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2012 (1)2011 (51)
August (1)

Wednesday Micro Hits
Wednesday, August 17, 2011
July (1)

Is it worth getting an education?
Thursday, July 7, 2011
June (2)

Tuesday, June 28, 2011

It Gets Better
Thursday, June 2, 2011
May (4)

Wednesday Micro Hits
Wednesday, May 11, 2011

My first experience with science writing (Part 1 of 2)
Tuesday, May 10, 2011

This is why we get vaccinated
Thursday, May 5, 2011

Monday Morning Jam
Monday, May 2, 2011
April (2)

Saturday Morning Serenade
Saturday, April 23, 2011

So long, farewell ...
Friday, April 1, 2011
March (10)

Stay Tuned ...
Thursday, March 31, 2011

From the Union of Concerned Scientists
Tuesday, March 15, 2011

Week 23 - Hockey Pool
Monday, March 14, 2011

March Madness
Monday, March 14, 2011

Saturday Morning Serenade
Saturday, March 12, 2011

What a bargain!
Wednesday, March 9, 2011

Wednesday Micro Hits
Wednesday, March 9, 2011

Technique Overload
Monday, March 7, 2011

Saturday Morning Serenade
Saturday, March 5, 2011

Et tu FDA?
Wednesday, March 2, 2011
February (10)

Saturday Morning Serenade - A Hip Edition
Saturday, February 26, 2011

Saturday Morning Serenade
Saturday, February 19, 2011

Wednesday Micro Hits (on Thursday!)
Thursday, February 17, 2011

Wednesday, February 16, 2011

Happy Valentine's Day
Monday, February 14, 2011

Saturday Morning Serenade
Saturday, February 12, 2011

The GOP War on Science
Wednesday, February 9, 2011

Wednesday Micro Hits
Wednesday, February 9, 2011

People, how about some ...
Tuesday, February 8, 2011

Saturday Morning Serenade
Saturday, February 5, 2011
January (21)

Saturday Morning Serenade
Saturday, January 29, 2011

Friday, January 28, 2011

Are you married to your reagents?
Thursday, January 27, 2011

Wednesday Micro Hits
Wednesday, January 26, 2011

Common Sense Tip #1
Tuesday, January 25, 2011

Saturday Morning Serenade
Saturday, January 22, 2011

From the Baby Boomers, a Big "Screw You"
Friday, January 21, 2011

Student Worker - More Student or More Worker?
Friday, January 21, 2011

Wednesday Micro Hits
Wednesday, January 19, 2011

Saturday Morning Serenade
Saturday, January 15, 2011

Holy moly!
Friday, January 14, 2011

Thursday Pondering
Thursday, January 13, 2011

The Electronic Office
Thursday, January 13, 2011

Wednesday Micro Hits
Wednesday, January 12, 2011

Saturday Morning Serenade
Saturday, January 8, 2011

The Plug - January Edition
Friday, January 7, 2011

Bits 'N Pieces
Thursday, January 6, 2011

Latest Manuscript Review
Wednesday, January 5, 2011

The $4 gallon of gas
Wednesday, January 5, 2011

Our slowly shrinking (and dying) planet
Tuesday, January 4, 2011

It's 2011 already? For reals?
Monday, January 3, 2011
2010 (46)
December (9)

Saturday Morning Serenade
Saturday, December 11, 2010

The State of Microbiology
Thursday, December 9, 2010

Wednesday Micro Hits
Wednesday, December 8, 2010

2010 blogging meme
Tuesday, December 7, 2010

The Environmental Impact of the Christmas Season
Tuesday, December 7, 2010

Music Snobbery
Thursday, December 2, 2010

Phantom Power
Thursday, December 2, 2010

What's Your Name?
Wednesday, December 1, 2010

Wednesday Micro Hits
Wednesday, December 1, 2010
November (8)

Saturday Morning Serenade
Saturday, November 27, 2010

Awakening from the food coma ...
Friday, November 26, 2010

Wednesday Micro Hits
Wednesday, November 24, 2010

Donor's Choose Final Followup (Recipes #3 and #4)
Tuesday, November 23, 2010

A Monday Mess
Monday, November 22, 2010

Saturday Morning Serenade
Saturday, November 6, 2010

Wednesday Micro Hits (Peer-Review Edition)
Wednesday, November 3, 2010

Day 2 of the ASA-CSSA-SSSA Meeting (#ACSMtg)
Wednesday, November 3, 2010
October (29)

ASA-CSSA-SSSA Meeting - Day 1
Sunday, October 31, 2010

Stayin' Alive
Sunday, October 31, 2010

Saturday Morning Serenade
Saturday, October 30, 2010

Wednesday Micro Hits (Vol. 4)
Wednesday, October 27, 2010

ASA-CSSA-SSSA Early Career Program
Monday, October 25, 2010

Saturday Morning Serenade
Saturday, October 23, 2010

Wednesday Micro Hits (Vol. 3)
Wednesday, October 20, 2010

Donor's Choose - Family Recipe Number 1
Sunday, October 17, 2010

Making Good on Donor's Choose Bribe - Comfort Food Recipe 1
Saturday, October 16, 2010

Saturday Morning Serenade
Saturday, October 16, 2010

Friday Wrap-Up and Random Thoughts (Vol. 2)
Friday, October 15, 2010

First I Begged, Now I Bribe
Thursday, October 14, 2010

Finding Out Things The Hard Way(TM)
Wednesday, October 13, 2010

Wednesday Micro Hits (Vol 2)
Wednesday, October 13, 2010

Here's where I start begging ...
Tuesday, October 12, 2010

#UnK3rn3d: Life Outside the Lab?
Tuesday, October 12, 2010

First fleas, now frogs?
Tuesday, October 12, 2010

No Fleas Please
Monday, October 11, 2010

My next Research Blogging article has been chosen ...
Sunday, October 10, 2010

Saturday Morning Serenade
Saturday, October 9, 2010

Donor's Choose
Friday, October 8, 2010

Friday Wrap-up and Random Thoughts
Friday, October 8, 2010

RB: Waste Not, Want Not.
Thursday, October 7, 2010

Research Blogging
Wednesday, October 6, 2010

Wednesday Micro Hits
Wednesday, October 6, 2010

What if I were not a microbiologist ...
Tuesday, October 5, 2010

TJ's Tips on Manuscript Review
Monday, October 4, 2010

Chinese plagiarism and the death of English-language journals
Friday, October 1, 2010

Allow Me a Formal Introduction
Friday, October 1, 2010
Blogger Profile

Thomas Joseph

It's a Micro World after all is a blog dedicated to discussing pretty much whatever I feel like. When I delve into scientific matters it will primarily be discussing microbiology (agricultural, bioenergy, and environmental focus). Otherwise, I'll probably ramble on about sports and life.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Awesome Stuff
Views: 1506 | Comments: 1
Last by Brian Krueger, PhD on Feb 03, 2012, 3:18pm
... have only been slightly exaggerated. Life certainly has been busy lately, but I have been keeping note of some items that I definitely wanted to blog on. In particular, my efforts to go fully-electronic in my lab/office dwelling. So, I'll be back soon to blog on those efforts as well as review some of the software/apps as well as hardware that have helped me progress my lab forward. . . . More
Views: 584 | Comments: 1
Last by JaySeeDub on Aug 17, 2011, 3:56pm
1. This article sums up the "Republican problem". The money quote is as follows:

Do not underestimate the willingness of a whole lot of Republicans to vote for someone that they want more than someone that they think can win.

And that is the problem in a nut shell. What most Republicans fail to comprehend, or just don't care about, is that when you vote for a candidate in an election, you are voting for an individual who will lead and represent the entire country. Not just you and your own ideology. Not only that but they are our face to the wider community, so on the national level they represent us on a global scale. When you nominate someone to run in an election, you should really consider if they're going to be palatable to the broader population (i.e., centrists and independents) because if they're not, they're not going to win. I'm not sure what the GOP could have done differently in 2008 (not including the gaffe of picking Palin for VP). John McCain was as a good a candidate as the GOP could have mustered. He is mainly a centrist, though he started attempting to lean right as th . . . More
Views: 1806 | Comments: 8
Last by old timer on Aug 08, 2011, 11:15am
So maybe I'm not the best person to ponder this question, given that I already have several college degrees.

Or, perhaps, that makes me emminently qualified to answer this question.

Either way, the following article by John Stossel got me thinking (which is always a dangerous thing).

Now, we're not talking about refusing to teach children. Rather, the question revolves around the importance and worth of a college education. Stossel is right when he states that professors at universities, most universities at any rate, care more about research than teaching. After all, it is what their career is measured by, and they'd be foolish to ignore it. However, I believe that there are any number of colleges and universities where the teachers are more dedicated to the task of teaching the next generation, than performing research.

I just never attended one.

My education is the product of two state schools, which both have extremely well-funded federal research programs. Did I get a good education? I think I did, but I'd say that came more from my graduate coursework. My undergraduate education revolved around rote memorization an . . . More
Views: 529 | Comments: 6
Last by Thomas Joseph on Jul 07, 2011, 9:05am
After a couple weeks hiatus, which saw me run off and get hitched, honeymoon in the tropics, party with Mickey Mouse, and then try to settle back down into the daily grind, I am back (again). Not sure how regularly I'll be posting, because there are still plenty of manuscripts which need writing, data which needs analyzing, and experiments that need running and troubleshooting.

