Friday, February 29, 2008

Friday Dial Stopper

Here's another Friday Dial Stopper that breaks the rules. I don't think I've ever heard this song on the radio. However, if it ever were to be played, my dial would come to a screeching halt faster than Roger Clemens's plans for a post-baseball life of celebrity benefit appearances.

And speaking of baseball, today's Dial Stopper is for you, Johnny B.

Wednesday, February 27, 2008

Listen closely

Watch this trailer for the movie "The Fall" and see if you do a double take like I did. The whole clip is thoroughly bizarre, yet there is one thing that jumps right out at you as being totally out of place.

(hat tip to Acephalous, via Pharyngula)

Tuesday, February 26, 2008

Encyclopedia of Life now online...sort of

I was pretty excited to get an email announcing the launch of the Encyclopedia of Life. Unfortunately, they do not appear to be quite ready to receive the multitude of visitors that are trying to get there and the site is "Temporarily Unavailble". There was also a link to a newsletter in the email I recieved, but the link brings up the dreaded "Page Not Found" error.

I suppose it is not so bad a thing that folks are overwhelming the server to get EOL. It means there is lots of interest in the project. I assume that they have IT folks working on the problem as I write and the situation will be resolved soon.

For the time being, you can check out this NY Times article on the project, courtesy of Carl Zimmer.

UPDATE: the site now appears to be accessible. However it is loading very slowly.

Sunday, February 24, 2008

Clearly, I'm in the wrong business...(alternate title: People Are Dumber Than I Thought)

Out at breakfast this morning, I came across a catalog for Learning Connections, which "offers a wide variety of short courses, trips, and seminars designed for adults in Rhode Island and the South Coast region of Massachusetts." At first glance through the courses they offer, it looked like the sort of stuff you find at a local community center - classes in cake decorating, introductory Spanish, ballroom dancing, etc. There were even some classes that looked intriguing to me - like the "Seasonal Italian Cooking Series" and "Scotch Whiskey: An Exploration into Malt". And then I flipped to the pages in the back and find "classes" such as:

Spirit Flame Pictures

Those in the spirit world communicate with us in various ways. In this fun, eye-opening class, use index cards and a candle and see what spirit wants to show you. Discover visual evidence from the spirit world; you may even get a picture of a loved one, an angel, or a family member who has passed into the spirit realm. Kathleen has pictures to show, and each person who attends will leave with their own spirit flame picture.


Healing Yourself through Past Life Regression
Why are people afraid of heights, water or speaking in public? Do you have a health issue that hasn't been helped any other way? Some people are simply curious about past lives while others want to know why they have so many challenges in their life. These issues are very often because of a past life experience. Topics discussed include meditation, connecting with your spirit guide, and the workshop includes a group past life regression.

and my personal favorite:

Divine Intervention: How to Pray and Get Results

Do you ever feel like you are having a one-way conversation with God? Are you hearing a lot about prayer in the media? Join this discussion and learn the 10 tips to getting your prayers answered. Talking and listening to God takes time, patience and faith; but the exchange is life-changing.

That's right folks, the reason your prayers are going unheard is because you're not doing it right. You need to spend $39 for a two and half hour class to learn how. It must be like taking candy from a baby.

The list goes on and on - "Meeting Your Spirit Guide", "How to Activate Your Ability to Become a Healer (with Eric Pearl)", "Crystal Healing", "Scrying: Seeing Though the Crystal Ball". Yes, you read that right - scrying! If you don't believe me (and I wouldn't blame you), go check it out yourself.

I'm pretty cynical when it comes to American intellect, but I have to say this left my jaw agape. Even though I get rather haughty about being from an area that is both intellectually and socially liberal/progressive (New England in general, and Massachusetts in particular), I knew that even we had our fair share of kooks (well, maybe not our fair share, but enough anyways). But these "classes" are taking place not 10 minutes from my own house. That's just too close for comfort.

