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.