One of those days ...

Blast from the Past

If you don't know the proper conditions with which to precipitate DNA using EtOH, here is an article that will show you how it's done ... old school style* (PDF, 2 pages).

Moral of the story: Spin your DNA down for 30 minutes.

*Old school in this case being 1985.

It's Always Something ...

Currently playing on iTunes: Hells Bells by AC/DC.

So just got back a review on a manuscript I'm a 2nd author on. It's a collaboration I struck up with the help of a senior researcher at the institution I work at. He was friends with a couple of guys, and they needed some microbial work done. Since I'm the lone microbiologist here, the match was made fairly easily. Bonus, they've become good drinking buddies (and at this point owe me lots and lots of free beer).

At any rate, we put together a manuscript on a problem that my collaborators face in their neck of the woods. It involves agent X, used to deal with issue A. When exhausted, it is disposed of in manner NG (which stands for "not good"), which creates issue B, and effects crop 1 and 2. Got all that?

It's some fairly straightforward work, and I was asked to look at the impacts on microbial diversity. They shipped me samples, I did my work, I wrote it up and sent it off to them. They worked it into the overall manuscript, we beat and banged on it a bit and then sent it off. Well we got the reviews back last week.

Reviewer 1: Loved it. Had nothing but praise for it. Comments were all of a paragraph in length. Either they did a last minute review and couldn't be bothered with it or not, I have no idea. I love Reviewer 1 regardless.

Reviewer 2: Someone pee'd in their Wheaties before they did this review. They picked every nit that could be picked. Heck, they even took issue with my use of the word "microbial". I mean really, dude? All told, their review was three single space pages long. We've all decided that we don't like Reviewer 2, but would love to take Reviewer 1 out for a beer.

So now ... off to address the comments of Reviewer 2. Hopefully we address them to the satisfaction of the Associate Editor so this puppy doesn't have to go out for a re-review.

Odd packing?!?!

Taping a cellphone to a Pepto-Bismol bottle and stuffing it in your suitcase is NOT an example of odd packing. I still don't know why, if you had them flagged before they left the US, you let them get to Amsterdam. Whiskey Tango Foxtrot TSA!

No hablo Español.

But I'm trying to rectify that. Just installed Rosetta Stone's Latin American Spanish, Level 1 onto my work laptop. Now I just need to find time to wear the dorky headset and I should be able to curse in a foreign language in no time!

Anyone ever use Rosetta Stone, and what did you think of it?

Woo hoo!

A plethora of PLFA data arrived on Friday, which means for most of today I'll be analyzing the data and prepping it for my next collaborative manuscript. Probably not much blogging today unless the data analysis breezes by.

Friday Video

Urine Luck

Using urine to power daily life.

Botte's brainwave was to use urine instead of water. By weight, urine contains roughly 2 per cent urea, and each urea molecule contains four hydrogen atoms, which, crucially, are less tightly bound to the molecule than the hydrogen in water. Splitting these bonds would require less energy, making hydrogen production more efficient.

Last year, Botte's team reported that they had been able to generate hydrogen from urine using an electrolytic cell with cheap nickel-based electrodes running at only 0.37 volts- much less than the 1.23 volts it takes to split water (Chemical Communications, 2009, p 4859). Pure hydrogen bubbled off at the cathode, while nitrogen and carbon dioxide formed at the anode.

Doing this would have two advantages. First, you can generate electricity. Second, it removes the urea from the environment. Urea is broken down to ammonia (NH3) which can cause environmental problems such as ecosystem acidification and eutrophication.

Food Recall

Listeria monocytogenes contamination of lunch meat.

The products subject to recall include:

* 25.5-pound cases of "Marketside Grab and Go Sandwiches BLACK FOREST HAM With Natural Juices Coated with Caramel Color" with the number 17800 1300.
* 28.49-pound cases of "Marketside Grab and Go Sandwiches HOT HAM, HARD SALAMI, PEPPERONI, SANDWICH PEPPERS" with the number 17803 1300.
* 32.67-pound cases of "Marketside Grab and Go Sandwiches VIRGINIA BRAND HAM With Natural Juices, MADE IN NEW YORK, FULLY COOKED BACON, SANDWICH PICKLES, SANDWICH PEPPERS" with the number 17804 1300.
* 25.5-pound cases of "Marketside Grab and Go Sandwiches ANGUS ROAST BEEF Coated with Caramel Color" with the number 17805 1300.
* The packages also bear vendor number "398412808" and the USDA mark of inspection.

All the above were sold at Wal-Mart.

The US has a "zero tolerance" policy with L. monocytogenes. That means that when inspecting food, even if one colony of Lm shows up, the food needs to be removed from the market. It's not a bug that plays well with people, especially pregnant women.

I hate cats ...

... to the people in my neighborhood who let their cats roam freely ... if you'd like to come pick up the trash in front of my house that your cats ripped open and dragged over my front lawn between 6AM and 8AM, I won't stop you.

This really doesn't come as a surprise ...

... if you're on Facebook, you cannot block the founder Mark Zuckerberg. Though I doubt he'll spend all his free time looking at my page, it is something people should consider carefully. While it doesn't appear to be the case that anyone else is blockable yet, the time may come when someone figures out how to do it and pilfers people's private information.

Probably not hugely newsworthy, but yet another reminder to keep the information on Facebook to a minimum.

Too much literature?

Either I read too much literature, or I am citation happy. This latest manuscript is pushing 100+ citations. The journal I am sending this article too doesn't have a reference limit, but it's still an awful lot of the literature I'm going back to. Oddly enough, I've had to make links back to articles from the 1970's because from that time, to the time we did this study ... no one reported on these linkages from a molecular biology standpoint, at least in this particular ecosystem.

Music

Seems that the Genomic Repairman is having a music crisis. Here, I have over 120 GB of music, with very little I wish to listen to. However, I do have a few bands that I have on my iPod which I've turned to.

1. Them Crooked Vultures - A sweet mix of Queens of the Stone Age (Josh Homme), Nirvana/Foo Fighters (Dave Grohl), and Led Zeppelin (John Paul Jones). What isn't to like about this super band?

2. Queens of the Stone Age - Awesome beats, kick-butt lyrics.

3. Shinedown - Sound of Madness, awesome song.

4. Brand New - Daisy and The Devil and God Are Raging Inside Me are two of the best albums of the first decade of the new millenium.

5. Beastie Boys - And if you don't like it, then hey **** you!

6. Here Come the Mummies - Most people will not have heard of this band, but if you love funk ... you'll love these guys. And they'll love you right back!

Link Love

I'm starting to update my blog links because a few people can't sit still long enough to keep my links relevant. At any rate, if anyone would like to do a little quid pro quo, drop me a link to your blog, put my blog up as a link on yours, and I'll include yours here.

Bed Bugs

Saw a report on the Today Show (video) this morning about bed bugs in NYC movie theaters. Seriously, whiskey tango foxtrot. Problem is, bed bugs are not all that easy to treat, and you can pick them up almost anywhere (especially if you stay at a hotel that is infested). Perhaps it's time to bring back DDT?

