Wednesday, December 14, 2011

Depression Wednesday

Found this quote from Bruce Bartlett, a former Reagan advisor and a Treasury official under Bush. Here's where I found it.

Here's the quote.
Basically we’re still stuck in the situation we were three years ago and we haven’t made any progress at all except that our problems are much worse because of political reasons, because we now have a crazy party in charge of one of the Houses of our Congress and they won’t allow anything to happen because it’s in their vested interest to make things worse,” Bartlett explained in his typically exasperated way. “Plus they have a theory that is completely nuts…. I’m very depressed. I’d love to see some program like this [paper] enacted. I see zero chance of it happening. The most we can hope for is that a complete crazy person like Newt Gingrich gets the Republican nomination, the Republicans lose so badly that they lose control of the House and don’t get control of the Senate and then maybe in a year we can finally talk about doing something rational such as what is discussed in this paper.

Sunday, December 11, 2011

What might be over there

(Picture from here.)

The news last week, among other things, is Kepler-22b, a planet about 2.4 times the radius of Earth orbiting a G-type star, Kepler-22.

Kepler-22 is about 600 light years from her. Kepler-22b appears to be orbiting in the habitable zone: the orbit around the start that gets enough sunshine to neither turn water to steam nor to freeze it utterly. It is/may/possibly be/we wish it were liquid water.

Why? Because liquid water is one of the prerequisites for our kind of life. Not that life that isn't ours isn't possible on some of the other planets found by Kepler. Just that with only a sample number of 1 we don't have much to compare it to.

We don't know the mass of the planet simply because of the way Kepler finds things. It looks for a blink in the star it's looking at to determine that something passed in front of it. Hence, we have an idea of Kepler-22b's size but not what fills it.

There's a good article over at Life Unbounded that discusses what it might be. It might be pure rock, pure ice, pure iron or a mix-- like our lovely home. If it is like our planet, things are going to be much heaver. Volume, and hence mass, is a cube function not a linear one. An increase of radius of 2.4 doesn't make the mass 2.4 times earth. If Kepler-22b were only made of rock and ice, it's gravitational pull would be about 5 times earth. A mix of ice and rock gets you 10 times earth. If it were like earth the pull would be better than 40G! But for arithmetic convenience, let's postulate it is of the composition that there are only 10Gs on the surface. Your average couch potato American Super Bowl watching male will weigh 2000 pounds, not 200-- more than a Holstein or a small rhinoceros.

Let's wax speculative for a moment. Let's say mammalian life evolved on Kepler-22b. That would mean a relatively modest size animal, such as a human, would have to have skeletal and musculature systems beefed up to be comparable to cattle. It's certainly possible-- cattle do quite well. But what would that mean?

Think about land vertebrates. They would have to either evolve these load bearing structures early or they'd never get on land. Let's start with salamanders, an early land vertebrate. If you look at a salamander the arms come into the body structure at nearly right angles. Earth's really huge salamanders would have required significant musculature around the shoulders to lift themselves off the ground. Or they could have just dragged themselves around.

Now, take that ancient 200 pound salamander and make it 2000 pounds. It's not moving, dragging or otherwise. I have a strong suspicion that land based animals would have significant difficulty. Flight might well be evolutionary impossible. I suspect verticality would be problematic-- humans would be on all fours and not have much chance to develop hands.

But that line of speculation only suggests that the evolution de novo of such structures on land would be difficult. Not impossible-- living systems manage many things. Just our kind of mammalian life being so suited to the conditions that birthed would have difficulty evolving the same sort of adaptations under such heavier gravity.

But let's go to the ocean.

Two things immediately leap to mind for ocean based life on Kepler-22b. For one thing, the gravity problem drops away. Archimedes pointed out that buoyancy is a function of how much water something displaces. If you displace 1 gallon of earth water you get a buoyancy of 8 pounds. If you displace 1 gallon of Kepler-22b water you get a buoyancy of 40 pounds. Of course, there's 5 times more pressure on that empty gallon jug so it would need to be stronger. But water is incompressible. That's why fish can go up and down the water column easily.

We can presume that we have aquatic life if there is any life at all.

