Wii update

Since MXX asked ...

Now that I have gotten over the initial disappointment of the whole Adobe/Hulu/Nintendo/Opera fiasco (they all still suck by the way), I'll focus on some of the more cool features of the Wii.

I love making Mii's. They're simple, but funny, and you can post them on the internet (there's a channel for that, and I forget what it's called at the moment) and people can vote for them if they like them. They also hold contests, giving "Mii Artisans" a theme and allowing them to submit Mii's that they developed based on the theme. I think it's cool.

We've tried two of our games: AMF Bowling Pinbusters! which totally sucked and Acme Arsenal which was tough to handle but interesting. AMF Bowling was way worse than the Wii Sports bowling. You can't use your Mii's, the characters repeat the same lines and actions after every turn and it gets annoying real fast. The Wii Sports bowling is much more fun. Fortunately we got AMF Bowling for under $10 (technically free because it was a "buy 2 get 1 free" promotion and that was our 3rd game).

Hooking it up to the internet was good because if you like old arcade games, the Wii has a virtual console which will allow you to buy a lot of old arcade games. Most run for $5 to $10. I got Golden Axe for $8 and it plays just like I remember it. I also got PacMan for $5. They have the Donkey Kong series, the Mario series, and about 80 additional games. It'd probably be cheaper to see if Midway or Atari comes out with a "Greatest Hits" collection, but eh ... I wanted instant gratification. They even have some old Commodore 64 games available for purchase/download ... so I'm so waiting for M.U.L.E. now.

Do the Republicans need something to rally around?

If so, why are they looking past the deficit?

The White House estimates that the government will rack up an unprecedented $1.8 trillion budget deficit this year. That would be more than four times last year’s all-time high.

Adobe sucks ...

... and to an extent, so does Nintendo. So, as I mentioned earlier, one of the draws for me was that the Wii could go online, which would allow me to check out sites like Hulu and possibly Netflix. Well, I knew that Netflix was currently off the table, but now I find out that the Wii cannot check out Hulu either because the Wii Internet Channel (powered by Opera) only runs on Adobe Flash v.7 and Hulu runs off Adobe Flash v.9. That means that while I can go to the Hulu site, all I get is a "Update Your Flash" message.

That sucks.

So, Adobe you suck for not opening up the source code for v.9 to let Opera make the necessary changes to their browser, and Nintendo you suck for not pressuring Adobe further into speeding up the entire process. Oh, and Hulu sucks for not coming up with a solution (like YouTube has) to allow the maximum number of viewers possible. And lastly Opera sucks for not demanding that their customer, Nintendo, get with the times.

The United States of China

Soon, no company will be American owned. Today, the Hummer division of GM was sold to a Chinese company. Does Hummer still make military vehicles? If so, does that mean that China will be making American military hardware? If so, that makes absolutely no sense whatsoever ... but this is the situation we find ourselves in, for better or worse.

I'm thinking worse.

I am addicted ...

... so I bought a Wii. And now all I can think about is the games I can get for it. Heck, I'm excited about the potential of being able to blog from it. How sad is that? Other than "pretty sad" that is.

So I hooked it up last night, and decided that I need a new widescreen LCD television to complement the Wii. Then I played Wii Sport which is a fun game ... you'll certainly break a sweat. It's easy to see why some people get hurt (or damage expensive living room items) playing the Wii. Then on to Wii Play. The only benefit to this game is the controller that comes along with it, and if I had known the game was lame, I would have ponied up the money for the controller and saved the other $10 to buy a used game which will have a longer lifespan in my game playing repertoire. The shooting gallery is fun, as is billiards, but everything else is sort of lame.

Oh, and I have to get Golden Axe on the Wii Virtual Console. I loved that game growing up!

Shoes

I like Red Wing Shoes. They're great, and durable. I've owned one pair of steel-toed Worx shows for about 7 years. They're getting up there now, and they're not as comfortable as they used to be, so I've been in the market for a new pair of shoes. However, after eight years of competitive Cross Country and Track and Field in high school and college, where I literally logged thousands of miles a year during that period, my feet and knees are shot. Not arthritic yet, but I would not be surprised if they eventually got there. So I prefer a shoe on which I can stand for long periods of time, but which leave my legs fresh. The Red Wings fit the bill, but they can be pricey. However, I have found that you get what you pay for.

Well, I stumbled upon a pair of Ecco's which were on sale, were stylish and which have turned out to be comfortable. They're pictured below.They're the Ecco Street Fusion Hydromax (#48804) and they're great. Got them on sale (just shy of a Benjamin), but they're living up to the praise people heap on this company. So perhaps I've found myself a new shoe.

Am I the only shoe snob out there (I also refuse to wear anything but Asics or New Balance when I actually do take to the track)?

h/t: Physioprof (over at Drugmonkey)

You too can go to Mars ...

I want to be an astronaut. I think it would cool. Slightly dangerous, but cool nonetheless. I doubt, given my "advanced age" (ok, I just feel old) I will ever get into space, which bums me out.

So, I'll do the next best thing ... I'll send my name to Mars. If you click on the link, you can too.

h/t: Science Cheerleader

I wonder why ...

... this is.

Obama has inspired a collective fawning. What started in the campaign (the chief victim was Hillary Clinton, not John McCain) has continued, as a study by the Pew Research Center's Project for Excellence in Journalism shows. It concludes: "President Barack Obama has enjoyed substantially more positive media coverage than either Bill Clinton or George W. Bush during their first months in the White House."

The study examined 1,261 stories by The Post, The New York Times, ABC, CBS and NBC, NEWSWEEK magazine and the NewsHouron PBS. Favorable articles (42 percent) were double the unfavorable (20 percent), while the rest were "neutral" or "mixed." Obama's treatment contrasts sharply with coverage in the first two months of the Bush (22 percent of stories favorable) and Clinton (27 percent) presidencies.

Is it because the media has shifted further towards the Left (as compared to the days of Clinton -- and possibly in reaction to Bush)? Is it possible that people don't want to be critical and have the race card played against them? Or is it something else?

Ok, one last post for today ...

... this is a truly awesome story.

By the 1980s, nearly one in three turtles that nested on Matura Beach were killed. When the government asked for volunteers to help protect the endangered creatures, Baptiste and several others answered the call. In 1990, they started Nature Seekers, one of Trinidad's first environmental groups.

What effect did they have?

Gradually, her message of conservation turned the tide of public opinion, and after nearly two decades under Baptiste's leadership, Nature Seekers has largely won its battle. Today, the leatherbacks' survival rate on Matura Beach is virtually 100 percent.

Over 5000 leatherbacks nest on Matura Beach a year now.

Here is their website: Nature Seekers.

Busy ...

... have two manuscript reviews I really need to finish today. Also need to finish the revisions on my own manuscript I hope to send out the beginning of next week. All the while I'm waiting for the peer-review to return on my last submission (110 days and counting ... WTF!). Busy times ahead, but I really will try to get my ASM overview (can I really call it a blog diary at this point?) done next week as well. At least it'll start me off with my May blogging on the right foot. Until then ... everyone enjoy their weekend.

The Wii and Netflix

I love Netflix, the Wii looks interesting. I already have Netflix and I'm probably going to get a Wii this weekend. Yay! My dream has always been to have a computer in my living room, hooked up to a nice big large screen LCD "monitor" and use it as a total home entertainment system. Part of the appeal of that would have been because I could then use the NetFlix "Watch Now" feature without having to sit in the office and gaze at the 17" monitor that my home computer is attached to (plus the current NetFlix software and need to use IE sucks).

The Wii has some very nice, rudimentary features (including WiFi capability that allows internet access) and I thought it would be great if I could access NetFlix and watch movies. If that were possible, I'd probably give up, at least for the near term, my desire to get a multimedia computer for the living room and focus on acquiring the LCD television.

Currently the Wii has no such feature, but that may change. So if anyone from Nintendo reads this blog ... allow the Wii to stream movies directly from Netflix, sooner rather than later. Please!

North Korea is on crack

North Korea's 150 Day Battle. I'm not exactly sure who they're fighting, but they seem to be really excited about it (or at least trying to muster some excitement ... though one can only imagine how much verve one can wrestle up on an embargo-related empty stomach). I like the poster that's quoted in the story (at the very end).

