Wednesday, September 26, 2007

Good times never seemed so good

This post has nothing to do with biology...unless I decide to delve into the nuerobiology of being a Red Sox fan...but if PZ Myers can allow a student to post about Drew Brees, I figure it's OK to open Archaea up to sports.

Anyways, my wife and I were at Fenway last night to watch the Sox beat the A's 7-3. This was our first (and only) game of the season (in fact, it has been a couple of years since we've managed to get to a game), and, man, I couldn't have asked for a better experience. I got to see just about everything that I could have hoped to see. Here are the highlights:

  • We got to see Schilling pitch. He wasn't overpowering, but he was very good - scattering 6 hits over 6 innings, striking out 6, and only giving up 1 run.

  • Manny Ramirez actually decided to play after sitting with an oblique "injury" for 24 games. BTW, Manny wears number 24. Coincidence? Knowing Manny, no. He got a standing ovation from the crowd (why oh why do we encourage him?) and went 1 for 2 before quiting being taken out of the game in the 5th. He won't be back here next year, so it was good to see him one last time.

  • I got to see my favorite current player, Mike Lowell, hit an RBI double off the wall. What can I say, I was hoping to see him get a hit and he did, so I was happy. He likewise probably won't be here next year (which is a damn crying shame if you ask me, especially if A-Rod is here instead), so it was good to see him before he goes.

  • J.D. Drew actually hit the ball. He went 3 for 4 with an RBI. Maybe he's needed 156 games to get used to Boston.

  • After being sidelined with a wrist injury for a while, Kevin Youkilis was back. He received a standing ovation and was showered with a full chorus of "Youuuuuuuuuuuk!"

  • A's pitcher, Ruddy Lugo had to wait to pitch in the bottom of the 8th while the crowd finished singing "Sweet Caroline". The PA had cut off the song and announced "Now pitching, Ruddy Lugo", but we could care less. 35,000 fans standing and belting out "Sweet Caroline, BAH BAH BAH, Good times never seemed so good. SO GOOD SO GOOD SO GOOD" while the players just stood around, watched and waited. If you don't know what I'm talking about, you'll just have to go to Fenway and experience it for yourself (in the meantime, here's a little taste). Gotta love this place.

  • The crowd erupted when the scoreboard showed that Tampa Bay was beating the Yankees. This was followed by 35,000 fans chanting "Yankees suck...Yankees suck...". I wonder how insignificant the A's felt at this point.

  • Jon Papelbon pitched in relief. This might have been was the most electrifying part of the entire game. As he ran in from the bullpen, 35,000 fans were on their feet and cheering. While he warmed up, 35,000 fans were on their feet and cheering. Let me repeat, while he was warming up, the crowd noise was at jet-engine decibel levels. And then 35,000 fans stood and cheered as he threw what turned out to be his only pitch of the evening to get a pop-out to end the inning and get the Sox out of a jam. The place went nuts. (BTW, excellent use of the Dropkick Murphy's "Shipping up to Boston" during his warmup.)*

  • David Ortiz hit a 3-run shot over the right field wall. Every fan wants and expects Big Papi to do this every time he's up, yet it never gets old. Again, the place went nuts.

  • Did I mention that the Sox won? (and the Yankees lost)

There was really only one lowlight of the game (what? did you think I'd leave well enough alone and be happy with the aforementioned highlights? what kind of Sox fan do you think I am?):

  • Eric f-ing Gagne: he couldn't (once again) get the job done in the 8th and Francona had to go to Papelbon with the tying run at the plate to quelch a potential A's rally. I'll be shocked (and enraged) if this guy is given the ball in a close game in the post-season.

Even with the disappointing Gagne, this was easily the best game I've ever been at.

*When Papelbon emerged from the bullpen, the PA played "Wild Thing", which I didn't think was right. It's cheesy and ripped off. This made the switch to the Dropkick Murphy's all the better.