Then again, this blog entry in 2009 states that bed bugs are not as susceptible to DDT as we might think.

When men drink ...

... saw this "science-related" article on MSNBC. It supposedly is on the "beer goggle effect".

To make matters even worse, another study shows liquor makes guys more likely to misinterpret a friendly female glance as a bold come-on.

So they spend some time discussing what this all means, and then come up with a "solution".

What to do? Women who want to just have a good time -- and not go home with a guy -- would be smart to dress conservatively, says University of Texas psychology professor Kim Fromme. "That's the more obvious cue."

That's right ladies. When men drink, you need to dress more conservatively. Got to love how the burden shifts from the individuals actually undertaking a behavior and the individuals who are more than likely minding their own damn business.

Correlations

Correlations of my latest gene abundance data set and environmental variables. The sheet is roughly 30 inches by 25 inches. Think this would make a good supplementary data set? ;)

One two many cooks ...

... so I've begun writing a new manuscript. We have a number of additional collaborators that we generally would not have, so I decided to, before I started my outline of the manuscript, email everyone and ask how they envisioned this manuscript taking shape. I detailed where I was thinking I'd take the manuscript (in philosophical terms ... not vacation destinations). I went so far as to let them know of the journal it was going to, and that I had already talked to the editor-in-chief of the journal about this manuscript (which is somewhat off the beaten path of what they routinely deal with) and that he was extremely receptive to this article.

I figured this was a nice courtesy email, and didn't expect much fallout from it. Yah, I was stupid. Turns out that everyone else has their own idea on the path this manuscript should take, and while some parallel my own ideas, the heaviest hitter on this manuscript (other than the one who is writing it, moi) is the most esteemed member of the group. So ... what to do? I can certainly see their point of view, but the approach they want me to take (and which other people have fallen in line with now), while it is the safe approach, does not bring the problems I wish to address front and center. It's not that I'm intending on making a huge splash with this paper, though if it happens to partly revolutionize the field I'll gladly take as much credit as people are willing to give me, but I really hate beating around the bush. My collaborators are much more conservative, thinking that you don't upset the status quo, you go for the sure bet, you play it safe, you don't fight the reviewers, you get results, and you accept it and be happy about it. With most publications, I'm happy to take that course of action. I did not want to take that action with this manuscript. Bollocks.

Where I disagree with Drugmonkey ...

... and I'm sure he's devastated. However, he's just plain wrong in celebrating the demise of Supplementary Material from the Journal of Neuroscience. I say as much in his comments section, but I'm going to start a discussion (for the two or three people who read this blog) here anyways. It's my perogative!

At any rate, Bobby Brown aside, here is what I had to say to his celebrating.

I seriously hope that not all journals go this route, and I’ll tell you why . As part of my postdoc, we did an MLST project on a common pathogen in the food industry. We managed to get strains from all over the world, from state and federal agencies, and from international organizations. In the end, the project had several hundred isolates. Where were we supposed to list them and all the supporting data (date collected, place collected, food it was isolated from, serotype, etc etc)? In the article itself? It would have taken a dozen or so pages just for that one table! And that’s not including the several phylogenetic trees we generated all of which took up an entire page. It would have been half the issue if we had incorporated it all into the text. It seemed that that was a PERFECT use of the supplementary material section. Instead of the editors taking proper control of their reviewers and authors, they’ve banished the practice altogether … bye bye baby, but at least we don’t have to worry about that bathwater any longer.

I'm not the only one who thought that there were good uses for Supplementary Material, and I do think that my anecdote is one good example of why Supplementary Material needs to remain as an option. In an age where we can generate millions of base pairs of data sequence in a few short hours, but where journal issues are not increasing accordingly in size, something has to give. I know there are repositories for most data of this sort (such as GenBank for sequence and GEO for microarray data), but I think we still need the Supplemental Material option for certain descriptive elements of a manuscript.

I agree with J. Neurosci when they said that additional experiments added as Supplemental Material were allowing things to get out of hand, but as I said in my comment ... instead of cracking down on such practices, they just threw the baby out with the bathwater. If all journals take this route, things are going to get a bit hairy. I know a couple of my manuscripts, where I provide background information that would dominate a manuscript's page total if I could not include it as Supplemental Material, is descriptive in nature, and is provided as a courtesy to the reader* would have a hard time finding a place to published. So, why is it too much to ask that journals, and their editors, spend a bit more time sorting the issue out, rather than torpedoing it wholesale? I bet part of the issue is money ... it's probably no small fee to host that data in perpetuity.

*It also saves me countless emails being asked for that last bit of information which some people might hope to glean some ideas from for their own data sets, but which for me didn't factor at all in my own study.

Invasion of my aural space

Aural Space - Aural space is a term used to describe moments when listeners are hearing a lack of noticeable sound.

Sometimes when I am at work and at home, I prefer to have that "background noise" going on. I make no attempts to drown it out by having a television on, or a radio, or my computer playing tunes. I figure that if I'm in my office, or my home ... I should be able to choose which noises I want going on within my immediate space. Sometimes at home my dogs disagree, and they'll bark til the cows come home, but I can live with that ... for the most part.

What I cannot live with, is websites which have now taken to playing video automatically. ESPN dot com is notorious for this, and it drives me freaking batty. I go to ESPN dot com to read the news, not hear it. If I wanted to hear it, I'd go to my television and turn on ESPN the channel. It's a downright pain in the rear, and a total invasion of my aural space.

I remember way back when, when Al Gore had just invented the internets, that putting MIDI music files on ones website was cool ... the tin-sounding music really added pizazz to any website that featured it. Ok, not really ... it was cool for all of a couple minutes but really started sucking as soon as the file looped back and played the same crappy music all over again. But it seemed like most people figured it out pretty quickly (except for anyone who has a Geocities or Homestead account) and discontinued their use.

There are a few other websites, most of which evade my memory right now, which I've caught doing this as well ... but ESPN dot com is, by far, the worst offender in my book.

Anyone else have any other websites which have taken up this annoying habit?

What am I reading today?

An article from 1972. Characterization of the Oxidized and Reduced Zones in Flooded Soil. I can't believe you still need a subscription to view this article. How long do copyright protections exist for articles published prior to 1978?

The oxidized and reduced layers in flooded soil were characterized by vertical distribution of the oxidation-reduction (redox) potential and concentrations of manganous manganese, ferrous iron, sulfide, nitrate, and ammonium. Redox potential was measured with a special motor-driven assembly which advanced a platinum electrode at a rate of 2 mm/hour through the flooded soil profile. Vertical distribution of reduced forms of manganese, iron, and sulfur and of nitrate and ammonium was determined by freezing and slicing the flooded soil into segments 1 or 2 mm thick. The apparent thickness of the oxidized layer was different when evaluated by the distribution of the various components in the profile, with the sulfide profile indicating the thickest oxidized zone, the manganese profile indicating the thinnest oxidized zone, and the iron profile showing an intermediate thickness. The thickness of the oxidized layer increased with duration of flooding.