"Let's run like a storm, riding on a flying horse," one street poster said. "Let's all become winners in the 150-day battle."

Eh? What the hell does that mean? North Korea has pegasi? Or is it pegasuses?

I didn't get tagged with the meme, but damn it ...

... I'm going to do it anyways.

My vote is for Nirvana’s cover of Lead Belly’s Where Did You Sleep Last Night? (aka: In the Pines).

Currently ...

Listening ToBleed It Out
Yeah here we go for the hundredth time
Hand grenade pins in every line
Throw 'em up and let something shine
Going out of my f--king mind

Filthy mouth, no excuse
Find a new place to hang this noose
String me up from atop these roofs
Knot it tight so I won't get loose

Truth is you can stop and stare
Run myself out and no one cares
Dug a trench out, laid down there
With a shovel up out of reach somewhere

Yeah someone pour it in
Make it a dirt dance floor again
Say your prayers and stomp it out
When they bring that chorus in

I bleed it out, digging deeper just to throw it away
I bleed it out, digging deeper just to throw it away
I bleed it out, digging deeper just to throw it away
Just to throw it away, just to throw it away

I bleed it out, go, stop the show
Choppy words in a sloppy flow
Shotgun, I pull, lock and load
Cock it back and then watch it go

Mama help me I've been cursed
Death is rolling in every verse
Candy paint on his brand new Hearse
Can't contain him he knows he works

F--k this hurts, I won't lie
Doesn't matter how hard I try
Half the words don't mean a thing
And I know that I won't be satisfied

So why try ignoring him?
Make it a dirt dance floor again
Say your prayers and stomp it out
When they bring that chorus in

I bleed it out, digging deeper just to throw it away
I bleed it out, digging deeper just to throw it away
I bleed it out, digging deeper just to throw it away
Just to throw it away, just to throw it away

I bleed it out
I've opened up these scars
I'll make you face this
I pulled myself so far
I'll make you face this now

*cry*

I have to do another GenBank submission using Sequin. I hate Sequin.

Hate.

It. Burns. My. Brain.

Those Kooky Ruskies

Russian scientist thinks alien ship saved the planet Earth.

Dr. Yuri Labvin, president of the Tunguska Spatial Phenomenon Foundation, insists that an alien spacecraft sacrificed itself to prevent a gigantic meteor from slamming into the planet above Siberia on June 30, 1908.

The result was was the Tunguska event ...

His evidence?

Labvin thinks quartz slabs with strange markings found at the site are remnants of an alien control panel, which fell to the ground after the UFO slammed into the giant rock.

"We don't have any technologies that can print such kind of drawings on crystals," Labvin told the Macedonian International News Agency.

Okay. Anything else?

"We also found ferrum silicate that can not be produced anywhere, except in space."

Someone can correct me if I am wrong but ... don't meteors come from outer space?

As an aside ...

... watched Kung Fu Panda this weekend. It's hilarious!

Yah, I know ...

... I didn't exactly blog "real time" about the ASM General Meeting. Honestly, from all the walking I did, I was dog tired every single day I was in Philly. By the time dinner was over and I brought my butt back to the hotel, I was zonked and out until the next morning.

With that said, I will talk about the highlights of the entire meeting (as I determined them to be) over the next couple of days. If you are really interested in the meeting, you can buy all the symposia (audio with slides) from Sound Images here. It's $299 for the entire conference.

For now, I have a review I need to do, as well as some patent work.

Memorial Day Tribute

Prayer of a Soldier in France
by: Joyce Kilmer

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

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

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

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

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

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

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

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

A Soldier of France to His Mother: Letters from the Trenches on the Western Front.
by: Eugène Emmanuel Lemercier
translated by: Theodore Stanton

"March 21

Dear Grandmother,
As the hour of trial approaches I seize the occasion to send thee my whole love it is all that I can do The situation is going to demand sacrifices in the presence of which we must forget all that binds us elsewhere But let us pray that the certitude of the Beautiful and the Good does not abandon us in the midst of our sufferings."

ASM General Meeting Blog Diary - Day Two

ASM "officially" opened on Sunday at 5 pm with the opening lecture. There were three presentations, all of which were stellar and revolved around the celebration of Charles Darwin. Unfortunately I didn't bring my notebook with me for the opening lecture, so I have very little notes other than the ones I put into my cellphone. of course all three lecturers have a multitude of publications so finding and reading their work won't be much of an issue.

The first talk was given by Nancy Moran of the University of Arizona. Her talk revolved around microbial obligate symbiosis with their insect hosts. She presented some fascinating research conducted in her lab (visit the link above for a glimpse). Next up was W. Ian Lipkin of Columbia University. His talk was entitled "Microbe Hunting in the 21st Century". Aside from the technical hiccup which meant that the last quarter of the right side of each slide was off the screen, his talk was also fascinating. He spoke about the various techniques his lab has employed for detecting a variety of existing and emerging pathogens. What I found particularly interesting was his mentioning of seasonal effects of schizophrenia and how it ties in with influenza season. Essentially there appears to be a correlation between the immune response and influenza infection in the womb.

The ASM Lecturer for 2009 was A.H. Knoll of Harvard who gave a bio-geo-paleontology lecture examining microbial life throughout the lifespan of the Earth. Simply put, there is evidence of microbial life for roughly 3.5 billion years. Of course, as a fan of astrobiology, this was very intriguing, and he hinted at performing such work. I'm jealous!

Overall, it was a wonderful opening session, the best I've attended.

Food-wise, it was also a great day. Went over to the Reading Terminal Market and visited Carmen's. Had my first cheese steak and it lived up to expectations. Got it with provolone cheese and roasted hot peppers. Good stuff! Prior to the session I took a short tour of Philly and went to the Academy of Sciences Museum. They have some great dinosaur exhibits (I got pictures on my cell phone so they're not the best quality) and the price to get in wasn't bad ($10). Not a bad day at all!

ASM General Meeting Blog Diary - Day One

Before I talk about the Workshop that I attended today, let me say one thing. Oh, and I hope that people who were responsible for setting the workshops up read this. Whoever had the brilliant idea of housing the workshops at Temple, and then thought it was a good idea to not have shuttles on Saturday to and from the workshops ... is an idiot. This was by far, one of the dumbest things that they could have done. Temple University IS NOT, IS NOT, IS NOT in a good part of town. Telling people they needed to take public transportation, or a taxi, to and from these workshops was a supremely dumb idea. Add to this the fact that a majority of the people who attended these workshops were not Philly natives, and you had a lot of lost people wandering those streets. That was inviting disaster, and if no one got mugged, it was a miracle.

Me? I walked from my hotel to the workshop. It was a two mile walk and I didn't have to go to far to remember that I hate large cities. One block from my hotel, passed the first individual passed out on the sidewalk, three blocks from my hotel, passed a puddle of slowly drying vomit. And the smell ... it was humid so the stink hung in the air. It smelled like your typical large city, like wet trash, and not just any trash ... if you;ve ever worked in a restaurant, and went near the dumpster ... that sort of smell. Bleh. When people talk about the sights and sounds of big cities, I don't know where they're looking at, or smelling.

Having grown up in NYC (Brooklyn and Queens), I know the rules of engagement. At all times, act like you know where you're going. If you're lost, act like you know where you're going. Do not act like a tourist, do not make eye contact with people on the street, do not respond to cars which pass by ... go directly from Point A to Point B. So when I approach Temple and I see cabbies dropping clearly lost people out on Broad Street, I thought "What a freaking mess." and tried to point out to people where they needed to go.

There was breakfast prior to the workshops in the morning, in the student center, but no signs pointing the way. Oy! Basic fare for breakfast, fruit, juice, danishes ... nothing to get excited over.

Then off to the workshop. I was in WS-04: DNA Sequence-Based Identification of Bacteria: Generation, Analysis of Data, and Interpretation of Results. Dag Harmsen of the University of Münster was the organizer. It was a good overview of sequencing, and phylogeny, and if you're new to sequencing, it's worth a looksee if they offer it next year. Most of it I already knew, but it was good to get some review and since we're encouraged to review and place such stuff on our IPP (Individual Performance Plan) and I was going to be at ASM anyways, I figured what the hey. It was geared primarily towards the clinical lab, though they did talk about phylogenetic analysis, and discussed matters purely from a direct sequencing approach (assuming pure samples, which means no talk of cloning and chimeras). Nothing really exciting or out of the ordinary, except for the one dude asking about dominant and recessive genes (eh?), and the dude from NCBI getting his knickers in a twist when it was mentioned that in a lot of cases, GenBank is a mess. He tried to cover NCBI's ass by talking about their new RefSeq project ... yah dude, but for a lot of 16S stuff, Genbank still sucks. Anyways.