On the one hand, I am tempted to check one of these things out - see what kind of person attends and just what sort of information is being given. A social experiment, if you will. On the other hand, I'm tempted to heed Mr. P.T. Barnum's wisdom and create my own ridiculous "class" and charge people 50 bucks to listen to a bunch of nonsense. There's surely a market for "Making Your Dreams Come True: How to Concentrate Really Really Hard and Make Gold Dubloons Appear Out of Thin Air", right?

Saturday, February 23, 2008

Weekly Urchin: Dreamlines

I've somehow managed to completely slack on last week's "Weekly Urchin" post. So much for giving them the respect they deserve. Oh well. To make up for it, please enjoy these lovely pieces of urchin art - generated by a program called Dreamlines created by Leonardo Solaas. (Hat tip to Kevin Z. for bringing Dreamlines to my attention).

Friday, February 22, 2008

Friday Dial Stopper

This week's Dial Stopper breaks the rules a bit. I've never heard this song on the radio, so technically, my dial has never stopped on it. However, it's one of the songs that I always hope to hear on my Pandora stations and one of those songs that will always cause me to stop what I'm doing at the moment to turn it up and listen. It's as close to a dial stopper as I can get in the absence of any actual dial. Not sure I get the video though.

Thursday, February 21, 2008

Going, going, gone

Here's a quickly-done composite of some photos I took last night of the lunar eclipse.

Wednesday, February 20, 2008

If you own an HP DesignJet 5500 large format printer... not, I repeat, do not press and hold down the "Form Feed & Trim" button.

This will not, as one might assume, feed out and trim a length of paper commensurate with the length of holding down the button so that you can start with a nice, clean fresh surface on which to print a nice, clean undergraduate research poster on. Instead, the machine will interpret such holding down of the button as a series of individual presses of the button and proceed to feed out and trim 100s of individual 2-inch strips of paper.

Please note as well:
The "Cancel" button does not, in fact, cancel this operation. Nor does the "Power" button. Nor does unplugging the machine. Nor does swearing at said machine such obscenities as to have made Blackbeard himself uncomfortable.

I hate this machine. Again.

Michael Pollan lecture

For those in the Providence area:

Michael Pollan, author of The Botany of Desire, The Omnivore's Dilemma, and In Defense of Food, will be speaking at Brown tomorrow night (Thursday, Feb. 21) at 6pm.

I recently read The Omnivore's Dilemma which I found outstanding. It was well-written, entertaining, and educational. I was particularly shocked about what I learned concerning the corn industry. Though I was already a aligned with the organic, hormone-free, antibiotic-free, locally-grown, free-range ideals, this book helped focus my energy on realizing some of them better. If his writing is any indication of his speaking ability, this should be an excellent lecture.

I'm planning on being there and then probably heading out for some "Green Drinks" at Nick-a-Nee's afterwards.

Tuesday, February 19, 2008

Cuttlefish chicanery

Scopped this cool cuttlefish video from Carl Zimmer:

Cuttlefish Camouflage (NY Times video)

We actually maintain a few cuttlefish (Sepia officinalis) here at RWU. They're definitely the stars of the "wet lab", though monstrously difficult to keep. Beyond being picky eaters and sensitive to environmental conditions, we've had a couple leap out of their holding tank. One perished on the concrete floor, the other was rescued and put back into the tank, but had fractured its cuttlebone and didn't survive long.

One of the PIs here is working with a student on diet imprinting in young cuttlefish. One of the reasons cuttlefish are hard to maintain in captivity is that they generally only eat live food. The student here is working on getting the cuttlefish to imprint on non-live food with the hope that as adults they will be able to thrive on a diet that is less a pain-in-the-ass to deal with.

Almost daily, when I get home from work, my kids ask me if I saw the cuttlefish and they always want to come to my work to see them. I have to admit, I'd probably spend hours watching them if I could.

Looking to buy me a gift?

You couldn't go wrong with this.

I already own this one.

I'm not kidding.


Stop laughing.

Sunday, February 17, 2008

Gotta get me a fedora

May 22 - mark your calendars

More here

Friday, February 15, 2008

Friday Dial Stopper

Going old school here. Pre-MTV so no good videos for this dial stopper, so I went with just the music this week. Legendary band with countless classic songs, but this one is my favorite. Enjoy!

