestrial life would not contradict Christian thought.

As reported in L'Osservatore Romano, the official newspaper of the Vatican. The article isn't online yet (they appear to be a week behind), but MSNBC has a blurb on the comments by the director of the Vatican Observatory, Rev. Jose Gabriel Funes, SJ*. His thought, as far as the Catholic Church is concerned, all life is the work of the Creator, so it'd be fine. Of course, there is the problem of Jesus' sacrifice for our redemption. If alien life happened to be similar in attitude and behavior (what Christians would term "sinful") and they have no record of ever having religion or a redemption story ... for me, that'd be a big problem. I'm sure it's obvious why.

Of course, Mark Shea, he of Catholic apologist fame, has a much different take on it.

*SJ stands for Society of Jesus, aka Jesuits.

Tuesday, May 13, 2008

As a (micro)biologist ...

... it's always cool when you get to name something.
A biologist has named a newly discovered trapdoor spider after rock star Neil Young: Myrmekiaphila neilyoungi.
For microbiologists it's identifying and naming a new microorganism. For molecular biologists, it's naming a new gene. Unfortunately, the gene designation fucK has already been taken (fuculose kinase).

I missed this ...

... but agree with it wholeheartedly. So I'll link to it now: Why the PZ Myers Affair is Really, Really Bad for Science.
The simplistic and unscientific claim that more knowledge leads to less religion might be the particular delusion of Dawkins, Myers, and many others, but it is by no means the official position of science, though they often implicitly claim to speak for science. Nor does it stand up to mounds of empirical evidence about the complex relationship between science literacy and public perceptions.
... and ...
As long as Dawkins and PZ continue to be the representative voices from the pro-science side in this debate, it is really bad for those of us who care about promoting public trust in science and science education.
What more needs to be said? Science needs to stick to talking about science, not insulting religion or working people (atheist and theist alike) into a frenzy.

Progress on CCD ...

... Colony Collapse Disorder. Honey bees are a big deal, there are dozens of crops which rely on pollination. If you like apples, oranges, and peaches ... you can thank honey bees. If you like broccoli, carrots, and eggplant ... you can thank honey bees. They're handy little workers, and obviously big business. So a lot of effort is being taken to figure out what the deuce is going on (explained in the first link above). In the meantime, other efforts are being undertaken to provide pollination alternatives. Blue bottle flies as effective pollinators? You better believe it.

Panties In A Wad Alert!

Drama reigns supreme here! And I quote:
That is simply insane. It's a declaration that religion trumps everything, and gives students an escape hatch from learning — biology class would become an exercise in futility, in which lazy, stupid, or religiously indoctrinated students would simply parrot the book of genesis at their instructors, and expect to be given a good grade.
Fortunately, cooler heads prevail here, here, and here. And of course, as of this moment, they're being ignored. Instead, the masses allow themselves to be whipped into a frenzy over basically a non-issue.

What do I think about the issue? I think Rep. Kern should find something more important to do, but that's the way it is with state politics. The only thing Oklahoma has been able to do in the last several years, as a state legislature, AFAIK is institute a tax on the poor (i.e., lottery). Oklahoma has been renowned for their corruption and incompetence at the state level, which is probably why they can't get big business into the state. As a consequence, they rank in the bottom 10 in every category of note. And yes, I spent several years in Oklahoma, attending graduate school, so I know what I'm talking about. I think this bit of legislature is stupid, and I think Rep. Kern is stupid for continually trying to push it through. I think it'll get shot down again.

The other unfortunate effect is that I think it paints theists in a bad light, as if they're all quacks. They're not. I don't think this issue rises to the level of needing to get your knickers in a twist, like a lot of people want. Maybe they miss the days of their youth where they got picked on as kids and received wedgies from the "cool kids", only now they get to rant and rave and "do something about it". I don't know.

An interesting effect of rising gas prices ...

... old-fashioned gas pumps, can't handle the increase.
Mom-and-pop service stations are running into a problem as gasoline marches toward $4 a gallon: Thousands of old-fashioned pumps can't register more than $3.99 on their spinning mechanical dials.

