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!

Still revising ...

... though it's going much slower on a laptop, because my desktop whimpered and died on me. Graphic construction software (I use Gimp) is much more tedious on the laptop. As a matter of fact, I hates it. But, it's coming along. I hope to get it out by the first week of December ... and focus on the data analysis for my next manuscript.

Pragmatic Me

I was reading RPG's blog, and his latest entry is one which ultimately deals with why he is a scientist. It boils down to, as he states ...

I don’t do science because it’s useful, or important. I do science because I find it beautiful.

I have no problem with that, but that is certainly not how I found myself in the world of science.

For me, it started in high school. We took that awful preliminary SAT test ... called, oddly enough, the PSATs. When you take that test, it comes back to you with a list of careers you might be ideally suited for. At the top of the list for me: Medical Technologist. A career I had zero information about. So, I started looking around (this was a time before that series of tubes called "the internets") and got literature from a number of universities. They all painted a nice picture about their Med Tech programs. I always did better in my english, history, and political science classes as a student, but I just couldn't see myself in a career within those fields. Exactly what would I do? is something I constantly asked myself. Be a librarian? was the response that my mind often came up with.

I wanted no part of being a librarian.

A medical technology position wasn't "high profile", though it could be a good start towards getting into a med school. What med tech provided however was an almost guaranteed source of employment from the minute I was given my diploma. As a child who grew up solidly middle class, this was a big deal. I saw how my parents struggled with keeping food on the table and a roof overhead, I saw the intense work ethics of my dad and grandpa, I knew I'd have to eventually do the same ... and being a librarian didn't seem like a very good source of income. I don't say this to degrade librarians, because pay may be really good ... but no one ever gave me any information as a teenager on what it was like to be a librarian. When found in such a vacuum, you fill it the only way you know how *shrug*.

At any rate, so based on the results of that PSAT test, and the information I found on Med Tech (not to mention those PSAT's seem to be serve as a recruitment tool for colleges because every Med Tech program in the land started sending me brochures on their particular program), I figured I'd look at colleges that offered the program. I looked at several, and each one of them spoke to the point of a low number of Med Tech's but a high demand for them. Base pay was good $16/hour (at the time) and bound to increase every year, so I figured I'd give it a try. It certainly seemed more challenging than any other subject I'd considered majoring in.

Beauty alas, never factored into the equation.

Now, as I've progressed in my career, I've been excited by several aspects of my work ... most notably, I find it cool that if I do an experiment ... I may very well be the first person EVAR to do that particular experiment to answer that specific question on that specific organism. But that isn't what keeps me going. What keeps me going is that paycheck I receive. Now, it helps that I love what I do. I most certainly do, but my particular job affords me many benefits which allow me to love it, and want to persist in doing it.

I guess there are those who will persist in doing something because they find it beautiful. I'm happy for them. For me, that simply isn't the case. I think what I do is important AND useful, both for the environment, my field, and more importantly myself ... and all for different reasons. I'm afraid beauty simply doesn't fit into the equation, or if it does it's not a factor which is weighted very heavily.

Boomer Sooner!

The University of Oklahoma football team travels to Stoolwater this weekend to face their in-state "rival" OSWho? Typically only the OSU fans consider this "The Big Game" because to OU, the Cowboys are usually just a bunch of fumbling fools. However, this year OSU is ranked 12th, and OU trails Texass by .084 points in the BCS rankings. So, even for OU this ranks as a "Big Game". Beat OSU, hopefully handily, and OU stands to jump ahead in the BCS standings ... thereby earning themselves a trip to the Big 12 Championship to play Missouri. Beat Mizzou (which we did last year) and it's time to play for the National Championship!

I know, OU lost to Texass earlier this year. Doesn't matter. Strength of schedule, peaking at the right time, number of quality opponents ... they all favor Oklahoma. Boomer friggin Sooner!

Happy Thanksgiving

Hope everyone has a great Turkey Day!

Squee! Cuteness!

Max, one of my puppies.

New Computer!

Looks like I'll be back in business after the holidays. My new and improved computer has been ordered by IT, and should be here after the Thanksgiving holiday. Just in time too! Though the federal government has moved to rating its employees to coincide with the fiscal year (Oct 1 thru Sept 30) rather than the calendar year (Jan 1 thru Dec 31), the holiday season is still turning out to be pretty hectic. However, instead of cramming to get that final manuscript out by Dec 31 (complete with all the bureaucratic paperwork that comes with it) -- that sort of cramming happens at the end of September now -- there is just a lot of online training and other assorted junk this year.

Well, at least there is never a dull moment!

Linkage

Adopt a Microbe

Top Ten Favorite Microbes

In browsing the comment fields of my blog entries, I came across a comment by Rhea, blogger of The Apprenticing Lab Rat that got me thinking.

What are my favorite microbes?

So, I put my thinking cap on, and came up with the following list of my ...

Top Ten Favorite Microbes.

10. Nitrosomonas eutropha - I suppose you could put N. europaea here in this spot as well, they're very closely related. They make up one lineage of the Nitrosomonas genus, which happens to be the lineage you're most likely to find growing in wastewater treatment plants. This genus is also one of two major players (along with Nitrosococcus) in the first phase of ammonia oxidation, which sees the conversion of ammonia to nitrite, a necessary step in the Nitrogen Cycle.

9. Yersinia pestis - Any bug which can pretty much singlehandedly be responsible for what people would forever refer to as the "Black Death" gets my attention and respect.

8. Comamonas badia - Not an organism most people are going to have heard about, though I've blogged about it before. Nothing particularly exciting about this organism other than the fact that it forms flocs. Flocs are useful for wastewater treatment systems as it provides a matrix for organisms to grow on ... call them floating biofilms. If the flocs are of the right composition, they will settle out rapidly, a feature necessary for producing a quality effluent. It's on my list because in some of our genetic characterization studies, we've seen a relative of this organism but have yet to isolate it. I like challenges!

7. Escherichia coli - Come on, Who doesn't like E. coli? Of course, for the purposes of this question, we're excluding those individuals who are currently tied up with a bout of the Aztec two-step. For any gene jockey E. coli is an essential tool for cloning purposes. Heck, I even used E. coli for triparental matings way back when.

