Currently ...

Listening ToSo give me something to believe
Cause I am living just to breathe
And I need something more
To keep on breathing for
So give me something to believe
Believe, The Bravery

Neandertal Genome

The rough draft of the Neandertal genome has been released.

...the team has decoded 3.7 billion bases of Neandertal DNA from a bone of a female Neandertal fossil discovered in Vindija cave in Croatia. That DNA represents about 63 percent of the total Neandertal genome.

So, what have they found so far?

Analysis of the genome reveals that humans and Neandertals share genetic roots stretching back at least 830,000 years. Neandertals, the species Homo neandertalensis, were humans’ closest relatives, appearing about 300,000 years ago and living in Europe and parts of Asia until going extinct about 30,000 years ago.

That's just a glimpse. The article is a good read, go check it out.

Court Sez: No link between vaccines and autism

So anti-vaccine activists, get over it.

An attorney for the families did not respond immediately to a request for comment. But the head of one consumer group that questions vaccine safety, the National Vaccine Information Center, said the court's ruling will do little to change the minds of most parents who suspect a link between vaccines and autism. She said more studies are needed.

Exactly how many more studies are needed? It wouldn't matter how many studies were performed ... you'd always make the same claim: More studies are needed.

So, just shut up and get your kids vaccinated already.

No talking in class!

For all microbiologists not living in a cave, we all know that we're really losing the war against pathogenic bacteria, at least on the antibiotic front. Even the most potent antibiotics like vancomycin -- often considered the antibiotic of last resort -- have seen some organisms develop resistance to it. So, it's time for either new drugs, or a new approach. A New Scientist article discusses developing new antibiotics which target quorum sensing. The article is based on a communication in Chemical Communications, entitled: Towards quorum-quenching catalytic antibodies. The process of quorum sensing is described as following in the NS article:

Individual bacteria monitor the concentration of signalling molecules, and when it reaches a certain level, change their behaviour. That concentration provides a rough indication of when the number of cells in a particular population has reached a certain critical mass – known as a quorum.

So? This process, the authors hypothesize, can be targetted in what they call "antivirulence therapy".

Bacterial antivirulence therapies seek to avoid the development of treatment-induced resistance.

The NS article continues to explain:

But hacking the bacterial communication system could make it possible to prevent this transformation, and leave the cells waiting in a safe form for an attack signal that never comes. That would give the immune system extra time to naturally clear the bacteria from the body, says David Spring at the University of Cambridge, UK.

Of course, that does mean that the body needs to clear the infection on its own. In some circumstances, that may not be possible. But at any rate, how can they do it? They plan on designing antibodies to these quorum molecules. These antibodies will degrade the quorum molecules upon contact, or at least that is the hope/plan.

Reference
Prashant B. Kapadnis, Evan Hall, Madeleine Ramstedt, Warren R. J. D. Galloway, Martin Welch, David R. Spring (2009). Towards quorum-quenching catalytic antibodies Chemical Communications (5) DOI: 10.1039/b819819e

The Grammy's

I consider award shows a total waste of time. Waste. Of. Time. However, after watching Be Kind Rewind last night (Netflix rocks), I switched back over to the television and came across the Grammy's. So I decided to watch for a bit. I think I hit the Disney segment because both Miley Cyrus (can't stand her) and the Jonas Brothers (can't stand them) both did performances. However, I noticed something interesting ... it appears that Disney couldn't just get them up on stage to perform. Instead they actually had to have their acts chaperoned. Miley had to sit next to the much more talented Taylor Swift, and the Jonas Brothers had to act like fools next to Stevie Wonder. I hope both of these kidlet acts never succeed outside of Disney's purview.

Come on Denver!

Get with the program. It's a statue for crying out loud.

Alternate monikers suggested for the horse with the glowering eyes include "Bluecifer," "Satan's Steed" and "Blue Devil Horse."

Bluecifer. Heh.

When I saw the picture I thought it looked somewhat familiar, and wondered where I had seen something similar before. According to Wikipedia, Luis Jiménez, a sculptor was killed making this piece. Maybe the Bluecifer moniker is accurate after all. At any rate, it was based on a sculpting of his named Mesteño which is on display at my alma mater, Oklahoma. The one on the Oklahoma campus is just a wee bit smaller, coming in at approximately 8 feet in height (as compared to the 32 feet of the Denver airport sculpture). It's current location is outside OU's Fred Jones Jr. Museum of Art. There are pictures on flickr here (daytime) and here (nighttime). Why the nighttime shot? Take a look for yourself, and that's not photoshopped either.

Forward Contamination

Forward contamination is the passing of earth organisms to other space objects (of particular relevance, the Moon and Mars). The issue is discussed in Time Magazine.

Even though Phoenix was assembled in a special clean room to minimize bacterial contamination, and its arm, which would have direct contact with Martian ice, was heat-sterilized before launch, it's likely that dozens or more species of microbes hitched a ride on Phoenix's 10-month trip to Mars. Once on Mars, it's possible that bacteria shielded by the structure of the spacecraft from the harsh Martian UV radiation could stay alive, in dormancy, for hundreds of thousands of years. And if native microbes do exist on Mars — nothing has been found yet, but scientists hold out hope that the ice present on parts of the planet harbors life — there's a risk that foreign bacteria could contaminate or somehow change the development of their Martian counterparts.

The state of sustainable energy

New Scientist article.

Although scientists are agreed that we must cut carbon emissions from transport and electricity generation to prevent the globe's climate becoming hotter, and more unpredictable, the most advanced "renewable" technologies are too often based upon non-renewable resources, attendees heard.

Three cited examples are: 1. Iridium; 2. Platinum; 3. Land.

To everyone who has freaked out about the flu ...

... there is a reason to feel a bit more secure today.

Strep infections and not the flu virus itself may have killed most people during the 1918 influenza pandemic, which suggests some of the most dire predictions about a new pandemic may be exaggerated, U.S. researchers said on Thursday.

Yah, but ... something still killed those people.

Well, yes indeedy, but that something was a bacterium, and we now have antibiotics to treat bacterial infections, see?