Tuesday, September 25, 2007

Attack of the Killer Space Germs (or, Does Evolution Work Differently in Space?) reports that "germs" sent into space return home to Earth more virulent. I can't find the original PNAS article to which it refers, but this seems like a very interesting finding - a strain of Salmonella sent into orbit more easily infected mice and it took 3-times fewer bacteria to kill a host. (update: here's the PNAS paper)

The researchers have a hypothesis for this finding though it is not clear how from the CNN article why. They think that the bacteria evolved in response to the low fluid sheer shear that results from the low gravity environment. I am not able to figure out why the low fluid sheer shear would lead to a more virulent bacterium, but for some reason, the researchers have shown that over 150 genes have changed in the space-traveling Salmonella. Obviously, low gravity (and/or low sheer stress) has applied a strong selective pressure on these little critters. It would be interesting to know more about the genes that were affected.

I have a major issue with the CNN article though (which is one reason I wish I could find the PNAS article). Cheryl Nickerson, a professor at ASU, is quoted as saying:
These bugs can sense where they are by changes in their environment. The minute they sense a different environment, they change their genetic machinery so they can survive

Now, I am no microbiologist, but this statement reeks of an oversimplification of the evolutionary mechanisms at work here. It is this kind of carelessness (or bad reporting?) that helps perpetuate a misunderstanding of evolution in the general public. A scientist should be able to communicate basic evolutionary theory, especially when being quoted in a high-profile media outlet.

BTW, "fluid sheer" is not the same as "fluid shear". My biomechanics professor would be so disappointed (Sorry, Amy!)

Update: Using the correct terminology I was able to find this much more informative National Geographic article. It explains a little more about the possible mechanisms involved here (and doesn't have the same nocuous Nickerson quote)

Wednesday, September 19, 2007

There Be Pirates Here

If ye can't talk the talk, don't even think about walkin' the walk ye snivelin' landlubbers. It be "International Talk Like a Pirate Day"! So avast there me hearties, grab ye bottle o rum and belt out a mighty "ARRRRRRR!"

Listen to Talk Like a Pirate Day by Tom Smith:
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Tuesday, September 18, 2007

October forecast: cloudy with a chance of brimstone

RWU is an interesting place. For a small New England university it seems to become embroiled in more than its share of controversy.

First there was the whites-only scholarship nonsense .

Then there was the Inconvenient Truth brouhaha. This one even found its way onto the Colbert Report (unfortunately, the original Comedy Central video is no longer available, but you see the original CNN FoxNews interview with a RWU student and read the Colbert Report transcript over at Conspiracy Factor).

The next "controversy" will start In October when the campus tackles religion, science, and evolution. First up will be a Socrates Cafe discussion of "Are science and religion incompatible?" . This will be followed up later in the month with a seminar by Dr. Eugenie Scott of the National Center for Science Education as part of RWU's Civil Discourse Distinguished Lecture Series.

Given the recent history of the campus, I'm sure there will be no shortage of bobos in attendance at both events. I'm even willing to bet that there will be picketing and the calling down of fire and brimstone. Stay tuned. Should be fun.

Monday, September 17, 2007

Does God have a bookie?

Following up Dale McGowan's neurological explanation of the "bright light at the end of the tunnel" phenomenon, I think I've uncovered why some people experience the "hand of God". Concussions.

Detroit quarterback Jon Kitna expected people to snicker and laugh when they heard his explanation for his comeback against Minnesota after getting knocked out of the game with a concussion.

"It was a miracle," Kitna said Monday.

Kitna left the game in the second quarter, returned in the fourth and led the Lions to a 20-17 win over the Vikings in overtime on Sunday.

He said it was the third concussion of his NFL career, and the first since 2001. Kitna said he also had a concussion playing for Seattle against San Francisco in a 1997 preseason game.

"I've never felt anything like that, and for it to clear up and go right back to as normal as I can be, is nothing short of a miracle," Kitna said. "I just definitely feel the hand of God. That's all it was. You can't explain it.

"I have no headaches, no symptoms, no lingering effects. But that was the worst my head has ever felt, and the worse my memory was in the second quarter. Yet, after halftime there was nothing."

He was knocked out of the game in the second quarter and appeared to be out for the rest of the day, standing on the sideline without a helmet.

"I was out of it. I didn't know anything. I lost coherence," Kitna said. "It's one of those things, you shouldn't even been able to go back in the game, but it went back to normal and cleared up like it never happened."