1. I love the Nook 2. Compact and responsive, this little device is perfect to dragging along just about anywhere. Sure, I could read an e-book on my phone, but I love this puppy.

2. When in doubt with insurance coverage, appeal.

3. Is it just me, or does the science blogosphere seemed to have quieted down lately? I know I've been AWOL, but no scandals, no tempests in tea cups. Things seem a bit drab lately.

4. If the GOP nominated Michelle Bachmann, they'd deserve the butt-whooping they'd get in the election. And the argument for dec . . . More
Views: 451 | Comments: 2
Last by Thomas Joseph on Jun 06, 2011, 8:04am
Came across the following blog entry at the Big League Stew. It is about a PSA from the SF Giants, combatting homophobia. It's targetted to LGBT teens to let them know that life does get better beyond the bullying and to not turn to suicide. It is done in conjunction with the It Gets Better Project.

I'm sure there is a small portion of society that has not been bullied, or bullied. However, I think the majority have either experienced the shame of being bullied, or witnessed that shame when in the act of bullying. If you've gone through bullying, you'll know that no one else should have to experience such pain (emotional and physical), and if you have bullied, hopefully you've matured to the point that you are ashamed of your actions and would also like to prevent others from having to go through the torment of being bullied.

So, no matter what direction you are coming from on this issue, here is your chance to make a differ . . . More
Views: 439 | Comments: 4
Last by JaySeeDub on May 12, 2011, 10:53pm
1. This is one way to get a few vacation days. I suppose. Or would this fall under sick leave?

2. A fool and his money are soon parted.

3. For those finding themselves affected by flooding, take extra precautions against bacterial disease. A study conducted in 2004 (PDF, 8 pages) after flooding in Haiti showed good results from using PuR water treatment systems, though boiling should achieve similar results.

4. You would think that, after the Nick Adenhart tragedy two seasons ago, MLB would get their act together involving DUI charges. Nope, not yet. There is simply no excuse for this.

5. Not a big fan of bed bugs. . . . More
Views: 1843 | Comments: 4
Last by Alchemystress on May 16, 2011, 9:19am
NOTE: To avoid TL;DR responses, I'm going to break this story into two parts.

I think the experience I am about to relate is far enough passed that I can speak with a little more objectivity than I could have even a couple of weeks ago. I should note that, in the end, things did work out for the better ... for the most part.

The story starts about a year ago when a manuscript of mine was accepted for publication. It appears that the reviewers recommended the manuscript for "Featured Paper of the Issue" which meant that in addition to getting the manuscript published (the major goal), I'd get some press out of it as well. Totally win-win!

I was told that as the article approached the publication date I would be contacted by a member of the journal staff about what I would need to do in regards to the press release. I figured that eventually I would receive a call from a staff science writer who, having read the paper, would ask me some questions to flesh out the final details and proof what they had written.

So I waited. And waited. And waited. And waited some more. Ten days before the issue was to be released I was sent an email that contained a long list of items to consider for writing a press release. I was asked to get back to the . . . More
Views: 3698 | Comments: 5
Last by Alchemystress on May 16, 2011, 6:37am
If you happened to be wondering -- or needed it explained to you -- why people get vaccinated, here is your reason.

The United States seems to be on track to have more measles cases than any year in more than a decade, with virtually all cases linked to other countries, including Europe where there's a big outbreak.

So measles is making a comeback? I wonder how that could possibly be happening.

Europe, especially France, has been hit hard by measles, with more than 6,500 cases reported in 33 nations. International health officials are blaming it on the failure to vaccinate all children.

Surprise, surprise. "But surely", the anti-vax crowd will say, "this has nothing to do with not getting vaccinated. That reason is just a canard!"

Of the 89 cases reported through the end of last week, 79 were people who were unvaccinated or who had no documentation of it, Wallace said.

You were saying, anti-vax crowd?

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I'm still around. I promise.

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Last by Genomic Repairman on Apr 01, 2011, 10:42pm
... it's time to bid adieu.

As people may have noticed, I haven't been blogging much lately. A lot of it has to do with work -- I'm slammed here writing papers and analyzing data -- but I also haven't been into the scene here at LabSpaces as much lately. There are a number of reasons for my feeling this way, but I don't think I really want to get into them because I do appreciate Brian giving me the opportunity to blog here. He allowed me to bring my backwater blog into the light and get some traffic, and for that I will always be grateful.

However, now it's time to turn over a new leaf. I hope not to bounce around too much (for fear of losing what little readership I have), so I hope that my next stop is my last before I eventually hang up my blogging shoes for good. With that, I'm happy to announce that I will be joining Scientopia!

See you on the flip side!

And when my new digs are ready, I'll come back and post a link.

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Views: 294 | Comments: 0
... in the meantime. The evolution of Apache.

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Received the following in my email today, thought I would pass it on.

Dear Thomas,

Over the last several days, we've received many calls and emails from UCS members and supporters asking about the current crisis involving several of Japan's nuclear power reactors. Like most of you, we are deeply saddened by the terrible tragedy of last week's earthquake and tsunami, and our hearts go out to the many victims.

For more than 40 years, UCS has served as a nuclear safety watchdog and a reliable, independent source of information on nuclear power technology and its risks. UCS technical experts are working hard to provide timely, updated analysis of what is happening at the stricken facilities and what the implications may be.

You can find regular updates on our blog "All Things Nuclear" and learn about why events have unfolded in the way they have, where the situation may be headed, and what it may mean for the people around the facilities and the environment.

We are also being called on frequently by a wide range of media outlets to provide independent, unbiased information and analysis about the rapidly changin . . . More
Views: 783 | Comments: 6
Last by Lavaland on Mar 15, 2011, 1:10pm
So I guess it's my turn to broadcast the results of this hockey pool. A pool that I was doing fairly well in, until Cath made me brag. This resulted in me being jinxed for the remainder of the season. Ok, so I was doing well maybe for the first two weeks of the pool, and the trend is clearly for me to stink it up. In my defense though ... this has always been a Canadian sport, and I'm a fan of the Islanders. Those two things mean I was fated to fail.

Anyways, onto the results.Here are the results for Week 23. dreamsandhope (Chall, correct?) ran away with the point total this week with 42. Richardipus trailed her by 7 to come in 2nd. Cath had 31 for 3rd, and a gaggle of us scored 30 points for the week (ScientistMother, Gerty, and myself) for fourth. Bob scored 28, and Lavaland brought up the rear with 27. Since this is all about me, I didn't really gain any ground this week (again), and tying with Gerty meant I'm still solidly in DFL.

The overall standings? Lavaland's poor showing this week allowed Richardipus to sneak within one point of the lead. Everything else stayed pretty much the same except Chall moved into a tie for 5th with . . . More
Views: 238 | Comments: 2
Last by Thomas Joseph on Mar 14, 2011, 9:16am
My bracket

Click to embiggen.

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Views: 207 | Comments: 1
Last by Suzy on Mar 12, 2011, 12:58pm

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Last by Alchemystress on Mar 09, 2011, 5:00pm
you call this a bargain?

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Views: 278 | Comments: 6
Last by Thomas Joseph on Mar 10, 2011, 8:10am
1. I don't blame this father. I might even would do the same thing if I were in his position.

2. I'm not willing to give Comic Sans the benefit of the doubt, but I am a new fan of Bodoni MT. (Note: the article does not spell the name of the font properly).

3. Gas is well on it's way to $4 a gallon. For some states it is already there. But it's not just at the pump where you'll be hit. You'll get hit in the supermarket as well. Despite what some people think, food doesn't come from the grocery store. It's grown. On farms. By farmers. Doing such involves a lot of inputs, a good portion of which is fuel. Tractors, combines, irrigation machinery, and other farm equipment doesn't run on magic. Same for the trucks which haul the produce to the store where you pick it up. This all involves oil. So you can expect a hit at the supermarkets. To make matters worse, as more and more cropland is diverted to growing corn (for ethanol production), prices will also increase because there is le . . . More
Views: 427 | Comments: 5
Last by Thomas Joseph on Mar 08, 2011, 10:39am
The following article is a pretty good read, and once you comprehend how embedded this technology is in our lives, and in turn how simple it is to disrupt, it's also pretty scary.

Why would a GPS outage cause such disruption? These satellite signals now do a lot more than inform your car's satnav. GPS has become an "invisible utility" that we rely on without realising. Cellphone companies use GPS time signals to coordinate how your phone talks to their towers. Energy suppliers turn to GPS for synchronising electricity grids when connecting them together. And banks and stock exchanges use the satellites for time-stamps that prevent fraud. Meanwhile, our societies' reliance on GPS navigation is growing by the year.

Not that GPS technology is "new" (the full system has been up and running since 1994), but it's amazing at how many people have glommed onto it and integrated it into systems that GPS was never intended (nor designed) for. All of which reminded me of work, and how we can fall into the trap of leaning too heavily on a single technique for our research endeavors.