"Neither antimicrobial drugs nor serum therapy was available for treatment in 1918," Klugman's team wrote.

Now there are also vaccines that protect against many different strains of S. pneumoniae, which cause infections from pneumonia to meningitis.

That's not to say that if you come down with a fever you should just pop whatever antibiotics you have in your bathroom cabinet ... since you should have finished your antibiotics for what they were prescribed for ... but there is no reason to panic about some massive flu epidemic which will wipe out 10% (or more) of the worlds population.

That's Doctor Thomas Joseph to you!

On occasion, the scientific blogosphere gets into a tizzy about some subject or another. This week it's about Dr. Biden wanting to be called ... well ... Dr. Biden. Go figure.

"My feeling is if you can't heal the sick, we don't call you doctor," said Bill Walsh, copy desk chief for the Washington Post's A section and the author of two language books.

Heh. O-tay!

At any rate lots, and lots, and lots, and lots, and lots, and lots (and I didn't get/list them all) of Science Bloggers are blogging about it, and most are miffed!

Honestly, at work and especially in my private life ... I don't expect to be called doctor. Heck, when I received my degree and called my family, my own mother didn't even call me Doctor (though the rest of my family tried it out on me at least once), so I was brought down to earth fairly quickly. My mom of course denies that she did it to avoid me having a big head, but rather to the fact that she was road-tripping with my sister at the time and was paying attention to the road (even though my sister was the one driving).

At any rate, I can see what upsets people about the dismissive comments by Bill Walsh ("Mr." left off purposely). I especially understand that it can be upsetting to women, who often have earned their degree while fighting opposition and derogatory/sexist behavior -- much tougher odds than their male counterparts. I think everyone who earns their Ph.D. should be proud of it, and they should use it if they are so inclined. As for me, there are times I'm referred to as Doctor (it's the work culture I'm in actually), but I don't make a point of using it. I do have business cards that have Ph.D. after my name (they're cool) and I have a business card holder inscribed with my full name (and making mention of the Dr. as well) but that comes out only in certain instances ... such as when I attend customer workshops and people are looking to me for my scientific expertise. More often than not, I prefer to be called Tom, and my support scientists were instructed very early to use that, and only that to get my attention. What they call me behind my back is another story, and I probably don't want to know.

So, what does all this boil down to? If you earned it, and you want to use it. Use it! If you don't, don't! It's your call either way. All this typing to say that, eh?

Oh, and if you're one of those people who refers to all female teachers as "Ms." and all male teachers as "Dr." ... stop and think about it. Heck, why don't you ask them what they'd like to be called? There's a shocker for ya!

In the future, Big Brother will go by one name ...

Google.

Google also is promising not to retain any information about its users' movements. Only the last location picked up by the tracking service will be stored on Google's computers, Lee said.

Suuuuurrrrreeeee.

Requiescat In Pace

Michael Dubruiel. He was a blogger, an author, and most importantly to him a loving and caring father and husband.

Change we can believe in?

WTF is with all these Democrats who can't seem to file their taxes properly?

This is getting disgusting. The rich keep getting richer, and the rest of us get screwed. Fun times!

Irony ...

... I learned long ago that when one opens their mouth to be a wise-ass, it often comes back to bite you in the ass. And Biden has a big mouth, which means that chomp will often be painful (to the ego at the very least).

Keyword of the Day

The Nuclear Option

Is Nuclear Power Worth It? Link goes to a Scientific American article. It's definitely worth the read. Definitely some pro's and con's to this energy source.

A pro, as odd it may seem by reading this quote:

And nuclear power plants have been operating in the U.S. for 50 years without exposing workers or residents in surrounding areas to excessive radiation. "Radiation is mundane, it's a weak carcinogen," says Rod Reed, a senior health physicist at the NRC. "It leads to very mundane changes, not three-eyed fish."

In fact, a typical coal-fired power plant exposes local residents to as many as 18 millirems of radiation yearly, whereas a nuclear power plant emits less than six millirems per annum, according to researchers at Oak Ridge National Laboratory.

Reed adds: "Radiation should be respected, not feared."

And a con?

At issue in the failure at Davis–Besse is the alloy metal used to craft the nozzles—known as Inconel 600 or Alloy 600. The alloy of nickel, chromium and iron is resistant to corrosion generally—but slowly cracks when exposed to boric acid and stress.

But it isn't just reactor heads that are made from the stuff. The steam generators that transfer the heat from the solution of water and boron, which comes into contact with the nuclear reactor, to the water heated into steam that turns the turbines to produce electricity also employ the alloy. "The tubes in the steam generators were susceptible to cracking," says Ken Karwoski, senior level advisor for steam generators and material inspection at the NRC's Office of Nuclear Reactor Regulation. "It's a combination of the temperature and the water chemistry."

So is this an issue dealing with all nuclear power plants? Fortunately no.

As early as the late 1950s there was some suggestion that this metal would crack under pressure but "the decision was made to go with this material," Karwoski says. "The perspective was that it should last but it didn't." And, as of today, there are still 15 nuclear power plants, including Davis–Besse, employing their old steam generators made from the alloy.

The U.S. fleet of 104 nuclear reactors—most built in the 1960s and 1970s—produced 806.5 billion kilowatt-hours of electricity in 2007, a record, and ran almost 92 percent of the time.

Speaking of issues with nuclear energy infrastructure, here is another article from Sci Am about nuclear mishaps.

In all, there were 10 incidents at U.S. nuclear plants last year [2006] that merited ratings of 2—"significant spread of contamination / overexposure of a worker" and "incidents with significant failures in safety provisions," as the INES handbook puts it—or above, Jones says. "Two reactor events and eight nonreactor events."

Overall, I'm still of the opinion that nuclear energy is a reasonable source of energy for the United States.

More on ...

... the new process to create LED lights.

The cost of production has kept the LEDs far from homes and offices, however. Gallium nitride cannot be grown on silicon like other solid-state electronic components because it shrinks at twice the rate of silicon as it cools. Crystals of GaN must be grown at 1000°C, so by the time a new LED made on silicon has cooled, it has already cracked, rendering the devices unusable.

