Ahhh, Religion.

Yesterday, Morning Edition had a piece on sexual abuse victims making progress in using the Vatican. The duality of the Religion and Nation State of the catholic church has provided cover for the Pontiff and his lackeys, but its seems there may be an opening. Recently, an Oregon federal court and the Sixth Circuit Court of Appeals in Ohio said they are open to hearing arguments, based on the exception to the sovereign state immunity, called the "tortious act" exception. If the plaintiffs can show that U.S. bishops are officials of the Vatican, and that they harmed children by failing to report sex abuse, then there is a chance of getting to trial. Seems open and shut to me.

Meanwhile back at the Vatican...Gay people are going to bring the world to an end. Jesus.

NEWTS!

Newts (baby ones I think, man I am a terrible biologist) appeared at our home to this evening. As I was pulling into the garage, I noticed the first one on the downspout, then noticed the second one in the driveway. I am still trying to figure out what type of newt they are (terrible biologist). After snapping a couple of pictures, I herded the one in the driveway into the planter so he wouldn't get run over. Guess with all the rain be have been having, I'll need to be on newt patrol when moving the cars.

*************************************UPDATE*************************************

So, I did some research and I think it our visitors are Arboreal Salamanders (Aneides lugubris). I used this web page for the identification. This picture, along with the range, habitat description led me to my conclusion. If anyone thinks otherwise, I am interested in your opinion!

Foot in baby's brain

This post is graphic, but interesting. Doctors in Colorado removed a developing leg, hand, and intestine from a baby's brain. The news story is here and a big graphic picture here. The good news is the baby seems to be recovering well from the surgery. Although I don't agree with him completely, PZ Meyers had thoughts similar to mine on the matter:

Something struck me when I saw the photograph of this particular surgery. Here it is, a photo of a fetal foot flopping out of a bloody baby's brain (don't click if you're squeamish). As I'm sure you've noticed, anti-choice people love to parade about with gory photos of aborted fetuses, and they love to dwell on little details like a recognizable hand or face. This picture is exactly like those, yet realize this: there was no human being behind those little baby toes. The existence of these fragments of non-sentient tissue endangered the life of a child, and there was no question that they needed to be extracted.

This is also how we should view abortion. It's ugly and messy, and there's something disquietingly resonant of humanity in the pieces of the embryo or fetus, but we shouldn't be fooled. Those are beautifully patterned collections of differentiated cells, but there is no person there.

Now it is unknown if these organs were a growth from the baby that was born born or another fetus developing inside the baby that was born, but it provides interesting grist for really interesting scientific and ethical thought. I would ask PZ, "when is there a 'person' there?" I don't have the answer, but I definitely think it is interesting to think what makes us human (not that I think that makes us as a species 'special', just different). I am confident there will not be a definitive answer in my life time, if ever.

Depoliticize Prayer

Steven Waldman, co-founder of Beliefnet, was on Talk of the Nation yesterday and on Forum today. Both days Waldman suggested that the choice of Warren to deliver the invocation was an attempt to depoliticize prayer (because Obama, a liberal, was reaching out Warren, a conservative) Well, bullshit. There is one way to depoliticize prayer, keep it separate from politics. There should be no invocation at the inauguration. Separate church and state. That said, Warren has said bigoted things about the LGBT community. While I find his comments repugnant, I don't think that should disqualify him out right, I just think it is completely ironic in light of the Reverend Wright kerfuffle (Obama should have him give the invocation). I think this is strictly a political move and a savvy one at that, but time will tell.

Roy Zimmerman

Danny sent this video from Roy Zimmerman, I have seen other stuff from Roy, but I hadn't seen this particular one. If you aren't familiar with Roy Zimmerman, you should check him out. He is pretty funny and has a pleasing left perspective. He has songs gay marriage, evolution and other politcal issues.

Merry Christmas

As I mentioned in a post a few weeks ago, the Bush administration is sprinting to the finish, trying institute their policies in the final days. Stay vigilant, write to your senators and congressional representatives!

Master and Slave

I am constantly impressed with nature's ability to put humans in their place (that is, we are not as special as we think we are). The source of this amazement is frequently ants. Anyone not impressed by ants, just hasn't done enough research. One feature of ant society that is completely fascinating is ant slavery. That's right, ants enslave other ants. The nature of the enslavement varies, but in general it involves either killing the queen and hijacking the nest or kidnapping pupae. In the genus Polyergus, commonly called Legionnaire ants, workers are incapable of carrying out even rudimentary brood care, care for their queen, or even acquiring food. Polyergus species subsist solely as a ruling caste, maintaining a worker force by capturing ants of the closely related species in massive colony-to-colony raids and have evolved to efficiently capture slaves.