Clearly, God's a Lion's fan and knew He needed Kitna's help to beat the spread.

Saturday, September 15, 2007

Life Among the Eupatorium

The Eupatorium in our garden is in full bloom and the insects are loving it. Here are some pics from a single 1/2 hour photoshoot (there were others too - some fast, small buggers that I just wasn't able to get). I'm working on the IDs of the less obvious ones...

...update: All bugs identified. And I take no credit for most of them - the fine folks over at are the real experts. Thanks.

Megacyllene robiniae - Locust Borer
(thanks, BugGuide!)

Melanoplus sp. - Spur-throated Grasshopper
(thanks again, BugGuide!)

Danaus plexippus - Monarch Butterfly

Agapostemon sp. - Metallic Green Bee

Ancistrocerus antilope - Potter Wasp

Ancistrocerus campestris - Potter Wasp
I was sure that this was the same species as the one above,
but Richard V. over at has set me right

Polistes dominula - European Paper Wasp
An introduced species, first recorded in the U.S. in Boston, 1978.
Expanding range in the U.S. and possibly replacing native species

Lucilia sp. - Green bottle blow fly

Bombus sp. - Bumblebee

Bombus sp. - Bumblebee

Apis mellifera - Honeybee

Apis mellifera - Honeybee

Apis mellifera - Honeybee

Tuesday, September 11, 2007

Double trouble

I am late to the game on this, but just in case anyone somehow wanders my way without hearing about it elsewhere, I have to share. Not sure how I'm just finding out about this now...


(the x-rays and video are killer).

How have we not known about this anatomical phenomenon? I mean, we're not talking about some obscure creature here. Moray eels are found in just about every aquarium in the world. I feel like I've said this before, but the wonders of biology will never cease to amaze me.

Friday, September 07, 2007

A sea chanty?

In honor of my recent trip...

"I'm Shipping Up to Boston" by the Dropkick Murphys

I would have preferred a more "maritime" video, but they didn't ask for my input.

Order yours today!

This really must be seen. Words just can't do it justice.

Make sure you at least check out "Washlet 101"

(hat tip to Linda)

SEA Photos; part 1

Finally, as promised, some photos from my brief, but oh so wonderful, trip aboard the SSV Corwith Cramer. Four days of sailing and oceanographic adventure with Sea Education Association. This wasn't so much a scientific cruise as a chance to relive my days weeks months with SEA as an undergraduate and reconnect with a great organization. We sailed. We scienced. We kept a 24 hour watch. We even set the fisherman (sorry, can't find a link to help you with this one). If you ever get a chance to do this, you must. Encourage all your undergrads to look into SEA Semester as well - from a life experience point of view, its one of the best things they could do. Beyond hands-on, practical oceanographic research, SEA Semester builds leadership, self-confidence, teamwork, responsibility, problem solving, physical endurance, and plundering. Well, maybe not plundering. Anyways, on to the sure to check out Part 2 and Part 3.

The Corwith Cramer awaits

My bunk...and my hairy legs.

Couldn't find A through D

Ship's compass

"Steer a course for others to follow"

Just in case


Just in case, take 2
(AKA Gumby suits)

What good is a ship without her bell?

Had to (re)learn the ropes

How better to end the day?

Part 2 and Part 3

SEA Photos; part 2

Shipek sediment grab waiting to be deployed
(one of my favorite no-frills, old-school, bruiser of a scientific instrument)

the Shipek coming back onboard

Mmmm...mud from Menemsha Bight

I've been over this bridge about a billion times.
First time going under it.

Any guesses where we are?


Sailing through the night.
Red over Green; Sailing Machine

Sunset via porthole

Peeking in the doghouse.

Night lab work.

Not a bad office view, eh?

Part 1 and Part 3

SEA Photos; part 3

Furling the jib out on the bowsprit

Compass by night

Even Associate Deans have to swab the deck

This is what happens when you don't help swab the deck

Furling the tops'l

The carousel waiting to be deployed

12 Niskin bottles and a CTD headed down 50 fathoms

Anti-scurvy agents

Don't know who Louie is, but he's probably a bosun if I had to guess

Ship's lab

Coming home to the Hub

Part 1 and Part 2