The pumps, throwbacks to a bygone era on the American road, are difficult and expensive to upgrade, and replacing them is often out of the question for station owners who are still just scraping by.

Many of the same pumps can only count up to $99.99 for the total sale, preventing owners of some SUVs, vans, trucks and tractor-trailers to fill their tanks all the way.
Bummer! Guess that means that gas prices won't be allowed to go over $3.99. Right? Yah, I wish.

Monday, May 12, 2008

An update on the E-Fueler ...

... that I spoke about a couple of weeks ago. Here is a CNET article, with a picture of the entire machine, which is surprisingly not too large. One of those could fit at the side of your driveway if you so desired.

Can you Dig It?

Sure, The Warriors is one of the best movies ever, but I'm not talking about that at the moment. I'm talking about Dig It! The Secrets of Soil the Smithsonian Institute collaboration with the Soil Science Society of America. According to the webpage, it is described as follows:
The Soil Science Society of America (SSSA) is working with the Smithsonian's National Museum of Natural History in Washington, DC, to plan a soils exhibition entitled Dig It! The Secrets of Soil as part of their Forces of Change Program. The exhibition will include a display of state soil monoliths and educational, interactive sections to help the museum's more than six million visitors a year understand how soil is intricately linked to the health of humanity, the environment and the planet.
The main element of the exhibition will be at the National Museum of Natural History, where:
A soil monolith from each state, territory, and the District of Columbia will be displayed. Interactive stations include soil texture, color and parent materials, and the distribution of soils in the U.S. Models show water, nutrient, and gas movement in soil and relate soils to our daily activities. This 1.5 year interactive exhibition of 5,000 square ft will explain soils to 6 million museum visitors.
After the run at the MOHN, it will tour the country.

It's the right place ...

... just a different name. I've changed the name of this blog to "(It's a ...) Micro World (... afterall)" from Bio-Fuel!. Partly because I wanted to expand my base (even though I maintained such a disclaimer clause on my original blog) of topics, and partly because I liked the new title I had come up with a couple of weeks ago. The focus will remain pretty much the same, bioenergy discussion will be part of the primary focus, but I wanted to get more in the agricultural/environmental microbiology aspect of things. As far as I am aware, there is very little of that, so I fill a niche which may (or may not) need filling.

BTW: Is my new logo snazzy or lame? Trying to find a good globe (to make the "o" in Micro) was a bit of a pain.

Build a pond ...

... and help cut down on global warming.
Research led by Iowa State University limnologist, or lake scientist, John Downing finds that ponds around the globe could absorb as much carbon as the world's oceans.

Professor Downing found that constructed ponds and lakes on farmland in the United States bury carbon at a much higher rate than expected; as much as 20-50 times the rate at which trees trap carbon. In addition, ponds were found to take up carbon at a higher rate than larger lakes.
According to this report, the two major ways that carbon is stored in ponds is by runoff from the surrounding soil (which contains carbon - in the form of decomposing plant material), and from algae and other aquatic plants which use carbon dioxide for photosynthesis.

Friday, May 09, 2008

You too can understand science talk ...

... by grasping the meaning of the prefixes and suffixes commonly used by individuals in science.

I have used and explained several of them recently in this blog, but we'll go over them again, as well as a few others.

Yesterday I spoke about the Acidobacteria. Sometimes just looking at the word can reveal a clue as to the physical capabilities of the organism in question. As indicated, Acidobacteria fare extremely well in acidic conditions (pH's under 7.0). They are what is known as acidophilic.

Acido/philic (adjective)
Acido- = acid
-philic = loving

Acidophilic = Acid loving (i.e., they prefer to grow in acidic conditions).

So, acidophilic is an adjective. The noun would be acidophile.

Alkalo/philic (adjective)
Alkalo- = alkaline (basic solution, pH above 7.0)
-philic = loving

Alkalophilic = Alkaline loving (i.e., they prefer to grow in alkaline conditions). The noun is alkalophile.

