Wednesday, January 30, 2008

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".

Monday, January 28, 2008

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?

Saturday, January 26, 2008

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, January 25, 2008

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.

Wednesday, January 23, 2008

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.


Friday, January 18, 2008

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)

Sunday, January 13, 2008

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:

Thursday, January 10, 2008

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.

Tuesday, January 08, 2008

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

Monday, January 07, 2008

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).


Thursday, January 03, 2008

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?