Pressure changes would be much more rapid. On earth, we get about 33 feet/atmosphere. That means if you go down 99 feet you are under 4 atmospheres of pressure: 1 from the surface + 3 for the depth. On Kepler-22b that would be much more rapid: 1 atmosphere every 3.3 feet. However, that's an earth atmosphere. About 14.7 psi/atmosphere. I would expect surface atmospheric pressure on Kepler-22b would be significantly greater. I don't know how much.

Regardless, the pressure gradient in the ocean would be significant. This would completely change the ecology and physiology of marine life. We know there are some pretty strange animals living down about 5000 feet. On earth, that's about 152 atmospheres. Light does not penetrate down that far so animals have two big issues to face: no photosynthesis and pressure issues.

On Kepler-22b we get the same pressure at 500 feet. Much, much closer to the surface. Many animals on earth manage quite nicely migrating from the surface down to that depth and return, though whether they'd be able to withstand the pressure gradient on Kepler-22b is open to question.

Kelp can grow as deep as 200 m-- around 180 feet. This relationship between depth and growth is purely defined by how much light is received by the organism and is independent of pressure. We can imagine that our Kepler-22b kelp beds are surviving under 56 earth atmospheres of pressure rather than a little over 5.5.

So, Kepler-22b's attempt at vertebrate life would give us some surprises. Ocean life, maybe not so much.

We can forget marine mammals, icthyosaurs, plesiosaurs, seals and sea otters. All of those animals started on land and made the return. If a land animal actually evolved and returned to the sea, it would carry with it the characteristics that made it successful on the land. Kepler-22b's dolphins aren't going to look like ours if they happened at all. There would be too much differing heritage.

But advanced organisms can evolve in the sea. We have cuttlefish, tuna and octopuses, all of which are very bright. If/when we get to Kepler-22b we might find cultures based around them.

My money's on the cuttlefish.

Friday, December 9, 2011

Sunday, November 27, 2011

Consideration of Works Past: The Green Rain

Usually, I talk about science every two weeks. But the turkey tryptophan is still coursing through my veins and I can't face it. So I'll wax literary for a bit.

Over the past few years I've been re-reading works that I found interesting and provocative back when I was a mere babe. (You can read previous ruminations here, here, here and here.)

The Green Rain was published by Paul Tabori back in 1961. It's a short book-- barely 70,000 words, if that. It's premise is simple: there's a mistake with a chemical missile and something goes wrong. The chemical seeds the clouds. It rains and the result is that everyone caught in the rain turns green. General hilarity ensues.

Well, only if you count political destruction, death and riot as hilarity. Perhaps I have a skewed sense of humor.

There were a lot of odd books written in the sixties and seventies, many of them better known. The Muller-Fokker Effect by John Sladek, for example. Adam M-1 by William C Anderson. Rally Round the Flag, Boys! by Max Shulman. Most of these works were fairly light even though they might be handling fairly dark material.

The Green Rain reads like a bitter, eloquent Ron Goulart at the height of his powers. It opens with a quote from one of the characters, a bitter old professor named Pelargus, who says "Something goes wrong. It always does." Then, it wanders over to a satyric biochemist who has created "chlorophylogen", a chemical precursor to chlorophyll. It has the property of generating plant like behavior upon contact with light. NASA (the ISS in the book) decides to send a rocket to the moon to make it earth like. It fails in launch and returns to earth, seeding the rain with chlorophylogen. Something happens to the chemical in the return. It's no longer simple chlorophylogen, it turns human beings green.

You can't change the color of people's skin without dealing with race. Tabori does. You can't change skin color without political repercussions. Tabori gleefully traces the downfall of the cold war. You can't change skin color without religious overtones and you can't have a religion without con artists-- at least not in southern California. Tabori wanders over there, too.

It's a romp. Or, at least it is in the beginning.

Things go dark about half way through. It's not like Shulman or Anderson. There's no easy, happy ending. The bitter Pelargus may have the last laugh after all.

This is what fascinated me when I first read it long ago and it fascinates me still. Though the science is dated and the political world is different, there's a lot that still rings true in this book. There's a scene where a young actress discovers herself pure green and comes out screaming and then faints. When she wakes up her first words are "I'm going to sue for a million bucks!"

And we're off and running.

What's curious about this book, and some of the others mentioned, is how thoroughly vanished they are in popular culture. Certainly you can find them. All of the above books are mentioned in wikipedia and you can get used copies at Amazon. The internet never forgets anything.

The impact at the time of Sulman and Anderson was considerable. Tabori, less so, but he was well known. Almost none of these names are mentioned now.