When I first arrived at the institution I now . . . More
Views: 181 | Comments: 1
Last by Genomic Repairman on Mar 05, 2011, 1:22pm
Not much time to blog lately. I have a couple in the works, but real life demands just have to take precedent. So, with that said, here is another tune.

. . . More
Views: 412 | Comments: 6
Last by Thomas Joseph on Mar 07, 2011, 8:08am
When you go to the FDA website and click on the link that says "About the FDA", it asks you a simple rhetorical question "Do you know ... what the FDA does?". Immediately after asking this question, they inform you with the first answer being:

FDA is responsible for

protecting the public health by assuring the safety, effectiveness, and security of human and veterinary drugs, vaccines and other biological products, medical devices, our nation’s food supply, cosmetics, dietary supplements, and products that give off radiation.Note, the FDA is primarily* responsible for protecting the public health.

So, given that ... why this?

At the same time, government documents obtained by showed that federal Food and Drug Administration inspectors knew about problems with contamination and sterilization at a plant run by the Triad Group of Hartland, Wis., as early as July 2009.

So the Triad Group had serious issues revolving around their sterilization procedures. These issues put hundreds, if not thousands, of . . . More
Views: 206 | Comments: 1
Last by Suzy on Feb 26, 2011, 12:28pm
It's a bit of a long song (the video is over 9 minutes long), but it's the Tragically Hip at their best. If you want more of The Hip, click on their listen page. And if you can ever catch them in concert, do it! They're awesome!

Gordon DownieGordon Downie from 5 feet away

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Views: 190 | Comments: 1
Last by Genomic Repairman on Feb 19, 2011, 10:45am

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Last by Thomas Joseph on Feb 23, 2011, 10:24am
Wednesday Micro Hits is a compilation of news and ideas that have popped in my head over the past week or so. I usually collect them in a queue and then post them in one fell swoop. This way I don't clutter the blog section of LabSpaces with a million tiny blog entries that will probably interest no one other than myself. So sit back, relax, and click on the links ... maybe you'll find something interesting (or amusing at the very least). Oh, and yes, I realize today is Thursday, but I pushed this off a day because the HR1 issue is more pressing and I didn't want to pull attention away from it with my inane ramblings.

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Views: 1536 | Comments: 7
Last by JaySeeDub on Feb 16, 2011, 6:18pm
There are a number of people currently writing about the proposal HR 1. Problem is, all they're whining about is the cuts to NIH funding. I'm here to tell you though that more than just NIH is going to be taken to the woodshed with this proposal.

I received the following from the ASA-CSSA-SSSA trisociety today and they paint a picture that is just as, if not more so, dire than what the medical folks are seeing in this proposal. In effect, it is going to gut agricultural and environmental science research.

. . . More
Views: 221 | Comments: 2
Last by Genomic Repairman on Feb 12, 2011, 1:25pm

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Last by Katharine on Feb 10, 2011, 2:14pm
The GOP in the House have come out with a list of cuts they want to have added to the continuing resolution (CR) slated to be brought up for vote soon. The cuts total $74 billion and will be (if I read it all correctly) applied to this years budget. That means the cuts will be immediate. Looking at the list, some of the things don't bode well, as a good chunk is directed towards science funding.

1. A 1 billion dollar cut from the Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States.

2. A 1 billion dollar cut from the National Institutes of Health. The NIH is the nations major medical research agency.

3. A 246 million dollar cut directed at university-based agricultural research. This m . . . More
Views: 617 | Comments: 14
Last by Suzy on Feb 10, 2011, 9:52am
1. I love my AppleTV. For years I've wanted a home media center. After scrounging and saving (for about as long as I've been pining for it) I was finally able to put one together. Nothing too big (though a 42" television looks big unless it's side-by-side with a 50") or too fancy. I did promise myself I'd keep it all Panasonic so all the components would mesh together nicely, so the AppleTV is the exception. With that said however, it compliments the rest of the system. The sweet thing is, since all of my media is on my desktop and sorted (in a very anal-rententive manner) in iTunes, it was almost a no-brainer to go with the AppleTV (also looked at the WD TV Live Plus but it doesn't come standard with wireless). The wireless connection between the desktop in my home office, and the AppleTV in my living room is perfect for someone (i.e., me) who didn't want to run wires throughout the house. It doesn't currently have Hulu access, but that's about the only downside I've seen so far. Now that I've got my home media center, I can focus on the less important things ... like furniture.

. . . More
Views: 335 | Comments: 5
Last by Lab Mom on Feb 10, 2011, 10:33pm
... perspective?

"We're still figuring out what our rights are, whether damages come into play or not," he told CNN. "This is more than just a breach of contract. ... This was a very traumatic experience for a lot of these people."

Really? Traumatic? Dude, tickets were going for $800 a pop, minimum. You know what's traumatic? Not having a job. Not knowing if you'll pay your heating bill or buy food this week. Wondering if they'll start foreclosure proceedings on your house this month. Not knowing where your next meal is going to come from. Those are traumatic.

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Last by Thomas Joseph on Feb 07, 2011, 9:33am

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Last by Thomas Joseph on Feb 07, 2011, 9:33am

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Last by Thomas Joseph on Feb 07, 2011, 9:34am
Honestly, I'm surprised that I haven't seen more coverage of the Challenger tragedy in the news or the blogosphere today. It was a pivotal moment in our history, and it seems as if it's being forgotten. With that said, today is the 25th anniversary of the Challenger tragedy. It's hard to believe that I was in grade school when this happened, but I was. I remember watching the launch because Christa McAuliffe, a teacher, was one of the crew members. She was supposed to be the first teacher in space, but instead shared a more ominous fate with the six other NASA astronauts.

Challenger Crew (Courtesy: NASA)

I don't think, at the time at least, that I ever really gave it much thought as to why they were doing what they were doing, just that they died doing it. I certainly don't think Christa McAuliffe went up into space just to be the first teacher in space, though I must admit the challenge in and of itself might have been part of the motivation to do so (it would have been for me). Instead, I think as a teacher, she was doing it to inspire a whole generation of children. As a matter of fact, she was slated to . . . More
Views: 418 | Comments: 10
Last by Thomas Joseph on Jan 28, 2011, 11:35am
I imagine that most scientists are creatures of habit, and some superstition as well. Speaking from experience, I know I have protocols which I've worked with for a decade or more and I'm loathe to change or tweak them. They work, why reinvent the wheel? This same thought process extends to reagents that are typically used in the lab. There were certain manufacturers that I "grew up" using, and remained loyal to that particular brand throughout my graduate and postdoc work. When putting my own lab together, while I was willing to negotiate some* on equipment**, by and large I was more than happy to stick with the "tried and true" microbiological and molecular reagents that I had used for years. For instance, I would never consider buying my restriction enzymes from anywhere but NEB. They work, why switch?

Problem is, projects change, which means conditions change. This point was eloquently brought home to me this past week. We had received some free Taq. We were told that in our system, this Taq would most likely perform better than any other Taq we could find on the market. For general amplifications we use what I would consider a "middle of the line" (in terms of cost) Taq which has worked pretty well in our hands. After all, Taq is Taq, no? Now there were inst . . . More
Views: 481 | Comments: 5
Last by Genomic Repairman on Jan 26, 2011, 11:23am
1. Goodbye Jack LaLanne. I had no idea he invented the "jumping jack".

2. Couldn't have happened to a nicer guy. What I don't think is that this is not to the level of Hillary Clinton's move to New York, or Alan Keyes running over to Illinois, for their runs for Senate. ETA: The ruling has been stayed, so he's currently still on the ballot.

3. Pets have many beneficial attributes, but they also carry some risk. Also, while this should go without saying, I have to say it anyways because some people are stupid ... never ever let your pet lick an open wound.

4. . . . More
Views: 335 | Comments: 3
Last by Geeka on Jan 27, 2011, 3:25pm
You know, there are some things which you really shouldn't have to tell people. Like the following little gem of common sense that I'm about to tell you:

When you run a service lab, and someone calls you to inquire about said service, call them back.

Now, there is some work we've been planning to do, and we've been ramping up our efforts. We have all of our ducks in a row and we're ready to launch into the data acquisition portion of the project. We wanted to do it in one big go because doing it "in bulk" would reduce our costs. I've spoken with other collaborators, friends, friends of friends, and a few have mentioned the service lab of a particular university as having unparalleled service. So I sent them an email. Never heard back. I waited awhile and sent off another email. Never heard back. I made a couple of phone calls. Never returned.

Now, in their defense, I was told that they are routinely hard to get ahold of, but if you could get ahold of them, the work they did was great. Ok, fine ... habitually lazy when it comes to getting in touch with people, but do great work. I was willing to put in the effort to eventually make contact (even if I had to drive there as a last resort). And if they were booked solid, I could always go with another option tha . . . More
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Last by Genomic Repairman on Jan 22, 2011, 11:47am

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Last by Thomas Joseph on Jan 25, 2011, 9:20am
This article got my blood boiling.

Americans overwhelmingly say that in general they prefer cutting government spending to paying higher taxes.

