Wednesday, December 31, 2008

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.
"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!

Tuesday, December 30, 2008

Math Made Easy


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*


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.

Monday, December 29, 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!


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 ...


Listening To

Thursday, December 25, 2008

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!

Saturday, December 20, 2008


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!

Friday, December 19, 2008


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.

Thursday, December 18, 2008


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.

Wednesday, December 17, 2008


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

Tuesday, December 16, 2008


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

Monday, December 15, 2008


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

Sunday, December 14, 2008


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".


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.

Saturday, December 13, 2008


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.


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.

Friday, December 12, 2008


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).


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

Thursday, December 11, 2008


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.


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.

Wednesday, December 10, 2008

More Financial Crisis Victims

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).

Tuesday, December 09, 2008


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.

Monday, December 08, 2008

Puppy cuteness

This is Kode, our most recent adoptee.


Sol Light - Creators of the LightCap

Friday, December 05, 2008

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.

Wednesday, December 03, 2008

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

Tuesday, December 02, 2008

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.


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!