One solution is to grow the LEDs on sapphire, which shrinks and cools at much the same rate as GaN. But the expense is too great to be commercially competitive.

Now Colin Humphreys's team at the University of Cambridge has discovered a simple solution to the shrinkage problem.

They included layers of aluminium gallium nitride in their LED design. These layers shrink at a much slower rate during cooling and help to counteract the fast-shrinkage of pure gallium nitride. These LEDs can be grown on silicon as so many other electronics components are. "They still work well as LEDs even with those extra layers inside," says Humphreys.

Currently ...

Listening To

Well, that's thanks for ya

Woman saves bosses life, only to be "downsized" a couple of months later.

The firing comes just months after Hegyi, a registered nurse, saved the life of station finance manager David Breed, who suffered a severe heart attack at work in September.

Linkage

Astronomy
SEDS Messier Catalog
TUMOL - The Ultimate Messier Object Log (Software)
Stellarium - Open Source Planetarium (Software)
Astronomy POTD - NASA's Astronomy Picture of the Day

Microbiology
The Microbe Zoo

Gah!

I hate the Steelers. Arizona should have had that game wrapped up. Too many penalties and bad plays cost them.

I wonder if the Jets will ever make the Super Bowl again. In my lifetime would be nice.

So ...

... what do people think of the new background? Yucky? Worth keeping? Needs a touch-up or two?

Cheaper LED's coming soon

LEDs now grown on silicone vs. sapphire wafers.

GaN, grown in labs on expensive sapphire wafers since the 1990s, can now be grown on silicon wafers. This lower cost method could mean cheap mass produced LEDs become widely available for lighting homes and offices in the next five years

Energy resources are going to improve in typically one of two ways. First is to find new sources of energy. Second is to find better ways to conserve. LEDs fall into the second category.

First sign of the Apocalypse

Currently ...

Listening ToBest song on the album: Six Days (Soulwax Mix)

The song was originally sung by Colonel Bagshot back in 1971, under the title Six Day War, and was remixed by DJ Shadow in 2002.

Six Days
At the starting of the week
At summit talks you'll hear them speak
It's only Monday
Negotiations breaking down
See those leaders start to frown
It's sword and gun day

Tomorrow never comes until it's too late

You could be sitting taking lunch
The news will hit you like a punch
It's only Tuesday
You never thought we'd go to war
After all the things we saw
It's April Fools' day

Tomorrow never comes until it's too late
Tomorrow never comes until it's too late

You hear a whistling overhead
Are you alive or are you dead?
It's only Thursday
You feel a shaking on the ground
A billion candles burn around
Is it your birthday?

Tomorrow never comes until it's too late
Tomorrow never comes until it's too late
Make tomorrow come I think it's too late

Netbooks and Linux

This article makes no sense to me. Rather, the opinions of the users of netbooks, makes no sense to me.

“Linux just isn’t a platform for the mass market,” he said. “All the early reports of lots of returns of Linux netbooks were because people bought them with that and didn’t know what to do with it.”

Say again? What's so difficult about Linux? I have an Asus EEE Pc (900 model) which has Linux on it. It's a sweet little machine. 20GB flash drive, with an additional 16 GB in the SDHC slot that comes standard on the side (the 16GB SDHC card cost me ~$16 dollars from Amazon ... not a bad price to effectively double the memory of the machine). Oh, and I haven't had a single problem with it, especially when all I'm doing is surfing the net, or taking down quick notes with the Open Office software which comes installed. Yes, it take a bit of brain power to get full functionality, but it really does come with time and use.

Are people just lazy, or do they rely on "Windows for Dummies" books more than I realize?

How are you going to spend your ...

... extra five months?

Between 1978 and 2001, Americans’ average life span increased almost three years to 77, and as much as 4.8 months of that can be attributed to cleaner air, researchers from Brigham Young University and Harvard School of Public Health reported in Thursday’s New England Journal of Medicine.

I guess this means we'll all live longer, allowing us to see global warming armageddon. w00t!

You said it Jack Cafferty!

Stimulus package is loaded with crap. The link is mostly about how Limbaugh is a loud-mouth, but read the last paragraph.

The stimulus package is not going to be a walk in the park either. Republicans are yelling it's too costly and doesn't stimulate enough. And they might have point. It's at $825 billion now and could go higher. Hundreds of millions for condoms and other contraceptives doesn't belong in there either, unless it's for what's about to happen to the American taxpayer.

So ... who's ready for "what's about to happen"? I'm not.

Synthetic Biology

I'm not a Craig Venter fan, but you have to hand it to him, he's motivated and doesn't back down from a challenge. Here is a talk of his on his quest to create life. It's a 15 minute video. The organism he plans on creating is Mycoplasma laboratorium.

Currently ...

ReadingThe best portable star atlas in production (IMNSHO).

Listening To

Nuclear Power

I'm not sure that many people actually consider this, but ... nuclear power is going to be as finite as fossil fuels are. Current estimates peg nuclear power as being capable of powering the world at current rates for the next 200 years. Then, that's it folks.

According to the NEA, identified uranium resources total 5.5 million metric tons, and an additional 10.5 million metric tons remain undiscovered—a roughly 230-year supply at today's consumption rate in total.

There are a couple more options though ...

Two technologies could greatly extend the uranium supply itself. Neither is economical now, but both could be in the future if the price of uranium increases substantially. First, the extraction of uranium from seawater would make available 4.5 billion metric tons of uranium—a 60,000-year supply at present rates. Second, fuel-recycling fast-breeder reactors, which generate more fuel than they consume, would use less than 1 percent of the uranium needed for current LWRs. Breeder reactors could match today's nuclear output for 30,000 years using only the NEA-estimated supplies.

That's a bit more comforting. The question is ... would future developers actually develop these technologies sometime other than the 11th hour like we're currently experiencing with oil?

If you talk to someone in the know ...

... when it comes to environmental issues, and you ask them what the next "Big Deal" is, they'll tell you "Water". Water is a hot commodity, and we totally take it for granted. I mean, admit it ... you literally flush drinking-grade water down the toilet every day without even drinking it. I've blogged about it before. However, despite our cavalier attitude about water, it really is a finite resource. One only need look at Atlanta of last year to realize that, and farmers in California this year are going to be squeezed very tightly thanks to new regulations.