A comforting thought, and a bit of a no-brainer. Problem is, as we will see, that these Americans, who more than likely belong to the Baby Boomer generation, haven't given much thought beyond this sentiment. So, when they're pressed with specifics, they back off.

Yet their preference for spending cuts, even in programs that benefit them, dissolves when they are presented with specific options related to Medicare and Social Security ...

This paragraph, if I read it correctly, is poorly written. What happens is that when specific cuts are proposed, to programs that will benefit them, people back off from the desire of wanting cuts. Who is them? Baby Boomers would be the logical guess. Medicare and Social Security are two programs that Baby Boomers have banked on ... yet they're also the ones who have elected politicians who have routinely expanded those programs which have dwindled their reserves. Of course, the Baby Boomers want to pass the buck and keep those programs intact.

Nearly two-thir . . . More
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Last by Thomas Joseph on Jan 24, 2011, 8:08am
Happy times! Collaborations have my lab bursting at the seams. We literally have hundreds of samples waiting to be processed, and with the projects we're already neck deep in taking up all of our time, I've realized that I need to do something to break the sample processing bottleneck. DNA does not extract itself.

So to reduce the bottleneck I've hired a student worker. This will be my third. So far I'm 1 for 2 in the category of "productive student worker". The first was a disaster. They were handed over to me from a coworker who "couldn't use them". Hindsight being 20:20 and all, the reason my coworker couldn't was because the student was a bum ... ok, maybe not so much a bum as entitled. As in "this is beneath me." I could sit down with them, outline experiments, have my support scientist hover over them ... in essence, do everything short of running the whole thing myself and it still resulted in a mess. We did get a couple of figures for a proceedings paper (hopefully a manuscript in the near future), but it was an opportunity lost. I shoulder the blame for the lack of productivity out of this student. I was new, it was my first student, and I was still trying to work out of my supervisory style and there are things that I know I could have done better.

Fortuna . . . More
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Last by Thomas Joseph on Jan 21, 2011, 8:06am
1. An article, IMO, worth reading. Sometimes we can be like moths to a flame, pulled towards the bright lights, completely oblivious to the fact that we're leaving even the basic necessities behind. Politics is that bright light, and until we start letting common sense dictate what we do -- and more importantly we convey this desire to our politicians -- we'll be stuck in this endless spiral which will lead to has resulted in a massive crisis.


3. You know, I'm getting sick and tired of Facebook "slipping in features" that divulge personal information. I'm pretty wary about what I reveal on the site, and keep sensitive information off the site, but really ... these practices are simply shady. I know Facebook needs to make money, and this is how they do it, but they really should be upfront about it. The adage "It's easier to ask for forgiveness than permission" is being abused.

4. Dear sequencing service provider, I appre . . . More
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Last by Thomas Joseph on Jan 18, 2011, 9:52am
A new Cake album. Woo hoo!

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Last by Cath@VWXYNot? on Jan 14, 2011, 12:58pm
If I had ever entertained the thought of going on camera, for any reason ... this video has dissuaded me entirely.

I feel no sympathy for Sarah Palin, and this thing is freaking hysterical, but goes to show you that once you put something on the web, you're bound to lose control of it.

h/t Salon.

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Last by becca on Jan 17, 2011, 12:20pm
Viewing this, and came across this (#13) ...

“Gun control advocates tell us that removing guns from society makes us safer. If that were the case why do the worst shootings happen in gun free zones, like schools? And while accidents do happen, aggressive, terroristic shootings like [the Mumbai massacre] are unheard of at gun and knife shows, or military bases. It bears repeating that an armed society truly is a polite society.” - Ron Paul

Comment was made by Ron Paul in December of 2008. It can be found at his Congressional website here.

I bet he felt like an idiot when Major Hasan shot up Fort Hood almost exactly a year later.

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Last by JaySeeDub on Jan 25, 2011, 3:05pm
These are tough times. Everywhere you look money is tight, budgets are stagnant or shrinking, we're being asked to cut costs, and incorporating money saving methods to keep those costs down are becoming commonplace. I started out 2011 (actually ended 2010) intent on doing my part in not only cutting costs in the operation of my lab/office, but greening them up as well.

As I looked about my office there was one thing that jumped out at me. The volume of paper which was cluttering my desk and shelves (I actually have a set of metal shelves I purchased two years ago to hold all the scientific papers I've printed out in the past several years).

Paper, paper, everywhere,

Until all the trees were dead.

Paper, paper, everywhere,

Nothing interesting to be read.

Coleridge, if he had ever seen my office.

Between the cost of paper and the price of ink, I imagine that I have spent a lot of institutional money printing out versions of my manuscripts, other peoples scientific papers, progress reports, and other assorted stuff. It all adds up over time.

I'm not sure how much my institution pays in paper and ink costs each year (though I'm going to ask), but I'm sure it's significant. As such, it seemed like an . . . More
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Last by Cath@VWXYNot? on Jan 12, 2011, 7:17pm
Yes! It's another edition of Wednesday Micro Hits! I haven't been blogging regularly enough to incorporate it into my blog rotation, but since I'm back (for the time being), I figured I'd throw one together and give the one or two people who read my blog something to do for a minute or two!

1. A new blog that should be interesting, on the topic of soil science, called Wired for Soils. Check it out!

2. No Labels. I like.

3. If you thought twitter was next to useless, you need to check out this site.

4. Been having a lot of neck pain lately. Don't know if it's the way I'm sleeping (I'm a horrible sleeper) or what, but ... bought myself a memory foam pillow and my neck felt great this morning! Those things are awesome! Never thought they would make a difference, but a coworker raved about his so I figured I'd give it a whirl. Now, will the feeling/comfort last?

5. That's a lot of snow. Can't sa . . . More
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Last by Thomas Joseph on Jan 12, 2011, 12:40pm

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Last by Genomic Repairman on Jan 07, 2011, 10:10am
I thought I'd start a blog series where I plug a particular product. It's probably something I've come across which I think is cool and useful in my own work. I'm going to try to do this (i.e., remember) once a month, and here is January's edition.

Rite in the Rain's All-Weather Notebooks. I stumbled upon these puppies at the 2010 ASA-CSSA-SSSA trisocietal meeting. It was in the "swag bag" you get upon registering, and was really the only thing worthwhile. If you do field work, you'll know how hard it is to take notes when the weather sucks (when it's raining or even when it's damp). These notebooks go a long way in reducing that angst. While I prefer to write in pencil (yah I know, patent people have a fit when you do stuff like that ... hopefully I can get an electronic notebook system established where I can scan all my field notes into a more "permanent" format) they have some cool pens as well (albeit slightly expensi . . . More
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Last by Thomas Joseph on Jan 07, 2011, 2:26pm
1. I'm thrilled that NetFlix has started to improve their offerings on Instant View. This is especially evident in their television section, and I'm now hooked on Dexter.

2. Downloaded two albums from Amazon over the holidays. They were doing a $5 special for the Best Music of 2010 (still seems to be going on at the moment). I bought Cee Lo Green's The Lady Killer and Kings of Leon Come Around Sundown. So far I'm liking the KoL album more.

3. To the idiots of the world that own SUV's ... when you pull up alongside someone who was in front of you and is looking to make a turn, you do realize that you've now effectively and entirely blocked their view of incoming cars from that direction? Which means they now have to sit and wait for you to make your turn, or otherwise face the risk of getting into an accident by pulling into traffic blindly. Wait . . . More
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Last by Thomas Joseph on Jan 06, 2011, 8:26am
After having read and reviewed a particular manuscript three times (the original and two revisions) I only had this to say to the Associate Editor:

I have now reviewed this manuscript three times. I believe it is safe to say that all of my concerns have now been sufficiently addressed. Please accept this manuscript posthaste. While I have indicated that I would be willing to review yet another revision of this manuscript, I fear I'll have a brain hemorrhage if it shows up in my email inbox again.

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Last by Evie on Jan 05, 2011, 4:44pm
Was reading a HuffPo article this morning and choked on my beverage (after reading this article I need something a bit stronger) when I came across the following line ...

"A dollar more per gallon isn't that much – probably about $750 more per year for each motorist, but there's a psychological aspect to gas prices," he said. "People are going to be up in arms about this."

Only $750 more per year? Only? ONLY? Excuse me, but lets see how far $750 could go. $750 could ...

1) Pay my car insurance for the entire year,

2) It's a brand new 42" LCD television (with stand),

3) It's a movie night for two each week of the year (if you lay off the soda and popcorn),

4) It's what I typically set aside for two and a half months of groceries (including food for my two dogs),

5) It's over a year and a half of gym membership dues (for me at my gym at any rate).

Yah, $750 can go a long way ... and I'll readily admit that I'm fairly well off. And lets not forget that thats ON TOP of what we're already paying out for the year on gas as it is. But what about those people who are not as well . . . More
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Last by Thomas Joseph on Jan 12, 2011, 2:11pm

Coruscant - an ecumenopolis

What are sci-fi movies trying to tell us with images, and themes, like the above? The term ecumenopolis comes from the combination of the two Greek words ecumene and polis -- in other words, a city made of the whole world. It is featured in Star Wars (as an example) as the planet of Coruscant (pictured above). Watching the movie one may note that there is no visible greenery on the planet, no visible water, and even major landscapes are dwarfed or have been wiped out by buildings. It is a theme that has been mentioned numerous times in science fiction, and a listing can be found in Wikipedia. While it seems like a thing of fantasy, the view of North America from space at night suggests otherwise (see below).