Another issue with GenBank

So received an email today from GenBank that started with the following:

Complete feature annotation has not been included for some or all of the sequence(s) you have submitted. We prefer to accept sequences that have been annotated by the submitting authors.

Of course they prefer to accept sequences that have been annotated by the submitting authors. It's one less thing they need to do, and I completely get that ... no problem with that from me.

So what annotation was missing? Protein translations for the sequences from my phylogenetic study of environmental samples. It's not a very large sample set (more than fifty, under a hundred) but it was (I believe) enough to get the job done for what we were looking at. We looked at a real time PCR amplification product, which was slightly on the long side (a tad over 400 base pairs) as far as qRTPCR goes. It's a partial sequence of the gene we are looking at, so I have no idea how things look 5' or 3' of the gene in question. As a matter of fact, the gene has about a 1000 base pairs of sequence upstream of the site we are looking at, and extends about an additional 250 to 300 base pairs downstream of our site as well. It's a fairly big gene which encodes a pretty large protein product.

So GenBank wants to know the protein translation of these clones from this environmental study. Me? I think it's a waste of time. Since they're partial sequences, we have no way of knowing if this sequence is even going to be used to make a protein. Since there is over 1,000 bp of sequence upstream, with any number of potential stop codons or frameshift's before we even get to the sequence in question ... it seems like a fruitless exercise. Do we really need these environmental sequencing projects, similar to mine and many many others, cluttering up BLAST reports? GenBank calls them "conceptual translations" and they DO show up in blastp reports. Since there are so many of them, they oftentimes dominate those reports. Now, I know GenBank has a "exclude uncultured/environmental sample sequences" as an option (which can be found under "Exclude" oddly enough) but it seems silly IMNSHO to automatically incorporate the thousands of these sequences in these reports. I suppose there are pro's and con's to each approach, and I know some people prefer to use protein sequences; though I've always read we want to find possible silent substitutions so you can't go wrong in choosing/preferring to use DNA sequences.

I don't know. Maybe my inner-curmudgeon is getting the better of me today. It just seems that, especially when it pertains to environmental samples, there can be something as "too much information" especially when that information is based on conceptual models. Do I think that these sequences are wrong simply because they're rooted in bioinformatics? No, I do not. I just don't see the utility in providing them in each and every case. Especially since it'd be simple enough to work them up when you download the DNA sequences. Of course, one would argue that it's simple enough to just submit them.

Educate me folks.

Food for thought ...

... very interesting article on staying connected. Could I do without a cell phone? Probably.

Titanic

Iceberg four times the size of Manhattan works its way into the Arctic Ocean shipping lane. So who cares? Well, just about every oil rig in the Arctic Ocean.

Large enough to threaten Canada's offshore platforms in the Grand Banks off Newfoundland. Wohlleben said iceberg control companies can redirect smaller icebergs, by towing them or spraying them with water cannons.

"I don't think they could do with an iceberg that large," she said. "They would have to physically move the rig."

Fun stuff, huh?

BankIt - I hate you GenBank

Why I can't set my "Clone ID" to use the "Sequence ID" is beyond me. Why does it have to be "You use the same property for every item, or construct some stupid tab-delimited table to upload"? Why not have a damn button which says "You want to use the Sequence ID for the Clone ID"? How hard is that? Does no one ever do that?

Fin!

Manuscript out the door. Now onto the next one. Fun fun!

In the meantime, I'm jamming to the following iTunes mix ...

Don't Talk to Strangers - Dio
Mexico - Incubus
Dream Brother - Jeff Buckley
Life in Technicolor - Coldplay
Dyers Eve - Metallica
Dam That River - Alice in Chains
Next To You - The Police
We Build Then We Break - The Fray
Get Off My Cloud - The Rolling Stones
Been Around the World - Cracker

Maybe I won't get a smartphone ...

... after I read this article.

Many people are banking on their iPhones, for example. Watch out. Citigroup recently revealed that its mobile-banking application for the iPhone was secretly storing personal information, possibly including account numbers, access codes, and balance information.

So nice.

Friday Video

Happy Birthday

To Neil Armstrong!

Mix Tapes ...

... are cool. Though technically, they're more like Mix CD's now, eh?

1. I'm a Believer - The Monkees
2. Bus Stop - The Hollies
3. God Only Knows - The Beach Boys
4. Just You 'N Me - Chicago
5. Never My Love - The Association

Thor ...

... looks like it's going to be pretty darn awesome.

China - Food for Thought

Read this commentary over at Reuters and it raises some interesting points, but the most interesting point IMNSHO was raised by a commenter who said:

Population control takes many forms, does it not? Every government is guilty and bloody handed. Do they care? Unlikely.

As I was reading that commentary, that very thought was going through my head. I simply do not think that China cares about its population*, and if a number of them die so that China can progress economically, then they died for a good cause. It's a horribly shortsighted position to take, considering the long term effects that pollution will have, but at least to me it appears a route that China is willing to take. I don't think anything will happen in the near future unless the people demand it, and that can't happen or won't be allowed to happen.

*We already know China has stringent population control measures in place, so we know they consider themselves overpopulated to begin with.

Weekend Reading

Effects of Medium Composition on the Growth of Chlorella vulgaris During Photobioreactor Batch Cultivations

A promising alternative to petroleum-derived fuels lies in microalgae-produced biodiesel. Compared to major terrestrial crops, microalgae have higher rates of oil and biomass production and appear to be the only source of renewable biodiesel that can meet global demand for transport fuels. Chlorella vulgaris may be suitable for biodiesel production due to its faster growth and easier cultivation compared to other strains. Lipid production is achieved in two steps: a biomass production phase, and a lipid production phase, in which the lipid content of algal cells is increased by submitting them to environmental stress such as nitrogen starvation. As a preliminary step towards the optimization of the biomass production step, the effect of different nutrient concentrations in TAP medium on the photobioreactor cultivation of C. vulgaris was studied. The results showed good growth of Chlorella vulgaris in 2X TAP, reaching a biomass concentration of 6.0 g/liter. Growth inhibition was observed at concentrations of the nitrogen source, NH4Cl, between 500 and 1000 mg/liter in the medium. Varying the concentration of the phosphorus source, K2HPO4 in the medium had no effect on cell growth within the range studied, provided phosphorus sufficiency is ensured. Other medium components are non-limiting at the levels studied.

Link.

... and ...

