... had one of those days that made you want to scream, and then go home and just go back to bed?
Yah, that's been my week so far.
Thursday, December 03, 2009
Wednesday, December 02, 2009
Six weeks?
Read this article over at ESPN: From Hunk to Chunk, and Back Again. Crazy dude decides to gain 90 pounds so he can relate to his clients. I can see where he's coming from, but this is the part that scares me the most.
I should probably start soon ... right after I finish all the Thanksgiving left overs. Nom nom nom.
James says it took about six weeks of training and willpower to finally kick his addiction to junk food and start eating healthy food consistently again.Yikes! This is what I'm looking forward to as I attempt to lose the 20 pounds I've gained since I stopped running competitively in college.
I should probably start soon ... right after I finish all the Thanksgiving left overs. Nom nom nom.
How microbes can save the world ...
7 ways microbes may solve our energy woes by MSNBC.
I think our best efforts (and greatest impacts) would be by focusing on butanol and methane.
I think our best efforts (and greatest impacts) would be by focusing on butanol and methane.
Interesting read ...
... over at Mark Shea's. He reported on a Dick Cheney hullabaloo yesterday as well, and it gets interesting in the comment section. Here is a comment by a reader named Sean O'Kane:
Washington D.C. has become a place, at least it seems that way to me, where politics is the fabled perpetual motion machine. It doesn't need anything but itself to run. To hell with economics, to hell with sound military policy, to hell with medical health care experience. All they need to know is how to wiggle out of their fumbles and scandals come election time, and how to bring home the bacon to fund projects which really only impact a few people in their districts but have a nice dollar value on the bottom line.
It also points out to me that the populace is naive at best, stupid more likely, and downright apathetic at worst. Instead of clamoring for individuals experienced in things outside of how to perform the perfect "back stab" or "reach around", we continue to elect people, seemingly for life, who continue to flush this country down the toilet (I'm thinking particularly of people Barney Frank and Chris Dodd). Why didn't Colin Powell run for President? Probably because he didn't want to deal with the backroom crap and negative campaigning, part and parcel of politics. I think that if he could have been allowed to just do the damn job of running the country and not deal with all the whiny pissants who scuttle around the Capital, he could have been convinced to do it.
I guess what this boils down to is that I would prefer someone with actual military experience to run this country. They are, after all, Commander in Chief and a knowledge of what our forces are capable of, how they can be usefully deployed in a way that they are the most effective, not over-extended, or put into a losing situation thanks to politics (notice a trend here with politicians?) would be great. We're not going to get that in this Presidency, we sure as heck didn't get it in the last Presidency (or the one before it). You can think through a situation as much as you like, but sometimes actual experience will prove the most valuable commodity. Right now, I don't see much of that and haven't in a very long time.
Mr. Powell, would you consider running for President?
A further problem with Cheney's "tough guy" stance is that when he was a young man he went to great lengths to avoid serving in the armed forces during the Vietnam war. Cheney fully supported the Vietnam war yet he sought 5 deferments to avoid the fighting because he "had other priorities." He was content to let others do the dying & dirty work. I find his "tough" stance to be very hollow and hypocritical.Being President of the United States calls for an individual to wear many hats. He has to make sure the country is safe and secure from threats, has a strong economy, sound social policies, and that the citizens are happy, healthy, and productive. There is a lot more to it, and I know that I'm probably overlooking a great many things but I think that only further supports my point that whoever takes on the position of President has to have a wide range of experiences and knowledge.
Unfortunately, his experience was the norm among top Bush adm people. The notable exception was Colin Powell had expressed the most caution about going into Irag. Powell served in Vietnam.
Washington D.C. has become a place, at least it seems that way to me, where politics is the fabled perpetual motion machine. It doesn't need anything but itself to run. To hell with economics, to hell with sound military policy, to hell with medical health care experience. All they need to know is how to wiggle out of their fumbles and scandals come election time, and how to bring home the bacon to fund projects which really only impact a few people in their districts but have a nice dollar value on the bottom line.
It also points out to me that the populace is naive at best, stupid more likely, and downright apathetic at worst. Instead of clamoring for individuals experienced in things outside of how to perform the perfect "back stab" or "reach around", we continue to elect people, seemingly for life, who continue to flush this country down the toilet (I'm thinking particularly of people Barney Frank and Chris Dodd). Why didn't Colin Powell run for President? Probably because he didn't want to deal with the backroom crap and negative campaigning, part and parcel of politics. I think that if he could have been allowed to just do the damn job of running the country and not deal with all the whiny pissants who scuttle around the Capital, he could have been convinced to do it.