Oh, the other annoying thing was that even though they said there would be WIFI available, there wasn't. Highly annoying, and when it was pointed out to the staff, they acted like they didn't know anything at all. Also highly annoying. That was however, the only hiccup in the entire day. Boxed lunch, and then finished out the workshop and walked back to the hotel. Hopefully no one died getting back to their own hotels.

After that, freshened up and set about the town. Took in more of Chinatown, and ate dinner at Ly Michaels which was a nice modern Asian cuisine restaurant. It was a bit pricier than the place I ate the night before ($12.95 for the main course, as opposed to the $6.95 Pho) but still reasonable and excellent. Had the summer rolls with hoisin sauce and the curry chicken. Both excellent! A good way to end the day.

Tomorrow, more sight seeing and dining. Going to make it to the Reading Terminal Market for a cheesesteak!

ASM General Meeting Blog Diary - Day Zero

Nothing doing with the American Society of Microbiology General Meeting today, but I did have to travel to Philadelphia. Man, what a trip. First, let me say that I hate Mapquest. I didn't pay attention when I printed out the directions, so I get half way and then I notice that every major city I have to go through, Mapquest has directed me around. So I have to get off one highway, get onto another, get off that one, get back onto the main one. And I have to do this three or four times. That is a pain in the tookus, especially when I'm traveling alone, the roads are crowded, and I have to now read directions and drive?

Ain't gonna happen.

Fortunately for me, I was just recently handed my BlackBerry, and it has an application called TeleNav on it.

TeleNav sucks.

Hard.

So I figure that there is no way I'm going to read directions while driving through major cities, so I pull into a rest stop, I pull out my BlackBerry, open up TeleNav and punch in the address to my hotel. TeleNav tells me to get back on the road and all is good for the first 30 miles or so. Then, as I'm approaching the first major city on my route, it directs me to a highway that I've never heard of. I figure it knows what it's doing, so I follow it. About 10 minutes later and I'm freaking downtown! I'm not on the highway, I'm on the side streets of a major city, and it's freaking packed. Kids are graduating from college and there are tons of people in the streets, which means there are a ton of cars ... and my GPS is navigating me through this crap ... constantly telling me of accidents 5 miles up the road and that I may encounter some congestion. Whiskey! Tango! Foxtrot! What are the hundred cap-n-gown wearing kiddos walking on the curb, if not congestion?!?!?!!!!11!!!

So, I finally get back to the main highway (why it needed to take me downtown to get back on the major highway I have no freaking idea), and everything proceeds smoothly until I hit the next major city, and before I know it ... I'm downtown again! Jimminy Crunchy Fishsticks! So I spend another hour and a half navigating another downtown traffic mess.

I finally make it to Philly, and I'm about 10 miles away from the hotel. What should TeleNav do? Oh, and I expected this would happen ... it freezes up on me. Now I'm on the last stretch of I-95 and I have no idea where the heck I'm going. Oy vey! The hate, it burns my brain!

Despite TeleNav's best efforts to kill me I eventually make it to my hotel, to find out that they don't have a parking garage (Yah, I guess I should have checked that ... grr). And I also find out that I left all my forms at work on my desk! Call work, the secretary faxes them to the hotel (so I can hand in my tax exemption form), and I have to pay $24/day for valet parking (I better get reimbursed for that!).

Get my crap up to the hotel room and inquire about dinner. Fortunately there was stuff down the block, and I came across a nice little Thai/Vietnamese place. Ordered some Pho (it's pronounced "Fuh" as if you're about to tell someone to do something really nasty to themselves) and it was just like I remembered it, which was excellent*. I hadn't had Pho since graduate school (some five odd years ago at this point). Reminded me of some of the not-so-good 'ol days. Heck, the best part of those days was the section of town called "Little Vietnam" with the excellent restaurants, shopping markets, and bubble tea shops.

So, while the day sucked it ended on a good note. I just might have Pho tomorrow night too. So, that was Day Zero. Tomorrow, ASM Workshop day, where I have to wake up at the buttcrack of dawn to get a bus to get to Temple University for the class, because ASM isn't offering shuttle service tomorrow to the workshops. Grrr!


*If you've never had Pho, start simple ... flank steak and brisket. You can eventually move up to the tendon and tripe.

Yeah Carrie Prejean ...

... you should do what Shanna Moakler did. Pose for racy pictures* AFTER you do your stint as Miss Cali**.

"I want to be a role model for young [women] with high hopes of pageantry, but now feel it more important to be a role model for my children."

Yah, because allowing Playboy to objectify you for millions of men is really setting a sterling example for young girls across the country. Oh please. Besides, what a senseless bit of stupid drama***, but that's what you get when anything involves Perez Hilton. Drama. Does anyone even really care about the Miss America pageant anyways? Anyone? Anyone? Oh, and Donald, you don't count.



* According to WIKI, she was December 2001's Playmate of the Month.

** SARCASM for the humor impaired.

*** The question Perez Hilton asked was a valid one, and Carrie Prejean should have responded in a much better fashion, but the resultant outcry from people like Perez Hilton and Shanna Moakler, milking it for all that it was worth for their 16th minute of fame, was pathetic.

They're back ...

I haven't blogged about them, but they've been back for at least a couple of weeks now. My chimney swifts have returned. I assume they're in the process of building a nest, laying eggs, and adding to their numbers. I'm fine with that.

If you want to play a small role in wildlife conservation, it is as simple as removing the chimney cap off the top of your chimney. If your chimney isn't made of metal, you may wind up having a chimney swift family take up residence. They eat a third of their own weight, a day, in flying insects ... so they're a boon to your backyard.

Chimney Swift Information (PDF, 4 pages).

The Origin of Life: RNA?

So says John D. Sutherland, chemist at the University of Manchester.

Scientists have long suspected that the first forms of life carried their biological information not in DNA but in RNA, its close chemical cousin. Though DNA is better known because of its storage of genetic information, RNA performs many of the trickiest operations in living cells. RNA seems to have delegated the chore of data storage to the chemically more stable DNA eons ago. If the first forms of life were based on RNA, then the issue is to explain how the first RNA molecules were formed.

So how did they (Matthew W. Powner (lead author) and Beatrice Gerland co-author)) do it?

Instead of making the starting chemicals form a sugar and a base, they mixed them in a different order, in which the chemicals naturally formed a compound that is half-sugar and half-base. When another half-sugar and half-base are added, the RNA nucleotide called ribocytidine phosphate emerges.

A second nucleotide is created if ultraviolet light is shined on the mixture. Dr. Sutherland said he had not yet found natural ways to generate the other two types of nucleotides found in RNA molecules, but synthesis of the first two was thought to be harder to achieve.

Article is here. (PDF, 4 pages, Subscription Required). The abstract:

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the ‘RNA world’ hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that ‘activated’ ribonucleotides can polymerize to form RNA it is far from obvious how such ribonucleotides could have formedfrom their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis—cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate—are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence fromthe start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

Cool work. As the Times article states, a lot of people figured that RNA was the first organic molecule formed that started the "chain reaction" called "life", there just was very little evidence that it was possible. This article changes all that.

I smell a Nobel.

Reference
Powner, M., Gerland, B., & Sutherland, J. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Nature, 459 (7244), 239-242 DOI: 10.1038/nature08013

Pay those in the minority no mind ...

The Notre Dame and Obama fiasco.

Gibbs also cautioned the press to recognize that those who are against the Obama's visit are in the minority. "I think it's important to understand it appears as if the vast majority of students and the majority of Catholics are supportive of the invitation the president accepted," he said. "And I know he's greatly looking forward to -- to seeing them."

Is this the message the Democrats want to send? "You don't hold the popular opinion, therefore we shall pay you no mind. Better yet, just go away"

Social Security ...

... to go belly-up sooner than expected?