So? We need more water, and we need is yesterday. And scientists may have stumbled upon something which may help us achieve that goal. Desalination done cheaply, also an item I mentioned in that blog entry I linked to earlier in this entry.

National Food Poisoning Death Toll At Seven

Salmonella is to blame.

A seventh death was linked Friday to a nationwide outbreak of salmonella associated with tainted peanut butter and paste sourced to the Peanut Corp. of America's plant in Blakely, Ga., authorities confirmed.

Although their exact causes of death have not been determined, all seven people have died after being infected with the bacterial strain Salmonella Typhimurium, the Centers for Disease Control and Prevention said on its Web site.

Actually, it's Salmonella typhimurium (note capitalization/italicization), but who's counting?

At any rate, the USDA's Food Safety and Inspection Service (FSIS) agency has a FAQ sheet on salmonellosis. Here is a sample from the FAQ.

Q. What are the symptoms of salmonellosis?
A. Most people experience diarrhea, abdominal cramps, and fever within 8 to 72 hours after the contaminated food was eaten. Additional symptoms may be chills, headache, nausea, and vomiting. Symptoms usually disappear within 4 to 7 days. Many people with salmonellosis recover without treatment and may never see a doctor. However, Salmonella infections can be life-threatening especially for infants and young children, pregnant women and their unborn babies, and older adults, who are at a higher risk for foodborne illness, as are people with weakened immune systems (such as those with HIV/AIDS, cancer, diabetes, kidney disease, and transplant patients).

As you can see, it can be a nasty bug, especially those who do not have a strong immune system.

The FDA also has Salmonella listed in their "Bad Bug Book". According to the chapter on Salmonella, the infectious dose is only about 15 to 20 cells, so this is a very contagious organism.

Unfortunately, with this case in particular, give its ubiquitous nature (found in a variety of non-cook ready-to-eat food items) it's very hard to suggest a method to ensure that if you eat some of this food, what you can do to avoid getting sick. In this case, just avoid these items for the foreseeable future.

Currently ...

Listening ToU.N.K.L.E. - War Stories

Burn My Shadow
I have burned my tomorrow
And I stand inside today
At the edge of the future
And my dreams all fade away

I have burned my tomorrows
And I stand inside today
At the edge of the future
And my dreams all fade away

And burn my shadow away
And burn my shadow away

Fate's my destroyer
I was ambushed by the light
And you judged me once for falling
This wounded heart will rise

And burn my shadow away
And burn my shadow away

An' I see the light, too light for love
An' I see the light, too light for love
An' I see the light, too light for love
An' I see the light, too light for love

An' I see the light, too light for love
Burn my shadow
An' I see the light, too light for love
Oh...
An' I see the light, too light for love
Burn my shadow
An' I see the light, too light for love
Away

And burn my shadow away
And burn my shadow away
Oh, how I loved you

Ok, now what?

According to this CNN article, we've finally come to the consensus that global warming is real.

Human-induced global warming is real, according to a recent U.S. survey based on the opinions of 3,146 scientists.

The study was produced by the University of Illinois and according to the article asked two major quesitons.

Two questions were key: Have mean global temperatures risen compared to pre-1800s levels, and has human activity been a significant factor in changing mean global temperatures?

About 90 percent of the scientists agreed with the first question and 82 percent the second.

A little late in the game if you ask me. We needed to be working on solutions years ago. It's also interesting to take note of who were the biggest doubters of global warming. Petroleum geologists and *drum roll* meteorologists.

Petroleum geologists and meteorologists were among the biggest doubters, with only 47 percent and 64 percent, respectively, believing in human involvement.

Heh. Meteorologists can't even get the short term weather correct, what makes anyone think they're reliable in the long term?

So ... now what? This really is an issue that needs to be addressed NOW. Enough with these questionnaires, and onto some solid, workable solutions.

For my part, I work on greenhouse gas emissions from agricultural waste, so attempting to understand the microbial involvement (which is rather large) and how we can curb it, will hopefully be my contribution.

Perhaps ...

... we should have children write any complaint letters we ever need to write.

"Dear Mr. Claudet," the letter from the 7-year-old girl began. She described in four sentences problems at Southdown West Park, the small greenspace by her home. The plastic slide needed to be more slippery, she wrote, and an electrical panel near the tennis court was "dangerus."

When she mailed the letter, little did she know that she would set the parish's bureaucratic wheels in motion.

All her requests for improvements were met during the holidays after the letter landed on Parish President Michel Claudet's desk. He opened it himself, he said, and took the young girl's input seriously.

Edolphus Towns (D-NY) is a Moron

With all the problems our country is facing, you know what with the two wars we're fighting, an economy in shambles, the mortgaging of our future with almost a trillion dollars in bailout money with very little strings (or expectations) attached, this fool wants to hold hearings about the Bowl Championship Series because he doesn't think a "true #1" came out of the BCS.

"I think you really do not get a true No. 1 out of (the Bowl Championship Series)," Towns told the newspaper. "Nobody questions the Super Bowl. The team that wins is the best team that year. I think we can do the same thing at the college level where once it's over there is no questions about who is No. 1 and who is No. 2."

WHO CARES!?!?!!!!

This is all this fool can think about? Jimminy Christmas! Everyone who voted for this guy should be summarily slapped upside the head for picking such an obvious "winner".

At least someone speaks common sense at the end of the article though.

Former house Majority Leader Dick Gephardt of Missouri said he thinks Congress won't have time to deal with this issue with so many issues, particularly the economy, facing lawmakers. "I think this is something that colleges will have to figure out together," Gephardt told USA Today. "I'm not sure this is what the public wants Congress to be spending their time on."

And I repeat ...

I'm not sure this is what the public wants Congress to be spending their time on.

Damn Friggin Skippy!

So, while I think a playoff would be nice ... I don't think Congress should be wasting my tax payer dollars making it so. I can certainly live without a playoff. I cannot live without my government functioning properly and ensuring that the services I pay for actually work for me (now and when I retire).