6. Legionella - How many organisms do you know that can spread through an air-conditioning system? I know of one in particular, and this one is it.

5. Pseudomonas aeruginosa - As a clinical microbiologist, P. aeruginosa is one of those organisms that is very easy to identify. If it smells like Welch's grape juice, it's P. aeruginosa. That, and it fluoresces. It does have this nasty habit of being very harmful to burn victims though. The damn bug grows just about everywhere, and is a friggin pain in the posterior to eradicate from a system once it takes root.

4. Borrelia burgdorferi - Say that fives times real fast. I've never had Lyme disease, and I never want to either. Spirochetes look cool too.

3. Vibrio cholerae - Two words for you: rice-water stool. Some things/phrases stick with you forever, and those two words are one such phrase I will never forget. I've also always been fascinated with quorum sensing, and this organism along with other Vibrio species, has seen the lion share of such research. V. cholerae was also responsible for helping Robert Koch refine his postulates, as well as bringing about the birth of epidemiology (see John Snow).

2. Neisseria gonorrhoeae - Spent more time working on this organism than any other. It's an exquisite organism, being an obligate human pathogen it has no vector and must rely on one of the few activities that most humans have a proclivity for -- sex -- for transmission. There is a documented case of fomite transmission as well.I crack up everytime I see that. The actual letter ... is a bit disgusting when you read it.

1. Deinococcus radiodurans - The coolest of the cool. Any organism that can take dosages of radiation that would kill a human a couple hundred thousand times over is neat! Not that this organism evolved after Chernobyl. Instead, this "super power" is most likely the result of surviving dessicated environments. That is why this xerophile (arid condition surviving organism) is at the top of my list! All extremophiles rock by the way!

So, what are some of the favorites of everyone else? Hmmm, should I make this a meme?

My Favorite Microbe

According to Rhea, her favorite organism is Helicobacter pylori.

H. pylori is indeed a cool bug, but it's not my favorite. Actually, this is a good idea for a blog entry. I'm going to list my Top Ten Favorite Microbes. Stay tuned!

Yup ...

... the desktop is still down for the count. Something about my 24" monitor being too much for the graphics card that currently resides in the bowels of that damned machine. It will need to be upgraded, but that won't happen until after Thanksgiving.

At least I managed to recover the data/text I need for the revision of my grad school manuscript. Now hopefully my co-author will come through today with the request I made of them, and we'll get this thing out!

Quid Pro Quo

Even after blogging for most of this year, my blogroll is rather small. So, I'm opening up my blogroll! If you read my blog and wouldn't mind putting up a link to mine on yours, I'll return the favor! Just leave the relevant details in the comments section!

It's hard to believe ...

... that my first alma mater, the University at Buffalo, may actually be going bowling this year. It looks like they clinched the Mid American Conferences East Division, and will probably play undefeated Ball State (if they don't get upset) in the MAC Championship game in a few weeks. I haven't really been a big fan of UB football. When I went to UB, the football program sucked. They were getting their asses kicked by every team they played. In the meantime, our XC and Track and Field teams were winning conference championships ... and who got the glory? The pathetic football and basketball teams, and those guys had the egos to go along with it ... though they sucked.

No, I'm not bitter. I mean, with three individual conference championships (1000m, 1600m, 5000m), and a fourth team title (XC) under my belt, what do I have to be bitter about?

Anyways, these new kids aren't the old losers I had to deal with, so I'll root for them. Though, I must admit, my loyalties run much deeper for the University of Oklahoma. At least until UB puts me into their athletic Hall of Fame *hint* *hint*.

Yep ...

... my desktop here at work is still broken. So I guess I'll blog a bit more today.

The Alternative Scientist

My latest addition to The Alternative Scientist is up. Go read it!

Does my breath smell?

It appears that Helicobacter pylori may be the cause of halitosis (aka 'bad breath') as well.

H. pylori is a very interesting bug. It appears to have first been identified in the 1800's, though the work didn't really go anywhere. The issue was readdressed in the early 80's, with the work of scientists Barry Marshall and J.R. Warren, who linked the organism to stomach ulcers. This was met with a fair bit of skepticism, but Marshall showed them (did he ever!) by drinking a flask of the bug and promptly coming down with a stomach ulcer. In addition to being a really stupid thing to do, it eventually earned them the Nobel Prize in 2005. There are also links between H. pylori and stomach cancer, which makes the issue of halitosis rather small potato's in the grand scheme of things. It's estimated that roughly 50% of the worlds population carries the organism, though only a percentage of those carriers ever present with any sort of symptoms.

Does this water taste funny to you?

Water from urine recycling machine broken in space station. $250 million dollar system? I think the Boy Scouts of America can do it for much less.

I hate Murphy ...

... and his stupid Law. So I have this manuscript that I'm revising and I've finished all but maybe 1/8th of it. So what goes and happens? Blue screen of death on my computer followed by a total crash (a little cursor blinking in the top corner, nothing else). All my data is on that computer, so now I have to wait for IT to recover my revised manuscript and new figures from their backups. So much for getting it finished today. Dang it.

J-E-T-S!

Jets! Jets! Jets! Jets!Jets defeat the previously unbeaten Titans.

Now, hopefully I pulled out a win in my fantasy football league. If I win, I get a berth in the playoffs.

ETA: Looks like I pulled out a 10 point win in fantasy football. Huzzah!

Yet another reason ...

... to stay a leg up in the scientific world.

The report, based on a global survey of experts and trends, was more pessimistic about America's global status than previous outlooks prepared every four years. It said that outcomes will depend in part on the actions of political leaders. "The next 20 years of transition to a new system are fraught with risks," it said.

Review #1

These reviews are taking a bit longer than I expected. Not that I've had much time myself to address the reviewer comments if I had gotten them sooner, so I guess no harm/no foul. At any rate, the work I had done during graduate school received a review requesting some minor edits: a change to the introduction; a change to a figure; a request for a figure; and more explanation on a third. Easily done, and very satisfying. According to the reviewers, the manuscript was well written, and the literature is adequately cited. That works for me. Now to get it turned around. I'm especially pleased because I have the work they requested, so I don't get into an ugly game of trying to do work I finished several years ago in my lab which doesn't deal in the slightest with pathogens.