I guess what this boils down to is that I would prefer someone with actual military experience to run this country. They are, after all, Commander in Chief and a knowledge of what our forces are capable of, how they can be usefully deployed in a way that they are the most effective, not over-extended, or put into a losing situation thanks to politics (notice a trend here with politicians?) would be great. We're not going to get that in this Presidency, we sure as heck didn't get it in the last Presidency (or the one before it). You can think through a situation as much as you like, but sometimes actual experience will prove the most valuable commodity. Right now, I don't see much of that and haven't in a very long time.
Mr. Powell, would you consider running for President?
Ho boy ...
Kerfluffle over PETA ad. Bill Donahue is about as bombastic an individual as you'll ever meet, so I'm sure PETA is thrilled that he's on the case. Mr. Donahue's problem is, he seems to fail to realize that every time he rails against something, he only gives those people more exposure. He fell into this trap with Dr. Pharyngula, he's falling for it here. Let the idiots have their rambling, don't give them their fifteen minutes of fame too.
It's typical PETA crappola, but this really caught my eye:
Besides, given that St. Francis of Assisi (Patron Saint of Animals and the Environment) is such a celebrated figure in Catholic circles, I really find the charge leveled by Ms. Krupa a bit odd.
It's typical PETA crappola, but this really caught my eye:
Krupa issued a statement responding to the Catholic League, saying: "As a practicing Catholic, I am shocked that the Catholic League is speaking out against my PETA ads. I'm doing what the Catholic Church should be doing, working to stop senseless suffering of animals, the most defenseless of God's creation."Wow. I guess Ms. Krupa doesn't keep up with the times, and seems to overlook the generation-long struggle of the Pro-Life movement. I would not be surprised if Bill Donahue points out the unborn and asks if they're not defenseless too? If he doesn't, he's just a loud idiot.
Besides, given that St. Francis of Assisi (Patron Saint of Animals and the Environment) is such a celebrated figure in Catholic circles, I really find the charge leveled by Ms. Krupa a bit odd.
Tuesday, December 01, 2009
Please God, No!
Dick Cheney in 2012.
"Why would I want to do that?" he replied. "It's been a hell of a tour. I've loved it. I have no aspirations for further office," Cheney said in an interview with Politico.Yeah, it was hell alright.
Joe Mauer as a Met
Oh that would be sweet. Spring training can't get here soon enough!
The Mets’ plans at catcher are fluid ...With the exception of Francisco Rodriguez, Johan Santana, and David Wright the status of the entire Met's franchise (including their GM, Manager and Owner) is fluid.
Good riddance to bad rubbish
Cop killer dead.
Before I was against the death penalty, I was for it. There are instances, like this one and others* that force me to reconsider that stance. I think it's no surprise that they didn't bring this piece of crud in alive, but the point is ... he should never have been out on the street to begin with. I also believe that there is no way Huckabee will run for President now in 2012. These sorts of things tend to haunt people for their entire lives. I know the families of these four police officers will have to live with it, so it's not as if Huckabee will suffer alone through all of this. Besides, he still has his television show ... those families don't have their sons and daughters, moms and dads, brothers and sisters.
*Jessica Lunsford is another one that comes to mind. While that scum died in jail, every breath he took was an insult to humanity.
Before I was against the death penalty, I was for it. There are instances, like this one and others* that force me to reconsider that stance. I think it's no surprise that they didn't bring this piece of crud in alive, but the point is ... he should never have been out on the street to begin with. I also believe that there is no way Huckabee will run for President now in 2012. These sorts of things tend to haunt people for their entire lives. I know the families of these four police officers will have to live with it, so it's not as if Huckabee will suffer alone through all of this. Besides, he still has his television show ... those families don't have their sons and daughters, moms and dads, brothers and sisters.
*Jessica Lunsford is another one that comes to mind. While that scum died in jail, every breath he took was an insult to humanity.
Monday, November 30, 2009
NASA finds Martians
Martians exist(ed). They're also (well, were) bacteria.
Close examination suggested that about 25 percent of the crystal structures were chemically consistent with being formed from bacteria.So at some point, there was life on Mars. The question one must ask now is ... is it still there?
"We feel vindicated. We’ve shown the alternate explanation is absolutely incorrect, leading us back to our original position that these structures are formed by bacteria on Mars," Dr Mackay said.
Dennis Bazylinski, an astrobiologist from the University of Nevada who peer-reviewed the findings, said: "Until now I was on the fence but this paper has really thrown out the non-biological explanation."
What I learned when I was in Pittsburgh ...
Note: I'm a bit late with this one. Had it 80% of the way written and then forgot about it.