It's what I call the Bret Harte phenomenon. If you've taken an American lit course, you've ran across the name. He was a contemporary of Mark Twain. However, now we remember Mark Twain and Harte is barely remembered. Now, I'm not saying Harte was as good a writer as Twain-- he was not. But he was worth reading and popular for a time. You can make a similar statement about William Saroyan or my own favorite author, John Dos Passos. Both brilliant writers and rarely read these days out of literature courses.

The Green Rain is a lovely little science fiction book that will make you think. Don't take my word for it. Go over to Amazon here and buy it. Read it.

We'll bring these guys back eventually.

Wednesday, November 23, 2011

Happy Thanksgiving

I'll be too busy preparing to, doing and recovering from stuffing my face for the next couple of days to put anything up.

But never fear. The Oatmeal is here.

Monday, November 21, 2011

UC Davis Spraying

I have nothing to say about this that hasn't been said. It's an outrage. I am reminded of setting dogs on protesters in the south in the 1960s.

However, if you want a real analysis of it go to James Fallows articles, here, here and here.

Simple Solutions

Gordon over at Gordon's Notes has an interesting discussion on handling ICU complexity: the checklist.

Sunday, November 20, 2011

Welcome to the Monkey House

I've been avoiding getting too political here. My last foray into that realm was back in 2008. Sure enough, both my readers were turned off.

But there's just too much crap being thrown around.

One nice place to read about is Wonkblog, Ezra Klein's recurring articles in the Washington Post. Unlike so many blogs he actually cites where he gets his facts and figures.

I like Klein's work. So let's look at them.

Paul Ryan's inequality plan increases inequality: This should not be a surprise to anyone above the intellectual level of a starfish since the Republicans appear to have a vested interest in such inequality. But, like Captain Renault in Casablanca, some people are shocked-- shocked!-- that it could occur.

Bush tax cuts are tripping up the supercommittee: ...and the Republicans are lying about it. What a surprise. What's interesting is his graph. If you look closely it and notice the debt without the tax cuts and the wars, the debt actually begins to decrease or stay the same, depending on how you look at it. But like a giant orange slug, the tax cuts crawl over everything.

Rick Santorum is right about Europe: In which we discover that in this country there's a tightly coupled relationship between father's earnings and son's earnings. This translates into the US have less upward mobility than, say, Finland or Canada. So much for the American Dream.

The corporate income tax in two charts: Corporate taxes range at close to the lowest point ever.

Land of Missed Opportunity: Little points along the way that we could have salvaged something. Anything.

The benefits of doing nothing: If congress does nothing, the deficit drops by $7.1 trillion over ten years. Deadlock now has my vote.

Go enjoy.

Saturday, November 19, 2011

Frank Miller, RIP... Sort of

Frank Miller was a mover and shaker in the comics world back in the 80s with The Dark Night Returns. TDNR was the equivalent of William Goldman's amazing Robin Hood film Robin and Marion.

Go to the link to learn about TDNR. The quick synopsis is that Bruce Wayne is 50+ and Batman is retired. He returns but given his age and the times it is purely a last hurrah. It was brilliant and strange. Age usually doesn't touch superheroes and it paved the way for several treatments of the superhero genre that included the passing of time.

Probably the purest legacy is Mark Waid's Kingdom Come.

Miller then went on to create the Sin City series which I found initially interesting. But graphic violence can only take you so far and I lost interest.

Well, Frank Miller has officially entered the community of Old Farts.

Miller put out this screed about the Occupy Wall Street movement. He thinks they are protesting the War on Terror.

You can criticize OWS for a lot of reasons but they are not attempting anything against the War on Terror. That is, unless you conflate the WOT with the wars in Afghanistan and Iraq. The two are not the same except in those who are either poorly misinformed or reflexively jerk up the flag like a frog in an electric current whenever they feel threatened. I suspect Miller falls in both categories.

I'm sad but unsurprised. Miller falls into that group of people who praise individual action as long as it doesn't happen. You can see this throughout his work: iconoclastic men who take matters and the law into their own hand when they see injustice. But when somebody actually does this it upsets the status quo and these same people are terrified. Miller goes so far as to suggest the OWS protesters join the military to fight terror. Which is fine if it had anything to do with what the OWS is trying to do. Anything at all.

