Thursday, November 29, 2007

Next Tagled Bank

The Tangled BankI read somewhere that one of the responsibilities of hosting the Tangled Bank is to announce the next location one week ahead of time. So, in fulfillment of my duties (a day late), I hereby inform you that Tangled Bank #94 is to be held over at Life Before Death. The last post over there is over a month old (rather ironically titled "Don't worry, I'm still here"), so I hope Felicia is ready for the multitude of submissions that will be coming her way.

I can't seem to find an email for Felicia, so please send an e-mail message to host[at]tangledbank[dot]net containing the words "Tangled Bank" somewhere in the subject line, and a link to your article, along with a sentence or two of descriptive summary. PZ will take care of the rest.

Research posters

Well, here I am sitting in a back room off a computer lab printing off posters for the BioNESUR meeting being held here tomorrow. There's a class going on in the computer lab, so I am effectively stuck here for at least an hour and twenty minutes. The good news is that we've just inherited a beautiful poster printer - an HP DesignJet 5500 - it prints beautiful, big posters. The bad news is that I am trying to figure out the machine by trial and error, on the fly - what kind of paper is this? what are the proper ink settings? how do I load new media? damn it, the ink is running - try new settings.

Just like my digital camera, I'm having mixed feelings about this new-fangled piece of technology. What happened to making posters one 8.5 by 11 inch sheet of paper at a time, carefully cut and pasted on a colored piece of construction paper and assembled piece by piece? Remember those?

Damn it. (do I sound curmudgeony enough?)

UPDATE: Damn it, I forgot rubber bands

UPDATE II: All better now. I figured out settings that work and the posters look stupendous. Forget what I said about old-school posters. I still need rubber bands though.

Tuesday, November 27, 2007

digital cameras - blessing or a curse?

I got my first digital camera just over a year ago - a Pentax K100D. Since that time I have taken nearly 3,000 photos - mostly of the kids with a smattering of other family. Unfortunately, most of those photos are sitting on my computer's hard drive. When I was shooting film I took fewer photos, but at least I had really nice prints that went into albums and that I could give to family and friends. Now I am simply overwhelmed with digital files.

So, I recently plunged in and formated a small subset of these pictures and got them online and had prints made. I decided that I should start with the most recent (Jack on skates) and work my way back through the summer. I'm rather proud of myself and these images and what good is taking pictures if you don't share them. So, if anyone is interested, go check out my online photo albums. (you'll need Flash Player to see them)

Wednesday, November 21, 2007

Tangled Bank #93

The Tangled BankAhoy me mateys and welcome to the 93rd edition of the Tangled Bank, humbly hosted by yours truly. For those of you returning to from Archaea to Zeaxanthol, welcome back. For those new to my blog, let me give you a quick introduction.

from Archaea to Zeaxanthol started out as a space to share all things biological with my AP Biology class during the stage of my life when I was crazy enough to try my hand at teaching high school science. I lasted one semester before I ran, almost literally, screaming from the profession. I have now thoroughly entrenched myself back in academia at Roger Williams University in Bristol, Rhode Island as part-time biology faculty and coordinator of the Undergraduate Center for Marine Life Sciences, where I am involved in various projects that revolve around supporting undergraduate research in the life sciences. And yes, I am a pirate. Two hundred years too late. Please feel free to peruse the site - you'll see a variety of posts ranging from reports on "pure" science to rants about students and teaching to the joys of being a sports fan in New England.

As for this edition of the TB, I've decided not to break submissions into topic categories. Instead I am posting them in the order that I received them. First come, first served. This way your promptness or procrastination are clearly displayed for all to see. So without further ado, please enjoy this Thanksgiving/Lebanon Independence Day/Feast of St. Cecilia edition of the Tangled Bank. (and forgive me for my one-liners)

Greg Laden wins the award for being this edition's first submission. Greg, your prize is in the mail, just like the iPod I won from Seed. Anyways, Greg has two interesting posts reviewing some recently published work. This first post tells you everything you ever wanted to know about glial cells but were afraid to ask. The second post explains why your sister smells kinda funny - it's those darn MUP proteins helping you avoid any incestuous urges. By the way, you probably smell just as funny to her.

John at a DC Birding Blog helps us answer the age-old question, "Which came first, the chicken or the blue jay?". Ok, not quite, but he does show us what claws can tell us about bird evolution.

GrrlScientist continues the avian theme with a review of some recent work on the importance of blue-light photoreceptors in bird migration. In another post, GrrlScientist reports on genetically engineered Supermice. We should start stockpiling Kryptonite now.

Archaeozoology offers a thorough description of the pathology of two similar bone diseases, osteomalalcia and rickets. Now get out of your house, go outside in the sunshine and get yourself your daily dose of vitamin D!

Alvaro at SharpBrains reminds us that our greatest asset as a human species is not our intelligence per se, but the flexibility of our intelligence. Flexibility is always a good thing, isn't it?