What are some other words:
aero- = involving air (e.g., aerobic)
an- = without (if we couple an- with aero- we get anaerobic which means lacking air)
anti- = against
bi- = two (e.g., biphasic means two phases)
di- = two
-phobic = fearing (e.g., acidophobic means fear of acid)
pseudo- = false (e.g., pseudogene)
psychro- = cold (e.g., psychrophilic means cold loving)
-phore = carry (see next)
sidero- = iron (e.g., siderophore means an iron carrying molecule)
therm- = heat (e.g., thermophilic means heat loving)

So, that's a few examples, and how some of them work together to give us common terms used in microbiology. A lot of these prefixes and suffixes have Greek and Latin roots. A book I first used, at least a decade ago, was compiled by Gylys and Wedding entitled Medical Terminology: A systems approach. You can find early editions of this text at places like Abe Books for cheap (by cheap I mean $1).

Koalas affected by climate change ...

Read the Science Daily article here.

From the article:
Professor Hume's group have shown in the laboratory that increases in CO2 affect the level of nutrients and 'anti-nutrients' (things that are either toxic or interfere with the digestion of nutrients) in eucalypt leaves. Anti-nutrients in eucalypts are built from carbon and an increase in carbon dioxide levels will favour the production of anti-nutrients over nutrients.
Biology is sometimes very finicky. Just because humans are capable of adapting to wide changes in environmental conditions doesn't mean other species can as well. I think a lot of people don't contemplate that reality.

Thursday, May 08, 2008

Ethanol in the tank ...

Ethanol producers hurting. Big time.
While environmentalists have warned that the rapid growth of ethanol posed a danger to sustainability, the alarm may be somewhat misplaced. Oil has topped $122 a barrel and could be heading to $150. But the ethanol bubble has already popped. The recent poor results from ethanol producers is far more likely to hinder further development than any change in government policy.
Well, it was fun while it lasted, no?

That sure was quick.


The Acidobacteria are an order of bacteria which are found in abundance in soils. In some soils they can be as much as 30% to 50% of the identifiable bacterial species. As the name suggests, they're acidophilic (acid loving). This order is a relatively new player in the Bacteria kingdom. We often find 16S rDNA Acidobacteria sequences when we do our sampling. I'm attaching a phylogenetic tree of one such study. Each branch of the tree (separated by differently colored boxes) indicates a different Acidobacteriaceae genus.

These microbes have proven difficult to culture, however there are cases of it occurring. It is believed that these microbes may be able to play a role in bioremediation.

The platypus (Ornithorhynchus anatinus) is one odd duck ...

... or maybe that's "one odd reptile", or "one odd marsupial"? Who the heck knows? Well, we all do now, thanks to the genome of the platypus being sequenced. First link is to a New Scientist article, the second is to a commentary by Nature magazine where the peer-reviewed manuscript is located.

Taken from the conclusion of the manuscript:
Since its initial description, the platypus has stood out as a species with a blend of reptilian and mammalian features, which is a characteristic that penetrates to the level of the genome sequence. The density and distribution of repetitive sequence, for example, reflects this fact. The high frequency of interspersed repeats in the platypus genome, although typical for mammalian genomes, is in contrast with the observed mean microsatellite coverage, which appears more reptilian. Additionally, the correlation of parent-of-origin-specific expression patterns in regions of reduced interspersed repeats in the platypus suggests that the evolution of imprinting in therians is linked to the accumulation of repetitive elements.

Translation: The platypus is obviously a mammal, but they are mammals which are much more primitive than just about every other mammalian species known to exist today, with the lone exception of the spiny anteater (echidna). Studying the genome of the platypus will give us important clues as to how the other mammals evolved.

Lock 'em up and throw away the key ...

... disgusting, simply disgusting.
But in a rare example of an attack apparently motivated by malice rather than money, hackers recently bombarded the Epilepsy Foundation's Web site with hundreds of pictures and links to pages with rapidly flashing images.

The breach triggered severe migraines and near-seizure reactions in some site visitors who viewed the images. People with photosensitive epilepsy can get seizures when they're exposed to flickering images, a response also caused by some video games and cartoons.

You have to be a total waste product to even think about doing something like this. I hope the FBI catches them and punishes them to the full extent of the law.

