Weekly Urchin: Sea Urchin 101

Despite what some people think, sea urchins are not morally reprehensible. Sure, they've got sharp, pointy spines and a predilection for destroying kelp beds, but they're not bad characters. They're just misunderstood. Well, I think it's time sea urchins got more respect and no longer crept in the shadows of their echinoderm brethren - the popular, good-looking sea stars (yes, 'sea stars', not 'starfish'), the mysterious and sought-after sand dollars and the quirky, fun-loving sea cucumbers (what about the crinoids you ask? Forget them - they're just weird).

So, in an attempt to raise much deserved good will toward these dark and brooding echinoids, and in the spirit of MBSL&S's That's A Moray Monday, DSN's TGIF series, and Pharyngula's Friday Cephalopod, I've decided to take it upon myself to offer a weekly urchin post.

I'll start with some sea urchin basics...

Sea urchins are spiny marine invertebrates that comprise, along with sand dollars, sea biscuits, and heart uchins the Class Echnoidea within the Phylum Echinodermata. Sea urchins differ from the other echinoids by having a more-or-less spherical body-plan and are thus referred to as "regular" or "globose" echinoids. Like other echinoderms, sea urchins utilize a hydraulic system of tube feet for locomotion and display pentameral or five-rayed symmetry - most clearly delineated in their test (a.k.a. shell). Although relatively small (generally less than 15 cm in diameter), some species can have spines over 20 cm long. With somewhere around 800 extant species, sea urchin are a cosmopolitan critter - found from the Arctic to the Antactic and from the intertidal zone to the deep-sea.

External anatomy
Sea urchin tests are are comprised of calcium/magnesium carbonate plates, specifically, five alternating pairs of columns of ambulacral and interambulacral plates. The ambulacral plates contain pores through which the tube feet protrude. Both kinds of plates have tubercles - ball-and-socket type spine attachments (urchin spines are capable of moving somewhat like your index finger around the first knuckle). The test and spines are all covered in a thin epidermis.


The oral surface of an urchin is on the bottom where its five teeth can be found (contained within "Aristotle's lantern", one of nature's most impressive feeding structures - more on this in a later post). The aboral surface is on top and contains the anus, surrounded by aptly-named anal plates, which are in turn surrounded by genital plates, each of which contains a gonadopore, through which gametes are released. One of the gonadal plates (known as the sieve plate) contains the madreporite - the structure through which water is drawn to power the water vascular system, the hydraulic system used by echinoderms for locomotion.


General Ecology
Sea urchins are epifaunal, using their Aristotle's lantern to graze upon algae and sessile organisms. Their spines are used for protection against predators (otters, fish, sea birds). Some urchin species have specialized spines that are capable of injecting venom that causes intense pain. Urchins can be voracious eaters and, if their numbers are unchecked, a population of urchins can completely strip an area of vegetation, resulting in a seriously-altered ecosystem generally termed an "urchin barren". Likewise if urchin numbers crash, the resulting algal growth can severely alter the local ecosystem.


Ok, it's quite late, so that's all for now. More on these lovely, non-evil creatures next week.

Term papers

The inevitable question: "How many pages does it have to be?"

I think John McCain will be our next President

(note: I am a political moron. What follows is not based on any facts, statistics, trends, or analysis of key issues. It is just some random thoughts from a generally apolitical mind. You have been warned.)

If there was ever a year where the Democrats could put a president in the White House, 2008 seems to be it. It just seems ripe for the picking. If only Al Gore or John Kerry were running this year. Hell, I'd take Michael Dukakis. I mean no slight against Barack Obama or Hillary Clinton - I think they'd make great presidents. I agree with their stance on most of the important (to me anyway) issues. In fact, it was difficult for me to decide on who to vote for in the Massachusetts Democratic primary - I easily could have gone either way. Unfortunately, I have serious doubts about whether either one can win the national election.

I've questioned Obama's and Clinton's electability for a while. I'll admit that I had hoped Al Gore would throw his hat into the ring once more. Barring that, I assumed John Edwards would need to be the one. Why? Because I don't think a black man named 'Barack Hussein Obama' or a woman, especially one towing Slick Willy behind her, will get the votes. It's superficial I know, but then again we are talking about the United States. Sure, either candidate will get the hard-line Democratic vote, but I think there will also be a huge push from the right to keep either out of the White House - there will be a large population, nationwide, that will not vote for a candidate, but against a candidate.

For a bit there though it looked like my fears were unfounded. I think neither Mitt Romney nor Mike Huckabee is electable either. I figured just about anyone could beat those two bobos. But now McCain has it all but wrapped up. Really, it must have been like taking candy from the proverbial baby. So now, the socially- and economically-conservative will vote for McCain (or at least, against Obama or Clinton) and the moderate, undecided vote has an appealing (white, male) choice.