Semi-continuous Cultivation of Chlorella vulgaris for Treating Undigested and Digested Dairy Manures

The present study, based on a previous batch-wise experiment, investigated a lab-scale semi-continuous cultivation of green microalgae Chlorella vulgaris (UTEX 2714), as a useful means for nutrient reduction as well as production of algal biomass which can be used as potential feedstock for the production of biofuel and other commodities, on 20x diluted dairy manures. Both undigested and digested samples were applied in parallel experiments for comparison regarding the requirements of hydraulic retention times (HRTs), removal efficiencies of nitrogen, phosphorus, and chemical oxygen demand (COD), biomass productivities, and CO(2) sequestration abilities. It was demonstrated that algae grown in undigested dairy manure achieved removal rates of 99.7%, 89.5%, 92.0%, and 75.5% for NH (4) (+) -N, TN, TP, and COD, respectively, under a 5-day HRT, while the HRT had to extend to 20 days in order to achieve 100.0% removal of NH (4) (+) -N in digested one with simultaneous removals of 93.6% of TN, 89.2% of TP, and 55.4% of COD. The higher organic carbon contained in undigested dairy manure helped boost the growth of mixotrophic Chlorella, thus resulting in a much shorter HRT needed for complete removal of NH (4) (+) -N. Moreover, algae grown in digested dairy manure provided more penitential than those grown in undigested one in CO(2) sequestration per milligram of harvested dried biomass (1.68 mg CO(2)/mg dry weight (DW) vs 0.99 mg CO(2)/mg DW), but did not surpass in total the amount of CO(2) sequestered on a 15-day period basis because of the better productivity gained in undigested dairy manure.

Link.

Guess I'm going to be interested in algae this weekend. What about everyone else?

The hotties of science

Over the past few days there has been a bit of discussion about the place of women in science. Part of it revolves around this ill-advised post which clearly objectifies women. Creepily, in my not so humble opinion. Sheril Kirshenbaum of the Intersection responded in a very calm and rational manner, and some other bloggers have weighed in as well. I found the discussion particularly interesting given the fact that Newsweek just had an article discussing the "Beauty Advantage" and how looks do matter, more than we'd like to admit actually, and that women do have it worse. So it goes without saying, but needs to be said despite some people's objections, that everyone really should use a more critical eye towards their own verbal regurgitation's ... before they spew them into the workplace, cyberspace, the street, or wherever they happen to be at the time.

Remember, it's better to keep your mouth closed and be thought a fool than to open it and remove all doubt.

With that said, one thing that was unfortunately lost in the entire discussion is that we can talk about the hotties of science without objectifying anyone. Yes, there are many good looking men and women in science -- myself included -- but it still overlooks another important facet ... the science itself.

So with that, I would now like to present the true hotties of science, or at least the ones I can pull from the top of my head.

1. Pyrolysis. Pyrolysis is a process by which organic material is exposed to extremely high temperatures and often pressure, in the absence of oxygen. This material is broken down into several components for the generation of energy. It is a player in the emerging biofuel discussion and has the benefit of being able to use multiple feedstocks. A common utilizable energy product from pyrolysis is methane which can then be used for natural gas in homes, vehicles, workplaces, you name it. It can also be used to generate bio-oils (PDF, 42 pages) for liquid fuels. As mentioned, people have looked at a number of feedstocks including cellulose and other plant materials, such as rice husks and even coconut shells. Oh, and people have looked at cooking swine manure as well (PDF, 8 pages) with excellent results.

2. Gasification. Gasification is the dizygotic twin sister of pyrolysis. Like pyrolysis, gasification is playing a visible role in the bioenergy discussion. Pretty much anything that contains carbon can be gasified, and fossil fuels such as coal are often gasified to produce electricity. Since the process typically occurs at over 700 degrees Celsius, this is a very hot science topic indeed. There are several approaches to gasification, as well as feedstocks. Gasification of biomass (PDF, 23 pages) has been studied to a great degree (PDF, 64 pages).

3. Thermo-tolerant bacteria. Now we get into my own wheelhouse! The blood always gets pumping when talk turns to the extremophiles, groups of organisms which live in the most inhospitable of environments. From the extremes in pH and temperature, to salinity and arid environments ... places we would never expect life on earth, seemingly harbors entire communities. These organisms have been used as models for exobiology, and been used in applied science the world over. Heck, one can easily argue that if it were not for the thermophile Thermus aquaticus (from which we got Taq polymerase), we would never have experienced the genomic revolution.

4. Lasers. I blurbed about this already today, but man weaponized lasers are pretty cool/hot/awesome/no longer the stuff of science fiction alone. Maybe the end-product isn't science itself, but to get it to that point some serious applied science needed to be performed, and these systems are the end result. These directed-energy weapons (DEWs) literally evaporate their targets. That's some serious heat!

5. The Hubble Telescope and Astronomy. Ok, so the telescope itself isn't hot per se, but what it typically views generates some pretty serious heat. The core of our own star, Sol, tips the thermometer at a mere 15,000,000°C, which by all estimates is pretty hot. Launched in 1990, the Hubble Telescope continues to produce amazing pictures of our universe today. Recently, astronomers detected a "monster star" which outweighs our own sun by ~300 fold.

6. Climate Change. So, is the world really getting warmer? It's a debate that has certainly generated a lot of heat, which in and of itself warrants it's placement on this list. I wish I could say that there are things that both sides could agree on, but I'm not so sure that there are. There is plenty of research being conducted on greenhouse gases, such as nitrous oxide, methane, and carbon dioxide. Scientists continue to look into how these gases are generated, how to reduce/sequester them, and the impacts they play on the environment. From my own vantage point, these gases are all part of two important nutrient cycles, nitrogen and carbon (PDF, 33 pages). Life goes on, and one thing is for sure ... marmots are getting bigger.

7. Heat shock proteins. There is a reason life can tolerate extremes in temperatures. Some cannot handle the extremes as well as others, but we all have a way of dealing with increases and decreases. The heat shock proteins regulate the responses of cells when exposed to elevated temperatures. There are a variety of proteins which handle this chore, and they are found in a range of organisms as well, from bacteria, to insects, to mammals. In addition, some of these proteins have been manipulated to serve a biotech purpose. You have to love applied science sometimes.

So, that's but a small primer on the hotties of science. As I think of some more, I'll definitely add them to the list. If commenters wish to add to the list, provide them in the comments or send me a link to your own posts. Perhaps the most important imparted lesson from this entire mess is that if we can find it in ourselves to look beyond things such as the gender of coworkers, collaborators and peers, and instead focus on the areas of science which really matter ... we'll wind up opening doors to bigger and better things. One can always hope.

ETA: Updated on 07/22/2010 to expand the list.

Nightmare cruise

Thousands of spiders found on ship from South Korea. It was a cargo ship, rather than a cruise ship, but still. Gah!

The Guam Department of Agriculture says hundreds of large spiders and thousands of smaller ones were seen when stevedores began offloading insulation and beams for housing units from the ship, the M.V. Altavia.

They blocked the offloading of materials for fear that the influx of spiders would damage the local ecosystem. I don't blame them.

Cool

Killer lasers.

Goodbye George ...

... Steinbrenner dead.

I never liked the Yankees. Heck, I hate the Wankees. But you have to give it to George Steinbrenner ... he wanted to win. I would like that in the owner of my favorite team. You hear that Wilpon?

One Funny, One Serious ...

... note.

Based on this article.The funny is the picture of a bunch of mice, on the right hand side. The caption: These mice have preferences. Seriously? That's your caption? Duh.

Now, for the serious stuff.

A GENE has been discovered that appears to dictate the sexual preferences of female mice. Delete the gene and the modified mice reject the advances of the males and attempt to mate with other females instead.

Which gene, and how?