Other than learning that GPS systems are stupid and suck and should never be used, I did learn a few interesting things. I'll relate them here in this post. Some will be rants, some will hopefully be useful bits of information for other people as well (or at the very least drum up a bit of discussion).
1. The American Society of Agronomy is losing members. Hemorrhaging might be the more appropriate word. The society has lost approximately a third of the membership over the last decade, and the trend still points downwards. This is part of the reason that ASA is planning a restructuring which will be coming to a vote probably some time in November.
2. The Cherry Quadzilla at Church Brew Works was awesome. It also only comes in 750ml bottles, so you'll want to take a cab (which we did). Also, bring a camera ... it's a very interesting pub. The chicken pot pie was also really good. As were the perogies.
3. When you are arranging the poster sessions, and you map out where the posters are going to be, discuss the lighting situation with the people at the Convention Center. There was at least one section that after the sun went down and cut out all of the natural light, was in the dark. It was dark enough to hinder reading posters from afar. The rest of the hall was just fine, but at least 40 poster boards were placed underneath an overhang that had absolutely no lighting. That means that approximately 120 people (40 boards over 3 days) had to put up with those cruddy conditions. Unacceptable. I find it hard to believe that after realizing people were sitting in the dark on Monday evening, that something could not have been done to redirect the posters to a better lit area ... which would have required moving some poster boards maybe 40 to 50 feet away. A sign pointing in the direction would have sufficed. The meeting was filled with Ph.D.'s ... if they couldn't handle a redirection of poster boards, they had no job being there anyways.
4. If you plan a business meeting for the 30 minutes before a poster session you are hosting, make sure the business meeting doesn't start with a 45 minute presentation on restructuring. Some of us really had to get to the poster session because we were, you know ... presenting.
5. Metagenomics fraught with pitfalls. I know metagenomics, especially deep 16S sequencing, has taken the microbial ecology world by storm. A whole lot of people have been swept up in the frenzy, including yours truly. Now, I can be a worry wort, and after attending a session where people talked about various metagenomic projects, I just had to go up and ask a question. What about the chimeric sequences? I have a long-ish blog entry on chimeric sequences (which I really need to get out onto the site, it's still a draft), so I won't go into too great a depth on them now, but they're PCR artifacts which can increase your microbial diversity artificially. As pyrosequencing reads get longer, the chances of getting artifacts are probably increasing as well. Any amplification based system is going to have this problem.
So how do you avoid it? Well, I had hoped the people at this session, who have done metagenomic sequencing now for a few years, would have the answers.
None of them did. They figured (rightly, I might add) that the rates would be about the same for these approaches as they would with regular sequencing schemes, but it doesn't help with how to deal with them. Let's do the math.
If you have a 6% chimeric sequence rate (a reasonable value I believe), then you'll have to throw out 6 sequences for every 100 you do. If you have a 200,000 read metagenomic project that's 12,000 sequences you have to throw out. Problem is, how do you find them? Chimera_Check and Bellerophon, the two major programs on the net that do chimera checks, are really hands on programs. You have to really check the results. That's impossible (I won't say near impossible because who is going to read a quarter of a million chimera check reports, other than no one). So what we're seeing is ... no viable (and reliable) way (that I can see) to check metagenomic projects for chimeras. That sucks.
Other than learning that GPS systems are stupid and suck and should never be used, I did learn a few interesting things. I'll relate them here in this post. Some will be rants, some will hopefully be useful bits of information for other people as well (or at the very least drum up a bit of discussion).
1. The American Society of Agronomy is losing members. Hemorrhaging might be the more appropriate word. The society has lost approximately a third of the membership over the last decade, and the trend still points downwards. This is part of the reason that ASA is planning a restructuring which will be coming to a vote probably some time in November.
2. The Cherry Quadzilla at Church Brew Works was awesome. It also only comes in 750ml bottles, so you'll want to take a cab (which we did). Also, bring a camera ... it's a very interesting pub. The chicken pot pie was also really good. As were the perogies.
3. When you are arranging the poster sessions, and you map out where the posters are going to be, discuss the lighting situation with the people at the Convention Center. There was at least one section that after the sun went down and cut out all of the natural light, was in the dark. It was dark enough to hinder reading posters from afar. The rest of the hall was just fine, but at least 40 poster boards were placed underneath an overhang that had absolutely no lighting. That means that approximately 120 people (40 boards over 3 days) had to put up with those cruddy conditions. Unacceptable. I find it hard to believe that after realizing people were sitting in the dark on Monday evening, that something could not have been done to redirect the posters to a better lit area ... which would have required moving some poster boards maybe 40 to 50 feet away. A sign pointing in the direction would have sufficed. The meeting was filled with Ph.D.'s ... if they couldn't handle a redirection of poster boards, they had no job being there anyways.