Can't they just go to Lowes?

Spacewalkers loose toolbox.

The briefcase-sized tool bag drifted away from astronaut Heidemarie Stefanyshyn-Piper on Tuesday as she cleaned and lubed a gummed-up joint on a wing of solar panels on the space station.

Home Depot delivers too, right?

Open Letter to Cingular

Dear Cingular (AT&T),

You suck. You've been a pain in my rear several times. Mostly because of the stupid fact that even though I paid for my rollover minutes, you seem to have the ability to axe them whenever you want. However, the last straw was when, after 6 years of service with you guys, one of your customer service representatives reset my phone upgrade date two years back when I moved and changed my number (though I specifically asked if this would be a problem, and that I WOULD NOT do the number change if anything was going to get mucked up). That meant -- according to you folks -- that I had to go four years without getting a new phone ... or I could pay out the wazoo. Well, I wasn't about to pay out the wazoo, and your customer service didn't seem particularly keen on helping me sort out the issue either. So, I found someone else, and you lose a customer that you've had for the better half of a decade.

I'm sure you're crushed. As am I.

Eat poop,
Tom

Mars likely had an ocean ...

... which probably covered up to 33% of its surface.

The younger, inner shoreline is evidence that an ocean about 10 times the size of the Mediterranean Sea, or about the size of North America, existed on the northern plains of Mars a few billion years ago. The larger, more ancient shoreline that covered a third of Mars held an ocean about 20 times the size of the Mediterranean, the researchers estimate.

Where there is (was) water, there is (was) also the strong possibility of life.

If I ever fly Qantas airlines ...

... I want to avoid one particular plane. This one as a matter of fact.

A Qantas jetliner that was damaged by a midair explosion in July collided Tuesday with another of the airline's planes on an Australian airport tarmac, airline officials said.

Yes, I'm a tad bit superstitious. So either I avoid the plane, or the pilot (if the same yahoo was involved in both instances).

Janella Spears is an idiot

She truly is. I mean, really. REALLY. IS. AN. IDIOT.

Her family and bank officials told her it was all a scam, she said, and begged her to stop, but she persisted because she became obsessed with getting paid.

She lost over $400,000, burning through her husbands retirement. Her reply?

"The retirement he was dreaming of — cruising and going around and seeing America — is pretty much gone for him right now," she said.

Pretty much gone right now? Hopefully he has a shred of sanity left, otherwise his freedom will be pretty much gone for him after he kills you for your stupidity in an insane rage.

What a tool.

Enough! Just crown him Czar already ...

... and be done with it. You know that's what they want anyways.

Nebraska is for parents ...

... that don't want their teen-aged kids any longer. I personally know a couple of people who saw this coming, but who were derided on the internet for their speculation.

Nebraska's safe haven law was intended to allow parents to hand over an infant anonymously to a hospital without being prosecuted. Of the 34 children who have been dropped off at hospitals, officials said not one has been an infant.

All but six have been older than 10, according to a Nebraska Department of Health and Human Services analysis.

Bold emphasis mine. What a sad state of affairs.

Bioinformatics

So, for the microbiologists/molecular biologists/geneticists who read this blog (I know there are a couple), what programs/software do you use for sequence analysis/protein analysis/molecular biological applications?

Here's my list:

IN HOUSE

Geneious ($249 subscription/year)
Used: Daily
Official description:
Geneious Pro is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, contig assembly, primer design and restriction analysis, access to NCBI and UniProt, BLAST, protein structure viewing, automated PubMed searching, and more. It even includes an API for creating your own plugins.

What I use it for:
Geneious is the workhorse application for DNA sequence analysis (chromatogram/sequence quality) and editing (vector and quality trimming) in my laboratory. Geneious is also used for contig assembly of genes/organisms and for alignment of 16S sequences for downstream phylogeny analysis (see programs MEGA, DnaSP, DAMBE). It can also be used to construct quick phylogenetic trees for routine examination. The subscription package allows me to receive regular updates. The only other comparable software application that I’ve found that works well on Windows XP is Sequencher (2007 quote for purchase was $2975. Major updates would require another purchase).

Artemis (freeware)
Used: Moderately (several times a month)
Official description:
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.

What I use it for:
Artemis is a valuable tool for examining completed genomes. Search by gene/sequence/functional category for items of interest. GenBank houses over 630 completed microbial genomes (631 as of 02/08/08).

MEGA ver4.0 (freeware)
Used: Moderately
Official description:
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

What I use it for:
MEGA is the primary phylogenetic tree building program. It constructs publication quality phylogenetic trees. It is used for molecular evolution and population genetic analysis. In terms of alignment data, MEGA is an established format and most programs export/import alignments in MEGA format. Geneious exports alignment data in MEGA format, allowing these two programs to be used in conjunction. MEGA also has a sequence editor for quick/minor alignment editing.

DnaSP (freeware)
Used: Infrequently/Rarely
Official description:
DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé, Tajima, McDonald and Kreitman, Fu and Li, and Fu tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

What I use it for:
DnaSP is primarily used to determine genotype numbers. Genotypes are based on SNP information derived from DNA sequencing (typically MLST – multi-locus sequence typing) closely related strains/isolates.

DAMBE (freeware)
Used: Infrequently/Rarely
Official description:
Data analysis in molecular biology and evolution. t is an integrated software package for retrieving, organizing, manipulating, aligning, and analyzing molecular sequence data. Allele frequency data can also be used by DAMBE for calculating genetic distances or phylogenetic reconstruction.

What I use it for:
DAMBE does not see frequent usage in the lab, but it is sometimes useful for determining genotype numbers (it ignores gapped sequences for example) from complex sequences.

TotalLab 120 DM ($6,000)
Used: Moderately
Official description:
The TL120 version in the TotalLab range is an advanced image analysis solution which offers an extensive range of features for the in-depth analysis of 1D electrophoresis gels and performing band pattern matching studies. TL120 DM is the TL120 analysis software complete with the DM database component so you can archive all your analysed results and perform cross experiment investigations.