The gene the team deleted is for an enzyme called fucose mutarotase, which adds the sugar fucose to proteins. Park believes that disabling the gene exposes parts of the developing mouse brain linked with sexual preference in adult life to extra oestrogen. The hormone masculinises the brain in mice - though not in people.

In a normal female mouse fetus, this extra oestrogen would be "filtered out" by a substance called alpha-fetoprotein. But AFP only functions properly when adorned with fucose. So without the gene that makes the enzyme, AFP cannot keep the flood of oestrogen at bay.

As a result, the female mouse brain develops as if it were a male. "The mutant female mouse underwent a slightly altered developmental program in the brain to resemble the male brain in terms of sexual preference," says Park.

I don't really intend to get into the whole nature/nurture debate on homosexuality. To me, I honestly don't care if it is a personal decision, or has some sort of genetic basis, or is a mixture of both, or varies dependent upon the person.

What I do care about is the road that such studies could go down. So what if scientists could establish a link between a single gene and lesbianism? Seems like it'd be to screen for. That is where my concerns arise. And they are not concerns I hold alone. The US Council of Catholic Bishops have a page discussing the moral implications of prenatal testing. Here is the "money quote" from that page, and they cite Pope John Paul II in his encyclical Evangelium Vitae (The Gospel of Life).

But since the possibilities of prenatal therapy are today still limited, it not infrequently happens that these techniques are used with a eugenic intention which accepts selective abortion in order to prevent the birth of children affected by various types of anomalies. Such an attitude is shameful and utterly reprehensible, since it presumes to measure the value of a human life only within the parameters of “normality” and physical well-being, thus opening the way to legitimizing infanticide and euthanasia. (no. 63)

Bold emphasis is mine. I do not think it is such a large leap to think that some people would consider homosexuality to be considered an "anomaly" just like one might view a child with Down's Syndrome to be considered an "anomaly". I think we need to be very careful when we head down these roads. It is one thing to wish to understand the things we experience in this world. I think it is another thing entirely to create tests to screen for them afterward. I don't think any small amount of irony should be lost on the fact that the Catholic Church -- an institution that many (not all, but many) of the more liberal-minded people in this country despise -- would be the first to step up in the defense of all people who could be construed as an "anomaly".

Further reading: Evangelium Vitae

I don't do chain emails ...

... but the information in this one was pretty sound (in my estimate) so I'm posting it here. So here is some advice, for those that want it and/or need it.

1. Give people more than they expect and do it cheerfully.

2. Marry a man/woman you love to talk to. As you get older, their conversational skills will be as important as any other.

3. Don't believe all you hear, spend all you have, or sleep all you want.

4. When you say, 'I love you,' mean it.

5. When you say, 'I'm sorry,' look the person in the eye.

6. Be engaged at least six months before you get married.

7. Believe in love at first sight.

8. Never laugh at anyone's dreams. People who don't have dreams don't have much.

9. Love deeply and passionately. You might get hurt but it's the only way to live life completely.

10. In disagreements, fight fairly. No name calling.

11. Don't judge people by their relatives.

12. Talk slowly but think quickly.

13. When someone asks you a question you don't want to answer, smile and ask, 'Why do you want to know?'

14. Remember that great love and great achievements involve great risk.

15. Say 'bless you' when you hear someone sneeze.

16. When you lose, don't lose the lesson.

17. Remember the three R's: Respect for self; Respect for others; and Responsibility for all your actions.

18. Don't let a little dispute injure a great friendship.

19. When you realize you've made a mistake, take immediate steps to correct it.

20. Smile when picking up the phone. The caller will hear it in your voice.

21. Spend some time alone.

If I were to assemble ...

... a soccer *ahem* football team, I would insist on the following:

1. The uniforms would be red.

The psychologists found that when the competitors appeared to be wearing red, they were awarded an average of 13% more points than the blue competitors, even though every athlete was presented in both colors at some point. What’s more, points awarded seemed to increase after the blue athlete was digitally transformed into a red athlete and decrease when the red competitor changed to blue.

2. I would field my team with short players.

Based on evolutionary and linguistic research which has revealed that people associate the size of others with concepts such as aggression and dominance, Van Quaquebeke and Giessner speculated that ambiguous fouls are more likely to be attributed to the taller of two involved players.

3. I'd insist on playing all my games at home.

Analysing over 2,500 English Premiership matches, researchers discovered that referees were statistically more likely to award yellow and red cards against the away team – even when home advantage, game importance and crowd size were taken into account.

4. I'd ensure that my team always played left to right (leftward).

It's been documented that individuals who read languages which flow left-to-right are more likely to have a negative bias for events moving in the opposite direction, from right-to-left. In the Penn study of twelve members of the University of Pennsylvania's varsity soccer teams (all native English speaking), researchers found that participants viewing the soccer plays were more likely to call a foul when seeing a right-to-left attack.

Doing all of this, my team would be unbeatable!

World Cup 2010

La Furia Rojas!


ETA: GOOOOOOOAAAAAAALLLLLLLLLLL!

ETA2: And I win the pool!

I love Maglites ...

... and after this article, I love them even more.

Maglica is obsessed with upgrading automation and fine tuning work flow in the plant to wring out speed and efficiency — the only way, he says, that he can compete with imports from China where labor is so much cheaper. The company has invested tens of millions in automation against pressures to go overseas — a strategy that has worked remarkably well, according to distributor Rich.

“The amazing thing with Maglite is we have sold their product for at least 10 years and they have never had a price increase,” he says. “I’ve never seen anybody not have a price increase every year. Not any other product line we’ve ever sold … and the quality has remained.”

If you need a flashlight, spend the couple extra dollars it'll cost you to buy a Maglite. I have a couple which I've had for over a decade a piece. The only thing that has worn down on them is the batteries.

River in the Road

by: Queens of the Stone Age

Fast approaching monsters,
Marching in a row,
Grab what slips your mind,
And what your memory won't hold.
Run, darling run.
I'll stall them if I can,
You'll escape and I'll be left rotting on the vine.

Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.
Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.

Run, darling run.
I'll stall them if I can,
You'll escape and I'll be left rotting on the vine.

Avert the children's eyes,
Forget left untold,
Don't look back to see,
The blood,
River in the road.

Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.
Ruuuuhhuuun, run run run.
Oh, Oh, Ohhhhhh.

Get sweet revenge with my blood,
River in the road .

Video Tuesday

What happens when coal is gone?

Well?

But a combination of sources, perhaps including saltwater-grown plants, could get us there in the relatively near term. “Oil will disappear and there’ll be no change at the gas pump because there’ll already be technologies in place,” predicts Laughlin. “The good news is once you build these [Fischer-Tropsch] plants, you can use anything, including garbage, for the biofuel conversion. The big problem is the initial capital cost.” We can adapt the facilities over time.

Spot on ...

He's got a good point ...

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
An Energy-Independent Future
www.thedailyshow.com
Daily Show Full Episodes Political Humor Tea Party

h/t: Mark Shea

Who wants to live forever?

Me.