Photo Credit: Alex Wild

Photo Credit: Alex Wild

As the stolen brood matures, the captured ants imprint on their captors' colony and perform the usual labor of foraging, brood care, and nest maintenance as they would for their own colonies. Polyergus ants are obligate parasites that cannot survive without the labor of the ants they enslave. Below the red slave-raiding Polyergus species is shown living with black/silvery slave ants, Formica argentea.

Photo Credit: Alex Wild

So, do slaves ever fight back? Commonly, the queen and workers of the raided Formica colony evacuate to nearby vegetation to wait out the raid, but there is documentation of some species trying to fight off raiders. There is also evidence that post-enslavement resistance has also evolved. In studies conducted by Susanne Foitzik of Ludwig-Maximilians University in Munich, slave nursemaids killed some 80 percent of their captors' young queens and some 60 percent of the young workers. Nature loves an arms race.

I guess this means no more shoes on airplanes.

First of all, I am impressed with W's reactions time. Second, it's too bad the guy missed.

MCB Follies

Every year the graduate students in the MCB department put together funny videos and skits and have a big party to watch them. The video below, made by my labmate, is my favorite. There others here.

What would Faux News say about this?

The Daily Show With Jon StewartM - Th 11p / 10c

Moment of Zen - Santa Fist Bump

Barack Obama Interview
John McCain Interview

Sarah Palin Video
Funny Election Video

Prop 8

The other night Jon Stewart held Mike Huckabee's feet to the fire on gay marriage. I like Mike Huckabee, I think he is a good guy, but I disagree with him on most topics ranging from science to gay marriage. The interview is good and worth watching. the second part is about gay marriage. They came back the other night and looked at alleged conflict between the black and gay communities.

The Daily Show With Jon StewartM - Th 11p / 10c

Proposition 8

Barack Obama Interview
John McCain Interview

Sarah Palin Video
Funny Election Video

Steven Chu to head Department of Energy

Berkeley MCB professor, LBNL Director and Nobel Laureate, was named by Obama to head the Department of Energy. I think this is great. Although it was not intended to be, I see this appointment as repudiation of the know-nothing, anti-intellectual, cronism of the Bush administration. During his tenure at LBNL, Chu has changed the direction of LBNL initiating the Helios project and bringing the labs focus of funneling sunlight into our gas tanks. He was also instrumental in founding the Energy Bioscience Institute, a "collaboration" between Berkeley and BP (personally not a big fan of public private collaborations, but that is another post). Chu's tenure has not been without controversy (he came up during the UC salary controversy), but as a visionary with scientific experience, I think he is top notch.

Biodiesel fo' Shizzel

For those of you who don't know, Liz and I have a 2000 Volkswagen Golf TDI that we run on Biodiesel. We purchased the car in 2006 with approximately 70,000 miles. We (mainly liz) has run the mileage you to 113,000 miles. We purchase our biodiesel at the biofuels oasis, a worker owned co-operative in Berkeley. So far, Liz and I love the golf and are happy with the biodiesel. I hope to make regular comments and analysis on biofuels and biodiesel in particular. Sustainable carbon neutral renewable liquid fuels are needed to displace petroleum-derived transport fuels that contribute to global warming. Biodiesel and bioethanol are being produced in increasing amounts as renewable biofuels, but their production in large quantities is currently not sustainable. One alternative is the production of biodiesel from microalgae. Algal biomass can be grown in photobioreactors, but a rigorous assessment of the economics of production is necessary to establish competitiveness with petroleum-derived fuels. Currently there needs to be approximately a ten fold reduction in cost to be competitive with petroleum fuels, but achieving the capacity to inexpensively produce biodiesel from microalgae is of strategic significance to an environmentally sustainable society. Public and private efforts are already underway to achieve commercial-scale production of microalgal oil, but for the moment barely any biodiesel is being made from microalgae.

Ants!
(kinda)

Technically, speaking these are not ants, but spiders (count the legs and eyes) that have evolved to look like Ants. Nature is amazing!



Although many of these spiders hunt ants, it is not this visual deception that facilitates their hunting. It appears that the visual mimicry protects them from predation by other predators that generally avoid ants because they produce formic acid. The spider's mimicry of ants is not just visual, but chemical as well. The integrity of social insect colonies is maintained by members utilizing chemical cues present on the cuticle of nest mates and any intruder. Some of these mimicking spiders use chemical mimicry to gain access to these nests, which can be acquired through biosynthesis or through contact with the hosts or their nest material. For example, This paper shows that the chemical resemblance of the spider does not arise through physical contact with the adult ants, but instead the spider acquires the cuticular hydrocarbons by eating the ant larvae. You are what you eat.