So, Mr. Towns get your ass in gear and do something USEFUL and IMPORTANT! You damn fool.

I am not a number, I am a free man!

RIP Patrick McGoohan.

Currently

Listening ToCaravan is one of the best songs of all time.

Screwed

If you haven't accepted it yet, perhaps think about this one as well.

One of the nation’s largest health insurers has agreed to pay $50 million dollars in a settlement announced today after being accused of overcharging millions of Americans for health care.

How?

New York Attorney General Andrew Cuomo says Ingenix has been manipulating the numbers so insurance companies pay less. In a just-released report, he contends that Americans have been “under-reimbursed to the tune of at least hundreds of millions of dollars.” Although UnitedHealth Group and Oxford Insurance were the only entities investigated, other major insurers use Ingenix, including Aetna, CIGNA and WellPoint/Empire BlueCross BlueShield.

If you've been screwed, don't ever expect the screwer to say "Sorry".

Where I have been

I've visited 31 states (62%), and I've lived in 4 of them. Create your own visited map of The United States. I haven't been outside the United States (aside from Mexico and Canada) so I won't bother with that little meme. Oddly enough, I grew up in New York, and I've never bothered traveling up into New England.

h/t to Phil from DC Dispatches.

Anything but Normal, in Normal IL

Wedding in Taco Bell.

"We have the same brain, just in two bodies," Paul Brooks said.

No comment. Well, other than to say I guess that explains getting married in a "Toxic Hell". Having half a brain will do that to ya I suppose.

Lay off the VapoRub

So says new study.

The strong-smelling ointment often dabbed under noses or rubbed on the soles of feet can be an irritant, increasing the production of mucus and decreasing how fast it’s cleared, potentially causing dangerous breathing problems in infants and very young children.

I don't know why people even bother using that stuff. It stinks and it doesn't really do anything. If I'm feeling like crap, and I use Vicks ... I just wind up stinking AND feeling like crap.

Jessica Rosenberg, 32, of Santa Clara, Calif., said she rubs Vicks onto the soles of her kids’ feet to quiet nighttime coughs. The new study is interesting, she said, but not enough to make her stop.

What?!?!

Dear God. Why would rubbing menthol on your kids foot keep them from coughing? Idiocy abounds.

This urban legends site dispels the silly "menthol on feet is good for you" myth. Though this 1908 explanation is amusing, and so very very backward: "internal morbid processes may at times be relieved by creating external irritations". In other words, if you have a headache, hit your hand with a hammer. It'll make you forget all about the headache. Oh,the fun we could have with this one.

Requiescat In Pace

Reverend Richard John Neuhaus, editor of First Things.

I think ...

... I know how I'm going to make my money and get myself to early retirement. I'm going to steal a supertanker filled with Saudi oil.

Quote of the Day

Don't try to be happier than happy. - Colin Cowherd

As if there wasn't enough to worry about?

Now NASA is warning that solar storms could knock out a large portion of the world's electronics, and electrical infrastructure if we're really, really unlucky. And who can really claim to have good luck right about now?

Damage to power grids and other communications systems could be catastrophic, the scientists conclude, with effects leading to a potential loss of governmental control of the situation.

Hmm, if this happens perhaps that crazy Russian would be right. I don't really want to be a part of the EU though ... if they even still existed.

Boomer Sooner!

Thrash the Gators!

Nifty Agricultural Tool

Was at a Soil and Water Conservation meeting earlier in the week and saw a talk on compost. This product was mentioned, and boy is it a neat idea. Gardensoxx. Just place it where you want it, cut a slit to insert your seeds and Viola! within a week, you have the starting of a garden. These soxx are multipurpose, used for erosion control, agriculture, gardening ... and relatively inexpensive when compared to what you'd pay for a garden's expenses anyways.

Five Ways the World Might End

Here's a really chipper story for the new year. Good news? None of these are predicted to happen tomorrow.

Linkage

Bureau of Communication

Funny stuff.

Currently ...

Listening To

Did You Make a New Years Resolution?

If it involves working out and/or losing weight, here is a handy tip chart for you. Me, I'm not into the whole resolution thing. I have been committed to losing a few extra pounds that I gained during graduate school, but I didn't feel the need to make a resolution on Jan 1st at 00:00:01 for it. I have found that losing the extra pounds can be done slowly but surely by two things. Exercise and portion control. No need for a fancy diet, or pay out the butt to have a company mail you food. Four to six ounces of meat at dinner along with a healthy salad and a generous helping of green vegetables works just fine.

If you're gonna go ...

... you might consider going in a National Park.

[At] least 33 people who chose to end their lives last year in a national park. The number is higher than recent years, although the National Park Service hasn't consistently tracked suicides.

"It's some place where, toward the end of someone's life, when they're feeling a total sense of despondency, they want to return to a place of natural beauty ... for their final moments," Suddath said.

Personally, I don't believe suicide is the answer. As they say, it's always darkest before the dawn. I truly believe that, and I hope I always will. Nevermind the terrible wake of psychological damage that is inflicted on those left behind.

Happy New Year

2009 - International Year of Astronomy

How many seconds in a minute?

It's not a trick question, unless you're talking about 11:59 PM tonight. The last minute of 2008 will be 61 seconds long.

Immediately before midnight a leap second -- the first for three years -- will be added to atomic clocks around the world by official timekeepers.

Why?

"The difference between atomic time and Earth time has now built up to the point where it needs to be corrected, so this New Year's Eve we will experience a rare 61 second minute at the very end of 2008 and revelers... will have an extra second to celebrate."

Enjoy that extra second folks!

Math Made Easy

Eh?

It appears that FOXNews considers these laws "wacky". Admittedly, some of them are stupid, but ...

4. In Michigan, it is legal to kill a dog for attacking chickens, livestock or people, but you can't snuff the pooch in a high altitude decompression chamber or by electrocution.

So preventing people from killing animals by two very painful methods is wacky?

... and ...

10. In Alabama it is against the law to exploit a bear by promoting, engaging in or being employed at a bear wrestling match, or by subjecting a bear to surgical alteration of any kind, including, but not limited to, declawing, tooth removal and severing tendons.