I wonder sometimes if artistic success such as has been enjoyed by people like Frank Miller or Tom Cruise or others makes people a little psychotic. They get such enormous positive feedback they lose the ability to correct themselves and go off the rails.

A very good critique of the screed is by Tony DiGerolamo here.

I don't quite understand why the OWS movement pushes the buttons it does. I find it fairly hopeful if inarticulate. I hope it will make the transition from inchoate movement to political action much as the Tea Party did. The Tea Party was every bit as incoherent and odd as the OWS but it had an inherent authoritarian organizing principle that pleased some big money people who then co-opted them.

Where's George Soros when you need him?

Neat TED Talks

Some very cool TED talks came across my desk recently:

Friday, November 18, 2011

Thursday, November 17, 2011

Hitler was a Creationist

There's a really good analysis of Nazism, Creationism and Darwin here by Coel Hellier. Hats off to Jerry Coyne for the link over at Why Evolution is True.

The article specifically destroys the pernicious lie that either Hitler or the other Nazis embraced Darwinism or were atheists.

This spectacular untruth is spouted constantly by those who also lie about Christian persecution in this country.

Christians are not persecuted in this country. There is no evidence of it save in the tormented minds of the chronically paranoid.

Sunday, November 13, 2011

Signs of Life

(Picture from here.)

I apologize for this post being late. There were... technical challenges that had to be overcome.

Throw your mind back to any Star Trek or similar movie or television. The ship approaches a new planet. The captain says to whatever passes for a science officer: "What's down there?"

The SO replies: "Life signs, Captain."

Just what does that mean? What are signs of life?

We know there is something different about biochemical systems that are alive versus biochemical systems that are not alive. We don't necessarily have a good idea of what that difference is.

Can we in fact recognize it when we see it?

Martin Hanczyc has a TED talk here that talks about the line between live and non-life. He makes any good points including that living systems have to have containment and metabolism.

(Hanczyc rightly points out that living systems are hard to define and brings up the bugaboo about viruses not fulfilling the definition of life. My own feeling about viruses is that they are elaborate biochemical systems that parasitize living systems. I don't think they can be called alive. What they can prove is that natural selection can occur with biochemical systems that have independence from the underlying living systems. But that's another discussion. I think for our gross purposes we can neglect them.)

The National Research Council tried to derive some idea about how life can be identified that bears no relationship to our own. They came up with the following criteria: (This is all in the TED talk, BTW.)

  1. The system has to be in non-equilibrium: energy is absorbed by the system, used and waste materials/energy discarded. Living systems are, in effect, a turbine on the downhill slope of energy. If the turbine isn't moving the system is dead.
  2. Life needs to be in liquid form. Materials in the living system must be mobile. I quibble with the word "liquid" here. I think the mobility implied by liquid is what's necessary. Solvents allow materials to come in intimate chemical contact with each other, allowing chemical activity.
  3. The making and breaking of chemical bonds.
These are extremely general qualities and one could easily see a designed system meeting them. I would personally add in the susceptibility to natural selection but that may be quibbling.

We divide chemistry into two worlds: organic chemistry, based on carbon, and inorganic chemistry, everything else. This is sort of like the archaic view of life: vertebrates and everything else.

Lee Cronin is a chemist (TED talk here) that is interested in inorganic biology. He's posited three basic questions:
  1. What is life?
  2. Is biology special?
  3. Is matter 'evolvable'?
Where he gets interesting is that he's turning the process backwards and starting with question three: Is matter 'evolvable'? By this he means can chemical systems be induced to present the opportunity for natural selection.

Cronin believes that the physics of life is encoded into the rules of the universe in the same way as the physics of stars. He refers to life as a "flame in a bottle."

Cronin starts with the idea of contained chemical systems. He's been repeating Miller-Urey's experiment with multiple interconnected compartments with some interesting results. Now, though, he's been attempting to make synthetic biological systems without carbon. (See here and here. Paper here.)

He calls these "cells" iCHELLS: inorganic chemical cells. iCHELLS have membranes to contain chemical reactions. They have chemical processes and the ability to store electricity. He's interested in creating evolvable matter-- which, to his mind and my own, is the essential definition of life. In place of carbin he is using polyoxometalates. These are molecules made up of multiple metal atoms bound together by oxygen.