Wednesday, May 07, 2008

Science Czar

Why something to this effect isn't a Cabinet Level position, I'm not sure ... but perhaps it should be.

Newsflash: Bioethanol Still Bad Idea

According to this article at least.
Indeed, many livestock operations are getting hit with a double whammy. First, they’re paying more for each ton of corn-derived feed. At least as importantly, a new study finds, the corn product that’s they're feeding to their animals can be anticipated to carry triple the normal load of fungal toxins.

Because those fungal poisons — or mycotoxins — threaten the health of animals, farmers can look for reduced livestock growth, especially in swine.

The new analysis conservatively estimates the current cost to U.S. hog producers from just one of those toxins, fumonisin, at about $9 million a year.

Personal Genome Scans

Don't count me as one of the people who'll opt for this type of service, though $1,000 isn't all that much to have it done.
Navigenics, 23andMe and deCODE specify that customers own their personal data. But executives keep the door open to use their growing databases for research with commercial or nonprofit partners. Such studies should take place under research protocols, not as an outgrowth of consumer marketing, the CDC’s Khoury argues. For now, he says, the best tool available to personalize medicine is low tech and low cost: family health history.

So we'll move from companies selling your personal information like addresses, phone numbers and the like to selling your genotype. Not for me.

I'm happy ... or am I?

Liberals Miserable, Conservatives Overjoyed.

Honestly, I just think Conservatives are happy right now because they're watching the Liberals rip themselves apart in the Democratic Party Primaries right now. Get that damn thing over and done with!

My question is, where do the moderates fit into this?

Q: Is your glass half empty or half full?
A: It's 50% water, 50% air.

I can relate ...

Compliments of PhDComics.

Tuesday, May 06, 2008

Isolation Is Fun!

I'm not talking about sitting in a locked room for days upon days, I'm talking about isolating bacteria! Bacteria are everywhere, and depending on where you're considering, they're different from each other. On your skin alone, there are a multitude of different types of bacteria. These bacteria also differ from the bacteria in your mouth, which differ from the ones which are in your gut. Depending on the type of bacteria you're trying to study, you'll need to use different media (either liquid or solid) that you'll use to grow your organism on/in, grow it in the presence of oxygen (aerobic) or not (anaerobic), and supply it with different carbon and nitrogen sources, as well as additional nutrients (Ca, Fe, K, Mg, Mn, etc etc).

Different organisms respond to different culturing methods, and these methods can be exploited by the microbiologist to select for certain types of bacteria. In essence, you're "dissuading" a certain type of bacteria from growing, which allows the others to grow relatively uninhibited. That's what I'm doing today.

I have identified the major players in a bacterial community that we're really interested in, for use in agricultural applications (mainly to remediate animal waste). Now I'm trying to isolate them from each other so we can study them on their own. Now, we might not be able to grow each one of them, but I'd like to isolate at least the ones that are found the most abundantly in the system. Today, I start with a Halomonad. Given the name, these organisms typically like growing in conditions which have higher than normal salt conditions (halophilic - which means "salt loving" as opposed to halophobic which means "salt fearing"). Not all organisms can tolerate such conditions, so we'll use that to our advantage. So what we'll do is make up media containing a range of salt (NaCl) concentrations and plate out some of our bacterial containing solution. If all goes well, only the identified Halomonas strain will grow.

Afraid Of Heights?

This guy obviously isn't. Best of luck to him. He goes in approximately 18 days.

Le Grand Saut.

Viral Outbreak In China Ahead Of Olympcs

Article here.
Although the outbreak is another headache for China's Communist government as it prepares to host this summer's Olympic Games, WHO's China representative, Hans Troedsson, said the disease was not a threat to the Beijing Olympics because the disease mostly sickens young children.

It mostly sickens children, so the Olympians will be safe. Well thank God for that! Sheesh.


Article here.
More than 100 hours of classic footage from NASA's Mercury, Gemini and Apollo space missions have been restored for high-definition television — and will be made available to the world through the space agency's archives.

Can't wait to see them.

Monday, May 05, 2008

It rained today ...