An ecumenopolis in the making?

My thoughts turned to such notions as I was reading the following article, which is definitely worthy of a read. The article discusses the issue of mesopredator release, which is when small- to mid-sized predators are released from the pressures of their own predation by large-sized predators. Since they are no longer pre . . . More
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Last by Thomas Joseph on Jan 04, 2011, 8:23am
I hope everyone enjoyed the holiday season. I'm sure quite a few people took an extended break, recharged the batteries, and are now ready to launch themselves back into the daily grind. I did something of the sort myself, though I started early when my car broke down the day before my vacation officially started ($50 dollar repair for a blown fuse ... who knew the fuel pump had a fuse devoted to its operation? Not me!).

I intentionally stayed out of pocket, in part because I've done so much writing and reviewing (three papers revised/accepted, and four manuscripts reviewed in the last month) that I just couldn't face doing more writing on my down time. So when the time came to amscray, I packed up the car and headed out to the family for the Christmas holiday. Lots of food (though I actually didn't gain any weight), lots of laughter, and lots of rest. Very little drama (which is a nice thing), but lots of time in a car (over 2500 miles by the time I turned in the rental).

So here we are now in 2011, and I have made a couple of resolutions, which I haven't done in a long time.

1. Lose 10 to 15 more pounds. I dropped 10 pounds this past year ... little less than half of what I gained in the past couple of years. It's all been diet (low carbs, which is hard for . . . More
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Last by Genomic Repairman on Dec 12, 2010, 3:16pm

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Last by Evie on Dec 13, 2010, 5:20am
So, this press release that I forwarded to some people at work today generated some interesting email discussion. Me and my colleagues do a fair amount of work on animal waste and their byproducts, and when I say "waste" I mean it literally ... poop and pee, on a massive scale. We do a lot of work with CAFO's (Concentrated Animal Feeding Operations), so there are lots of animals (thousands if not tens of thousands) in a small area. If the waste is not handled or treated properly, it can have some dire environmental -- as well as animal and human health -- impacts. So, my job (and the job of my colleagues) is to find ways to improve on current waste treatment systems, which often leads us to cooperate with municipalities (and nations) to draw from their own applications (with reciprocation when they draw from us as well).

However that is really just a tangent to what we discusses this morning over a few emails. You see, the press release talks about a group of organisms called the PVC (Planctomycetes, Verrucomicrobiae, and Chlamydiae) which this research consortium have call "the missing link" between microbial life . . . More
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1. Brett Favre has announced his retirement seventeen times!?! Wow.

2. This laptop doesn't look chrome plated to me. What gives?

3. Can't say that I followed much of the Edwardses drama over the past couple of years. I do think it's sad that she has passed away from cancer, especially with her family in such a disarrayed state. It also makes me think about my own personal health, which I think is something I'll blog about in the future.

4. Speaking of which, this is the time of year where I start giving away some of my annual leave. I am allowed to accumulate only so many hours before they start falling into a "use or lose" bin. The holiday season will use up about half of those hours (if I take a solid week or more off) but the rest need to be used somehow. I've tried to pick several people who need the hours badly (because th . . . More
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Last by Thomas Joseph on Dec 07, 2010, 1:35pm
h/t - Drugmonkey.

January - I figured to start off the new year I'd do something a little different. [What's Your Name?]

February - If you love strategy games, you have to try the Advance Wars series. [Currently]

March - I'm on record as saying before that the HSUS is a farce. [I repeat again HSUS is a farce]

April - Honestly... what were these people thinking? [Honestly]

May - - --- -.. .- -.-- / -- .- .-. -.- ... / - .... . / .- -. -. .. ...- . .-. ... .- .-. -.-- / --- ..-. / - .... . / ..-. .. .-. ... - / -- . ... ... .- --. . / ... . -. - / -... -.-- / -- --- .-. ... . .----. ... / -.-. --- -.. . .-.-.- [--. ..- . ... ... / .-- .... .- - / - --- -.. .- -.-- / .. ...]

June - Wo . . . More
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Last by Thomas Joseph on Dec 14, 2010, 10:50am
So, now that Thanksgiving is over I've had to start decorating for Christmas. If I had my druthers, I'd decorate ... never ... or possibly on the 23rd or 24th, but the decision is not mine to make alone. So up into the attic I went, and down came all the wreaths, ornaments, stockings and holders, holiday DVDs and CDs, garland, and lights ... and the big artificial tree. This tree has seen much better days and so this is probably the last year it'll be used, but it's gotten me to thinking (yah, scary thought). What is going to happen to that tree when I'm done with it, and what sort of environmental impact is it going to have?

Before I go any further though, I have to say that one of my favorite parts of last evening was breaking open my favorite Christmas CD of all time "Favorite Carols of Christmas" and listening to it. I've just completed ripping and adding it to my iPod, so I won't get stuck listening to all the cruddy Christmas music out there on the radio.

At any rate, I've gone around looking for information on the environmental impacts of artificial Christmas trees and come across a f . . . More
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Forget all these "music snob/warz" posts. You know where it's at? Nick Cave & the Bad Seeds.

Everyone else needs to go find some real music. Really.

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Last by Thomas Joseph on Dec 02, 2010, 3:17pm
Black out to phantom power, and like there's nothing on. - Something On.

No, I'm not talking about one of the best albums ever made (by The Tragically Hip), but rather the phenomenon known as phantom (also known as standby or vampiric) power. Phantom power is when a machine draws an electrical current even when it is in the "off" position, when technically it's in the "standby" position. This can run you upwards of $10 a month! And if you're a cheap SOB like myself, that's a lot of money that can be saved.

So, this Christmas, buy yourself a present. Get a few . . . More
Views: 461 | Comments: 8
Last by CK on Dec 02, 2010, 1:42pm
I am fascinated by some of the naming conventions I come across when looking at new bacterial species. Having cultured, and identified novel organisms myself (currently working up four novel strains), I always find this subject fascinating, so much so that I've blogged this topic once before. Most times the names given to these organisms are very conservative, but sometimes the people who have identified them get "creative" … or the names themselves just turn out to be amusing to me.

So, I’ve collected a handful here to giggle over.

Case #1: Fervidicoccus fontis -

Fervidicoccus ('di.coc'cus. L. adj. fervidus hot; L. masc. n. coccus a berry and, in biology, a coccoid cell; N.L. masc. n. Fervidicoccus coccus which grows at high temperatures).

fontis (fon'tis. L. gen. ma . . . More
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1. Holy Cannoli! Imagine buying a house and then finding out it's entirely uninhabitable. Not only that, but then you find out there are no legal repercussions for those who sold you the house. It happened to this couple when the house they purchased turned out to be a meth-house. There is a list kept by the DEA that you can search, by state, to see if a house may have been used to create meth.

2. Yesterday ended Native American Heritage Month. If you're up for a little culture, this YouTube video, released by the Smithsonian is good. It's a bit lengthy (47 minutes), but worth it.

3. "You've got to look like a hobbit." Exactly what does a hobbit look like? Well, they're obviously white donchaknow?

4. Consider me . . . More
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Last by Genomic Repairman on Nov 28, 2010, 3:54pm
I hope everyone had a nice Thanksgiving. I'm probably in Kentucky right now doing some field work so I'll leave you with a video from a band which hails from this state, Cage the Elephant.

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Last by Thomas Joseph on Dec 03, 2010, 7:07am

So the food coma is over, and yesterday was a rousing success. Had not one, but two, Thanksgiving dinners. I have not yet stepped onto a scale today, but if I gained less than five pounds I'll be supremely happy! I did try to eat as healthy as I could yesterday, trying to skip using too much gravy, or eating too much dressing, so I am slightly optimistic.

Tips to cooking your bird ... if you take the tin-foil off for the last hour, and rub some butter on the skin, it browns very nicely. In addition, the tin-foil cover really keeps the bird moist. I've used the turkey bags before, but all the juices collect at the bottom and I don't like a soggy bird.

Today, I'll be making turkey soup (which is why it looks like a chest burster took out the turkey I cooked yesterday). Take the dark meat you have remaining (in particular the wings) and drop it into a half pot of boiling water (use a large pot). Let it simmer for about an hour or so and pull out the meat. This will help flavor the water (making a turkey stock of sorts) and will loosen up the meat on the wing bones. You can also add 15 ounces of chicken broth/stock and remove an equal amount of water. Throw away the skin and pull off whatever meat you can. Put the wing meat back into the soup . . . More
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1. I hate sore losers, and Joe Miller is a sore loser. Underlined emphasis mine.

Murkowski claimed victory last week when a hand count of write-in ballots by the state Division of Elections showed she led Miller by more than 10,000 votes. Even subtracting the ballots challenged by Miller's representatives, Murkowski still led by more than 2,100 votes.