Obama and The Internet

In light of the 533,000 jobs lost in November, we are going to need a lot of jobs. On Saturday Obama outlined his vision for the reviving the American economy. He plans to create jobs with WPA style projects upgrading roads, schools and energy efficiency in a public-works program whose scale has been unseen since construction of the interstate highway system in the 1950s. One of the programs that excites me is the expansion of broadband access across the country.

“It is unacceptable that the United States ranks 15th in the world in broadband adoption,” Mr. Obama said. “Here, in the country that invented the Internet, every child should have the chance to get online.”

Now, I don't think the internet will solve educations problems per say, but this sort of investment is what we need. These sorts of programs will create jobs now and increase the efficiency and robustness of our economy in the future. Science funding works the same way, it is an investment in our future as a nation and a global community.

Good Recipe

Liz has recipe for cranberry cake on her blog. Let me say it is delicious. If anyone is looking for a good dessert dish this holiday season, I highly recommend it.

Robert Reich Gets It Right
(again)

Robert Reich had a great post on December 3rd, discussing how our society has lost sight of what makes America great, the people and the people that we educate here.

"Our preoccupation with the immediate crisis of financial capital is causing us to overlook the bigger crisis in America's human capital. While we commit hundreds of billions of taxpayer dollars to Wall Street, we're slashing our outlays for public education."

I couldn't agree more. It is short sighted to slash funding for education in these times of economic difficulty. The education of student makes our economy more efficient, robust, and productive in the future. Reducing already anemic educational budgets may be penny wise, but it is pound foolish.

Reading List

I have added a reading list to the right hand side of my blog called "primary literature". I hope record my thoughts on interesting papers as I read them here on my blog periodically. I plan on posting a new paper each day (but not comment everyday) with a link to the paper. I think it will be a mix of old literature relevant to my interests and new stuff that comes across my screen (desk just doesn't seem like the correct phrase anymore). If anyone comes across interesting stuff, send it on over. Today I came across

Dynamic spread of happiness in a large social network: longitudinal analysis over 20 years in the Framingham Heart Study

In this article, the authors James Fowler and Nicholas Christakis suggest that happiness is contagious in social groups over three degrees of separation. If you are happy or be come happy it increases the likelyhood that your friends are happy or will be come happy and that effect is detectable on friends of a friends as well. I have not yet read it in detail, but I want to see how they control for the association of happy people. Anyway, I hope everyone is happy.

Why study choanoflagellates?

An Evolutionary Perspective.

Multicellularity has arisen several times in the course of evolutionary history each with unique features and attributes. As Leo Buss noted animal multicellularity is unique, compared to plant and fungal multicellularity, because animals have the capacity to move relative to one another, that is they lack a rigid, confining, cell wall. To understand the evolution of animal multicellularity, the reconstruction of the correct evolutionary antecedents is essential. Specifically, understanding of the character evolution prior to the evolution of animals it is critical to understand the biology animals close living relatives. The closest known living relative of animals is a group of collared flagellates called the choanoflagellates. Choanoflagellates are aquatic heterotrophic eukaryotes characterized morphologically by a single apical flagellum that is surrounded by a collar of actin filled microvilli. Many species of choanosflagellates live a solitary life style; however, some species have the capacity to form colonies. This is particularly interesting because it raises the possibility that the last common ancestor of choanoflagellates and animals may have shared this characteristic, thus understanding choanoflagellate colony formation will be inform our understanding about the evolution of animal multicellularity.

Yesterday's Forum

Yesterday KQED's Forum had a good program on the end of the Bush Presidency (many of the things discussed were not unique to the Bush Administration) but should serve as a reminder for us to remain vigilant in the final days of the presidency.

Bush Presidency Winds Down
The Bush presidency is winding to a close, but his term is not over yet. This 'lame duck' period of the presidency is often a time for last minute executive orders and pardons. We look at the waning days of the Bush administration and consider his legacy.

The War On Christmas

The Colbert ReportMon - Thurs 11:30pm / 10:30c

A Colbert Christmas: Toby Keith Sings

Colbert at Christmas
Colbert Christmas DVD

Green Screen
Bill O'Reilly Interview

Only thing is, I think Toby is serious...

That Conservative Whine

The classic claim of fiscal conservatives is that private corporations are more efficient than government. So setting aside the fact that I think several aspects of society should not be run for profit i.e. education, health care, insurance, I still take exception to the claim. A recent two part story from NPR touches on topic. Surprise (if you have had your head up your ass for the last 8 years), there has been a sharp increase in no-bid contracts. How the hell are no-bid contracts market based? this exposes these people for what they really are, greedy. Interestingly, the story also discovers that

"industry shouldn't collect the nation's taxes; public servants should do that crucial job. And the IRS's own calculations even show that government employees are more efficient: for every dollar spent trying to collect taxes, government workers collect three times as much as the collection companies do."