So animal cruelty is wacky? Hamstringing a bear is wacky?

Some people need to get a clue.

Surely ...

... I did NOT read this blog right. Herm Edwards as a potential candidate for the Jets coaching vacancy?!!?!! Is this guy on crack?

Yes, after starting 8-3, losing 4 of the last 5 was seriously disappointing. But the answer was not to get rid of Mangini. Jimminy Christmas. It's the Jets of old. The sucky, sucky Jets of old. *sob*

Acceptance!

Thank you, you love me, you really love me! - Jim Carrey in The Mask.

One paper accepted (the one from my graduate school days). Working on getting the other revised and sent back out for further review. Then, onto this years major project!

In the meantime, a white paper, and two presentations for customer workshops in early January. Which is only a couple of days away. How time flies!

Don't be like Caroline Kennedy ...

... you know?

In a 30-minute session with The News on Saturday, Kennedy punctuated her answers with "you know" more than 200 times. "Um" was fairly constant, too.

For scientists who must regularly present their science in a public setting, be it seminars, symposiums, or other invited presentations ... these verbal tics can definitely overshadow their work. That's definitely not a good thing. One piece of advice is to go slow. Allow a pause between your thoughts. When changing a slide, step back, collect your thoughts and then and only then, speak. Even a pause for a second can give you that precious time needed for your brain to catch up with your mouth and prevent you from a verbal tic. Saying things like "you know", "ah", "uh", or "umm" can definitely distract the audience. I imagine everyone who reads this blog and has attended seminars has sat in attendance and counted verbal tics for at least one presenter. It's awful!

So, before your next seminar, sit down with a co-worker and give your talk. Have them listen for those verbal tics and then work on eliminating them. Your talk will improve and it'll pay off in the long run as well.

Hopefully your slides don't suck either ... but that's a talk for another time.

Germ Warfare ...

... just took on a new meaning.

Scientists noticed that two neighboring colonies of P. dendritiformis never grew to touch each other on an agar plate.

Interesting, but what happened next ...

The research team, led by Avraham Be’er at the University of Texas at Austin, next wanted to know whether the bacteria were just inhibiting the growth of their sibling colony or were actually killing the other colony. Upon closer examination, the team found that dead bacteria littered the fringes of both warring bacterial colonies, showing researchers the smoking gun.

Cool! Look for the article in the Dec 29 issue of PNAS (article not currently available at the time of this blog post).

Astronomy Highlights of 2008

FOXNews' Top Five Amazing Astronomy Discoveries of 2008.

United States to Dissolve

So say the Russians.

So, where will you wind up? Me? I'll be a part of the European Union! w00t! I worry about those who will wind up being Chinese though. Beware of the melamine!

Home

Back at home. Went on a road trip to visit family. Took two of my dogs along for the "vacation". All in all, I should have stayed home. Weather didn't exactly cooperate either. Any good to come out of it? Of course! Here is a cute pic of Kode in the car. He's not the best traveler, but he toughed it out like a little trooper.

Guess this means I'm available to blog again.

Currently ...

Reading

Listening To

Merry Christmas!

I hope everyone has a Merry Christmas and a Happy New Year! Though I do intend on getting back to blogging* before 2009!


*Being able to set posting dates and times is a nice Blogger feature!

M

ycoplasma laboratorium. As much as it pains me to give props to Craig Venter (when I was in graduate school, he was "the enemy"), this is too cool to pass up. M. laboratorium is the name of the organism that has been planned to be "created" as part of the Minimal Genome Project. M. laboratorium is actually M. genitalium with bits and pieces removed. Essentially, if it was considered (and proven by transposon mutagenesis) to be a "non-essential gene", it was excluded from the final "blueprint". Once they have the base template/blueprint, they will synthesize the genome and then pop it into a cell so it can "take off" on its own. Venter has even filed a patent on this idea, and they've published on their efforts as far back as 2006 in PNAS (PDF, 6 pages). So, while this organism doesn't actually even exist (as far as I know), I'm going to put it at the top of my "Merry Christmas" list.

Hopefully everyone has enjoyed this little "series". It was definitely not intended to be a full-fledged repository for these organisms. Instead I hope that it exposes (excuse the pun) people to some organisms that they may not have heard of before. Even better if people have contributed additional information in the comment fields.

At any rate, I hope everyone has a great holiday season!

E

lizabethkingia meningoseptica (further referred to as Em). Em is a Gram negative bacillus from the phylum Bacteroidetes. It is ubiquitous in the environment, having been isolated from soil, as well as both fresh and salt water. The genus derives it's name from CDC bacteriologist Elizabeth O. King, who first identified this organism as having caused meningitis in infants. She originally named it Flavobacterium meningosepticum.

R

uminococcus albus. Three guesses as to where Ruminococcus can be frequently isolated. According to the MicrobeWiki (a neat little site hosted by Kenyon College), Ruminococcus can be isolated from ... yep, you guessed it ... the rumen of cattle, sheep, and goats. R. albus is a gram positive organisms, belonging to the phylum Firmicutes. It is anaerobic, does not produce spores, and is non-motile. They produce a number of cellulose degrading proteins, which is useful for the organisms they inhabit, as it allows them to obtain energy from cellulose which they cannot otherwise digest.

R

aphidiopsis curvata. This organism was first identified and classified in 1929, and it's been a problem ever since. R. curvata is a cyanobacteria and produces a number of toxins which can be lethal for certain animal species. Two identified toxins produced by R. curvata are cylindrospermopsin (CYN) and deoxy-cylindrospermopsin (deoxy-CYN), both are toxic to the liver and kidneys.

R. curvata

Y

ersinia enterocolitica. Y. enterocolitica (Ye for short) is one of the etiological agents of yersiniosis, and according to the CDC, Ye is the main cause here in the United States. The disease typically presents as fever, abdominal pain, and diarrhea and is often contracted by eating undercooked pork. It can often be confused as appendicitis. It's main target is children, though anyone is susceptible, especially those who suffer from hereditary hemochromatosis.