Coturnix blogs about the newly described Nigersaurus taqueti, one of the most morphologically interesting dinosaurs I've ever seen. I just stared at those photos of the skull shaking my head in amazement. A must see if you haven't already (and even if you have, go see it again).

Speaking of being awed by biological variety, Stephen at Quintessence of Dust reviews a recent paper that addresses the question of why there isn't even more diversity out there, in particular in plant's inflorescent morphology. It's an interesting piece that shows how evolutionary theory can be used to create a testable developmental model. It also introduces us (or at least me) to the concept of "evolutionary wormholes". Mr. Darwin may I introduce you to Dr. Einstein?

Over at Metamagician and Hellfire, Russel gives us an excellent rant about science being a major part of "rational inquiry" and not merely "a way of describing the world, among other ways". I particularly like his statement that

At this stage of human understanding, it would simply be irrational to reject such scientific findings as that certain diseases are caused by bacteria or viruses, that the Earth revolves around the Sun (not vice versa), that our own species, Homo sapiens, evolved from earlier life forms, that DNA encodes for proteins in a way that provides a mechanism for biological heredity - and many others.
Hear, hear!

On a completely different topic, Russel touches upon the relationship between "binge" drinking during pregnancy and fetal neurolodevelopment. Not quite Russel's take, but this reminds me of when my wife likes to say (rather Darwinisticly), alcohol only kills the weak brain cells and we don't want our kids having weak brain cells do we?

(Russel has also provided a couple of good posts concerning irrational and unfounded calls to morality in issues of bioethics - see here and here )

Tara Smith gives a concise description of methicillin-resistant Staphylococcus aureus (aka MRSA) and its growing prevelence in non-hospital communities. While some grim details are discussed, Tara's presentation is a far cry and a refreshing change from the Armageddon-like press MRSA has been receiving lately. Tara also discusses a disturbing finding that shows MRSA infections spreading rapidly in swine populations - and the ability of these infections to easily jump to humans. Please, please, tell me I can still eat bacon.

Ed at Not Exactly Rocket Science has an interesting post on cooperation and communication in bacteria and the evolutionary pressures on bacterial slackers. Apparently, bacteria have their own versions of Jeff Spicoli to worry about. Ed seems to have a thing for cheaters too - he provides us with a post about the multiple disguises used by the bluestriped fangblenny. I bet his next post involves awkward, misunderstood porcupines that dress in black and listen to the Cure.

Ouroboros discusses potential problems with calorie restriction. Sure, you may live longer and avoid getting diabetes, but you'll probably have worms. I think I'll go eat a cheeseburger now.

CL at planet doom? (aka the Scourge of the Southern Seas) invokes the Law of Unintended Consequences in questioning the sensibility of seeding the ocean with iron to counteract global warming. Next thing you know, he'll argue against importing Cane toads.

The Agricultural Biodiversity Weblog discusses some newly discovered traditional planting techniques in the Amazon that facilitate cross-pollination in casava, which results in "making the casava stronger". ABW also has an interesting post about the intersection of culture and nutrition that explains why Kenyans don't eat polenta.

Mike at 10,000 Birds has some great photos and a description of the Northern Gannet. Some day I hope someone refers to me as 'pulchritudinous'.

The physics arXiv blog reveals a new medical toy in our near future - the micro MRI. It's sure to be the hot item next Christmas.

Science and Reason has a really nice piece that describes the role of sirtuin proteins and the sirtuin-encoding gene sir2-1 in extending the lifespan of C. elegans. Too bad they haven't found a gene that increases nematode pulchritude.

A Mad Tea Party provides us with all the nauseating details of Norovirus, aka the Cruise Ship Virus. I suggest reading this one before you sit down and gorge yourself on turkey, stuffing, and cranberry sauce.

Unbelievably and with amazing symmetry (I'm not making this up), Greg Laden, who started us off with the first post, finishes us up with the last. In this one, Greg discusses Neutral Theory and the Adaptionist Program in relation to some new work on the evolution of the nematode vulva. I think I best let that one alone.

Well, that's all folks. Hope you've enjoyed this edition of the Tangled Bank. I've certainly enjoyed writing it. Enjoy your Thanksgiving, Lebanon Independence Day, Feast of St. Cecilia, or just another day in November as appropirate. Stay tuned for Tangled Bank #94 to be hosted by Life Before Death

Friday, November 16, 2007

RWU starting to get it?

A couple of weeks ago, I expressed in passing my hope that Roger Williams University would someday join the ranks of Bowdoin and Penn State (and a slew of others) in "greening" the campus. Looks like folks here were ahead of me on this and in recent weeks the University has brought sustainability to the forefront with the unveiling of the campus shuttle converted to run almost entirely on used canola oil. It's name is still up in that air (or rather stuck in committee), but I've heard two possibilities I like - 'The Canola Rolla' and 'Deep Fried Ride'.