I've got to admit, the thought is somewhat intriguing. And just think ... all this awesome scientific knowledge I possess, what a shame to let it all go to waste!

iTunes - Next Ten

1. Welcome to the Working Week - Elvis Costello
2. (Don't Fear) The Reaper - Blue Oyster Cult
3. Mr. Brightside - The Killers
4. Albert Goes West - Nick Cave and the Bad Seeds
5. Champion Sound - Fatboy Slim
6. Nice to Know You - Incubus
7. Fight With Tools - Flobots
8. Highway 61 Revisited - Bob Dylan
9. The Needle and the Damage Done - Neil Young
10. Walking On the Moon - The Police

Video Thursday

Going through my iTunes, I came across this gem from a bit back. My goodness, what was I thinking? Catchy beat, those crazy Europeans.

Biofuel Roadmap

Document issued by USDA. From an article at Biofuels Digest:

The USDA projected in its report that the US, in order to meet its 2022 RFS target of 36 billion gallons of renewable fuel, would produce 13.4 billion gallons formed educated energy crops, including perennial grasses, energy cane, and biomass sorghum; 500 million gallons from oilseed crops, 4.3 billion gallons from crop residues (corn stover, straw), 2.8 billion gallons from woody biomass (logging residues only) and 15 billion gallons from corn starch ethanol.

The report, entitled "A USDA Regional Roadmap to Meeting the Biofuels Goals of the Renewable Fuels Standard by 2022" can be found here (PDF, 21 pages).

Asian Carp in the Great Lakes? I have a solution ...

... just let BP into Lake Michigan. That'll kill off the carp!

Asian carp found less than six miles from Lake Michigan.

CHICAGO – An Asian carp was found for the first time beyond electric barriers meant to keep the voracious invasive species out of the Great Lakes, state and federal officials said Wednesday, prompting renewed calls for swift action to block their advance.

Commercial fishermen landed the 3-foot-long, 20-pound bighead carp in Lake Calumet on Chicago's South Side, about six miles from Lake Michigan, according to the Asian Carp Regional Coordinating Committee.

What a mess we've made of our world. I always say that life doesn't come with a "reset" button, but in this case I really wish we had one.

My hatred of BP ...

... grows by the minute.

BP "oil containment practices" threatening extremely endangered wildlife populations.

"They drag a boom between two shrimp boats, and whatever gets caught between the two boats, they circle it up and catch it on fire. Once the turtles are in there, they can’t get out," Ellis said.

Ellis said he had to cut short his three-week trip rescuing the turtles because BP quit allowing him access to rescue turtles before the burns.

... and ...

Ellis said most of the turtles he saw were Kemps Ridley turtles, a critically endangered species. Harming or killing one would bring stiff civil and criminal penalties and fines of up to $50,000 against BP.

$50,000? Chump change for BP at this point.

I will NEVER buy gas from a BP station ever again. EVER.

To the Algerian witchdoctor ...

... that gave his favorite team a tie in the World Cup against England. Can you leave the pigeon home for the game against the United States? Thanks.

Science as fad ...

One of the most impressive, and revolutionizing, advancments in science (IMNSHO) was the ability to sequence DNA. And not just sequence DNA, but sequence billions upon billions of base pairs in minimal time.

The problem now is ... it's gone mainstream.

The first full genome was sequenced in 2003 after 13 years of work. Today, analyzing a genome takes three months and costs about $40,000.

You know it's gone mainstream when people are chatting up sequencing Ozzy Osbourne's genome. Oh of course, it's all for the "betterment of man" because some of us may go on a decades long bender and will need to know if our genes can handle it ... right?

Smile at someone today ...

... you never know what effect it may have on them.

A smile cannot, of course, save everyone; the motivations behind suicide are too varied. But simple kindness can be surprisingly effective. Mental health professionals tell the story of a note left behind by a man who jumped off San Francisco's Golden Gate Bridge. If one person smiles at me on the way to the bridge, the man wrote, I will not jump.

In the last stages ...

... of pushing out a manuscript for review. I'm feverishly trying to get this darn thing presentable, and since it's on a project I hate, it's not going well. But I'm motivated now so I'm spending much energy on it. Trying to juggle personal life as well, which is also cutting down on my time. In the meantime, enjoy some QotSA.

What?!?!

Sack-tapping, a new form of bullying. My goodness gracious. What is wrong with people?!?!

I like Mark Shea ...

... article on Copernicus.

Geekdom

Oh, almost forgot ... one other good thing came out of San Diego. This. This puppy definitely gets worn at our next customer workshop.

IAwareables

Little brown balls ...

Link between malaria and algae.

"These tiny organisms have a huge impact on humanity in very different ways," says Keeling. "The tool used by dinoflagellates and Chromera to do good -- symbiosis with corals -- at some point became an infection mechanism for apicomplexans like malaria to infect healthy cells.

Wow ...

... toddler, smoking.

Aldi smokes an average of 40 cigarettes daily.

Aldi is also two years old. RJ Reynolds would be proud.

Memorial Day

Uhhh ...

... am I missing something out of this article?

Inside many undersea hydrothermal vents, magnesium-rich rocks react with sea water. Such reactions create a heat source that could drive miniature convection currents in nearby pores in the rock, claim Christof Mast and Dieter Braun of Ludwig Maximilian University of Munich, Germany. They propose that such convection could concentrate nucleotides, strands of DNA, and polymerase, providing a setting that would promote replication.

Supposed model for DNA replication without life. Reading this it looks like they've found an environmental equivalent to the conditions found in PCR. Yippee. Only problem is ... where is that naturally-formed, pre-life polymerase coming from?

Back from the ASM 110th General Meeting

And all I have to say at the moment is ... I love San Diego, but the meeting was a huge disappointment.

So sad ...

... Boyzone news. I don't really care about Boyzone, honestly, I don't ... but this section had me a bit perplexed and amused.

The band reformed in 2007 and 2008, and the following year group member Stephen Gately died suddenly aged 33 while on holiday on the Spanish island of Majorca.

I didn't know death by "sudden aging" was possible! I'm not sure what the number 33 has to do with it ... just that whoever wrote this article was probably as enthused writing it, as I was reading it.

Crickets nom nom nom

Bugs as food.

Tuesday Video (May Not Be SFW)

Maybe smallpox wasn't so bad after all?

Found a link to the following article in my ASCP "Daily Diagnosis" e-mail newsletter.

The worldwide eradication of smallpox may, inadvertently, have helped spread HIV infection, scientists believe.

Experts say the vaccine used to wipe out smallpox offered some protection against the Aids virus and, now it is no longer used, HIV has flourished.

For reals?

To test if the events may be linked, the researchers looked at the white blood cells taken from people recently immunised against smallpox and tested how they responded to HIV.

They found significantly lower replication rates of HIV in blood cells from vaccinated individuals, compared with those from unvaccinated controls.

The smallpox vaccine appeared to cut HIV replication five-fold.

How?

The researchers believe vaccination may offer some protection against HIV by producing long-term alterations in the immune system, possibly including the expression of a receptor called CCR5 on the surface of white blood cells, which is exploited by the smallpox virus and HIV.