A year ago, the trustees projected that the Social Security trust fund would start paying out more in benefits than it collects in taxes in 2017 and that the trust fund would be depleted in 2041.

Yah, right around the I was set to retire, go figure. But hey ... guess what?

But many analysts said the worst recession in decades will produce a bleaker forecast for both Social Security and Medicare in the new trustees' report. The downturn has resulted in a loss of 5.7 million payroll jobs since it began in December 2007 and an unemployment rate that hit a 25-year high of 8.9 percent in April.

Ah yes ... by the time I retire Social Security won't be around any longer. Fun stuff! Let's see if we can spend our way out of this one!

Sonofa ...

... frak! Isn't this the way things always go? First you drop a hundred and change on a new set of front tires. A day later you notice a slightly sweet smell coming from your vents. You turn the car off, return an hour or so later to find a mysterious, huge puddle underneath your car, and it's definitely not water. The liquid, whatever it is is slick, clear, and odorless. Oh, and you check your radiator fluid and there isn't a single drop in the reservoir. Oddly enough, you had the water heater replaced about two months ago to the tune of ~$400 because you own a Pontiac and they built the thing such that to replace the water pump, they need to take the timing belt off, and that's one hell of an expensive repair.

So, could I be so lucky as to have a simple burst hose? Doubt it. If the new water pump is defective, that means that while I may not have to pay for the part, I'll get stuck with an ~$300 labor charge repair.

At this point, is this damn car (12 years old, 120K miles) worth it?

A sobering reminder ...

... to those of us who work (and more importantly supervise those who work) in the lab. It's not child's play, people can get hurt and sometimes killed.

Among the findings of the October lab inspection was that PPE was not fully used in the lab in which the 23-year-old Sangji worked. She was not wearing a lab coat in December when pyrophoric material she was handling splashed and ignited her clothing.

The Cal/OSHA report says that, when the incident occurred, Sangji was drawing approximately 20 mL of 1.7 mol/L tert-butyllithium in pentane into a 60-mL syringe when the syringe plunger was either ejected or pulled out of the syringe. An undetermined amount of the liquid splashed onto her hands, arms, and torso. The ensuing fire burned more than 40% of her body. One of the postdoctoral researchers used his lab coat to extinguish the flames and called for help. Sangji died of her injuries on Jan. 16 (C&EN Online Latest News, Jan. 22).

Safety standards, and safety issues are not something to be brushed aside as trivial. Sometimes, it is the difference between life and death.

The New Star Trek Movie ...

... was awesome! The special effects are wicked cool, the acting is pretty good (better than the original, which isn't saying that much), and the plot is pretty interesting as well. Suffice it to say, I predict there will be at least one sequel, and they came up with a pretty interesting way to ensure that it doesn't hinder the established Star Trek canon. I promise not to post any spoilers! The only thing I'll say is that Kirk does manage to get his ass kicked a lot in this movie.

Anyways, while I enjoyed the movie for the action, it got me thinking on the way home. Not because there is any deeply moral question posed by the movie, but because it painted a future Earth that looked believable, and I was envious. I do not believe that for a single minute that we, as a species, have reached our pinnacle. I believe there is a lot more maturation our species can do and an equally large amount of technological advances we can make. I also don't believe I'll see these advances in my life time, but boy do I wish I could see them. It's not that I'd want to live forever, but I contend that life is simply too short to fit in everything that one could do. At least, this is the way I feel.

So, unless they manage to build a warp drive spaceship within the next few years, I'll only be able to dream of the future, instead of live it.

Hi ho, hi ho, off to ...

... make an ASM poster I go.

Super busy this week, so very little blogging. I hope to, however, blog about the goings on at ASM's 109th General Meeting in Philadelphia from May 16th through the 21st however.

Why should we care what the White House has to say ...

... about baseball? I mean really? Hey Gibbs, you ever heard of the response: "We're more focused on -- and concerned about -- the economy, Pakistan, Afghanistan, and the piracy issues plaguing the Gulf of Aden. Baseball isn't really on our radar right now."? I gather not. Sheesh.

Gibbs said any case where an athlete is using a drug to get ahead is a tragedy, a shame and a great embarrassment to MLB.

No duh Gibbs, but it looks like Manny wasn't doing it to "get ahead". You stupid fool.

Interesting blog entry ...

... over at Science Cheerleader about Twitter.

Her entry is about a student at U. Wisconsin-Madison, Adam Wilson, who twittered using only his mind. Neat.

h/t Science Cheerleader.

White House Task Force on the Middle Class

Green Jobs and the Middle Class (Feb 27th, 2009), viewable at C-Span here. I'd skip the first 37 minutes (most of it's VP Biden and other politicos blathering on and on), and focus on the middle 35-40 minutes where the invited speakers discuss green jobs. The best part of the discussion starts around 47:30 (and lasts for about 10 minutes) with Van Jones, Founder of Green for All.

The White House LiveBlogged the event, so you can use that as a time frame for choosing what you want to view.

Journal of Negative Results

Currently I've been able to find two such journals.

Ecology
Journal of Negative Results

Biomedical Sciences
Journal of Negative Results in Biomedicine

Anyone know of any others? I'm sorely tempted to submit something to the first one, if I come up with a study that doesn't prove useful in any other way. Though I'm not sure that my research leader would allow it.

Scientia Pro Publica - Carnival Issue #3

The Scientia Pro Publica Blog Carnival (Issue #3) is up. This time it's being hosted by Bob O'Hara of Deep Thoughts and Silliness, and yours truly has a blurb in it based on this post. Check it out, and thank Bob O'Hara for hosting it.

New Continent Discovered in Pacific Ocean

Only problem is, it's made entirely of plastic.

A high-seas mission departs from San Francisco next month to map and explore a sinister and shifting 21st-century continent: one twice the size of Texas and created from six million tonnes of discarded plastic.

Whiskey. Tango. Foxtrot.

Coolness abounds though, thanks to the efforts of Scripps and Brita:

With a crew of 30, the expedition, supported by the Scripps Institution of Oceanography and Brita, the water company, will use unmanned aircraft and robotic surface explorers to map the extent and depth of the plastic continent while collecting 40 tonnes of the refuse for trial recycling.

If that recycling proves to profitable it could be a boon! There are six million tonnes (at least) of plastic there, and we could tap into it all. Remember my post about limited resources? Bringing those resources back to the United States, and converting them for use by our country (and then keeping them here) would be great. These are, I believe, the technologies we need to work on if we're to stay relevant in the world economy of the future.

China?

I tried to think of reasons why I would want to visit China. The Great Wall is obviously one reason. The Terracotta Army is another. However, none of these sights are worth risking my entire vacation (and all the money I would spend on it) and my rights as an individual, on the whims of the Chinese government.

"In many cases we have gotten reports that they were being quarantined for the sole fact that they had a Mexican passport, whether or not they came from Mexico, whether or not they had been in Mexico, whether or not they had been in contact with someone else from Mexico," Guajardo said.

Hello Mercury ...

NASA's MESSENGER makes another pass by Mercury. Click here for MESSENGER's Mission page.

Combining observations of Martian crust recorded by MESSENGER and those recorded by Mariner 10 in the 1970s reveals that at least 15 percent of the planet’s surface is covered by a relatively blue, dim compound. Most of it is concentrated in craters and adjacent regions splattered with material excavated from craters. Solomon says the most likely candidate is a titanium-rich oxide that originated one to 10 kilometers below the surface and was exposed when space debris bombarded the planet.

The presence of titanium oxide would suggest that during Mercury’s first 100 million years or so, while the planet was still forming, it was hot enough to generate a magma ocean, with much of the surface and the interior liquid, comments Linda Elkins-Tanton of MIT. Titanium oxide would have been one of the last compounds to solidify, and it might have remained just beneath the surface.

MESSENGER is slated to make another pass of Mercury in September.

Just cut it in half ...

Halving carbon dioxide emissions by half by 2050 could stabilize global warming.

To contain global warming, and its risks and consequences, warming compared to pre-industrial times (pre 1900) should not exceed two degrees Celsius. Although, according to the reports of the Intergovernmental Panel on Climate Change (IPCC), there is no specific temperature threshold for dangerous climate changes, and the negative effects are gradually increasing, over one hundred countries have adopted this “2°C target”. Scientists have used a new probability model to calculate how much CO2 our atmosphere tolerates under these target specifications. This and another study, recently published in Nature, produced similar results: From 2000 to 2050, a maximum of 1000 billion tonnes of CO2 may be emitted into the atmosphere. Roughly speaking, today, around one third of this wad has already been shot.