Add to that the fact that Obama and Clinton may be duking it out with one another for months to come while McCain will be sitting pretty as the clear forerunner and can start his presidential campaign early. He can begin bringing the various Republican factions together, while Barack and Hillary continue to divide the Democrats. I've heard that right now the African-American voter turnout is through the roof. Will that be the case in November if Hillary gets the nomination?

I'm hoping a Democrat gets in - I'll be voting for which ever one gets the nomination. But I think McCain may be more electable, especially in swing-states like Ohio and Pennsylvania. 2008 might be the year the Democrat should have had, but didn't. I'm hoping I'm wrong.

Friday Dial Stopper

This is one of those songs whose video makes it a dial stopper. I like this song in its own right, but whenever I hear it I immediately think of the video, and that just makes me smile. I must have seen this on MTV about a half million times my sophomore year in college. It seems like such a happy song and the video has a feel-good vibe. Who'd have thought the song's about heroin addiction? Go figure.



Bonus trivia: this is the only song I know of whose video was the inspiration for another song

I was hoping for something grander

ORIGIN
mkrylvledg tiypgtgfga ttatvgelvf ntgmsgyqes itdqsyngei lmftyplign
yginrddhes ikptckgvvv hevarrasnw rnaqslddyl kqnaipgimd idtravtkhi
rtkgamkati vdnvlpdtvd rlkvtelnra vvaqsstnna ypnpatgpnv vvvdfglkhs
ilrelakrqc nltvlpyntt aseimalnpd gvmltngpgd pkdvpgalem irevekhvpl
fgiclghqlf alangadtfk mkfghrgfnh pvreiatgri dftsqnhgya vdrdslaqtd
llitheeind gtveglrhrd yaafsvqyhp daapgphdad hifdefidlm aanqatqkgs
qfna
//

What is it? Well, it's the amino acid sequence for the small subunit of carbamoyl phosphate synthase from Lactobacillus plantarum of course. The letters L-E-M-I-R-E correspond to Leucine-Glutamic Acid-Methionine-Isoleucine-Arginine-Glutamic Acid, based on the single-letter amino acid code.

(yes, I'm wasting time thanks to Carl Zimmer)

UPDATE: after refining my search techniques a little more, I have indeed come up with something grander - 'lemire' can be found in the humanRUVBL2 gene. Not too shabby.

Deep Sea News - Just One Thing Challenge

Do you want to help protect the deep sea?

Are you up to a challenge?

If you answered 'yes' to both of those questions then head on over to DSN and sign up for their weekly "Just One Thing Challenge".

Chuck D, Emma G, and spineless socks

Had to share some recently-acquired gifts. Yes, I'm showing off and want you all to be insanely jealous.

First up, a pair of finger puppets from my sister-in-law. That there's Uncle Chuck on the left and Auntie Em, "The Most Dangerous Woman in America", on the right:

These and much much more can be found at The Unemployed Philosopher's Guild. (and no, it's not entirely a coincidence that my daughter is named Emma. My son? Oh, he's named after a seafaring captain of course).

Second, a pair of home-knit socks from my mother-in-law that will make all you invert fans envious (yes, I'm talking about you, KZ). Besides being stylish and super-comfy, they're made from crab and shrimp chitin! (actually, from a yarn called TOFUtsies, which contains chitin fibers)


So, I've got radical, free-thinkers on my fingers and crustaceans on my feet. What could be better?

Synthetic life followup

I want to return to the topic of synthetic life and the Venter Institute's recent accomplishment of synthesizing a half-million base pair bacterial genome from scratch. Thinking and reading more about it I realized that my first reaction to this was quite simple - "Cool.". Not "Oh my Todd! What have they done now?" or even "Wow, that is absolutely amazing - I can't believe they figured out how to do that!". Just "Cool." Even back when the Venter team succeeded in inserting a whole genome into a DNA-less cell, I wasn't particularly blown away. I mentioned then that this sort of thing seemed like the next logical step in the world of biotech and genetic engineering. We've known for some time how to genetically modify organisms. In fact no one is really phased by this idea any more - at least from a feasible scientific and technological standpoint. Sure, people argue over whether or not genetically modified organisms (GMOs) are good for us or for the environment, but no one blinks an eye at our ability to create GMOs (hell, you can buy a kit and do it yourself).