2. Part of me wonders if the Cold War is coming back. But this time, it's China we're facing off against. I imagine these issues with the Korea's are certainly going to cast a pall over the next year or more.

3. And this article doesn't make my reflection on point #2 seem all that crazy, though a Cold War is much more preferable than an Asian/World War.

4. I'm a bit late on blogging the rest of my notes on the #ASCMtg, but I'm going to get to them. I promise. I also owe everybody two extra recipes for the Donor's Choose campaign. The delays couldn't be he . . . More
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I finally have some time to pay up on my Donor's Choose challenge. I made payment for Jade's generous donations to the cause, and then I went on a self-inflicted hiatus when Genomic Repairman was kind enough to donate his winnings to my kiddies as well. Thanks GR (and Brian who issued the challenge). In your honor, here are two more recipes.

Recipe #3 (TJ's Comfort Food)

Nacho Chicken Casserole


6 boneless chicken breasts, skinned, and excess fat removed

Bag of Doritos (a big bag)

Chili powder

Can of Cream of Chicken (15 ounces) *Can use Cream of Mushroom instead*

1 bag (8 ounces) Fiesta Blend Shredded Cheese *Any multi-cheese mix will do, preferrably spicy*

Onion, Paprika, Cumin (all optional)


1a. Grill the chicken breasts and cut into bite sized chunks (or shred).

1b. Cut a small slit into the Doritos bag to let air out. Then crush all the nachos into small bits.

2. Place a layer of nachos into the bottom of a 2 quart casserole dish.

3. Sprinkle some chili powder onto crushed nachos (can also put cumin or paprika and/or onion).

4. Lay a third of the chicken onto nachos.

5. Lay a third of the cream of chicken soup on chicken.

6 . . . More
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Last by Cath@VWXYNot? on Nov 22, 2010, 6:06pm
... I'm still around, but barely. Trying to wrap up some "minor revisions" for a manuscript which were not so minor when considering the fact that the Associate Editor wanted me to split my "Results and Discussion" into two sections, and Reviewer #3 waxed philosophical about some of my comparisons. So it's mostly busy work, though I really want to beg off having to rewrite and restructure half of my paper. Also annoying in the sense that looking at the AE's publications in same said journal ... and he's used a combined R&D for every manuscript he's submitted there. Gah.

At any rate, I will not be daunted by the task ahead of me ...

Muse "Uprising" Best Special Effects VMA 2010 from HUMBLE TV on Vimeo.

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Last by Namnezia on Nov 07, 2010, 7:39am
I LOVE this band! They have a new website, and just came out with a new album.

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Last by Thomas Joseph on Nov 05, 2010, 1:32pm
Ok folks, I just read possibly the worst paper I've ever had the misfortune of being asked to peer-review. To the editor who sent it to me ... you really don't like me, do you?  Anyways, here we go ...

1. Don't misspell the word "abstract". I mean, after the cover page, it's the first word on the first page! It's the first thing I read, and when I see that you spelled that word wrong, I am going to automatically assume that there are other misspellings. For you, the manuscript author, this is a bad thing (see #2).

2. I can understand grammatical errors, especially for foreign authors. It happens, and I realize the English language can be complex and hard to figure out. I make grammatical mistakes myself from time to time (I tend to misuse "that" and "which"). However, there is no excuse for spelling errors. Just about every program designed for document generation has a spell checker. If you can't be bothered to take the 10 seconds to spell check, I am going to assume that you are lazy.  Lazy is bad, because if you can't be bothered to check the manuscript, what makes me think you bothered to properly design your experiments? That you paid attention to detail ... that you gave a crap about any of the science? It's a rhetorical question because the answer is non . . . More
Views: 315 | Comments: 6
Last by Thomas Joseph on Nov 03, 2010, 3:03pm
So I lost my original post. I had about 80% of what I had wanted to write on my update from the ASA-CSSA-SSSA tri-societal meeting and my stupid touch-pad sent me back a page. Doing so left me with nothing, and if I can't get Brian to institute an autosave feature *nudge nudge* I'm going to be supremely bummed ... and will start writing all my blog entries in Word. ;)

Anywho ... Comic-Con ended on Sunday so there was no temptation to spend the day hanging out with Stan Lee rather than attending symposia, which I guess is a good thing. I never did make it to the Keynote Address Sunday night, though from what I heard it was quite the talk. The tri-societies have made a conscious effort to bring in well-known speakers who interface with our mission, and this year they did a great job in getting Thomas Friedman, Pulitzer Prize winner, and author of The World is Flat and Hot, Flat and, Crowded. I wound up not attending because I had an obligation to participate in another meeting/workshop. As a matter of fact there were several meetings running concurrently with the Keynote Address, which I view as a bit of a problem. Since the tri-society is making a strong effort to bring in excellent speakers, these "side meetings" are going to see diminished numbers, or they are going to h . . . More
Views: 381 | Comments: 3
Last by Thomas Joseph on Nov 03, 2010, 3:10pm
Some very interesting goings-on already.

First, they're holding Comic-Con at the same time here in Long Beach. Comic-Con is in Exhibit Hall A, ASA-CSSA-SSSA is in Exhibit Hall B. I feel the pull to enter Exhibit Hall A, but they tell me I'm too nerdy to enter ... oh, and that I don't have the right badge for admittance either. Phooey.

Second, shame on the Hyatt Regency. I arrive at 2PM, and they tell me that they were booked to capacity yesterday and they're still cleaning rooms. The lady at the desk complains that we're all arriving early. I ask her what time the hotels official check-in time is, and she tells me they don't have one. Question: If you don't have an official check-in time, how can you state that I've arrived early?

Monday is packed full. I'm going to make it a point to attend at least one "early career" talk, probably the one dealing with juggling work and home, but Monday is heavy on the microbial work (especially topics dealing with -omics) and I really want to attend as many of them as I can.

I have a meeting tonight, and it runs concurrently with the opening talk. Actually it runs an hour past the opening talk, which means I'll be attending only the last half of my meeting. Also, why schedule division meetings towards the back end o . . . More
Views: 195 | Comments: 2
Last by Genomic Repairman on Oct 31, 2010, 2:52pm
Well, I'm currently at the airport getting ready for my flight to Long Beach California for the ASA-CSSA-SSSA meeting. I'll be arriving this evening in time, hopefully, for the opening talks and beers with collaborators. I'll be blogging on the meeting, and have been extended access to the media room so it should turn out to be a really exciting event. It's definitely one I'm looking forward to. 

I noticed that Brian donated a princely sum to Donor's Choose, and as such I will be posting two additional recipes. Since I'm out of pocket and my recipe book is back home, I won't be able to do so until Thursday, but they shall be posted!

Toodles for now folks, and I'll see you all on the flip side.

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Last by JanedeLartigue on Oct 31, 2010, 2:06am

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Last by Thomas Joseph on Oct 31, 2010, 10:14am
1. They were still making Walkman's?

2. Will be attending the ASA-CSSA-SSSA tri-society meeting. I've already blogged about the early career scientist sessions, but I'm hoping that the meeting has some more sessions which grab my interest. This meeting is usually short on microbiology, and ASM is usually short on the agricultural issues, so it takes me two meetings to touch all my bases. Either that, or I need to find new societies and meetings to attend.

3. I'd love to be able to go into space at some point in my life. It appears however that it's going to have a severe impact on my carbon footprint.

4. I'm finally feeling better. Still have a runny nose, but I think I'm out of the woods. I may have dodged a sinus infection, so I guess it could come back and bite me in the rear sooner or later. Honestly, I think they should do away with sinuses altogether.

5. . . . More
Views: 304 | Comments: 2
Last by Thomas Joseph on Oct 26, 2010, 3:41pm
For those of you who are attending the ASA-CSSA-SSSA International Annual Meeting in Long Beach, CA this year (October 31 through November 4), there will be several Early Career Programs. I think all of them are considerably worth the time to attend.

They can be found here.

From granting writing, to interviewing, to how to write manuscripts. They also have an hour-long anti-#k3rn3d session called "Balancing Career and Home".

Brianna Blaser, Science Careers/AAAS, will talk about what work/life balance means in today's world while succeeding in your career. She will show you how to assess your time management needs, and make the most of your time at work and home.

So, if you are attending this years tri-society, and are a relatively new career scientist, I'd give these sessions some serious thought. I know I'll be attending several. I intend on independently blogging the conference too, in case people can't attend but would like to hear about the parts of the meeting I personally attended.

. . . More
Views: 246 | Comments: 6
Last by Nikkilina on Oct 21, 2010, 8:47am
1. Got to lay blame for this incident at the feet of the Olympic National Park Rangers. Their "fun" -- in the form of taunting this animal by shooting bean bags at it -- led to the death of a 63 year old hiker. Also, who in their right mind tells visitors to the park to hurl stones at a wild animal? Other than these idiotic park rangers that is. A tragic, completely avoidable, mess. Heads should roll over this.

2. Stupid people should not breed. Here is the evidence.

3. If anyone spots the truck which ran through my sinuses, can you take the number down please? I've actually got a Research Blogging post in the works because of my allergies, if I can only recover long enough to get my eyes to focus on the manuscript to read it.