One third of this wad has already been shot? WTF kind of reporting is this?

Agricultural Research

I'm all for increased spending for medical research, however I don't think it should come at the expense of, or the ignoring of, agricultural research. Why should we continue to invest in agricultural research? According to the Research for Development (UK) website:

Agricultural research is a particularly good way to spend aid money. The Surr Report cites research showing that the cost of lifting one person out of poverty through agricultural research is US$180-190 per person compared with the US$2,304 per person for lifting one person out of poverty through aid spending in general. According to the World Development Report 2008, investment in agriculture research has "paid off handsomely," delivering an average rate of return of 43 percent in 700 development projects evaluated in developing countries.

Those are some pretty good returns. Nevermind that no amount of medical research is going to save a person from starving to death.

Ethanols impact on food and greenhouse gases

A report from the Congressional Budget Office was released in April, 2009 with the title "The Impact of Ethanol Use on Food Prices and Greenhouse-Gas Emissions" (PDF, 26 pages). Here are a few exerpts:

Rising demand for corn also increased the demand for cropland and the price of animal feed.

Those effects in turn raised the price of many farm commodities (such as soybeans, meat, poultry, and dairy products) and, consequently, the retail price of food. Pushed up in part by those effects and by surges in the price of energy, food prices rose by almost 2½ percent in 2006, by 4 percent in 2007, and by more than 5 percent in 2008. That those increases coincided with higher prices for corn raises questions about the link between ethanol production, the demand for corn, and food prices.

Also:

Changes in food prices affect spending for federal food assistance. The federal government administers several assistance programs that are operated at the local level by state agencies and other providers. The largest of those programs are SNAP and the National School Lunch and School Breakfast Programs. Federal reimbursements and benefits for those programs are adjusted automatically each year according to the change in various food price indexes. The change in food prices from 2007 to 2008, the period covered by this analysis, determines the benefits for those programs for fiscal year 2009. As a result, the rise in food prices attributable to increased production of ethanol will lead to higher federal spending for those programs: specifically, an estimated $600 million to $900 million of the more than $5 billion increase in spending projected for fiscal year 2009 as a result of the rising price of food.

... and ...

Although WIC assistance is funded through a different mechanism than are SNAP and the school programs (WIC is not an entitlement program but instead receives an annual appropriation), ethanol’s effects on the cost of the basket of goods available through WIC could be similar to the impact that its production has had on food prices in the other federal nutrition assistance programs.

So not only did we see an increase in food prices, something I've been arguing for awhile now, but it's also impacting government programs. That increase in prices (totally up to a billion dollars) will do one of two things: either more money will need to be diverted into those programs (at the tax payers expense, in a time of already bloated budgets), or people who benefit from these programs will see a cut in services as there will not be enough money to go around. To me, neither option seems particularly appealing, but I see no other options.

So, despite the bad news, is there anything good coming from this?

Research conducted by the Argonne National Laboratory (ANL) and used by federal agencies suggests that in the short run, the production, distribution, and consumption of ethanol will create about 20 percent fewer greenhouse-gas emissions than the equivalent processes for gasoline. For 2008, such a finding translates into a reduction of about 14 million metric tons of carbon dioxide and equivalent gases (a standard measure of greenhouse-gas emissions), or CO2.

But, don't celebrate just yet ...

In the long run, the result is less clear. If increases in the production of ethanol led to a large amount of forests or grasslands being converted into new cropland, those changes in land use could more than offset any reduction in greenhouse-gas emissions— because forests and grasslands naturally absorb more carbon from the atmosphere than cropland absorbs.

So, in the short run we're benefiting from the use of corn-based EtOH from a climate change aspect, but that could easily be erased. They do go on to discuss the potential for cellulosic ethanol, which is the preferred route to go (it could replace corn-based EtOH) and uses waste which would otherwise rot and be converted to carbon dioxide and methane by biological processes.

The report then goes on to discuss the viability of the EtOH-as-Fuel market.

The Congressional Budget Office’s (CBO’s) analysis of current technologies and prices suggests that, without subsidies for producing ethanol, the “break-even ratio” of the price per gallon of retail gasoline to the price per bushel of corn is currently about 0.9. In other words, when the price of a gallon of gasoline is more than 90 percent of the price of a bushel of corn, it is profitable to produce ethanol. At that point, revenues from the sale of ethanol would be sufficient to cover the fixed and variable costs of producing it.

So?

It is unlikely that, on average, ethanol producers over the past several decades would have turned a profit if they had not received production subsidies. The average ratio of a gallon of gasoline to the price of a bushel of corn fluctuates substantially from year to year and has exceeded 0.9 only once, in 2005

Click on the attached figure below.So currently, EtOH is only viable thanks to government subsidy.

At the current subsidy of 45 cents per gallon of ethanol produced, the break-even ratio that would allow producers to cover their fixed and variable costs falls to 0.7.

So, what do we have? We have a fuel which increases demands on our food supply which increases prices on food and government programs. It is also currently only profitable given government subsidies. Lastly, it has so far shown benefits in terms of climate change, but those could easily be wiped out with massive land clearing for more corn production.

I'll leave it to you, reader, to judge for yourself whether or not EtOH is the fuel of the future.

Jerk of the Week

This award goes to two individuals:

1. Thomas O'Donnell
2. Aaron Reich

Both formerly of the California Highway Patrol. Why? Sending accident scene photos (showing a dead 17 year old girl) to friends and family. What a pair of insensitive losers. I also highly doubt that they did so as a "cautionary tale" to their friends and family.

Jerks. Losers. Shame on both of them.

The stupid, it burns ...

... over at New Scientist. It appears that Debora MacKenzie suffers from a lack of reading comprehension ...

So what are we to make of US Secretary of Agriculture Tom Vilsack saying: "There is no evidence or reports that US swine have been infected with this virus"?

This quote comes directly from Secretary Vilsack's release to the public about the safety of pork for human consumption, Release No. 0137.09. Taken in context, it reads as follows:

"I want to reiterate that U.S. pork is safe. While we in the U.S. are continuing to monitor for new cases of H1N1 flu, the American food supply is safe.

There is no evidence or reports that U.S. swine have been infected with this virus. USDA is reminding its trading partners that U.S. pork and pork products are safe and there is no basis for restricting imports of commercially produced U.S. pork and pork products.

This is not an animal health or food safety issue. This discovery of the H1N1 flu virus is in humans. Any trade restrictions would be inconsistent with World Organization for Animal Health (OIE) guidelines.

Regardless, Secretary Vilsack is correct, as far as I know when he says that there is no link between this current H1N1 virus and American swine. Whether or not it was ever in American swine is irrelevant, because that particular strain (or more likely strains) didn't jump from pigs to humans. If you compare those strains to the current strain causing all these problems, there will no doubt be some major differences which will explain why the former wasn't deadly to humans, and the latter is.

What is even more amusing is one of the comments, obviously made by a PETA member (MarkInColumbus), where he rants incessantly about "Animal Agriculture". It seems that he wants to wipe all animals off the face of the planet because they're evil ... with their belching and farting of methane, their propensity to drink water, and their ability to cause cancer, stroke, heart disease, and diabetes by transfixing their big bovine/swine/ovine gaze upon poor defenseless humans.

Jimminy Christmas!

And damn the animals to hell, why do we need them? I mean, we can just convert fossil fuels into ammonia and use it for fertilization ... I mean that won't hurt the environment none. No sir!

Better to keep your mouth closed and be thought a fool than to open it and remove all doubt.

Words of wisdom MarkInColumbus, words of wisdom.

Oh, and it appears that Debora MacKenzie likes blaming random animals for our viral woes. In 2006 she blamed migratory birds (geese in particular - the damned fowl) for spreading H5N1, and blamed ornithologists for being complict in their denial of the facts. Gee, sounds sort of like a regurgitation of this latest story, no?

ETA: Time has a piece on pigs and H1N1 as well: Don't Blame the Pig.

ETA2: Two hours later and they have not posted my response to MarkInColumbus.

