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.

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.

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.

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.

Likewise:
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.

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.

Acidobacteria

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.

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.