I wonder if it's possible to revive the smallpox vaccination program. Immunize those most at risk for the disease and then see if we can detect a drop in HIV rates of infection.

Environmental collapse by 2050

Fishless oceans by 2050.

"If the various estimates we have received... come true, then we are in the situation where 40 years down the line we, effectively, are out of fish," Pavan Sukhdev, head of the UN Environment Program's green economy initiative, told journalists in New York.

What?!?!

Seriously?

During sleep, the brain is in its most active state; anesthesia, on the other hand, depresses central nervous system activity. On the operating table, your brain is less active and consumes less oxygen -- a state of unconsciousness nothing like normal sleep.

Doctors do not know exactly how general anesthesia produces this effect.

Bold emphasis mine.

Note to self: Remain healthy.

I had not looked at it ...

... from this perspective.

BP’s incentives are obvious. A deep-sea oil well costs hundreds of millions of dollars to drill, so the company prefers to bumble through never-before-tried recovery efforts than destroy its investment. Furthermore, BP is probably hedging its bets—if it loses this well, lawmakers will likely ban it from drilling there again. In other words, if BP loses the well, it loses both the enormous sunk costs of drilling it and the expected cash flow from all the remaining oil. Thus, even in the midst of this crisis, BP appears to be just as concerned with protecting its shareholders as with stopping this catastrophe.

This is probably dead-on, and it annoys me to no end. Time to force BP to pull the plug on this whole operation and shut down that well immediately, using whatever means necessary.

Like a rainbow in the dark ...

... Ronnie James Dio dead at 67.

Tuesday Video

Idiot

Typical Phillies fan. Got himself tasered for going onto the field. I bet the cop was a Mets fan.

Warranted? Heck yeah.

Should I be honored?

So, I was recently asked to write a book chapter for a new book in the series "Methods in Molecular Biology". Unfortunately, there are a couple of problems with the request:

1. The book chapter deals with work I did about 5 years ago, which means I'm 5 years behind on the literature.
2. In my line of work, book chapters count for ZILCH. Since it's not peer-reviewed, the bean counters at my agency don't care, and at this point I've already pretty much established my impact in this area so a book chapter won't help further.

Now, I've never written a book chapter and my ego is a bit pleased about the invitation. Plus, it's Methods in Molecular Biology, and I've poured over these volumes for my entire career. However I also know what a slog they can be, which really gives me pause. So I'm leaning towards rejecting the offer. However, if someone can give me a valid reason to consider it, I'm all ears (or eyes as the case may be).

Through the looking glass ...

Article found on Science Daily.

Understanding the behavior of Antarctica's ice sheets plays a fundamental role in our ability to build robust, effective global climate models, which are used to predict future climate. "These models rely on constraints imposed by data from the field," the co-chiefs pointed out. "Measurements of parameters such as age, temperature, and carbon dioxide concentration provide invaluable inputs that help increase the accuracy of these models. The more we can constrain the models, the better they'll perform -- and the better we can predict ice sheet behavior."

--. ..- . ... ... / .-- .... .- - / - --- -.. .- -.-- / .. ...

- --- -.. .- -.-- / -- .- .-. -.- ... / - .... . / .- -. -. .. ...- . .-. ... .- .-. -.-- / --- ..-. / - .... . / ..-. .. .-. ... - / -- . ... ... .- --. . / ... . -. - / -... -.-- / -- --- .-. ... . .----. ... / -.-. --- -.. . .-.-.-

..-. --- .-. / .- / .... .. ... - --- .-. -.-- / --- ..-. / -- --- .-. ... . / -.-. --- -.. . --..-- / -.-. .-.. .. -.-. -.- / .... . .-. . .-.-.-

.--- ..- ... - / -.-. --- .--. -.-- / .- -. -.. / .--. .- ... - . / - .... . / - . -..- - / .. -. - --- / - .... . / - .-. .- -. ... .-.. .- - --- .-. / - --- / --. . - / - .... . / --. .. ... - / --- ..-. / .-- .... .- - / .. .----. -- / ... .- -.-- .. -. --. .-.-.-

- .-. .- -. ... .-.. .- - --- .-.

Uhhh ...

... not much I can say about this one. So here's the link.

Phooey!

My first bad bit of news for the new year. I didn't win the election for Division Chair in one of my societies. Of course, that is not necessarily a bad thing, given the increased work load I would have experienced, but it does hinder a bit my ability to establish impact in my field. Getting elected would have shown that a majority (of those who vote at any rate) of my peers appreciate my efforts, enough to place me into positions of thankless and never-ending work.

I'll have to panhandle for some other position now I suppose. Anyone looking for an Associate Editor? Yeah, I'm a glutton for punishment.

I was for it ...

... but now I'm against it. We don't need more off-shore drilling if these sorts of things cannot be guaranteed to not happen. I cannot believe there are not more fail-safes on these rigs to prevent this exact thing. I mean honestly ... what part of 210,000 gallons of oil released a day into the ocean doesn't raise enough concerns to ensure that a FAIL-SAFE is put into place properly?

Read the following article ...

... today, about the tree that this little girl mentioned three times, and I've decided that I'm going to grab a new copy of Anne Frank's diary and read it again.

All of this ...

... over a phone?!?!

Sheesh.

Bio-diversity: Why does no one seem to care?

Or at least, none of the people who can really effect the outcome of the problem?

But they clearly haven't worked too well. The problem, says Butchart, is that while there have been lots of plans on paper, "they have been inadequately targeted, implemented and funded". There are lots of protected areas, but they haven't been given enough money and are not in the most biologically important places. More than 80 per cent of governments have promised to tackle invasive alien species, but fewer than half have done anything.

The report can be found in the April 29, 2010 issue of Science (PDF, 9 pages). And what does the report say? The factors leading to loss of biodiversity continue to trend upward, with no promise of slowing down. The major factors? They are as follows:

The majority of indicators of pressures on biodiversity show increasing trends over recent decades, with increases in: (i) aggregate human consumption of the planet’s ecological assets; (ii) deposition of reactive nitrogen; (iii) number of alien species in Europe; (iv) proportion of fish stocks over-harvested; and (v) impact of climate change on European bird population trends. In no case was there a significant reduction in the rate of increase ...

They also mention habitat fragmentation and mentioned a pretty alarming trend there as well:

... 59% of large river systems are moderately or strongly fragmented by dams and reservoirs ...

Fifty-nine percent? Ouch!

So what is their conclusion?

Our results show that, despite a few encouraging achievements, efforts to address the loss of biodiversity need to be substantially strengthened, by reversing detrimental policies, fully integrating biodiversity into broad-scale landuse planning, incorporating its economic value adequately into decision making, and sufficiently targeting, funding and implementing policies that tackle biodiversity loss, among other measures. Sustained investment in coherent global biodiversity monitoring and indicators is essential to track and improve the effectiveness of these responses.

Let us hope that this report does not fall on deaf ears.

Stop the madness!

New Arizona anti-immigration law will impact MLB.