Sweet Release

All I need to do is finish the figure legends and then I can get this manuscript out to my collaborator! Within the next couple of weeks this manuscript should be on its way to the journal! w00t!

ETA: Done, and out!

ETA2: A couple of more hours and my ASM poster will be finished, and then it's time to move onto the next manuscript.

What mission?

"It's clear that the mission created confusion and disruption. I apologize and take responsibility for any distress that flight caused," Caldera said in a White House issued paper statement.

Yah uhhh ... exactly what would that mission have been? A photo opportunity? Good Lord.

GenBank Lesson for the Day - Ok, it's a rant

GenBank can sometimes be very usefulless. Ok, maybe not useless*, but a general pain in the toosh. Case in point ...

Our lab is doing some real time PCR to examine the gene densities of denitrification genes in a number of environments. In order to do so you need to make plasmid standards which will allow you to generate a concentration curve based on dilutions of that control plasmid. Then you can take your environmental sample, run the real time PCR on it with that particular primer set and match up the Ct value with your standard. From that, you can figure out how many copies you have in your sample (per mL, per g, per ng DNA ... whatever you choose).

What is important is that your plasmid be what you think it is and not just some amplified product of the correct size which works with the primers but was actually an unrelated gene. How can this happen? Well, the primer set for nirK ... the original manuscript published on that primer set uses amplification conditions starting at 43C and stepping down to 40C. That's not exactly a stringent condition, and so you get a whole mess of crap amplifying. The first time we tried it, we had a product of roughly the correct size but upon sequencing hit some gene encoding an enzyme in Nitrosomonas eutropha, and it wasn't nirK. As a matter of fact, the reverse primer was a 100% match to this particular non-nirK gene. Yah, that sucked.

At any rate, we started over again and got a better band. [If you read the original manuscript they don't even gel visualize their PCR products ... they did southern blots ... and claim that if you concentrate your sample down far enough you'll see a really faint band along with a huge smear. Ok, great ... thanks for that]. So, we did that, got a product, cloned it and shipped it off for sequencing.

The sequences came back today and I began analysis. So the first thing I did was blastn (BLAST against the nucleotide database) our data against GenBank. They came up, fortunately, to "nirK sequences" ... but they were all from uncultured isolates. Knowing the mess we had previously gone through I wasn't satisfied with that. There are a lot of things out there in the GenBank database which are not what they say they are (it's a non-curated database after all) so I wasn't taking that for an answer. So, I did a blastx (translate our DNA sequence to protein sequence and BLAST against the protein database) and came up with NirK, once again all from uncultured organisms. If it's uncultured, how did they get protein from it? Well, 99.9999% of the time they didn't ... it's just a translation of the nucleotide data and it hasn't been verified. Therefore there is no guarantee that the protein is what it is since the database is not curated. For example, if you submit a sequence that you claim is nirK, then the protein translation is NirK, even if the gene you accidentally cloned is fucK (for the sake of argument**, and an eventual pun). And from that point on, everyone who accidentally clones fucK thinks they have nirK, but they don't. Leaving them fucK'd. Add to this the fact that they'll submit their fucK'd sequences as nirK and you see how this can eventually snowball out of control.

And don't think that can't happen because it has happened before ... the first complete microbial genome ever sequenced, H. influenzae claims to have two lactoferrin binding protein operons. Problem is, it actually doesn't ... one of those operons encodes for a pair of transferrin binding proteins, it was just mis-annotated ... and will be forever. How many other sequences were subsequently mislabeled based on that GenBank comparison?

So just because GenBank told me at this point that I had nirK, I was not satisfied. What you need to do at this point is do a blastx but under the "Choose Search Set", select "SWISSPROT protein sequences (swissprot)" as opposed to the "Non-redundant protein sequences (nr)" most of which we now know are not really protein sequences but are rather unverified translations from nucleotide sequences (and there are distinct differences between the two). Why SWISSPROT? According to their website:

UniProtKB/Swiss-Prot; a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.)

It's a manually curated database of actual protein sequences. So while you won't get a large number of results, the results you get will have been verified many times over.

Fortunately for us, SWISSPROT informed us that our sequence did indeed match a curated NirK protein (from A. faecalis). Yay us!

So, a final word of caution. GenBank can prove to be very useful, but only if you take your results with a grain of salt ... and you're conscious of what the data is telling you. Knowing how to best frame your question so you can get solid results is also a very important skill when utilizing GenBank.

*It's a highly useful repository, but it's got some major flaws which can cause some big headaches if people aren't aware of them.

**As far as I know, fucK which encodes fuculose kinase and nirK which encodes a nitrite reductase do not share any sequence similarity so having this occur is infinitesimally slight.

The NFL Draft

So the Jets drafted Mark Sanchez in the 1st round (trading away essentially no one of note) and then picked up Shonn Greene in the 3rd round. They're set for at least the next year or so with Thomas Jones at RB*, but I wonder if this means we'll see a two back setup like the one that the Carolina Panthers employ. I also wonder what this means for Leon Washington.


*Of course now I'm reading that he's not exactly happy with his contract situation.


On a side note, Oliver Perez (SP for the NY Mets) sucks. We paid how much for this guy this offseason? I'd like to note that we could have had Derek Lowe for about the same price, and Lowe is currently 2-1 with a 3.10 ERA while Perez is currently 1-1 with a 8.50 ERA. Oh, and Jerry Manuel says the Mets pitching must improve. Yah well, Jerry ... that's like saying a bunch of illiterate individuals better start reading more proficiently. They can't do it better until they start doing it in the first place! Aside from Santana, the Mets have NO. STARTING. PITCHING.

Currently ...

Listening To

Hysterical

Oh man, I've got to stop laughing ... it hurts!

h/t PsD.

Come on guys ...

... it's a little bit of paperwork/legwork and wasting taking time to fill it out/do it would be worth it in the long run. It'd also save you from being publicly embarrassed, ya?

Vander Linden said the investigators know that several years ago an entire freezer full of biological samples broke down and all the samples had to be safely destroyed. But a complete inventory of what was in the freezer was not done before the samples were destroyed. Vander Linden said there's a "strong possibility" the vials were in that freezer and destroyed, but that isn't known for sure.

Where I work, we need to keep a complete inventory of what microbial isolates we have on hand*. As species/strains enter and/or leave the lab, the list needs to be updated. It's a bit of a pain in the toosh ... especially when we're talking about having to keep track of things even as simple/safe as E. coli K-12, but it's better than the alternative ... losing a sample and having it hit the news.

*I can't believe that I'm going to give kudo's to Microsoft but ... MS Access comes in really handy with this. It also helps in our chemical, plasmid, and primer inventories as well.

WTH?

Who in their right mind, when submitting the 16S rDNA gene sequence for a type strain, submits a sequence riddled with N*'s? It's a type strain for crying out loud ... you can't make sure you've got a clean sequence? I mean, WTF folks ... combined, a new forward and reverse read would cost you $7. You lazy sons of motherless goats.

Idiots!

*According to IUPAC nomenclature, N stands for aNy nucleotide, which certainly doesn't narrow the field for that position.

A Tale of Two Brothers

Once upon a time two brothers who lived on adjoining farms fell into conflict.

It was the first serious rift in 40 years of farming side by side, sharing machinery, and trading labor and goods as needed without a hitch.

Then the long collaboration fell apart. It began with a small misunderstanding and it grew into a major difference, and finally it exploded into an exchange of bitter words followed by weeks of silence.

One morning there was a knock on John's door. He opened it to find a man with a carpenter's toolbox. "I'm looking for a few days' work", he said. "Perhaps you would have a few small jobs here and there I could help with? Could I help you?"

"Yes," said the older brother. "I do have a job for you. Look across the creek at that farm. That's my neighbor; in fact, it's my younger brother. "

"Last week there was a meadow between us and he took his bulldozer to the river levee and now there is a creek between us. Well, he may have done this to spite me, but I'll go him one better. See that pile of lumber by the barn? I want you to build me a fence - - an 8-foot fence -- so I won't need to see his place or his face anymore."

The carpenter said, "I think I understand the situation. Show me the nails and the post-hole digger and I'll be able to do a job that pleases you."