... so no biking into work. That was a good thing because I had to lug two textbooks, the 1293 page Manual of Environmental Microbiology and the 1069 page Methods for General and Molecular Microbiology from home. I don't think I would have made it if I had to bike to work. BTW, the Manual of Env Micro is an excellent resource.

Primum non nocere - Part I

Translated: First, do no harm.

For those involved in the many scientific disciplines, this is a phrase which should be considered throughout the facets of their professional (and personal) lives. Earlier I mentioned that scientists need to behave responsibly when communicating with the layman because, like it or not, they represent science and scientists in toto. Act irresponsibly, and you tarnish the rest of us. Now, I'm sure that some people will take the Charles Barkley line of defense (i.e., "I'm no role model") and claim that each individual (and their message) should be judged on their own merits ... but we all know that doesn't happen. Never mind that some of the very people taking up this defense probably tend to lump groups of people into convenient, broad brush categories themselves.

Doing harm can come in many forms, but they all have the same outcome - that being, they serve to turn off the individual who is confused, disparaged, insulted or otherwise offended. How does it happen? It happens by talking over the audience, refusing to acknowledge non-scientist inquiries, open mocking of certain groups, and through insults and harassment of opinions and people holding them. I doubt this list is comprehensive, but I think my point is clear. Some people grasp these facts, others do not.

Case in point: Science Blogs. (Well, there goes my invite). I've taken to reading as many of the 71 blogs there as time permits, I stop to leave comments where appropriate, and I truly enjoy a number of them. I think denialism is a great read, and I also enjoy Not Exactly Rocket Science, particularly because Ed Yong spends a lot of time using Research Blogging. As scientists, I believe we need to be cognizant of the fact that our duties don't stop at the edge of the lab bench. That data needs to be interpreted and made known to society. And the thing is, 99.9999999% (a rough estimate) of the population are non-experts in the field we're reporting on. So, part of our role is making sure that we can distill down the important points and give it in digestible chunks for the layman. A lot of blogs do that, and to that end, I think they do the scientific disciplines a great service. The more people are informed the better their ability to grasp the importance of the work, and thusly, the more likely they are to support those efforts (in terms of policy and public funding).

But then, there is the opposite side of the spectrum. These blogs are, IMO, more noise than actual content. They're more screed than treatise. It's almost ironic that one of the entries of the linked blog (on May 4, 2008) was this one, lamenting that television programming devotes so little time to factually representing science. In the meantime, this same individual is taking pot shots at religion, here, and here, and here, and ... well, you get my point. And when he is talking about science, which he admittedly does well, he can't avoid putting in that last jab. And while I don't have the exact site statistics, judging by the numbers of comments left behind in his posts, I'd surmise his blog is one of the (if not the) most visited blogs on the site. So one must ask, what good results from this sort of screed? Other than the fact that he manages to insult a large portion of the members of American society ... the very people who pay the taxes which contribute to his research funding (if he has public sources of funding that is) ... I can't see what good can come of him professing that this is a scientific blog. It is this very type of screed which no doubt led to his being manipulated by Ben Stein. He got suckered because he has a big mouth, and can't keep it shut ... and because of that, the rest of us have to mop up his verbal diarrhea.

In my time doing research, I have found that people, regardless of political or religious affiliation, are more than willing to help you do your research and therefore develop applications which can benefit everyone. I try very hard to put a face to a name, for both their benefit and mine. When you establish that rapport (which for me isn't the most comfortable thing I have to do, being an introvert), you open a number of doors for the betterment of your own scientific program. I don't bite the hand that feeds me, I don't insult someone just because I have a platform to do so, and dozens of people will laud me for it. What exactly would it achieve?

As a microbiologist who currently studies microbial population structures in agriculture, I study microbial relationships which have obviously developed over long periods of time. I am constantly constructing phylogenetic trees ... plotting the evolutionary history of the organisms I am using to develop applications for advanced agriculture. My customers, none of whom are geneticists or microbiologists and who'd I guess are mostly evangelical Christians given my location (and probably have a dim view of evolution, and a probably even lesser understanding of it), see this and don't raise a fuss. They know I'm here to see to their problems and recommend solutions to it. I don't go around insulting their religious beliefs because I know that to do so would only make my life harder. If you don't want to get jabbed by the horns, don't poke the bull with a stick! It's as simple as that. And in the end, when they need to understand evolution, my hope is that they'll remember their discussions with me and they'll come to me for a way to understand it. This way, everyone wins.