What I use it for:
This program is integral for analysis of our ribosomal intergenic spacer analysis (RISA) data which is collected on a LiCor DNA sequencer. This allows us to look at archaea, eubacterial and fungal population patterns in a sample and then compare that gel image to other images/samples to construct a phylogenetic relationship between them. The DM option allows us to store this information in a database for comparison of data between experiments. This will enhance our ability to compare samples across time (date of analysis & time of collection) and space (place of collection).

ONLINE RESOURCES

NCBI (National Center for Biotechnology Information)
Site: http://www.ncbi.nlm.nih.gov/
Used: Daily
Official Description:
Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

What I use it for:
PubMed serves as a primary reference search tool which is linked to the U.S. National Library of Medicine. NCBI houses several major databases, ranging from nucleotide and protein, to taxonomic and structure/function. NCBI also has databases dedicated to SNP (Single Nucleotide Polymorphim), EST (Expressed Sequence Tag), and GEO (Gene Expression Omnibus) analysis. Databases cover all forms of life, from eukaryotic (animal and plant) to prokaryotic (archaea and eubacterial). NCBI also serves the BLAST (Basic Local Alignment Search Tool) which is used to examine sequence similarity to other previously identified sequences (nucleotide or protein).

Ribosomal Database Project (Michigan State University, J.M. Tiedje)
Site: https://rdp.cme.msu.edu/
Used: Daily
Official Description:
The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences.

What I use it for:
Upon sequencing 16S clones, we use the RDP database to classify (Phylum/Class/Order/Family/Genus/Species) them for separation, for further phylogenetic analysis. The RDP also has sequence match functions which will identify closely related sequences which are useful when building phylogenetic trees (typically using MEGA).

Bellerophon
Site: http://foo.maths.uq.edu.au/~huber/bellerophon.pl
Used: Daily
Official Description:
Bellerophon is a program for detecting chimeric sequences in a multiple sequence dataset by comparative analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries but can be applied to other gene datasets. A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point.

What I use it for:
Chimera detection in 16S sequences.

Farewell Phoenix Mars Lander ...

... you served us well. Hopefully this parting will be temporary and we'll see you again after the spring thaw.

Veterans Day

In Flanders Fields

In Flanders fields the poppies blow
Between the crosses, row on row,
That mark our place; and in the sky
The larks, still bravely singing, fly
Scarce heard amid the guns below.

We are the Dead. Short days ago
We lived, felt dawn, saw sunset glow,
Loved and were loved, and now we lie
In Flanders fields.

Take up our quarrel with the foe!
To you from failing hands, we throw
The torch-Be yours to hold it high!
If ye break faith with us who die
We shall not sleep, though
poppies grow
In Flanders fields.

by: Captain John D. McCrae

Open Letter to Tim Robbins

Tim,

Shut up. You're starting to look like an idiot.

Tom

Go vote!

It's too late to vote in the election for the Presidency of the United States, but you can make a difference in the life of a college student. It appears that there is a Blogging Scholarship (no, I'm not making it up) that pays out $10,000 to the winner (not making that up either). I voted for Brian Switek, author of Laelaps, and a student at Rutgers. There are several worthy candidates there, so go vote!

Sometimes ...

... you just can't make this stuff up. Really. Geocentrism (Thank God that the Earth is not moving).

Whiskey. Tango. Foxtrot?

Many people consider the Encyclopedia Britannica the FINAL AUTHORITY on all scientific matters.

Eh?

"The centrifugal force of Earth's rotation makes the planet bulge at the Equator. Because of this, Earth has the shape of an oblate spheroid, being flatter near the poles than near the Equator. Correspondingly, one degree of latitude is longer in high latitudes than it is in low ones." (Britannica vol. 4, p. 320).

Ordinary mortals cannot see this bulge however as it is visible only to the editors of the Britannica articles.

LOL.

Alas, I don't think this site is a spoof. I wish it were.

h/t to Mark Shea for the giggles.

Earth Four Hours From Destruction!

Ok, not really.

On the evening of Wednesday November 5, 2008 (for most of North America) a giant rocky body will pass through Earth's position in space less than 4 hours after Earth was there. If Earth were 3 hours and 40 minutes farther back in its orbit at that time, the collision would wipe out all life on Earth. In fact, it would render Earth's surface uninhabitable for millions of years.

Should the tabloids media run headlines like "Earth 4 Hours from Destruction"?

No, because there's a catch to this story. It's revealed by the question "What will the rocky body look like in our skies on the "eve of (near) destruction?" The answer is that the object will appear as bright as a first-quarter Moon. For a good reason — the object is the first-quarter Moon.

RIP Michael Crichton

The Andromeda Strain is one of my favorite sci fi books of all time. Eaters of the Dead, Jurassic Park, Sphere, and Congo are some of his other well known and often read works.

ETA: CNN link for added traffic.

After two years of an almost constant ...

... barrage of politics, it seems things will return to normal (whatever that is) for a bit. Here's to hoping that the next four years are a bit less stressful than the last four.

I've always wanted a mammoth ...

... and now it appears that I might be able to get one!

Scientists at the government-backed research institute Riken used the dead cell of a mouse that had been preserved at minus 20 degrees Celsius (minus 4 degrees Fahrenheit) -- a temperature similar to frozen ground.

The scientists hope that the first-of-a-kind research will pave the way to restore extinct animals such as the mammoth.

Why is this so exciting? The dead cell was not cryopreserved. Rather, it was simply frozen, as in, stuck in a plastic bag and stuffed into the back of a freezer for 16 years. No extraordinary efforts taken to preserve the cells of the dead mouse.

Therefore, scientists could potentially use cells from animals frozen in permafrost for centuries and "revive" them. Hello wooly mammoth! Here is a link to the PNAS abstract. The ability to gain access to the PDF can be found there as well.

Orion

I haven't really blogged about my astronomy exploits recently because the sky has not really cooperated. However I did notch a first a few weeks ago. I spotted my first constellation (without any assistance). You can probably guess which one.Orion.

I was pulling out of my driveway on my way to play racquetball at the ungodly time of 5:30am, looked up and Viola! there he was. Pretty friggin cool if you ask me.