So isn't it inevitable that we advance from inserting foreign genes into a cell to inserting whole genomes? Conceptually, it's just a matter of scale, right? So, that's what Venter's team did this past summer - they brought the field of genetic engineering to the next level by upping the scale. Was it easy? Hell no. Technically, the scientists had to overcome numerous barriers. They spent countless hours wracking their collective brains, performing failed experiments, and redesigning procedures. But in the end, it was never really a question of if they could do it, but how.

Same thing this time around. We've known how to build short stretches of DNA from constituent nucleotides for decades - we know the (bio)chemistry of it. But until now, we could only manage to make relatively small pieces of DNA - the longest synthetic strand of DNA had been approximately 30,000 base pairs long. So, Venter's team took us to the next level once again by upping the scale. And again, it was no small feat. Just an inevitable one. As Carl Zimmer has written, the advances we are seeing in synthetic genetics are largely technical, not conceptual.

So, no, I wasn't terribly surprised to hear about the synthesis of a 580,000 base pair bacterial genome. Impressed and excited, yes, but not surprised. And I won't be surprised when this genome is used to "boot up" a cell. Nor when the Venter squad whittles this genome down to the bare minimum that will drive a living cell - the so-called "Minimum Genome Project". Nor when GSOs - "genetically synthesized organisms" - replace GMOs in our regular lexicon. There's nothing Copernican here, the conceptual revolution is long past. DNA, nucleotides, nitrogen, phosphorus, carbon, electrons and protons. At this point it's all just different scales of biochemistry.

Friday Dial Stopper

Not sure why this one makes me stop the dial each time. Perhaps it's the bass hook. Perhaps it was their MTV Music Awards performance (see below for bonus link). Perhaps it's the fact that my almost 4-year old belts out "I think you're craaaaaazyyyyy" every time he hears it. Whatever the reason, I stop every time on this song. I even go searching for it sometimes.



(Bonus MTV Music Awards video here)

It's ALIVE...well, not quite yet

Folks over at the J. Craig Venter Institute have reported today in the journal Science that they have successfully synthesized an entire bacterium genome. An entire 580,000+ base-pair genome. From scratch. This is quite momentous as it brings the Venter team this much closer to their goal of synthesizing life de novo.

In case you have been living in a cave for the past 10 years, Craig Venter is one of the scientists that successfully sequenced the human genome back in 1999. For the past several years, he and his team of researchers at the JCVI have been working on creating artificial life - or rather synthetically recreating actual life. The first step towards this goal was accomplished just this past summer when Venter et al. successfully inserted the genome of one bacterium into another bacterium, essentially turning one species into another. Basically they showed that it was possible to insert whole genomes into another cell. The latest step just accomplished was to actually synthesize a whole genome. Next will be to try to get this genome inserted into a cell - which seems likely to happen considering their success in step 1. In fact, I would expect such an announcement in the near future.

This latest effort is quite interesting - they first sequenced the genome of Mycoplasma genitalium and then built "small" segments of the DNA (~5,000 - 7,000 bp long) from individual nucleic acids (Phase 1). To ensure that they could identify their genome, the researchers inserted their own "watermark" sequences that differentiated it from the natural M. genitalium genome. They also took some precautions by disabling genes for infectivity. They then assembled these "cassettes" into larger pieces of ~24,000 bp. These 24k pieces were then cloned into E. coli for replication so there was enough DNA to work with for the next phase. Phases 2 and 3 was similar to phase 1 - this time joining the 24k fragments into 72k pieces, which were again cloned into E. coli for amplification and sequencing, and then joining 72k fragments together to form 144k pieces, again cloned and amplified in E. coli. Phase 4 involved joining 144k fragments to create 288k fragments. However, at this point the researchers could not obtain E. coli clones with the 288k half-genome and had to move the operation over to the yeast Saccharomyces cerevisiae. Once that was done, Phase 5 was a simple matter (HAH!) of joining the half-genome chunks together through homologous recombination in yeast cells. Final sequencing showed that the team had indeed synthesized the entire M. genitalium.

What's next? Well, step three again will be to insert this synthesized DNA into a host cells to derive fully functioning M. genitalium. After that? How about creating an entirely novel genome from scratch? Then how about synthesizing self-assembling cell membranes to house these novel genomes? The rate at which the JCVI team is suceeding, I don't think we'll have to wait very long for true synthetic life.

Damn it!

I just typed up a nice longish post, full of science content and the program I used to create it (ScribeFire) lost it. I clicked "Post to Blog", it said "Post Successful" so I cleared the the editor. Yet, the post is nowhere to be found. Nowhere. I've had no problems with ScribeFire in the past, but now I can't post a damn thing with it - even though it tells me "Post Successful" every f-ing time. So instead, you get this rant.