Unfortunately, most people remember the bad. Probably because the bad is sexy ... everyone loves looking at the train wreck. Bad news and drama sell. Unfortunately, drama is the last thing scientists should be feeding into. Alas, not everyone feels this way and as a consequence they wind up harming us all.

Flu Epidemic? Stay at home ...

... but not for the reasons you might be thinking about.
To prepare, hospitals should designate a triage team with the Godlike task of deciding who will and who won't get lifesaving care, the task force wrote. Those out of luck are the people at high risk of death and a slim chance of long-term survival. But the recommendations get much more specific, and include:

* People older than 85
* Those with severe trauma, which could include critical injuries from car crashes and shootings.
* Severely burned patients older than 60.
* Those with severe mental impairment, which could include advanced Alzheimer's disease.
* Those with a severe chronic disease, such as advanced heart failure, lung disease or poorly controlled diabetes.

You wouldn't want to get into a car accident and get triaged if you get the flu.

The little ones ...

Recently I was extended an offer to give a science talk to a few classes of elementary school children, an offer which I accepted. A couple of weeks ago, I gave that talk and I must admit that it gave me hope for the future. The kids were well behaved, they were interested, they were intelligent. I spoke about energy and how it affects our lives, and what science is doing to help address the problems these kids hear their parents complaining about at the dinner table at night. The talk wasn't very complex, I didn't get into intricate microbial pathways. Rather, I laid out the basic premises and goals of not only my own research, but the goals and visions of my organization as well. I went in with a "Here is the problem, and here is how my research is going to help all of us."

Unfortunately, I think that message is lost on a lot of scientists. I read blog after angry blog, of scientists railing about stupid laypeople. They mock, they taunt, they openly insult. All of which results in deafening the general public to the good work that scientists do, day after day. However, this is a topic for another day. I'm going to do at least one entry on scientists and their responsibility to inform the public.

So back to the discussion at hand. I was pleased to see that the children ate up my presentation. We had a lengthy Q&A afterwards as well, where I got on the teachers good side by pointing out how a well-rounded education would help them achieve their eventual career goals as well. What floored me the most though was one question asked by one of the students when he asked: Dr. TomJoe, what's the difference in factors between the energy crisis of the Carter administration and the current energy crisis? This kid wasn't any older than 13 years of age, and he asked a question you'd expect from someone much older than him. Heck, you won't find this question being asked by many adults ... yet there he was. If this child can be that inquisitive, and that adept at asking a very important question ... I hope that he will be typical of the future generations. It is our obligation as teachers (for science doesn't stop at the bench) to foster these traits.

Sunday, May 04, 2008

The Nitrogen Cycle

ResearchBlogging.orgThis is my first attempt at using Research Blogging, hope I don't mess this up.

At any rate I've been reading a number of articles, for a paper I'm putting together, and I came across this review which I think is pretty good. It goes over the nitrogen cycle, of which I'm primarily concerned with nitrification and denitrification. Nitrification is the biological degradation of ammonia to nitrite and nitrates. Denitification takes nitrite and nitrate and reduces it to (hopefully) dinitrogen gas. I've illustrated (and simplified) the process in the following diagram. I'll also explain the "hopefully" comment towards the end of this entry.

Nitrification, since it is an oxidation reaction, requires oxygen (as one would surmise). Denitrification typically occurs under anaerobic conditions. As a result, the major players for both reactions are typically different, though there is some overlap. There are other processes involved in the nitrogen cycle, such as ANAMMOX (Anaerobic Ammonium Oxidation), Nitrifier Denitrification, and Aerobic Bacterial Denitrification, which have all gained increasing examination amongst scientists but have a long way to go before being as well understood as the classical systems mentioned above.

The field has also revealed that these processes are no longer the domain of bacteria, as once thought, but that the fungi and archaea also play a role in these processes. In fact, fungi in denitrification, and archeae in nitrification and denitrification, may be major players if not THE major players in particular environs.