The older brother had to go to town, so he helped the carpenter get the materials ready and then he was off for the day. The carpenter worked hard all that day measuring, sawing, nailing. About sunset when the farmer returned, the carpenter had just finished his job. The farmer's eyes opened wide, his jaw dropped. There was no fence there at all. It was a bridge -- a bridge stretching from one side of the creek to the other! A fine piece of work handrails and all -- and the neighbor, his younger brother, was coming across, his hand outstretched. "You are quite a fellow to build this bridge after all I've said and done."

The two brothers stood at each end of the bridge, and then they met in the middle, taking each other's hand. They turned to see the carpenter hoist his toolbox on his shoulder.

"No, wait! Stay a few days. I've a lot of other projects for you," said the older brother.

"I'd love to stay on," the carpenter said, "but, I have many more bridges to build."

-Over The Hills and Everywhere by Manly Wade Wellman, from the book Who Fears the Devil

Oh, by the way ...

... if you plan on donating any money to a humane society this year, don't give it to the HSUS (Humane Society of the United States). The "humane society" tag in their name is a total fabrication.

Humane Society of the United States

Despite the words “humane society” on its letterhead, the Humane Society of the United States (HSUS) is not affiliated with your local animal shelter. Despite the omnipresent dogs and cats in its fundraising materials, it’s not an organization that runs spay/neuter programs or takes in stray, neglected, and abused pets. And despite the common image of animal protection agencies as cash-strapped organizations dedicated to animal welfare, HSUS has become the wealthiest animal rights organization on earth.

Manuscript Homestretch

Got the office door closed, playing some Mighty Mighty Bosstones (currently Someday I Suppose off of their Don't Know How To Party album), and configuring the dozen or so phylogenetic trees I'm including as Supplementary Material for my manuscript (over 500 OTUs will do that to you). Once that is done, its off for a final reading of the manuscript to find typos, clean up the other figures, and catch any minor errors that I may have passed over previously. Then, it's off to the collaborators for their review prior to submission.

And then, I get to turn right around and work on the next manuscript. Whee!

So, no more blogging for today (and probably tomorrow).

Carbon Dioxide a Deadly Gas?

The answer to that question is: Yes.

Which is why the EPA was right in making the call that they did when they said that greenhouse gases, which includes carbon dioxide, pose significant hazards to humans.

The scientific analysis also confirms that climate change impacts human health in several ways. Findings from a recent EPA study titled “Assessment of the Impacts of Global Change on Regional U.S. Air Quality: A Synthesis of Climate Change Impacts on Ground-Level Ozone,” for example, suggest that climate change may lead to higher concentrations of ground-level ozone, a harmful pollutant. Additional impacts of climate change include, but are not limited to:

* increased drought;
* more heavy downpours and flooding;
* more frequent and intense heat waves and wildfires;
* greater sea level rise;
* more intense storms; and
* harm to water resources, agriculture, wildlife and ecosystems.

Bold emphasis mine, and here is Exhibit A.

In a "Perspective" published in the journal Science, Peter Brewer and Edward Peltzer combine published data on rising levels of carbon dioxide and declining levels of oxygen in the ocean in a set of new and thermodynamically rigorous calculations. They show that increases in carbon dioxide can make marine animals more susceptible to low concentrations of oxygen, and thus exacerbate the effects of low-oxygen "dead zones" in the ocean.

Carbon dioxide can pose more than the direct health hazard to humans, as you can see above. Those dead zones, mostly located near the coasts also will translate into reduced food supplies. I don't know about anyone else but ... I'd like to be able to continue to eat in the future.

Angling drives evolution in bass

Cool article over at Scientific American on fishing.

A new, 20-year study, led by University of Illinois at Urbana–Champaign ecologist David Philipp, "provides the first direct experimental evidence that vulnerability to angling is a heritable trait," the authors wrote.

So how'd they figure this out?

With the help of anglers, Philipp and his colleagues tagged and released largemouth bass in a state park pond in central Illinois beginning in the mid-1970s. Many fish were caught time and again, they found—up to 16 times in a single year. The researchers drained the pond in the 1980s and discovered that 200 of about 1,700 fish had never been hooked.

From there they did ...

From this stock, they have since bred the separate groups of "low-vulnerability" and "high-vulnerability" bass, and through three generations the offspring have stayed true to their parents' susceptibility—or aversion—to getting caught.

Pretty cool. So what does this mean?

"This type of selection experiment, which we propose has been going on in all bass lakes since the inception of angling, has the potential to alter, perhaps quite significantly, the behavior and even the life history of individual fish in those populations," the study said.

What form does the impact take?

Female largemouths swim away from their eggs after laying them; it is the male that guards them for their first month of life. The aggressive males are best at protecting their fry from predators—but they also may strike more readily at lures in their territories, making them more vulnerable to being caught.

Most times of the year male and female fish are caught in equal numbers. But during spawning season, males are caught the most. And hanging on to a caught male for longer than a few moments during nesting season could spell death by predation for the fry.

"Anglers may be negatively impacting the populations without knowing it," Philipp says.

That whacky South Pole!

Seems that the Antarctic ice is actually increasing in parts of the continent.

Extensive melting of Antarctic ice sheets would be required to raise sea levels substantially, and ice is melting in parts of west Antarctica. The destabilisation of the Wilkins ice shelf generated international headlines this month.

However, the picture is very different in east Antarctica, which includes the territory claimed by Australia.

East Antarctica is four times the size of west Antarctica and parts of it are cooling. The Scientific Committee on Antarctic Research report prepared for last week's meeting of Antarctic Treaty nations in Washington noted the South Pole had shown "significant cooling in recent decades".

... and ...

Ice core drilling in the fast ice off Australia's Davis Station in East Antarctica by the Antarctic Climate and Ecosystems Co-Operative Research Centre shows that last year, the ice had a maximum thickness of 1.89m, its densest in 10 years. The average thickness of the ice at Davis since the 1950s is 1.67m.

A paper to be published soon by the British Antarctic Survey in the journal Geophysical Research Letters is expected to confirm that over the past 30 years, the area of sea ice around the continent has expanded.

I'll see if I can link that paper when it comes out.

A must read ...

... by Bill Whittle of Eject! Eject! Eject.

... a dream becomes a goal once you make a viable plan and stick to it ...

Quid Pro Quo

Lately I've noticed that a few people have listed me in their blog links section. For that I'm most appreciative, and I'd certainly like to reciprocate. So ... if you've linked me and you're not listed in my Quid Pro Quo section, by all means shoot me off an email (or comment to this blog entry) and I'll rectify the situation. Once again, thanks!

Nom nom nom!

This weekend I decided to stay up late watching bad sci-fi movies, sleep in late with the dogs, and then treat myself to a nice thick sub at the local deli. That's the other half of my corned beef, pastrami, swiss on honey wheat sub. Finished off with a couple of dill slices, lettuce, tomatos, peppers and deli mustard. Wash it all down with a diet Mt. Dew (have to watch my figure ya know) and today is starting off rather well. Now I can work guilt free on a Saturday.

Oh jimminy ...

... trying to watch the movie Dark Star (Netflix rules!) but it's completely horrible. I don't know how it managed to get such a good rating.

I will say this though, if you manage to get through the first few minutes, you'll see the inspiration for the Bishop "knife trick" from Alien.

Don't give me any of that intelligent life crap, just give me something I can blow up!

Linkage ...

... to some web-based resources I've had to use lately.

Libshuff (Sequence Library Comparison) - To determine whether or not your various DNA (in my case microbial) libraries are statistically similar or not. It's hosted by UGA.

DNADIST - In order to use the web-based program above, you need a DNA distance matrix file. It's a part of the Phylip package. There is an online resource for this though hosted by the Pasteur Institute (which is what is linked above).

Or, if you don't want to use libshuff like I am, you can use UniFrac.

Is it a bad thing ...

... if I know the MCS sequence of pCR4-TOPO by heart?

Manually sorting through over a dozen 96 well plates of sequencing is a pain in the toosh. I'm dreading what's going to happen when I need to submit all of this to GenBank. Fortunately for me, it's mostly a descriptive study of a site, so I can probably get away with submitting it as an aligned environmental set!

Get off it ...

Read this article on MSNBC and had to laugh. They just don't get it.

The frugality of ... millions of other Americans who still have their good jobs feed back on the economy, holding down growth and encouraging other worried workers to trim their spending — causing the whole vicious cycle to run another lap.