This isn't biodiesel - it runs on straight vegetable oil (SVO) left over from campus dining. Unlike biodiesel, which can be used straight or mixed with conventional diesel in a diesel engine, SVO vehicles require an engine conversion to run properly. In addition to an engine conversion, SVO fueled vehicles generally preheat the oil before running it through the engine since it is more viscous than biodiesel, so most conversions include a two-tank system - one for PVO and one for diesel that will be used at start up and shut down to heat the PVO and clear it out of the engine so it doesn't gum up the works.

The PVO is recovered from dining service, filtered, and then stored in drums. The 'Canola Rolla' burns the PVO cleanly - releasing CO2 of course, but CO2 that was only recently removed from the atmosphere (via photosynthesis). Thus, burning PVO results in little net addition of CO2 to the present atmospheric carbon cycle, unlike burning fossil fuels which takes CO2 that had been sequestered away from the atmosphere for millions of years (and would have stayed there for millions more).

As an added benefit, I don't feel guilty about eating french fries. In fact, if I don't eat french fries, I'm being irresponsible, depriving RWU of a clean, renewable fuel source! Time for lunch.

Here's a short video on this project by The Feed:

Thursday, November 15, 2007

It's such a piddly thing, I know, but...

...I really hate it when students send emails with an attachment but no message. Is it too much effort to write "Here's my lab report!" or "Attached is my proposal. Thanks."? Sometimes I stare at the blank screen for a minute waiting for a message to appear thinking the server is just slow in loading it until I realize it really is completely blank. Have we truly become that lazy?

Wednesday, November 14, 2007

Fall Garden

Even without the flowers, our perennial garden is looking rather nice.

They giveth and they taketh away

Apparently I'm a lucky guy. Not only did I win a t-shirt from Seed, but I also won an iPod:
Hi there,

Congratulations! You've won a prize in the ScienceBlogs DonorsChoose Challenge Contest.

Your generous donation has helped to increase science literacy in a public school classroom. As if that weren't reward enough, you're soon to be the proud owner of a brand new iPod!! courtesy of Seed.

To claim your prize, please send a valid mailing address. We will pack up your winnings and get them to you shortly.

Thanks again for reading ScienceBlogs and giving to DonorsChoose through our blogger challenges. You're wonderful.

Best wishes,

The Seed Team

Then again, maybe I'm not so lucky. It turns out that my previous t-shirt win disqualifies me from my iPod win:

Hi again Jim,

I'm really, really sorry, but when I picked your name for the iPod I
didn't realize that you had already won a t-shirt. Our rules say that
the ipod drawing was only for names that hadn't yet won a prize, so
I'm going to have to choose someone else for the pod.

Totally my fault, and so sorry to disappoint you!

Ginny Hughes, Seed

I emailed Seed asking if they could give the t-shirt to someone else. You know, cause I don't want to be greedy. They said it was out of their hands now, but they're sorry for their mistake.

At least they'll be sending my t-shirt soon. Can't wait. Really, who would want an iPod instead of a yellow t-shirt?

Tuesday, November 13, 2007

Tangled Bank coming soon

Congrats to Greg Laden for being the first to submit a post for the next Tangled Bank (and thanks for reminding me that I'm hosting it!).

TB #93 will be up just in time for Turkey Day (if you're in the U.S.) or Independence Day (if you're in Lebanon) or the Feast Day of St. Cecilia (if you're a musician, poet, lover of Church Music, or a parishioner in Albi, France or Omaha, Nebraska). The rest of you will just have to enjoy the Carnival sans holiday.

So, submit away oh bloggers of science and medicine. jim.lemire[at]gmail[dotcom]

(or you could leave submissions in the comments)

Monday, November 05, 2007


I'm off to the National EPSCoR Meeting. Tough, I know, but someone has to do it. See you next week.

Job Posting: Assistant Professor of Evolutionary Biology & Bioinformatics

The Department of Biology, Marine Biology and Environmental Science at Roger Williams University invites applications from broadly-trained biologists for a tenure-track position in Evolutionary Biology with a specialty in Bioinformatics.

For more info, check out RWU's job announcement

Sunday, November 04, 2007

KZ Needs Help

I'm starting to think marine scientists that blog are all a bunch of helpless whiners. First Craig at Deep Sea News begged people to help him. Now Kevin Z over at the Other 95% apparently needs our help.

Next thing you know he'll be looking for someone to write his dissertation for him.

Thursday, November 01, 2007

My Jack-o-Lantern

Not the greatest picture I've ever taken, but here's the jack-o-lantern I carved during our local Audubon sanctuary's Spooktacular event. His Noodliness would be proud I think.

(thanks Sarah for sending the pic!)

(I should clarify - I took the bad photo. Sarah had the file on her computer and was nice enough to send it to me. Sarah's pumpkin photo came out much better)