Then, for good measure, the following morning I woke up a bit earlier, took out my binoculars and scanned Orion for M42 (Orion Nebula). What a sight!

Linkage

Check this website out:

Hunters Hope dot Org

Found it through a comment on Peter King's Monday Morning QB writeup for the NFL's week 9.

Good Guy of the Week

Jim Kelly, retired quarterback, Buffalo.

Kelly, who never could get the Bills over the Super Bowl hump in his Hall of Fame career, has a new mission these days -- to get every state to test for 54 potentially fatal diseases that could be diagnosed at birth. Only one state, Minnesota, tests for that many today.

He's on this mission because of the death of his son, Hunter, in 2005, from a rare brain disease called Krabbe Leukodystrophy. The disease (leukodystrophies afflict one of every 100,000 American births) could have been diagnosed at birth, but New York State did not test for the illness when Hunter was born in 1997.

"The tragedy for Hunter, and for so many children born with fatal illnesses, is that they're simply born in the wrong state,'' Kelly said the other night. "If you don't think that's something that just tears at your heart every day ...''

I've known Kelly for a long time, and I've always found him to be one of the biggest life-of-the-party guys I've covered. He was a prolific pre-curfew beer man in his Bills training-camp years, when the Buffalo players were as tight as a team could be. But when I saw him the other day, I saw he'd changed. There was a grimness to a once-carefree guy, with more lines on his face than I remembered. The grimness is not from giving up; it's a grim determination.

He's already seen governors of three states -- New York, Pennsylvania and Kansas -- and gotten each to increase dramatically the number of diseases tested for at birth. When babies are born, their heels are pricked and a blood sample taken to test for diseases. With Kelly's lobbying, New York has increased from 11 to 44 diseases tested for, Pennsylvania from 11 to 29, and Kansas from four to 29.

Parents can buy a kit to screen their children for the maximum number of diseases for less than $100, but Kelly, and his foundation, want the tests to be done for every child as a matter of course. Considering that the costs of caring for children with one of many known leukodystrophies can run from between $500,000 and $1 million per year, it seems like early-testing money would be well spent.

"I never won a Super Bowl,'' said Kelly, "and for a long time that really bothered me, obviously. But this is real. This is life. My Super Bowl victory will be to get every state to adopt universal newborn screening so we can save lives that are now being lost needlessly. When that day comes, that victory will be 10 times better than any Super Bowl.''

Because New York now tests for Krabbe, Kelly met a perfectly healthy boy, now a year and half old, who was diagnosed at birth and successfully treated. "Little Elmer,'' he said with a grin. Now his goal is to meet a lot more Elmers. If you'd like to help, or learn more about Kelly's mission, you can go to www.huntershope.org.

There is simply no reason that we shouldn't be performing these tests.

Microbial Life on Mars

Here it is, the slides (with some slight modifications and in PDF format) from my seminar on the possibility of microbial life on Mars given to the local Astronomy Club. The talk went well, from what I could tell, and I had a good time (and I hope everyone else did too, on top of learning something!). The slides are not "complete" in the sense that you might be able to glean all the information I spoke about by simply viewing them. That's because slides IMO should mostly be written from the vantage point of the lecturer, so as to be used as a guide for them and remind them of what they're going to say (if people are reading my slides, they're not paying attention to me speaking ... that's not a Good Thing). So you won't see many full sentences in these slides, just bullet points to jog my memory. And some snazzy eye candy (pictures). Alas, since it's PDF, all addtional eye candy (movement) is lost. I don't use special effects in my actual talks/seminars but for the local Astronomy Club, I figured what the heck. People thought the stuff I did was amusing (like the space-faring sea monkeys to illustrate the ideas of "forward contamination" and "panspermia".

Anyways, here it is: Martian Life

Get your own at Scribd or explore others: Science Biology bacteria microbial

Oh, and Scribd is a pretty cool site, and it's free!

This is what worries me about Obama ...

... sooner rather than later, I imagine I'll be considered "upper class" and I'll be taxed to death. Exactly what is his threshold for "middle class"? It seems to be a moving target.

IIRC, when Obama started this whole deal with defining the middle class, he pegged it at anything above $75K. No freaking way. As a married government employee, my wife and I come close to that, and we still live paycheck to paycheck. Student loans and a mortgage take out a considerable chunk of our pay. An increase in our taxes would kill us.

Then it was raised to $250K for a family. Pretty high ceiling there, but now it seems to be creeping down again. Where it actually stops, is anyone's guess. Give me a damn number, and then stick to it. Jimminy Christmas!

Uh, what?

Palin not going back to Alaska, even if she loses next week. And here I thought she was governor of the state. Does this mean she's stepping down?

If Obama and Biden win next week, I predict the death of the Republican Party as we know it. While quite a few people will rejoice at that, I don't think it's such a Good Thing. While a two party system is horrendous (essentially picking between dumb and dumber), a single party would be a damn nightmare. It'd be essentially mob rule.

Oh well, guess the Republicans brought this on themselves. I still blame Perot though. If he hadn't gone all loopy and pull his "I'm dropping out, no I'm here, here's my VP he's a total dumbass" stunt back in 1992 we might have a healthy three party system right now.

Busy again today ...

... preparing a talk for a seminar I'm giving on Friday to the local Astronomy club. Managed to find a way to put two of my favorite intellectual pursuits (Astronomy and Microbiology) together ... Astrobiology! So, I'll be talking about the potential for life on Mars. When I'm done, perhaps I'll put my lecture on the web.

Sheeple ...

So Obama paid for a thirty minute freakin infomercial during prime-time television, delaying the start (or end, as it were, damn Phillies) of the World Series game. Nevermind the fact that if he had kept his promise to accept public financing (read the entire article) this never would have happened ... but instead he's managed to pull in over half a billion dollars and has so much money left over, it appears that he'll just be throwing it to the wind in the next few days. Yay. Just what we needed ... wasteful spending when the economy is in shreds. Can't wait for those tax breaks and a rejuvenated economy and balanced budget. Oh wait, looks like that won't be happening.