Yersinia enterocolitica

C

lostridium difficile. Lookie! A Gram positive organism! It's an anaerobe, which means it doesn't need oxygen. This is ideal for it's environment, which is your intestines. "C. diff" isn't the kind of organism you really want however. It is most closely associated with antibiotic-associated diarrhea. What happens is that, when you're given a dose of antibiotics to treat some other infection, it winds up killing a portion of your normal flora in your intestines. This normal flora typically keeps C. diff in check, however with it now gone, C. diff takes over. Given C. diff's arsenal of toxins, you can then wind up with some nasty diarrhea and severe complications.

There is a rather ... ummm... interesting treatment for people suffering recurrent infections with this organism. Fecal transplants. I only wish I was kidding.

Scanning Electron Micrograph of C. difficile

H

aemophilus ducreyi. This organism can be summed up by one word: Chancroid. When you hear that word, you should envision a painful ulcer on someones genitalia. H. ducreyi is a sexually transmitted disease (STD), and it's the #1 cause of genital ulceration in the world. Dubious distinction, eh?

If you have an ulceration on your private parts and suspect it's bacterial in origin, there is an easy way for you to figure out whether or not you have contracted H. ducreyi or syphilis. Poke it. If it hurts, it's H. ducreyi. If it doesn't hurt, it's syphilis.

Fortunately for everyone involved here, I won't be showing any pictures of genital ulcers. Of course, it'll be interesting to see how many people Google brings here due to the search for the words "genital" and "ulcer".

R

hizobium leguminosarum. Like with Aa below, we'll simply refer to this bug here as Rl, because I'm not typing that out every single time. Rl is a soil organism which was first identified in 1889. These organisms are interesting because they pair up with legumes in a symbiotic relationship -- residing within root nodules -- and fix nitrogen. A portion of this nitrogen remains in the soil after the legumes are harvested, which cuts down on fertilizer costs. Because of this, you'll see legumes often used in crop rotations, rotating with other plants which do not fix nitrogen.

The nodulation process (formation of root nodules) is very intricate. The legumes release chemicals (flavinoids) which are sensed by the bacteria. In turn, the bacteria secrete chemicals (nod factors) which force the legume roots to undergo cell division and direct root hair growth. Eventually (with a few more steps) this forms the nodules in which the rhizobia reside.

Root Nodule.

I

sosphaera pallida. Isosphaera pallida is a species within the phylum Planctomycetes. The Planctomycetes are unique in that while they don't have a true nucleus, typically their DNA is enclosed within a double membrane (though this feature seems to be absent in Isosphaera. I. pallida is phototactic*, reproduces by budding, and displays gliding motility. Unlike most eubacteria, I. pallida (and other Planctomycetes) lack muramic acid -- a key component of peptidoglycan -- in their cell wall. It is therefore believed that these organisms went on their merry evolutionary way before peptidoglycan was ever heard of.

*I. pallida moves towards light sources.

S

hewanella putrefaciens. S. putrefaciens is a member of the Proteobacteria (Gamma class). It is a facultative anaerobe, and uses can use either iron or manganese as the terminal electron acceptor in electron transport (most organisms use oxygen). This organism derives its name due to the fact that it produces trimethylamines, which means it takes on a rotten fish smell. Yummy. Growing this organism will reveal that it has a pinkish color upon isolation. Another interesting tidbit is that this organism can also generate electricity.

People have also been unfortunate enough to find themselves infected with S. putrefaciens, though electrocution is not something they need to worry about.

T

hermotoga neapolitana. Another organism which has garnered a fair amount of buzz in bioenergy research circles. This hyperthermophilic organism can produce large amounts of hydrogen under anaerobic conditions (typically at around 80 degrees C). Like other organisms which have had their 15 minutes of fame, T. neapolitana is currently having its genome sequenced. The hope is that carbohydrates (generated/recovered as waste from other processes) can be fed to this organism so it can produce hydrogen for a variety of purposes (maybe hydrogen-fueled cars).

M

ethylococcus capsulatus. M. capsulatus is a methanotroph, which means it's able to use methane as their sole source of carbon and energy. This is useful as methane is a GHG that is approximately 26 times more problematic on a mole:mole basis than carbon dioxide. M. capsulatus uses methane by oxidizing it in a two step process, first to methanol, then to formaldehyde. The enzyme responsible for the first step of this process is methane monooxygenase (MMO) which comes in two forms, a soluble form (sMMO) and a particulate membrane form (pMMO). Different organisms may carry one or the other, or both (the organism in question, M. capsulatus encodes for both). Multiple labs have spent time studying M. capsulatus in the hopes that it can be exploited for methanol production.

M. capsulatus (Bath) has had its 3.3 Mb genome sequenced. As it's name suggests, M. capsulatus does possess a polysaccharide capsule, perhaps a tool to help it survive long periods of time in arid conditions.

Methylococcus capsulatus

A

ctinobacillus actinomycetemcomitans, which we will refer to simply as Aa from now on (because I'm not typing that out every damn time) is one of the "HACEK" grouping of Gram negative organisms that are all part of the normal human orophayngeal and/or urogenital flora. This organism (and the others) can, given the right circumstances, be found in association with endocarditis, bacteremia, and wound infections. Aa is a slow bugger to grow, often taking 48 to 72 hours, and forget about growing it on anything but enriched media. The most common infection associated with Aa is subacute bacterial endocarditis, though it is also blazing a trail in the area of periodontal disease as well. Aa has a decent sized virulence factor arsenal, including a leukotoxin, a PMN chemotaxis-inhibiting factor, resistance to complement killing, and bone resorption-inducing toxin.

S

erratia marcescens. S. marcescens is a Gram negative organism which belongs to the family Enterobacteriaceae. It can be pathogenic, most often found as a UTI, though it does also pose problems for immunocompromised individuals, especially those in a hospital setting -- leading to nosocomial infections. To make matters worse, S. marcesens has a habit of being antibiotic resistant, making it a very hard organism to clear. One of its hallmarks is that most isolates produce a reddish pigment called prodigiosin (see below), which assists in identification of the pesky bug.

From a historical, and religious, point of view, S. marcesens has been theorized to be the culprit in Eucharistic miracles involving bleeding hosts. However I'm not aware of it being confirmed in any such cases, if there have been any cases recently (of which I am also not aware).