4. I love my Blackberry. I love Poynt too, though it'd be even more spectacular if Poynt could work with my GPS system (AT&T Navigator) instead of just working with Blackberry Maps.

5. I suppose no one in the CIA ever played "hide ' . . . More
Views: 334 | Comments: 5
Last by Thomas Joseph on Oct 18, 2010, 9:31am
Here is my family recipe, as promised in my Donor's Choose challenge. If you like this recipe, and want more ... you've got to donate! As long as you donate, I'll make good on my promise and post two recipes. One will be a family recipe or my choosing, the other will be a recipe for one of my favorite comfort foods (so technically they will both be family recipes). If we get to $250, I'll post a family secret cheescake recipe, and if we hit $500, I'll post the other.

Now here we go, my family recipe of the week. It's pasta e fagioli (pronounced sort of like pasta fah-zule) where zule sounds like yule, as in the log. ;) It's typically a meatless dish, but you can add a pound of cubed beef to it if you can't go a meal without consuming animal flesh (I'm looking at you Brian). Some people and restaurants* use ground beef ... whatever you do, don't ruin this good meal using ground beef. I beg you.

Pasta e Fagioli


1 pound beef, cubed, and browned in olive oil (optional)

1 pound pasta (I grew up with ditalini rigati, which look like small tubes, but you could get away with penne rigate or gremiti here)

2 cans (14.5 ounces each) of beans (you can use red kidney beans, but I like cann . . . More
Views: 314 | Comments: 4
Last by Thomas Joseph on Oct 18, 2010, 9:34am
[Summary: Thomas Joseph makes good on the first donation to his Donor's Choose campaign.]

So Jade came through with a nice donation to my Donor's Choose campaign. Therefore, it's time I make good on my promise/bribe to provide two recipes (one a family recipe, the other a comfort food) for my readership. I said I'd post my Italian Wedding Soup recipe, but it's one that isn't in my cookbook yet. I'll be getting the recipe from my mom this weekend, so I may post it as a bonus recipe later this week. However, I do have a good soup recipe to post. Since Jade is a big fan of soups, I'll post my mom's stew recipe as my comfort food too. Most of these recipes are fairly simple and rustic, and don't take too much time to prep (at least I don't consider them too). If you have questions about any of the recipes, feel free to ask.

TJ's Mom's Stew (Comfort Food)


2 pounds of meat (beef or pork, but venison works best), cubed

1 large onion, diced and sauteed

Several carrots, peeled and diced

Several potatos, peeled and cubed

15 ounces of tomato sauce

1/4 cup of water

can of peas (12 ounce can, or a bag of frozen peas)

Teaspoon of Gravy Maste . . . More
Views: 187 | Comments: 2
Last by Thomas Joseph on Oct 18, 2010, 9:37am

There is no escape,
From the slave-catchers' songs.
For all of the loved ones gone.
Forever's not so long.

. . . More
Views: 223 | Comments: 4
Last by Thomas Joseph on Oct 15, 2010, 8:59am
So my second week at LabSpaces has come and gone. It was a pretty productive week, even with a holiday (Columbus Day, for those of you lucky enough to be able to take it off) thrown in.

1. Found out that my dogs decided they wanted to be flea-bags instead. Took it as an educating moment, letting people know about the human dangers inherent in living with pets with fleas. While bug eating may be a delicacy for some, I'd strongly advise against eating fleas. After that, I was visited by yet another plague.

2. Wrote a letter about/to Kern. Not that he'll read it, but other people had nice things to say about it.

3. We kicked off the Donor's Choose Challenge this week in earnest. I'm begging for money, and I'll keep begging until the challenge is up. If you want to shut me up, donate! I also decided to sweeten the pot by offering up some of my . . . More
Views: 313 | Comments: 10
Last by Thomas Joseph on Oct 15, 2010, 6:07pm
I've been thinking long and hard about this, and about what makes a suitable bribe to generate interest in getting people to donate to my Donor's Choose page. To be honest, while it'd be nice to see people fund projects on my page, even if they throw a few dollars somewhere else, I'd be happy. With that said however, I will offer something to "sweeten the pot" for people to donate through me.

Now, I don't knit. I can't beat you to a pulp. I've never been a bartender. I don't do cartwheels.

But oh, I can certainly cook.

I learned young, watching my grandma, my aunt, and my mom cook. I would help prep and I would watch over the sauces. I knew I had become a man when my grandma or m . . . More
Views: 491 | Comments: 14
Last by Thomas Joseph on Oct 18, 2010, 9:46am
[Summary: Where Thomas Joseph discusses an issue that changed the way he views the internet.]

This post by GR this morning really struck a chord with me. Not because I've found out that someone I knew passed away*, but it was certainly death related. The moment I'm going to refer to happened several years ago (back in 2003) when I was young(er), and dumb(er) than I currently am. It was back in the days when internet message boards (MBs) were all the rage, or at least they were all the rage for me. Discussions would often get downright nasty, and if you were intense enough about it, you'd throw down with complete strangers and say things that you wouldn't say to anyone's face -- even if they were your own worst enemy. I was that sort of jerk back in the late 90's early 00's, but it didn't last for much longer past that.

Back then I enjoyed debating. Actually, I didn't enjoy debating so much as I enjoyed winning debates. I think there is a distinct difference. If I could pummel my opponent into submission with a literary show of force, I considered it a huge success. I had my first taste of it my freshman year in college whe . . . More
Views: 406 | Comments: 8
Last by Thomas Joseph on Oct 13, 2010, 5:51pm
1. Can't even begin to say how much I love this new album by Brandon Flowers. Titled Flamingo, it's reminiscent of his Killers work, especially Sam's Town and Hot Fuss. Truly an awesome album.

Rolling River of Truth, can you spare me a sip?
The Holy fountain of youth has been reduced to a drip.
I've got this burning belief in salvation and love.
This notion may be naive, but when push comes to shove.
I will till this ground.

2. The Taliban can suck it. This lady was there doing nothing but helping, and they killed her. What asshats. It says something when the most technologically advanced items they have are weapons.

3. What Brett Favre did was majorly creepy, and clearly sexual harrassment. Won't be sorry to see him get the boot. Also, did anyone else note that his . . . More
Views: 269 | Comments: 2
Last by Thomas Joseph on Oct 13, 2010, 9:02am
I'd say please don't make me beg, but I'm already on my knees ready to ask you for your help.

The following project has 3 days left, and $200 to go. It's listed on my Donor's Choose page, but frankly I don't care if you link through me and support this project or not. Just go help Mrs. Radke's kindergarten class. Folks, here is our chance to get help to these kids who are on the ground floor. The skills they learn at this early age will stay with them for life. So lets donate, fund this project, and get tools into this classroom that will benefit these kids for a lifetime. Thanks!

PS: We cannot let these kids grow up thinking magnetism is magic!

. . . More
Views: 720 | Comments: 15
Last by Thomas Joseph on May 02, 2011, 1:33pm
[Summary: Thomas Joseph talks about why he went into the field he went into, and gives thanks to his parents.]

I really like this post by Zuska. As a matter of fact, my parents did the very same thing for me. The only exception being that I had to pay my last year of college because my dad was laid off from work* and so my folks couldn't help me with some of my tuition and fees that year. They didn't have to shoulder the entire burden -- I was on a X-C and T&F partial scholarship when we went to Division I my sophomore year, and I did work/study as well -- but they shouldered the majority of it. They wanted to give me a leg up on life, a life without being crushed by student loans the minute I flipped that tassle from right to left on my academic cap. And I couldn't be more grateful to them. Life wasn't always easy in the Joseph household, we were middle class, but that didn't mean times were always peachy. I remember my dad being on strike a few times and having to work odd jobs to keep food on the table, I remember him working 4PM to 12AM shifts for months at a time and him waking up at 6 or 7AM to see us off to school and t . . . More
Views: 1232 | Comments: 18
Last by Nikkilina on Oct 13, 2010, 10:03pm
So I related yesterday about how my dogs had fleas. Well as the night was winding down, I was given a heartattack when I saw something move out of the corner of my eye in my wash room.

It was this cute little fellow.

Froggie, Indoors

I feel like Jack Hanna today, if Jack Hanna dealt with flea ridden pets. Where this frog came from, I have no idea. He did collect a bit of dog hair in his travels through my house though, that much is obvious. And yes, that is where I found him ... on top of my washing machine.

Took him outside, where he promptly jumped out of my hand and onto a railing of my porch. That is a better place for him I think, even though I use a bug-free lamp on my front porch (makes using my porch swing that much nicer) there should still be plenty of eats out there for him.

. . . More
Views: 3097 | Comments: 21
Last by Thomas Joseph on Oct 13, 2010, 8:59am
[Summary: Thomas Joseph found a flea on his Husky. Now he tries to make everyone afraid of fleas.]