Grrrrrr.....

Songs that stop the dial

I might as well continue the lack of any science-based posting with something I thought of while driving into work today. As I was flipping through the radio channels I realized that there is a definite hierarchy to the songs that I listen to. Generally, I flip through a few channels, hear a few seconds of what's being played, and then decide which song to listen to and switch back to that channel. If I kept track of all the songs and my preferences, I could create a rather accurate ordered list of my favorites (hmmm, maybe I can't quite escape being sciency). However, there are certain songs that simply stop the dial - if it is on, I don't bother finding out what else is available.

Of course, these songs are a varied lot - some are all-time favorites, others are new songs that I'm currently excited about. Now, my taste in music is rather eclectic and I don't think I have the absolute best taste either (as my wife will surely agree) - I like what I like whether it's Led Zeppelin or The Chieftains.

On the way into work this morning, there were actually a number of stop-the-dial (STD?) songs, but I think the following gets top billing for today.

(and no, I'm not the least bit embarrassed admitting this)

It's the reason...

It's interesting how random memories collide sometimes. Just days apart, my kids were asking about my favorite TV shows when I was a kid (as part of our new nightly "Dinner Games") and Sarah over at Jake and Nina Save the Day posts part of an episode from one of them - a show I haven't thought about in years - what are the chances? I just had to go a-searching for more:

Rice close, but falls short

Even with the numbers to back up a Hall of Fame induction, Jim Rice fell short once again. The good news - he's closing in, garnering 392 votes this year, falling only 16 votes short of the requisite 75% of the votes. The bad news - next year is Rice's 15th and last chance to get in.

The Case for Jim Rice

Jim Rice is up for election to the baseball Hall of Fame. He has been for the past 13 years - failing to make the cut each time. Much has been written about why Rice belongs in the Hall (as well as about why Rice does not). There is plenty of speculation that, with the uncovering of the Steroids Era™ resulting in Rice (and indeed all pre-S.E. players) being seen in a better light, this is the year for Rice. Of course every year seems to be the year. Yet for the past 13 years it hasn't. I happen to think Rice belongs in the Hall - but of course, I'm a Sox fan and I had the privilege of seeing him play. The articles linked to above go into plenty of stats, but here are some compelling numbers:

Rice's best years were between 1975 and 1986. In those 12 years in the AL, Rice ranked 1st in runs, 1st in RBI, 1st in hits, first in HR, 1st in slugging, 1st in total bases and 4th in batting average. He also won an MVP and finished in the top five in five other years. From 1977-1979 he became the only player in history to hit 35+ homers and 200+hits in 3 consecutive seasons.

MLB Leaders 1975-1986

HOME RUNS	RBIs	HITS
Mike Schmidt* 440	Jim Rice 1,276	Jim Rice 2,145
Dave Kingman 365	Mike Schmidt* 1,221	Steve Garvey 2,121
Jim Rice 350	Dave Winfield* 1,147	Cecil Cooper 1,975
Reggie Jackson* 330	George Foster 1,114	George Brett* 1,961
George Foster 321	Steve Garvey 1,076	Robin Yount* 1,933
SLUGGING %	TOTAL BASES	RUNS
Mike Schmidt* 0.545	Jim Rice 3670	Mike Schmidt* 1,194
Jim Rice 0.520	Mike Schmidt* 3,448	Jim Rice 1,098
George Brett* 0.518	Steve Garvey 3,222	Dave Winfield* 1,069
Eddie Murray* 0.505	Dave Winfield* 3,221	George Brett* 1,021
Fred Lynn 0.494	George Brett* 3,201	Robin Yount* 995

* member of the Hall of Fame

What seems to be keeping Rice out of the Hall is his lack of longevity which prevented him from reaching career milestones in RBI and HRs - Rice only hit 382 HRs and only drove in 1,451 runs. Still he had more RBIs than Hall of Famers (to name a few) Duke Snider (1,333), Robin Yount (1,406), Roberto Clemente (1,305), and Kirby Puckett (1,085) and he hit more HRs than Hall of Famers George Brett (317), Joe DiMaggio (361), Carlton Fisk (376), Tony Perez (379), and Orlando Cepeda (379).

I'm not going to argue that he's in the same league as Ruth or Aaron or Williams, but Rice's career numbers match up with Hall of Famers and for 12 years he absolutely dominated the American League. I think he deserves to be in the Hall and I think the numbers back it up.

Perhaps this is the year. I certainly hope so.