Anyways, this infomercial was so special-rific that it's moved people to tears, definitely more than one it seems. You've got to be kidding me. Am I a curmudgeon or simply unmoved by the unabashed attempt to get people to vote emotionally rather than logically? You tell me.

Sometimes it's all about perspective.

There are plenty of times that I get frustrated with this country. For all the boneheaded decisions our politicians make, for all the greed that big businesses practice, for all the idiotic things that private citizens do ... it makes me want to pull out my hair and scream.

And then, I read articles like this one.

The condemned inmate, his body torn apart by guard dogs, slumped unconscious as the three executioners fired. The bullets shattered his skull, splattering blood near other prisoners forced to watch.

His offense: trying to escape from the remote prison camp in North Korea.

Compared to this, life here is pretty damn good. I don't say this to excuse the wrongdoings that go on here, because they most definitely need to be pointed out, stopped, and those responsible held accountable. However, I do think it's important to note that despite our problems, we still hold a lot of promise and potential.

Speaking of idiots ...

... Richard Dawkins is a bore.

The prominent atheist is stepping down from his post at Oxford University to write a book aimed at youngsters in which he will warn them against believing in "anti-scientific" fairytales.

Dawkins, it's called "fiction". Children don't grow up believing in witches and wizards, it's a good yarn. So what's next? Is he going to rail against Upton Sinclair's The Jungle, or Pearl S. Buck's The Good Earth? Or does he just have fantasy fiction literature in his sights?

Perhaps Dawkins would prefer if children just read The God Delusion? That'll certainly generate interest in reading, right? What ever happened to the imagination?

h/t to Mark Shea.

Idiots

1. What sort of idiot lets his 8 year old fire an uzi?

2. This one is just a plain idiot (well, they're all plain idiots). First she calls the cops complaining that the trunk of her daughters car reeks of death, and then when the cops concur ... she refuses to believe it.

3. How is this idiot still not in jail?

4. Yah, you thought you would never get caught, eh?

5. Ummm, what the hell you fool! First you call your constituents racist. Then you "apologize" by clarifying your comments to merely call them all rednecks. Why don't you just shut up you jackass.

Currently ...

Listening To
Rolled Gold Plus - The Rolling Stones

Order of the Science Scouts of Exemplary Repute and Above Average Physique (Post 1)

The first post outlining the badges I've earned in my career as a scientist.

BADGES

Talking Science Badge - Every geek talks about their science, don't they? Not that the non-science people in our lives really understand half of what we're saying, but the fact that we take the time to put it into layman terms (well, most of us do I suppose) must mean something.

I Blog About Science Badge - This one is pretty much a given since I blog here, right? Well, maybe this one is a bit suspect lately since I've done more blogging about music and sports than actual science, but since it's my blog I can do what I want. Then again, since I don't blog for Science Blogs ... oh wait, nevermind. Half of their blogs don't ever blog about science so who are we kidding?

I'm Pretty Confident Around An Open Flame Badge - Bunsen burners are cool. When that bunsen burner is simply a nozzle slapped on top of a can of butane, it gets even cooler. Yah, what can I say ... our lab doesn't have a gas hookup. It doesn't have vacuum or air either. *shrug*

"Sexing Up" Science Badge - I earned this one with my work on the STD Neisseria gonorrhoeae. I think I earn even more kudos for this badge given the fact that we actually tried to given gonorrhoea to baboons. It didn't work, though not for lack of trying. Next time you can claim that your P-1000 has been up the menstruating vagina of a baboon, come talk to me.


I've Frozen Stuff To See What Happens Badge - Whether it's throwing things in the minus 20, or better yet the minus 80, to see "what happens" -- in science we call that "making an observation" -- well, I've done it. What is especially cool is when you pull out the buffers for your restriction enzymes and it's still a liquid but when you flick the tube it immediately freezes solid. That's cool.

I've Frozen Stuff in Dry Ice to See What Happens Badge - Heck, in my graduate school lab we had a dry ice maker. It was this block of wood that you could connect a tank of carbon dioxide to and make the stuff. Scary as hell the first time you fired that baby up, but after that ... man the stuff you could put inside and then freeze. Total coolness!

I've Frozen Something in Liquid Nitrogen to See What Happens Badge - This is a bit scary. When you contemplate the fact that if you stuck your hand in the liquid nitrogen tank it'd die almost immediately and probably shatter into a million tiny pieces ... it's a sobering thought. So we had a few yucks with it, but that was about it. Of course one of the girls in the adjoining lab would use the LN to burn off warts. Weird. Effective, but weird.

Skynet?

Has it already begun to take shape?

The latest request from the Pentagon jars the senses. At least, it did mine. They are looking for contractors to provide a "Multi-Robot Pursuit System" that will let packs of robots "search for and detect a non-cooperative human".

Can I file this under "Bad Idea"?

You know ...

... when someone writes a perfectly damn good story, and someone else tries to make a movie out of it, the least they can do is be true to it! On that note, I suppose I should not be surprised by the stupid crap Hollywood does, so when I watch a movie which has been "altered" from the way the book ended, perhaps I shouldn't be surprised or upset.

The two movies which have recently irked me to this effect? [WARNING: Spoilers below.]

1. I Am Legend - I can't begin to count how many people don't quite understand the meaning of the movie's title. I've had to explain to them what the actual title of the movie means, because if he's NOT the only one (human) left, he's not really a "legend", at least not how Richard Matheson meant it.

2. The Mist - Typically Steven King movies suck, but this one was alright. That is, it was alright until they went and made Drayton a mass murderer at the end.

STD Greeting Cards

Did you give your partner an STD? Having a difficult time as to how you're going to break the bad news to them? Don't fret. Email them!

The site, www.InSPOT.org , is a way for people newly diagnosed with an STD to notify their partners to be tested, too. The e-cards, a sort of greeting card you’d rather not receive, are direct and to the point.

Sexually transmitted diseases. Never a fun thing I imagine, and not really a trivial matter. Some can be/are eventually fatal (syphilis and HIV), can lead to other life-threatening complications/diseases (HPV), or increase the risk of contracting a fatal STD (gonorrhea and chlamydia). The following link is to the CDC webpage on STDs.