Yes, it happened. I found a flea on one of my dogs. I was sitting there last night at dinner, minding my own business when my Husky came over to seek attention. He's the cutest thing you'll ever see with the lightest blue eyes, and a white and copper coat that is thick and luxurious. He's digging the cooler weather so is spending most of his time outdoors. Except for dinner time. So he nudged me and I leaned over to pet him. Holding his head in my hands I looked at his face and saw a speck. I figured at first it was dirt since he loves to dig. Then the speck ... moved. My heart sunk. My pup had fleas.

Now I give all of my dogs Frontline Plus, which is supposed to do a pretty good job of keeping fleas (and to a certain degree ticks) off of them. I follow the directions closely, so I was surprised to find a flea on him. So I grabbed the pyrethrin mist, worked a few good sprays onto his face, head and the remainder of his body and then proceeded to treat the kennels with an additional spray. I'll probably have to move up my Frontline Plus application to 21 days as opposed to the 28 I routinely wait between doses if I continue to see any fleas.

N . . . More
Views: 263 | Comments: 4
Last by Evie on Oct 12, 2010, 6:57pm
I've picked out the next article I'll be Research Blogging on. Want to know the topic? Here is a hint ...


Picture by NASA

. . . More
Views: 355 | Comments: 2
Last by Thomas Joseph on Oct 09, 2010, 12:55pm
[Where Thomas Joseph posts an obligatory YouTube music video].

ETA:This album by Brandon Flowers is pretty darn good.

. . . More
Views: 495 | Comments: 9
Last by Thomas Joseph on Oct 09, 2010, 4:28pm
Well, this finished off my first week of blogging here at LabSpaces, and so I'll try to wrap things up in style. Ok, not really in style, but with a rather inane blog entry. Now, this might look like my Wednesday Micro Hits, but really, this is my Friday Wrap-Up. Try not to confuse the two.

1. I think everyone should go over and donate a few dollars to this Donor's Choose project. I know GR will be especially fond of this one. I tried to tweet @RebeccaSkloot in the hopes that her publisher could do something about it, but it probably got lost in all the noise of the intertubez ... it's not as if she has only 30 followers like I do.

2. I continued the first of my weekly rituals, that being the posting of my Wednesday Micro Hits. Yeah, it's not all about microbiology, but rather very small (get it, micro/small ... I kill myself) blurbs that I didn't feel like writing large blog entries on.

3. I did my first (of hopefully many) Research Blogging articles here. I think it's a first for LabSpaces, but someone else wil . . . More
Views: 502 | Comments: 4
Last by Thomas Joseph on Oct 12, 2010, 10:32am
Ok folks, I've thrown my hat in the ring and set up my Donor's Choose page a couple of days ahead of schedule (officially starts on 10/10/10). That means, of course, that we have a couple of extra days to raise money. I've got seven projects listed on my donor page, a few of which are very close to being completed. Let's try to get those knocked out folks, and then we can progress to the larger projects. I have a widget to my project on the right hand side (you may need to scroll down a bit) if you want easy access to my chosen projects. Give early, give often folks.

ETA: HP is going to match all donations up to a total of 50K. Kudos to them.

. . . More
Views: 3515 | Comments: 13
Last by Thomas Joseph on Oct 11, 2010, 10:01am
Welcome to my first Research Blogging post here at LabSpaces! I'm not sure if this is a first for LabsSpaces, or simply a first for It's a Micro World after all, but regardless ... you're here now and you may as well stay for the fun! I grabbed a paper which caught my eye, and certainly generated a fair amount of buzz in the news, probably because it highlights the wasteful nature we've overlooked for far too long. As of the time of me writing this entry, the manuscript is available for download free from Environmental Science & Technology (link at bottom of page), but I have no idea how long this will last. So accordingly, here is the abstract for the manuscript:

This work estimates the energy embedded in wasted food annually in the United States. We calculated the energy intensity of food production from agriculture, transportation, processing, food sales, storage, and preparation for 2007 as 8080 ± 160 trillion BTU. In 1995 approximately 27% of edible food was wasted. Synthesizing these food loss figures with our estimate of energy consumption for different food categories and food production steps, while normalizing for different production volumes, shows that 2030 ± 160 trillion BTU of energy were . . . More
Views: 494 | Comments: 4
Last by Prabodh Kandala on Oct 07, 2010, 7:57am
I'm pleased to announce that I'm all set to start Research Blogging here at LabSpaces. Got my account established with the good folks over there, and have my first paper all picked out! I'll also probably try to bring my series What's Your Name? back to life* for your reading pleasure. Stay tuned!

*I claimed I was going to do it monthly, then promptly forgot about it after the first month. But it's a good concept so I'll try to run with it.

. . . More
Views: 658 | Comments: 3
Last by Thomas Joseph on Oct 07, 2010, 1:14pm
1. I'm getting used to Google Chrome. There are some things I don't like about the browser that I preferred on Firefox (no AdBlock, no NoScript support), but it's definitely growing on me. I use Chrome about 70% of the time now.

2. Who goes to jail for this egregious crime? Sure, insurance companies are about the bottom line, but when someone gets sick AFTER they've entered into the contract with you, the company needs to stick to their end of the bargain. Heads should roll for this, though I doubt any will.

3. This worm (Dracunculus medinensis) has always given me nightmares, hopefully we can successfully eradicate it in my lifetime.

4. Note to self: Avoid any sort of Sun Mountain rain gear when buying next round of gear for field work.
. . . More
Views: 767 | Comments: 12
Last by Thomas Joseph on Dec 14, 2010, 10:49am
The "What If?" blog theme for this month concerns what we feel our career path might have been had we not decided to do what we're doing now. I've mulled this question over in my head a number of times, not as often as I used to when I was still in graduate school*, so I have a pretty good idea of where I might have ended up.


Seriously. It started back in my undergraduate days. Back then at my university we had what was known as "general electives". The university was broken into eight disciplines, and in addition to your pre-reqs, you needed to take a total of nine classes from the discipline which did not contain your major. For me, my major (Medical Technology) was in the Life Sciences, so I needed to take classes from the Physical Sciences, Social Sciences, Arts, Foreign Languages and Cross Cultural Studies, etc. The class had to be three credits, and had to be on the "general education" list, and departments often taught courses which would stir student interest. The Geology Department at my university had a class entitled "Geology of National Parks" and it seemed like an interesting enough class. So I enrolled. And yes, there is a textbook for this . . . More
Views: 1504 | Comments: 11
Last by Cricket42 on Oct 13, 2010, 1:56pm
I remember the first time I was asked, in an official capacity*, to review a manuscript. I was excited because I had finally been asked by my peers to partake in one of the essential elements of publishable science ... the peer review. I was also extremely nervous. Would I review the manuscript with the same attention to detail as the other reviewers? Would I miss critical elements? Would I make a fool out of myself and recommend acceptance of a paper which was clearly junk (or vice versa)?

Fears aside, I proceeded with the review, which given all my anxiety took far longer than it needed to. In the end, I think I handed in a good review**, and I've been following a similar pattern of reviewing ever since then. Since I'm fresh off my latest review (a rejection, unfortunately) I figured now is a pretty good time to put my thoughts down on paper (the intertubez).

1. The first issues to consider will come when you get the email asking you whether or not you'd be able to do the review. First, do you have the time? IIRC, the typical reviewer reviews about seven papers and change a year (I'll have to find the data on that, but it was blogged about recently), which comes out to less than one a month. When I accept a review, I figure that it'll take me about an afternoo . . . More
Views: 3285 | Comments: 5
Last by becca on Oct 08, 2010, 9:56am
I blogged yesterday about a story I read in Biotechniques about the prevalence of plagiarism in Chinese journals. Here is the body of that entry reproduced here.

Begin blog entry ...

There have been several discussions on plagiarism lately on the intertubez (note to self: compile list), so when the following article was sent to my email this afternoon (via Biotechniques) I took note.

Over 31% of submissions to the National Natural Science Foundation of China English-language publications show signs of copying, self-plagiarism, or copyright infringement, according to Helen Zhang, journal director at the Zhejiang University Press in China.

Almost a third?!?

In an article published earlier this year in Learned Publishing, Zhang and her colleagues analyzed manuscripts submitted to the three journals between October 2008 and May 2009. They discovered evidence of plagiarism in 151 out of 622 . . . More
Views: 1415 | Comments: 18
Last by Thomas Joseph on Oct 04, 2010, 9:21am
I know my prior introduction was hardly on the verbose side, so I'm going to take this opportunity to introduce myself a bit more in-depth. Instead of running off a few dense paragraphs of text, I figured I'd break it down into a FAQ of sorts. I guess I've always wanted a FAQ about myself, and this is my chance, so by golly I'm going to take it! And yes, it won't be half as exciting/interesting as Psycasm's introduction.

1. Is your name really Thomas Joseph?

For the intents and purposes of this blog, yes. Would I answer to it if it was shouted out in public? Probably not.

2. Why did you come to LabSpaces?

As some of you may or may not know, I have a blog of the same name over at Blogger. I'd like to think that as a stand-alone, amateur blogger I did fairly well for myself. Obviously blogging at LabSpaces gives me a much larger platform from which I can blather from. I think it's going to be a challenge. LabSpaces is going to give me more traffic, which should increase the peer-reviewing of my thoughts/words. I'm taking it as an opportunity to gr . . . More