Oh, so because I'm not in the currently dire situation of losing my job I'm causing the economy to stay tanked because I don't spend my money like a fiend? Piss off. Who knows how long any of us have at any job really. Of course I have a bit more to worry about than the average individual since I'm coming up for tenure soon.

Economists say many still-flush consumers are handcuffed by psychological traps that cause them to tighten their purse strings even though economic hardship is not their reality.

Sorry, it's not a trap, it's what I call "common sense" and "living within your means". A lot of people thought they had nothing to fear prior to this whole collapse, and look at them. Things take unexpected turns. I'd hardly call it a trap to think that an unexpected turn can happen to me even though I haven't been hit yet. So, I cut down a bit more here and there. It's not that I've ever really been free with my wallet ... except when I first got out of college and wasted money on a 3DO system (what a friggin mess that was). I shop for clothes at Old Navy and Kohl's, not Abercrombie. I don't buy brand name food. I mean, I doubt the chicken I can buy from Wal-Mart is worse off than buying Purdue. And I avoid fads ... which is why I still don't have a Wii or PS3 (though I'm dying for one). So, now that I'm smart with money ... you know, I actually liked buying shares in my IRA at this reduced price ... I'm to blame for the economy staying in the doldrums?

Whatever.

Currently ...

Listening To

NUTS! and (*#@&#@!

Yesterday I was pleased with myself. I had finally wrapped up work on my Introduction, to the point that I merged it with the rest of the manuscript, saved it up and went home for the evening. When I got into work early this morning, I attempted to open it up.

Corrupted.

Whiskey! TANGO! FOXTROT!!!

We had a power surge last night, about the time I was wrapping things up, and I guess it fried the two files I had open. The two files? My Introduction file and my new Manuscript file. I still have my M&M and R&D seperate (THANKFULLY!) but my Introduction is gone. Forever. Fortunately I have most of the essentials memorized, but it means having to rewrite it. Mother----er!

And yes, I tried to recover the files. I spent 4 hours doing that, to no avail. It's probably easier for me at this point to just rewrite the damn thing.

*sigh*

WTF!

Lock up these idiots for the rest of their lives.

A mother and her teenage son are kidnapped. The kidnappers place a cell phone in the car of the boy's father so they can communicate their ransom demands. The son is burned with a blowtorch. The mother implores the father to pay the ransom.

A terrifying scenario, but one that the FBI and police say was all orchestrated by the mother to get some fast cash from her ex-husband.

The mother, Alejandra Arriaza, her boyfriend, Angel Ponce, and his nephew, Joel Boza, were charged Tuesday with federal kidnapping counts. If convicted, they could be sentenced to life in prison.

According to an FBI affidavit, all three have admitted their roles in the phony kidnapping.

This lady is a total tool. She kidnapped and tortured her own child!

I agree as well ...

... when I say that I think President Obama handled the hostage situation off the coast of Somali correctly. Not that I'm going to kid myself by thinking that he cares what I think about him. At any rate, I think our Navy did a great job. One shot, one kill. They're not the sort of people you want to screw with, especially when you're a strung-out teenager sitting in a friggin boat. As for Gates, got to agree with the article there as well. My only beef is ... I don't think he did enough trimming of the military budget. There are still some bloated carcasses sitting in that thing.

Sign me up ...

... for the Coalition of the Sane. I never have, and I never will ... tweet.

From a recent Sprint commercial.233,000 people just Twittered on Twitter. 26% of you viewing this have no idea what that means.

Notice what the twits are twittering. "me!" Heh. Is Sprint characterizing twits? Some people, including yours truly, think so. Not that I don't think blogs aren't self-indulgent, I just think they're more able to share ideas. Then again, I've never been on Twitter ... is the exchange of ideas as applicable to that platform? At a limit of 140 characters (IIRC) I can't believe it is.

Oh, and then there is this ... Twitter can harm a developing childs "moral compass".

"If things are happening too fast, you may not ever fully experience emotions about other people's psychological states and that would have implications for your morality," said researcher Mary Helen Immordino-Yang.

We're already in a state of constant information overload, Twitter (and other social networking sites) add another layer of noise to our daily lives. Oh, and for the record, I don't Facebook or MySpace either.

Bioethanol ... a drain on water resources?

Article in Science Daily.

The scientists made a new estimate of bioethanol's impact on the water supply using detailed irrigation data from 41 states. They found that bioethanol's water requirements can be as high as 861 billion gallons of water from the corn field to the fuel pump in 2007. And a gallon of ethanol may require up to over 2,100 gallons of water from farm to fuel pump, depending on the regional irrigation practice in growing corn.

If you look at the map, part of the area that is farmed for corn sits on top of the Ogallala Aquifer. Unfortunately, it's a water resource that feeds the nation, and it's beginning to fail. Back in 2007 the non-profit Environmental Defense issued a report on bioethanol and its impact on the Ogallala Aquifer. In the report titled Potential Impacts of Biofuels Expansion on Natural Resources: A Case Study On The Ogallala Aquifer Region (PDF, 18 pages) they state:

In the areas of highest Ogallala Aquifer depletion, new corn ethanol plants currently under construction or planned will increase the region’s ethanol production capacity by 900%. The area currently hosts only five ethanol plants with combined production of 71.5 million gallons per year, but another nine plants, with 639 million gallons per year capacity, are currently under construction. This dramatic expansion of ethanol production has substantial implications for already strained water and grassland resources in the Ogallala Aquifer region.

Water demands associated with individual ethanol plants—due both to ethanol processing and growing corn feedstock—are not exceptionally higher than demands from other industrial or agricultural users, but the construction of new ethanol plants in areas of existing water stress will exacerbate conflicts if water is already scarce. Water demands from new ethanol plants in areas of Ogallala Aquifer depletion may reach 2.6 billion gallons per year for corn-to-fuel processing alone, and between 59 and 120 billion gallons per year for increased water demand if there are local increases in irrigated corn production.

Now, look at those numbers and consider this ... if the above report (at the very top) is true, and water estimates may be 3 times as high as previously considered ... we're talking up to an additional 360 billion gallons of water per year drained out of that aquifer.

Once that water is gone, it's gone. You can't replenish that aquifer any other way that by rainfall, and that's just not going to happen.

Ridiculous

The cost of hiring a coach.

New Kentucky hoops coach John Calipari's eight-year, $31.65-million deal is the richest in college basketball.

Ok, well ... Kentucky is a basketball school ... so what?

College football coaches should feel the blessings, too. There's a good chance Calipari's deal will push the salaries of college football coaches even higher. Why? Football is a much bigger revenue-producer on college campuses than basketball, so it stands to reason the football coach almost always will be higher paid.

You know, I was an athlete in college. I didn't partake in any of the popular sports ... I ran Cross-Country, and both Indoor and Outdoor Track and Field. I was good, enough to be on scholarship, and unlike our popular teams, we were actually successful (I captained and led our team to a Division I Conference championship in XC my senior year). So, while I know about the tough work that goes into being a student athlete, I am dead set against athletes receiving pay for their athletic prowess. Why? Because only basketball and football players will benefit, and that doesn't seem fair to the rest of the athletic program. Of course, that comes tougher to defend when the colleges milk these athletes and bestow multi-million dollar packages to their coaches.

Things have gotten out of hand, just like they have in every other corner of the country. I just hope things don't blow up like I feel they're going to though.

Be more concerned with your character than with your reputation. Your character is what you really are, while your reputation is merely what others think you are. - John Wooden

Man's best friend? Riiigghhhtttt

I'm home sick today and trying to get something, anything, done today (other than watching the soaps). So I'm at the kitchen table with the laptop and other peer reviewed manuscripts spread out, trying to write ... and I have Max, my faithful Norwegian Elkhound mix at my feet. My two other dogs are elsewhere in the house, chewing on rawhide. So, to show Max I appreciate his company, I hand him a treat. What does he do? He runs off with it.

Gee, thanks for nothing buddy.

It's definitely spring ...

... know how I can tell? My sinuses clog, my teeth ache, my eyes water, and my throat gets scratchy. Oh, and I wind up swallowing about a gallon of mucus a day. Yah, spring is here, and I feel like poop. So here I am, at home, trying to mend by drinking lots of tea and getting high on Theraflu. Oh yah, and trying to write.