Take, for example, this scenario: An 18-year-old from Venezuela playing in the rookie league jumps in a friend’s car to head to the grocery store. The friend rolls through a stop sign. A police officer witnesses the infraction. The law, signed last week by Gov. Jan Brewer, requires that “where reasonable suspicion exists … a reasonable attempt shall be made … to determine the immigration status of the person.” The Venezuelan player, accordingly, is asked to furnish paperwork proving his legal residence, a new burden of proof under SB 1070. If he happens to have forgotten his passport and work visa at home, his friend would get a traffic ticket and the player would get significantly more.

“Under that scenario,” said Mike Philipsen, the communications advisor for the Arizona Senate Republicans, who drew up the bill, “he could be detained.”

In other words, hauled off to jail, even though he is in the United States legally.

“I’ve never seen anything like that in the United States, and Arizona is part of the United States,” Kansas City Royals designated hitter Jose Guillen said. “I hope police aren’t going to stop every dark-skinned person. It’s kind of like, wow, what’s going on.

“I was 17, 18. I’d forget things. Kids do.”

Here is my question, under pre-SB 1070 laws, at what point could there be an inquiry into the legal status of someone? Was it only after they committed (or were suspected of committing) a crime? Seems that would have been sufficient, no? This new law seems to go a bit over the top.

Just imagine, you're a tourist in some country and you leave your passport in your hotel room. You get stopped on the street for no apparent reason and get hauled off to jail because you're suspected of being in the country illegally. That would suck, no? Same difference with SB 1070 if you ask me. When I've traveled out of the country, I didn't always carry my passport with me. If it got stolen or was lost, I'd be screwed, so I kept it locked up back in my room.

It never ends ...

... so I was telling a friend that I was trying to finish up a lot of busy work this week, so I could hammer out this manuscript. I made mention of the fact that I KNEW, just KNEW, that once I finished my busy work, more would crop up.

So, I handled my two reviews and sent them off. Next day? Two more show up in my email. Fortunately, one is a re-submit of one I have already reviewed, so I'll take it on, but damn. Does anyone ASIDE FROM ME review manuscripts any longer?

Ethanol is dead, long live butanol

Butamax.

BD: What about the production economics?

BuMx: Using our process, a 100 MGy corn ethanol will make 80 Mgy of biobutanol, but every fuel molecule will have 25 percent more energy, so its a balance. Also, with 16 percent butanol, you are getting higher concentrations of a higher energy molecule, so you are getting real improvements in fuel economy and efficiency.

Butanol vs. Ethanol (Infrastructure)

And I will readily admit to being a bit biased. I've already said I think our best bet would be to focus on butanol and scrap the entire ethanol talk.

I want ...

... N8. Sexy.

To screen or not to screen

So in my copious spare time, I've been approached to co-write a metagenomics grant. We have the RFA and we have our system (rhizosphere). Now comes the fun part. Sketching out years 1 through 5, experimental design, and budget. If we're successful (we need to get past the "Letter of Intent" stage first), we hope to fund a post-doc to run with this project. I'm thinking that we start off with a good 16S rDNA deep sequencing run or two to establish the major players in our system, and follow that up with a metagenomic sequencing run. I favor the shotgun approach, just sequence everything we come up with and take it from there. I know other folks like the screening approach and only going for things that they think will be beneficial to know about. Off the top of my head, I can't think of an easy screen for our system, and while it'll be a lot of extraneous info to mine (and a more expensive proposition) I think it'll be worth it. From there, I hope to move us into transcriptomics which I think has the benefits of metagenomics while also giving us "real time" data on how the organisms are responding to environmental conditions.

Should be fun. Now I have a couple of days to put my letter of intent together.

Snippets

1. Good! So a Navy SEAL punched a terrorist, and the first SEAL was up for charges of not stopping it. Big whoop. Good news is, the tribunal wasn't phased. The only thing he should have been charged with IMNSHO is not letting the low-life get punched more! RIP Scott Helvenston.

2. Really Arizona? Really? If you wanted to be the laughingstock of the US, kudos. You earned it!

3. NEWSFLASH! The Sun is hot. Like, totally hot.

I like it ...

... remove divisions from baseball entirely.

Relax ...

... too many deadlines. Too much self-inflicted anxiety, too much, too much, too much. But not enough blogging. I'll get to it eventually. I hope. :)

I just love when ...

... in the beginning of your paper you talk about processes A & B and how they can negatively impact the environment, then you perform biological assays to measure A & B and show that in this particular instance, they don't amount to much ... but then you have to go on and say "Well, despite showing that there is almost nothing here, we went ahead and quantified just how much of the genes which encode for processes A & B were present anyways."

I mean, as if it makes any damn difference. Well, I suppose that's what I need to figure out now ... where COULD it make a difference? Maybe if we tweaked environmental condition X, and/or Y, and/or Z? I suppose I'm in a somewhat interesting position because while processes A & B don't appear to be going on at any high rate, the genes which are responsible are found in fairly high abundance. Why? In at least one case I have no idea, but I'll be damn sure to pull something out of my butt before all this is said and done.

This is why I hate projects that I walk into when half of the data has already been collected and they want me to get one of those "quick pubs". No doubt it'll go in somewhere, but it's not really what I wanted to be futzing with.

And to compound the fun ... another review showed up in my mailbox yesterday! Just two attachments ... not even text in the body of the email they were delivered in. Fortunately for them, I didn't just delete the email ... which I usually do when nothing but an attachment from a person I don't know shows up in my email box.

Dirt!

Just received this in my email today:

Dirt! The Movie is coming to you on PBS - Tuesday, April 20th at 10pm!

Check it out if you can.

You know what's a pain in the rear?

Buying flowers. DO. NOT. LIKE.

ETA: And by "DO. NOT. LIKE." I mean "thrilled with the response they generated". Lesson learned ... don't sweat the specifics and go with the flow.

Vid

What's wrong with me?

Why, when I'm trying to finish a manuscript, did I accept two manuscripts to review? Could I really be this desperate to put off writing?

On the plus side, I received a promotion last week. Woo hoo! What does it mean? It means I'm now eligible for international travel, and can submit proposals for agency post-doc lines. Doesn't mean I'll get either, but it's nice to know I can throw my hat into the ring now.

ETA: One review down. One more to go (fortunately it's a resubmit).

Day three ...

... of work in the field.

Today, I found out that I'm pretty much immune to fire ant bites. Didn't exactly set out to test that theory, but I managed to step onto a mound when collecting soil samples. Had ants covering my leg up to my knee by the time I realized it, had a few bites and stings but they haven't welted up yet (6 hours later) and I doubt they're going to at this point.

I do have a nice bruise underneath my ribcage, and blisters on both hands though. With the lack of rain those soils were dry and compact!

Thursday Funny

Thursday Video

Honestly ...

... what were these people thinking?

They had given him the trip as a graduation present. Anne Rucker told CBS4.com she knew about the reported violence in Mexico, but she thought her son would be safe in such a populated tourist area.

They're killing people in Mexico in BROAD DAYLIGHT! What made you think a crowd of people would make things any safer?

Sheesh.

Stay out of Mexico.