What has genomics told us? Genome sequencing has definitely sped up the process of understanding, and more importantly, identifying the organisms responsible for these processes. These studies have also shed light on the evolutionary paths these organisms have undergone as well. One such example is that of Nitrosomonas europaea (Ne). This intricate organism lacks all but one single, rudimentary synthesis pathway for siderophore production (citrate). Siderophores bind to iron, which are then picked back up by the organism via a receptor. With few exceptions, iron is a nutrient essential for life, which is why at first glance it makes little sense for Ne to not produce siderophores. However, Ne does encode receptors for many different siderophore types. What does this mean? It means it scavenges off of the siderophores of other organisms. This allows Ne to devote most of its energy into other pathways without having to worry about synthesizing means to acquire iron.

So back to the "hopefully" comment I made earlier. Why are nitrification and denitrification so important? Well, there are several reasons, one of the major ones being that nitrous oxide is a major green house gas (GHG). Nitrous oxide actually has 296 times more of an impact on global warming than carbon dioxide, which sort of makes it a "Big Deal". Nitrous oxide is produced when denitification occurs "incompletely". This incomplete denitrification occurs naturally in the environment. Some organisms don't have the genes which encode for the final step of denitrification, the conversion of nitrous oxide to dinitrogen gas. Sometimes the reason is regulatory, in that the environment is such that nitrous oxide is the final end product. Understanding how and why this occurs is the focus of current research by many individuals.

Hope this sheds some light on these two steps of the nitrogen cycle. I hope to post more on the matter in the future.


Hayatsu, M., Tago, K., Saito, M. (2008). Various players in the nitrogen cycle: Diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Science and Plant Nutrition, 54, 33-45. Article here.

Chain, P. (2003). Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea. Journal of Bacteriology, 185(9), 2759-2773. DOI: 10.1128/JB.185.9.2759-2773.2003

Resources to Learn More About Nitrogen Cycle
Online University Rankings
University of Missouri

I don't mean shoe size

Reducing your Carbon Footprint.

At this website you can calculate the total carbon dioxide emissions you'll incur as a result of a trip, and then offset them. Worth taking a look at if you ask me.

Saturday, May 03, 2008

Thursday, May 01, 2008

I was serious when I said ...

... I was going to do it.

Went out and bought a Slime kit (complete with Slime and air compressor) and repaired both tires on my bike. Washed the bike down and gave it a good rubdown with a microfiber cloth and checked my brakes and gears. Everything looks to be in working order, even though I did notice a couple of broken teeth on the outer chainring (which I'll eventually need to have replaced). So, come Monday, if the weather permits (and part of me is hoping it won't), I'm going to cut down on my carbon footprint a bit!

Clemens is so fuc... screwed

So who hasn't Clemens slept with? I hate the man. The fact that he's a Texass Shorthorn alum (Boomer Sooner!) alone makes him worthy of extreme hatred. Add to this that he pitched for the Evil Empire, the dreaded Yankers, is just the icing on the cake. I can't feel sorry for this bastard one bit. He thought he was untouchable, obviously he was wrong. Should Congress be spending our tax dollars more wisely, rather than wasting it investigating a waste product like Roger? Probably, but you know what ... he's got it coming to him. Say goodbye to the Hall of Fame Roger. Toodles!

Kudos to Obama

For telling it like it is.

Obama has said the tax holiday would save a typical American motorist no more than $28, and likely less according to economists because cheaper gas would increase demand and push up the price, putting more profit into the coffers of the oil companies.

"What working families need right now (is) not more of the same Washington gimmicks that are out of touch with the struggles of working Americans, but real change that will make a real difference in their lives," Obama said.

This is the change I spoke about earlier in my blog. Change that hangs around for awhile, change that is probably going to be uncomfortable for awhile, but pays off in the long run.
"But what we're talking about now is a Washington con game, and I think the American people are smarter than Washington and will see right through it."
Yeah, color me skeptical. I think if history shows us anything at all it is that American people can play the role of sheeple too damn well.