4. If you plan a business meeting for the 30 minutes before a poster session you are hosting, make sure the business meeting doesn't start with a 45 minute presentation on restructuring. Some of us really had to get to the poster session because we were, you know ... presenting.
5. Metagenomics fraught with pitfalls. I know metagenomics, especially deep 16S sequencing, has taken the microbial ecology world by storm. A whole lot of people have been swept up in the frenzy, including yours truly. Now, I can be a worry wort, and after attending a session where people talked about various metagenomic projects, I just had to go up and ask a question. What about the chimeric sequences? I have a long-ish blog entry on chimeric sequences (which I really need to get out onto the site, it's still a draft), so I won't go into too great a depth on them now, but they're PCR artifacts which can increase your microbial diversity artificially. As pyrosequencing reads get longer, the chances of getting artifacts are probably increasing as well. Any amplification based system is going to have this problem.
So how do you avoid it? Well, I had hoped the people at this session, who have done metagenomic sequencing now for a few years, would have the answers.
None of them did. They figured (rightly, I might add) that the rates would be about the same for these approaches as they would with regular sequencing schemes, but it doesn't help with how to deal with them. Let's do the math.
If you have a 6% chimeric sequence rate (a reasonable value I believe), then you'll have to throw out 6 sequences for every 100 you do. If you have a 200,000 read metagenomic project that's 12,000 sequences you have to throw out. Problem is, how do you find them? Chimera_Check and Bellerophon, the two major programs on the net that do chimera checks, are really hands on programs. You have to really check the results. That's impossible (I won't say near impossible because who is going to read a quarter of a million chimera check reports, other than no one). So what we're seeing is ... no viable (and reliable) way (that I can see) to check metagenomic projects for chimeras. That sucks.
Interesting article from Newsweek
On how America's economic woes could impact our standing in the world.
Friday, November 27, 2009
Today I am an Auburn fan ...
... I'd love to see the BCS blow up with Alabama losing to Auburn and then turning around in the SEC Championship and beating Florida. I'll also dream that Nebraska whoops it up on Texass in the Big XII Championship too, but I'll take what I can.
Currently after the 1st QTR, Auburn is beating Alabama 14-0.
ETA: 14-7 in the 2nd QTR.
Currently after the 1st QTR, Auburn is beating Alabama 14-0.
ETA: 14-7 in the 2nd QTR.
WTF people ...
... does everyone try to get a paper published before Christmas? I got requests for two more manuscript reviews today. It brings my monthly total to 4, only one of which I've completed.
I know what I'm doing today. Reviewing your damn papers!
I know what I'm doing today. Reviewing your damn papers!
Thursday, November 26, 2009
Tuesday, November 24, 2009
When science is abused ...
The United Kingdom provides us with a lovely example.
Britain has built the world's biggest DNA database without proper political debate and police routinely arrest people just to get their DNA profiles onto the system, the genetics watchdog said in a report on Tuesday.Good going PoPo.
What would Hell be like?
I imagine it'd be like this.
Rom Houben was misdiagnosed as being in a vegetative state after a car crash left him totally paralyzed.I read this story and I think of the Metallica song One. I truly cannot imagine being trapped for 23 years ... 23 YEARS ... without being able to communicate at all. I'm surprised the guy isn't totally insane at this point, and to think that other people might be in a similar condition? WTF!
But, in actuality, he was trapped in his own body the whole time with no way of letting friends and family know he could hear every word they were saying.
The 46-year-old, who can now tap out computerized messages and read books on a device above his hospital bed, has revealed: "I screamed, but there was nothing to hear.
"All that time I literally dreamed of a better life. Frustration is too small a word to describe what I felt," he said. "I shall never forget the day when they discovered what was truly wrong with me — it was my second birth. I want to read, talk with my friends via the computer and enjoy life now people know I am not dead."
His misdiagnosis was discovered by neurological expert, Dr. Steven Laureys, who fears there may be similar cases all over the world.
Monday, November 23, 2009
Microbial coolness
Video of nematode-eating fungi.
Video courtesy of Tom Loynachan, Professor of Agronomy (and Microbiology) at Iowa State University. All of the videos (accessible via the second link) are informative and worthy of a view.
Video courtesy of Tom Loynachan, Professor of Agronomy (and Microbiology) at Iowa State University. All of the videos (accessible via the second link) are informative and worthy of a view.
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