Best of the Deep Sea

As one of the honored judges of this year's Best of Deep Sea News, I'm happy to announce that Craig and Peter have got their self-congratulatory series of posts online - "The Best of the Abyss", "The Best of DSN", and the "Fuzzy Yeti Award", where you can cast your vote for the best DSN post of 2007 (sorta like an Academy Award for Best Picture if it were only awarded to films by James Cameron) . So, head on over to Deep Sea News and enjoy the best of the best (does that make Craig and Peter, the Eric Roberts and Chris Penn of the deep sea?)

Linnaeus' Legacy #3

Linnaeus' Legacy is "a monthly blog carnival devoted to the study of life's diversity, and the science of describing and understanding this diversity." The latest edition is up over at Greg Laden's Blog. My little rant on species naming rights is included in this edition, as well as a plethora of more intellectually enlightening posts (not written by me).

Enjoy!

Say it ain't so, AB

I'm shocked and disappointed - Alton Brown is a born-again Christian:

In 1992, Brown says, he found God, or maybe God found him, but he blundered away until he became a born-again Christian. The single biggest life-changing thing for me is I just got baptized last year. Everything else pales in comparison to acceptance of Christianity. That's number one.

I never would have thought. Unitarian Universalist, sure. Even United Methodist I could understand. But born-again? What's next? Bill Nye is a Jehovah's Witness? Richard Dean Anderson is an Intelligent Design creationist?

Lucky I had that quarter

So, I'm at blockbuster renting the 1st two Pirates of the Caribbean movies (the third is available on PPV). The total rental fee comes to $5.25. I give the guy $20.25. He punches in $50.25 by mistake.

Uh oh. What now? How can he possibly make correct change now?

Several minutes of blank staring and inactivity ensue.

Oh, thank Todd! There's a calculator on hand. 20.25 - 5.25 = 15.00

Disaster averted.

How did people ever do this sort of thing without cash registers or calculators? Are you kidding me? Give me a freaking break.

I guess I should have used a credit card instead.

Circus of the Spineless #28

The latest edition of the Circus of the Spineless is up and running over at Catalogue of Organisms. Head on over for all sorts of invertebrate fun.

I never knew

Litmus, the stuff of pH paper, comes from lichens.

How was this discovered?

Can lichens themselves be used to measure pH? If so, how come Les Stroud or Bear Grylls haven't taught us this yet?

Species naming rights

I'm not a taxonomist. I have never been involved in the discovery, description, or naming of a new species. Or even in the renaming of a species once considered something else. So, I really don't know the logistics of providing a name to a species.

I know that species are named for what they look like, where they are found, who discovered them, or in honor of someone else. I don't know the official rules of the game or even if there are official rules, but I never once would have thought that someone could buy the rights to a species name.

Well, that's what seems to be happening according to a story out of Scripps. Apparently, Scripps has a collection of new species that need to be named and has decided to use this as a fund-raising tool. They've got "an orange, speckled nudibranch, a hydrothermal vent worm, two types of worms found living on deep-sea whale bones, and several new species discovered in local La Jolla waters" all up for grabs. Naming rights start at $5,000.

I'm not sure I like this idea. Sure, they're raising money for the preservation of their specimen collection - something that I think is incredibly important, especially at a time where it seems natural history has been given a cold shoulder by "hard science" disciplines. However, the idea of commercializing this scientific process does not sit well with me. Maybe Scripps has a set of rules that must be followed and perhaps I'm being anachronistic, but do we really want to open the door to things like Polycera fedexii or Nereis walmartia?

Winter Garden

A cold front bringing a "wintery mix" came through here this past weekend, leaving a coating of ice on everything. I grabbed these shots this morning before work before everything could melt away. Compare to the shots of the garden a few weeks ago.

I'm a somebody

That's right, I'll no longer be wallowing in obscurity, now that I've been found by Montclair Publishing. Just check out this email I got:

Faculty Member at [email redacted],

It is my pleasure to inform you that you are being considered for inclusion in

"Who's Who in Collegiate Faculty" (2008/2009 Edition)

which is an exclusive section of Montclair Publishing's "Who's Who Among Executives and Professionals."

This upcoming national hardcover publication and website directory from Montclair Publishing LLC, was launched in 2007. Students, faculty, and staff members alike are helping to nominate the finest educators from schools throughout the United States and Canada.

Our goal is to recognize individuals for their commitment to and influence on teaching. There is no fee for publication.

If you are interested in being a part of our national publication, spend thirty seconds filling out your basic application below

I'm sure this nomination was very highly considered and that this is clearly a sign of accolades and success to come.

Next Tagled Bank

I 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.

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)

Tangled Bank #93

Ahoy 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

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:

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?

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?

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)

Aloha

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

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.

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)