Surprise, government beats industry three to one! And they do a more professional job. Don't get me wrong, I don't think government should do everything. The claim that companies are better just sticks in my craw. Looking at the corporations I see them suffering from many of the same ailments (bureaucracy, corruption, etc...) as those alleged against the government. Finally, there is limited to no accountability with private contractors. Think Halliburton and Blackwater...

A Couple of Daily Show Clips

Excellent (if gratuitous) use of the F-word:

The Daily Show With Jon StewartM - Th 11p / 10c

Mumbai Tragedy

Barack Obama Interview
John McCain Interview

Sarah Palin Video
Funny Election Video

Any doubts about the Daily Show? John takes Chris Matthews, Keith Oberman and MSNBC to task:

The Daily Show With Jon StewartM - Th 11p / 10c

MSNBC Replaces Fox News

Barack Obama Interview
John McCain Interview

Sarah Palin Video
Funny Election Video

Ants!

This is a cast of of an ant nest. Pretty cool!

In an effort to explore scientific issues in my blog I am going to try and blog about social insects on Tuesday and choanoflagellates on Thursdays. I will intersperse other science if it catches my attention, but as an exercise I am going to give this a try. I think ants are truly amazing. With a diversity of social structures they really cast human societies in a new light. Darwin, in the Origin of Species, described several ant societies that contain slaves. Slaves! How crazy is that but more about that in the future. There is also evidence for teaching and learning in ant communities. To start things off I point in the direction of an interview of E.O. Wilson, the father of sociobiology, by Andrea Seabrook (who I find kind of annoying, but Wilson is great.)

A couple of "New Rules" from Bill Maher

New Rule: Stop saying that we've overcome racism just because we've found a qualified black man and elected him president. Everybody knows we won't have true equality until we elect a dumb, unqualified black man. [slide of Bush doing African dance]...

...And, finally, New Rule: The rest of the world can go back to being completely jealous of America. Yes...our majority white country just freely elected a black president; something no other democracy has ever done. Take that, Canada! Where's your Nubian warrior president? Your head of state is a boring white dude named Stephen Harper. And mine is a kick-ass black ninja named Barack Hussein Obama!

That's right, everybody. I take back every bad thing I ever said about the good old U.S.A. I've gone from "God damn America" to "God damn, America!"

I feel like a hockey mom at the state fair getting felt up by Hank Williams Jr. While fireworks go off and Jesus appears in my cotton candy. It would be stupid not to be stupid about it.

So, I'd like to take this moment when we've finally got one right, to bask in a little unwarranted, unapologetic, irrational, faux patriotism. Or, as Fox News calls it, "regular programming."

Now, I might regret this. It's kind of like going grocery shopping when you're high. But, here goes, world...[with patriotic music under]

We're Americans. We built the Golden Gate Bridge and Hoover Dam and Joan Rivers. We're the only country that can look at a sandwich made of ice cream and chocolate cookies covered in fudge and think, "Ah, you think we could fry that?"

And you know what? YES, WE CAN!

They may have 72 virgins, but we have 31 Flavors.

You know what our favorite burger topping is? Another burger!

We invented rock 'n' roll, jazz, funk, R&B, and hip-hop. Without our music, your iPods would be filled with ABBA, Menudo and Men At Work. And you wouldn't have iPods.

Not only did we create the Internet, we're the ones who filled it up with porn.

Jefferson lived here. And Miles Davis and Mark Twain and Frank Lloyd Wright and a lot of other people Sarah Palin never heard of.

In America, strippers and Disney stars have an equal right to be named "Hannah Montana."

And I was freely able to make a movie saying there's no afterlife, and you could watch it while eating crap that'll kill you. But, that's okay, because our corn-fed high school sophomores are bigger than your soldiers, and they're better armed.

I ask you, in what other nation would they tax young people to make sure old people can afford erections?

What you call "football," we call "soccer." And what you call "war crimes," we call "football."

So, let me just say it again: we elected a black guy, and it was because he was the best candidate. Not because it was some cheap gimmick. And we should know, because we are also the country that invented cheap gimmicks.

Yes, America is like Jessica Simpson. Sometimes it's so stupid it embarrasses you, but, on the other hand, how about them titties?!

Godless Sodomites Unite!

On The Media, an NPR program, did a story on "new atheism" this week, you can listen to it here:



It is pithy and interesting, as are most stories from OTM. Now, I am not sure I like the idea of proselytizing, but I do see myself aligning with the "new atheists" and when asked (or not asked) advocate for a secular world view. That said, I am not sure the best way to advocate for secular world against a rolling religious juggernaut. As mentioned in the article it's self, organizing atheists can be like herding cats (no doubt a function of their embrace of evidenced based methodologies and aversion to dogma).

If you are interested in the out campaign you can find out more about it here.