The site featured in the first link is: inSPOT dot org which stands for [STD] Internet Notification Service for Partners or Tricks. You really can't make this stuff up.

Patent Crap

I'm handling patent stuff today so blogging will be scarce. I'll be back soon!

In the meantime, here are the next ten songs on my iTunes playlist:

1. White Rabbit - Jefferson Airplane
2. Piece of My Heart - Janis Joplin
3. For Those About To Rock - AC/DC
4. Heartbreaker - Led Zeppelin
5. Two Out of Three Ain't Bad - Meatloaf
6. Honky Tonk Woman - Rolling Stones
7. Heart of Gold - Neil Young
8. Tiny Dancer - Elton John
9. 25 or 6 to 4 - Chicago
10. Behind Blue Eyes - The Who

What's everyone else listening to?

The Happening - A Review

I can sum the movie up in three words.

What.

The.

Hell.

It was atrocious. I swear Marky Mark was in a coma in this movie. He speaks in monotone for most of the movie, and it's ... well, just plain stupid! If you've seen the trailers, you've seen the first five minutes of the movie, because all the "good stuff" is put right up front. I can't even begin to get into the details of the movie, like how Marky Mark is a science teacher, and he and his wife are in the middle of a bad marriage ... because, well it's not even integral to the movie except for about 10 seconds in the movie when Marky Mark uses his *ahem* skills as a science teacher to come up with the solution basically to "Run!" (away from the breeze).

I think the funniest bit is when, in the middle of a "terrorist attack" and people are told to evacuate NYC, Penn Station is friggin empty. EMPTY! IT'S NEVER EMPTY! 600,000+ people go through there each day ... and when the city is told to evacuate you think it's going to be anything other than shoulder to shoulder? Sheesh.

This movie sucks.

Currently ...

Listening To
Blue Oyster Cult - (Don't Fear) The Reaper is one of the best songs of all time. The song needs more cowbell!

Tom's Excellent Adventure

Went with Mrs. Thomas Joseph to Atlanta this weekend to catch her favorite team, the Chicago Bears, take on the Atlanta Falcons. Me, I'm not a fan of either team ... though I had to sort of root for the Bears, otherwise I'd have found myself in the dog house this week.

Anyways, the Superdome is a nice facility, the game food was good, the atmosphere was great, and the game was fun as well. If you're not a fan of either team, a close game is about all you can ask for. If it's a blowout, who cares ... right? This game was close, and then with about 2 minutes to go it got fast and furious. Orton (Bears QB) threw for a touchdown with less than a minute left to put the Bears up by 1 (see picture).Then Lovie Smith had a brain fart. A squib kick got the Falcons within striking distance. Then a pass by Matt Ryan, against a prevent defense, a play later and the Falcons were looking at a 48 yard field goal with Jason Elam about to kick the rock. His long is ~63 yard (IIRC) so this was a chip shot. Of course, as time expires, he knocks it through the uprights. Game Over. Atlanta Wins.Of course, this wasn't the only mistake Lovie Smith (the Bears head coach) made that day. His decision to run J. McKie on a 3rd and 1 at the goal line (instead of running Matt Forte) was dumb, and then foregoing the field goal (when they still needed two scores) to try to punch it in on 4th down is really what cost them the game IMO. Regardless though, it was a fun time ... and dinner at The Varsity afterward capped a great day.

Currently ...

Listening To

Who do I thank?

Since this time last year, the cost per share in one of my mutual funds has dropped 45%. w00t!

Fortunately, I have time on my side ... others are less fortunate. What about them?

The Happening

Netflix will be delivering this movie to my door (or my mailbox as the case may be) this afternoon. It has a horrible rating over at Rotten Tomatos, and was pretty much panned before it hit the theaters, which is why the wife and I didn't shell out our hard earned ducats to see it on the big screen. But now it's a cheap rental, so what the heck! Claims of "anti-science" have been thrown about when talking about this movie ... so it'll be interesting to see just how blatant it is.

Rabies - A survivors story

I've blogged once before about rabies, and how it's a severe and often fatal disease. As a matter of fact, it's so severe that only one survivor who did not receive the rabies vaccine after being bitten is known of. Her story is up at the Scientific American website.

How did she manage to become the lone survivor? Not by luck. She had some pretty smart doctors.

Instead of giving her up for dead, the doctors decided to "shut the brain down and wait for the cavalry to come" by inducing a coma to give her own immune system time to build up antibodies against the virus, says Rodney Willoughby, an infectious disease specialist who treated Giese at the Children's Hospital of Wisconsin in Milwaukee. Willoughby devised the treatment credited with saving Giese there, which has since become known as the Milwaukee protocol.

Rabies kills by compromising the brain's ability to regulate breathing, salivation and heartbeat; ultimately, victims drown in their own spit or blood, or cannot breathe because of muscle spasms in their diaphragms. One fifth die from fatal heart arrhythmia. Doctors believed that Giese might survive if they suppressed her brain function by sedating her while her immune system attacked the rabies virus.

This was the first time the therapy was attempted, and doctors had no clue if it would work or, if it did, whether it would leave her brain damaged. But Willoughby says it was the only chance doctors had of saving her.

This protocol is being used to treat another girl in Colombia (she's mentioned on the first page), and it appears to be working. If so, this is a great (but rather expensive) break through.

Hail Satan!

Doll delivers Satanic message, as well as a blurb about Islam.

Currently ...

Listening To

GFP!

Green Fluorescent Protein has won the Nobel Prize for Chemistry!

Ok, maybe the protein didn't actually win, but the people who characterized it did. They're Osamu Shimomura, of the Marine Biological Laboratory, Woods Hole, Martin Chalfie of Columbia University, New York, and Roger Tsien of the University of California, San Diego.

I remember when GFP first hit the commercial market, after the publication describing the vector pGFP (GenBank accession number U17997) by Chalfie et al. in Science in 1994 (PDF, 4 pages).

Congratulations to the winners, to GFP, and to all the wonderful uses it has found in science!

Go Fish!

Fish species takes the crown of "Deepest Living Fish Species Evar".

The fish, known as Pseudoliparis amblystomopsis, can be seen darting about in the darkness of the depths, scooping up shrimps.