Mistaken identity

While driving my kids to school this morning (actually while driving to Dunkin Donuts before dropping my son off at daycare and then my daughter off at the bus stop) I noticed a bumper sticker on the car in front of me. It was rather faded so I was having trouble reading it.

My first glance: I love...something something...picture of someone

Next glance: I love...German something with an 'S'...picture of someone

3rd glance - I thinks to myself: "hey that looks like a picture of Albert Einstein. Oh cool, it says I love German Scientists...picture of Einstein"

Me: "Hey kids, there's a really cool bumper sticker on the car in front of us,"

I'm now thinking of how best to describe Albert Einstein to an almost-4 and almost-7 year old.

Kids: "What does it say?"

And then the car in front of us slows down and I get a complete look at the sticker. It doesn't say I love German Scientists it says I love my German Shepherd. Now, that makes no sense with a picture of Einstein...wait a minute, that's not''s...


That's right folks, I confused a picture of Pope Benedict for a picture of Albert Einstein. Ugh.

Emma: "Daddy, what does it say? What does the cool bumper sticker say?"


Jack: "Daddy? What does it say?"

Me: "It says, I love my german shepherd."

Kids: "What's a german shepherd?"

Me: "It's a type of dog"

Emma: "Daddy, that's not a cool bumper sticker. That just means they have a dog."

Jack: "Yeah."

Me: "You're right. Let's go get a donut."

Thursday, February 14, 2008

Why Hillary can't win...

This is more telling than any poll.

Wednesday, February 13, 2008

I thought it was still winter

Last evening we had a nice snowfall and this morning I had to shovel a couple of inches of snow off the driveway. I had been thinking how nice it has been to have a real winter this year - plenty of snow, plenty of cold. It just seemed right - the way winter is supposed to be in New England.

Things changed in a hurry. The temperature shot up today over 50° and we've had rain of biblical Hadean proportions. So much for the continuation of our winter wonderland.

Tuesday, February 12, 2008

Happy Darwin Day!!

Charles Darwin was born this day in 1809 in Shrewsbury, England.

Coincidently, I grew up in Shrewsbury, Massachusetts. I wonder if my home town has a Darwin Day parade? I'll have to look into it for next year's Darwin bicentennial and see if I can't organize a town-wide celebration. Shrewsbury, MA after all is no stranger to revolutionary science - it's home to the Worcester Foundation for Experimental Biology Biomedical Research - birthplace of "the Pill" and early work on in vitro fertilization.

Anyways, go spend part of your Darwin Day over at the Guardian's (UK) online treasure trove of all things Darwinian.

Also, if you don't have enough to read these days, you can check out (almost) all of Darwin's publications online.

(note: the image above is from here)

Monday, February 11, 2008

And on the 8th Day, Todd said "Let there be junk DNA!" Not!

Stephen Matheson of Quintessence of Dust has a really nice, empirical refutation of the commonly held creationist claim that research on "junk DNA" has been repressed suppressed repressed suppressed by scientists.

Why do creationist's think "junk DNA" is so important? Well, they claim that "junk DNA" is evidence of Todd's handywork - non-coding yet conserved sequences of nucleotides that they claim scientists claim cannot be accounted for by natural selection. There are many problems with this line of logic, not least of which is the fact that "junk DNA" is an overly simplistic, archaic, and misleading term. As scientists began to realize that stretches of so-called "junk DNA" were functionally important, (even if they don't code for a protein) the idea that they were "junk" went out the window and their existence can readily be explained by natural selection. These stretches have been studied so intently in fact that whole new classes of non-coding DNA have been discovered. As Stephen points out very nicely with a little bit of research is that we are dealing with a problem of semantics - creationists are using the term "junk DNA" in a way that scientists no longer do.

Friday, February 08, 2008

Friday Dial Stopper

Great song. Awesome band. Really weird guy.

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.

Thursday, February 07, 2008

Term papers

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

Wednesday, February 06, 2008

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, February 01, 2008

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

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

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.