Tuesday, August 31, 2010

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!

Monday, August 30, 2010

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, August 27, 2010

Tuesday, August 24, 2010

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.

Monday, August 23, 2010

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.

Thursday, August 19, 2010

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.


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.

Wednesday, August 18, 2010

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.

Tuesday, August 17, 2010


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? ;)

Thursday, August 12, 2010

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?

Wednesday, August 11, 2010

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.


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?

Tuesday, August 10, 2010

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?


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, August 06, 2010

Tuesday, August 03, 2010