Sidenote: I like how the BBC video has a volume control that goes to "11".

Have we ceased to evolve?

According to one geneticist, the human rate of evolution is slowing down.

Although chemicals and radioactive pollution could alter genetics, one of the most important mutation triggers is advanced age in men.

This is because cell divisions in males increase with age.

"Every time there is a cell division, there is a chance of a mistake, a mutation, an error," he said. "For a 29-year old father [the mean age of reproduction in the West] there are around 300 divisions between the sperm that made him and the one he passes on — each one with an opportunity to make mistakes.

"For a 50-year-old father, the figure is well over a thousand. A drop in the number of older fathers will thus have a major effect on the rate of mutation."

Congratulations ...

... to the latest Nobel Prize Winners.

Medicine
Francoise Barre-Sinoussi & Luc Montagnier (France) - Discovering HIV.
Harald zur Hausen (Germany) - Discovering cancer-causing HPV.

Yay!

My Roth IRA has lost about 25% of its value in the last couple of months, and it's set to lose a bit more in the upcoming week. And who do I think should share a large measure of responsibility in this fiasco? Barney Frank, who it seems had a little* incentive to deregulate Fannie Mae.

Although Frank now blames Republicans for the failure of Fannie and Freddie, he spent years blocking GOP lawmakers from imposing tougher regulations on the mortgage giants. In 1991, the year Moses was hired by Fannie, the Boston Globe reported that Frank pushed the agency to loosen regulations on mortgages for two- and three-family homes, even though they were defaulting at twice and five times the rate of single homes, respectively.

*Maybe sarcasm isn't warranted here. Barney Frank had a huge incentive to fight for Fannie Mae to be deregulated. It's criminal, really.

Not a good day to be a mammal ...

... 1 in 4 mammalian species in danger of becoming extinct.

The new report updates the IUCN's Red List of Threatened Species, which overall includes 44,838 species, of which 16,928 are threatened with extinction. Of these, 3,246 are in the highest category of threat, critically endangered, 4,770 are endangered and 8,912 are vulnerable to extinction. The IUCN estimated that 76 mammal species have gone extinct since 1500.

That's a staggering number, and it's due primarily to man's own actions.

"Within our lifetime hundreds of species could be lost as a result of our own actions, a frightening sign of what is happening to the ecosystems where they live," added Julia Marton-Lefevre, IUCN director general. "We must now set clear targets for the future to reverse this trend to ensure that our enduring legacy is not to wipe out many of our closest relatives."

The word for today is: Conservation.

This little twirp ...

... needs a serious ass whooping for this stupidity. And his parents need to be levied a severely hefty fine, one they won't soon forget. Damn deadbeat parents.

Snowflake Sleeper Cells

Joe Biden claims:

At a Sept. 9, fundraiser, Biden addressed his national security credentials by talking about "the superhighway of terror between Pakistan and Afghanistan where my helicopter was forced down. John McCain wants to know where bin Laden and the gates of Hell are? I can tell him where. That's where Al Qaida is. That's where bin Laden is."

So, his helicopter was "forced down".

John Kerry explains:

"It went pretty blind, pretty fast and we were around some pretty dangerous ridges," Kerry told The Associated Press afterward. "So the pilot exercised his judgment that we were better off putting down there, and we all agreed."

"It" being a snowstorm.

[sarcasm]Well, at least we know that Biden, as Vice-President will be able to save us from inclement weather released upon us by the terrorists.[/sarcasm]

We were going to send Biden out to fight the Taliban with snowballs, but we didn't have to do it.

Well, at least we know it's an option.

Heaven help us ... this election is a total lost cause.

Shameless plug ...

... if something scientific in this blog tickled your fancy, nominate it at Open Laboratory 2008. Please?

If I want a camera ...

... I'll use a camera. If I want a phone, I'll use a phone. I won't use my camera to make a call. I won't use my phone to take a picture. Capeesh?

Nothing is simple anymore, is it? Besides, these extra "upgrades" to devices drain their batteries that much quicker.

While cell phone talk times generally range from 3 to 7 hours, once you add in extra duties, such as Internet use and video, all bets are off when it comes to figuring out battery life.

China: Use at your own risk ...

Sooner or later we're going to realize that China just has no control of just about anything that comes out of it. That is, until people get sick and die. Most often innocent children.

And you know what, with their aggressive population control measures, I honestly don't think the government cares if a few hundred children die. The only reason they then hunt down and kill those responsible is to put on a good face for the world in a "Hey, we don't tolerate this sort of stuff, see?" sort of way.

The reason why things are so cheap in China? They cut corners. They've got to make a profit too, right? So what makes any of us think that they're not cutting corners? It's a don't ask, don't even think about it sort of environment businesses that deal with China work in. Disgusting.

I'm honestly starting to look at where everything I buy is made. I'm not always going to find items not made in China ... heck, I doubt I'll always find items made in America (they do still make things in America, right?) ... but I'm definitely going to try. Even if it costs me a bit more in time and money. I think my health is worth it.

Death of a Postal Worker

The Post Office may not be long for this life.

The Postal Service lost $1.1 billion in its latest quarter. That number would be even larger if it weren't for direct mailings, which now constitute 52 percent of mail volume, up from 38 percent in 1990. Revenue from direct mail "is the financial underpinning of the Postal Service—it could not survive without it," says Michael Coughlin, former deputy postmaster.

But 89 percent of consumers say in polls that they'd prefer not to receive direct-marketing mail; 44 percent of it is never opened.

That's definitely not a good sign for the Postal Service. Worse yet, there is a company which, for a minimal fee, will contact businesses and tell them you want to opt out of direct-marketing mail. They're called GreenDimes. According to their website:

With GreenDimes, you can stop up to 90% of your junk mail - guaranteed. We work with you and the largest group of marketers and catalogs — over 4,500 and growing — to make sure you get only the mail you want.

Not bad, definitely a start. Plus ...

With GreenDimes, you'll make the world a better place by saving paper. We help you go farther: new Premium members, we'll plant 5 trees on your behalf. It's like growing your own tiny forest, in exchange for all your junk mail.

Woo hoo! They're green to boot. Their Premium service? $20.