Serratia marcesens

To Hell With Oil ... Where Is The Water?

Expect lots of droughts in the future.

At least 36 states expect to face water shortages within the next five years, according to a report from the U.S. Government Accountability Office. According to the National Drought Mitigation Center, several regions in particular have been hit hard: the Southeast, Southwest and the West. Texas, Georgia and South Carolina have suffered the worst droughts this year, the agency said.

This is obviously not a "Good Thing". With droughts come increases in food prices, which isn't something most people can handle right about now.

So, what can we do?

Water shortages don't have to remain a fact of modern life, drought experts say. Many offer the same solutions: Build better water delivery systems to accommodate population growth, develop more efficient uses of irrigation, and shift agriculture from the West to the East where it's easier and cheaper to water crops.

Infrastructure folks. More water storage capacity, both for on-farm and municipal use. I cannot stress the on-farm use enough either. I heard that costs in California for irrigation of a single acre in California is up from ~$30 last year to over $600 this year. If that report is true (if it was reported correctly AND I heard it correctly) that spells clusterf**k. Plus, it's about damn time we started working on inexpensive membrane technologies to desalinate sea water.

More Financial Crisis Victims

Pets.

In Arkansas, Cheryl Lang, a foreclosed-property inspector, found three dogs left locked in pet carriers in the back yard of a foreclosed home. Abandoned without food or water, the animals had died.

Whiskey! Tango! Foxtrot!

I've got to admit. This crisis still keeps me up at night, and puts a nice, tight knot in my stomach. I believe I'm very fortunate to have the job I do, and I'll do everything in my power to ensure that I continue to have it. Sometimes this world sucks.

Fair play

It appears that dogs can sense fair and unfair treatment.

To test the theory, Friederike Range and colleagues at the University of Vienna in Austria asked 33 trained dogs to extend a paw to a human.

The animals performed the trick virtually all of the time whether they were given a reward or not -- when alone or with another dog.

But the dogs' enthusiasm waned when they saw other dogs being rewarded but received nothing themselves.

Dogs that were ignored extended their paws much less often, doing so in only 13 out of 30 trials. They also showed more stress, such as licking or scratching themselves.

"They are clearly unhappy with the unfair situation", Range told New Scientist magazine. She also suspects that this sensitivity might stretch beyond food to more abstract things like praise and attention.

When we first adopted Kode, our Norwegian Elkhound mix, Max, became sullen and withdrawn. Then he took a very dominant approach towards Kode. We've tried our best to love equally on all three dogs we have, and things have definitely improved. Perhaps I spent too much time with Kode (who was undernourished and definitely skittish but still attention starved) when we first got him. Nowadays Kode looks to Max for cues, and Max is secure in his "alpha" role (I say "alpha" role because his owners are the dominant species in the house and they all know it).

Idiot

The title says it all really (MSNBC), guess it's Chicago politics as usual (CNN).

On November 5, Blagojevich allegedly told an advisor, "I've got this thing and it's [expletive] golden, and, uh, uh, I'm just not giving it up for [expletive] nothing. I'm not gonna do it."

What a tool.

Currently ...

Listening ToJeff Buckley - Sketches For My Sweetheart The Drunk.

Released post humously, this album has many a lyrical gem on it. My favorite song on the album is "Everybody Here Wants You". If you ever want to hear the love song to end all love songs, this is it.

Puppy cuteness

This is Kode, our most recent adoptee.

Linkage

Sol Light - Creators of the LightCap

Hello Ubuntu

The new computer arrived, but in the meantime I've been given a to-be-scrapped computer to use as a testbed for my "linux project". What I'm hoping to do is build a linux cluster. At first it'll just be two computers, but I hope to expand it as things go to surplus.

Why? Because with the amount of information we'll be acquiring (especially once we start 454 sequencing in earnest), I'll need the computing power for processing the data. I'd like a 64 bit computer, but from a Windows standpoint that means using Vista, and the government doesn't currently allow Vista on their computers without seeking exceptions ... and that paperwork is a bit of a pain. Besides, several of my programs don't work on Vista yet, which means I'd need to keep an XP machine around anyways (rendering the above moot). *sigh*

Anyways, if I cluster a couple of linux machines, I can achieve (I believe) similar results. So, anyone build a cluster recently? Also, what bioinformatic tools do you use regularly on linux? I've already installed Geneious and the Bio-Linux base programs (which is mostly Emboss) and Artemis.

ASM General Meeting

I'm putting the finishing touches on my ASM abstract for the 2009 General Meeting in Killadelphia. I hope everyone else is getting their abstracts done, the deadline is about a month away.

First Casualty of Global Warming?

Rare breed of possum may be extinct due to global warming.

Experts fear climate change is to blame for the disappearance of the highly vulnerable strain thanks to a temperature rise of up to 1.5 degrees Fahrenheit.

Currently ...

Listening ToUNKLE - Psyence Fiction

Societies, Memberships, and Fees

You know, I don't have a problem belonging to Societies. As a matter of fact, they're pretty much essential in my line of business. Stick around long enough, publish regularly in their journals, and do a fair bit of networking and in about a decade you get someone to nominate you for Fellow. In my business, becoming a Fellow in a Society is a big deal. It shows that you're regarded very highly by your peers, which shows that you've had what they refer to as "impact". That's a key word in my business ... impact.

Unfortunately, you don't just pick ONE society, you have to pick several ... because, being a Fellow in multiple societies is much better than being a Fellow in just one. Problem is, societies cost money. And they all want their money in December.

So here I am looking at what it's going to cost me, and I'm looking at a bill which will come in at around $500. That's money that I could use for Christmas shopping, holiday travel, and whatnot.

But it's tax deductible! Well, yes and no. Yes, it is ... but only if you meet a certain threshold, which last year the wife and I did not reach. It's doubtful we'll reach it again this year.

*sigh*

Well, time to ante up.

Always look on the bright side of life ...

... such as, we can expect a nuclear or biological terrorist attack within the next five years. Hey, at least we have five years and it's not going to happen tomorrow!