These compounds can form complex structures. Cronin points out that competition between molecules is also possible. If you have two compounds that can polymerize or otherwise form complex structures and those two compounds require the same root materials to do their magic, they are, in effect, competing for those resources against one another. The more efficient compound under the current conditions will "win." Changing the current conditions, such as changing temperature or pressure, can modify the selective advantage of one molecule over another.

This isn't life. But it does suggest that natural selection for biological systems may be a intrinsic reflection of the chemical selection between molecular systems. Cronin believes he may have "life" in two years. I think he's dreaming but we will see.

An interesting side effect of his work may be the creation of microscopic engineered complex systems. These won't be nanomachines but may be something I suspect will be more useful: micromachines: machines that operate in cell size domain.

So, if we subtract carbon from the equation, what's left? How do we detect life?

Enter Christoph Adami. (TED talk here.)

Adami is a professor at the Keck Institute of Applied Life Sciences. He's interested in simulating evolutionary biology with digital organisms. From this sprang Avida, a system that allows artificial organisms to compete with one another for resources. The organisms can change over time, allowing selection to occur and allowing the organisms to evolve.

Adami was approached by NASA to help them determine how to look for life. He boiled down the concept of life to ideas that were completely divorced from chemistry.

The TED talk is great. Please go watch it. In a nut shell, he had his little software organisms evolve and "metabolize" and then looked at the resulting environment outside of the organism.

Think about earth 4.6 billion years ago. It had a primordial soup containing concentrations of various chemicals. However, once life began the life forms exploited those chemicals, translating them to other chemicals. In a fairly short time the chemistry of planet earth changed.

Similarly, the resource environment of the artificial organisms could also be expected to change once life began.

The simulation he used had a built in mutation rate that could be tuned up or down. So if the "mutation rate" was tuned to maximum there was no retention of changes and nothing could be evolved. Consequently, the resource environment remained in the "non-living" state. As the mutation rate was dialed down, at a particular point "life" happened and the resource environment make a wild shift in a very short time.

Now, being an ex-biologist, I think he was looking at the effect of the inverse operation from mutation. He was dialing up or down the persistence of traits. Once that persistence reached a threshold level, life spontaneously occurred. This is an underlying concept in Cronin's work, too. Once the conditions are right chemicals become available to natural selection and once that happens they are alive.

The signature of life, then, is a recognition of a resource pattern that is not attainable without a living system, be it artificial, organic or made up of metal salts.

From the point of view of detecting life on other planets, this is both encouraging and disheartening. It's encouraging because it is an unequivocal sign of life: physical resource observations that can't occur without living intervention.

But it's disheartening, too. We could, for example, look at earth from some distance and figure out that it's not in equilibrium. The chemical signature of earth couldn't happen without living systems. However, that's not because there's anything special about earth. It's because we have enormous understanding and data about how earth works. We have vastly less knowledge about planets in our own solar system and almost no knowledge at all about exoplanets. Heck, we're seeing planets right now that we thought couldn't happen. How could we possibly look for an abnormal resource signature without knowing what a normal resource signature is?

For example, there's the problem of methane on Mars. Methane in the Martian atmosphere can only last about a year. Yet we see significant amounts of it. That means that something on Mars is making methane. On earth, we'd say that was the signature of a living system. That's where methane comes from here. But on Mars? We don't have a clue.

But life may be an inevitable quality of matter under the right conditions. Cronin said it as a hypothesis: is matter in and of itself evolvable?

I hope it is.

Friday, November 11, 2011

Insult Diplomacy

There's been a lot of yelling in Europe but you can't tell your insults without a scorecard.

Here's your scorecard.

Thursday, November 10, 2011

Scrat in Africa

You remember Scrat from Ice Age. Well, here's an independent film of Scrat in war torn Africa.

This one is strange. I'm not sure what to make of it.

Wednesday, November 9, 2011

Stupid vodka-shooting cat!

Deep in the wilds of the UK lives Adam, a man with an incredibly active (and audible) dream life. His wife, Karen, transcribes for him.

Hear him roar. Discussion here.

A few examples:
"Wow. I can't believe I got punched in the face by a cow! Those bovines have bad attitudes. Total bitches. Oh, that's gonna leave a mark."

"I've got some fabulous nail polish for that camel toe."

"You know, the world will be a much better place when we get to eat vegetarians. Furthermore, you get your five-a-day with one of those."

"So the prince and the mermaid lived happily ever after... Until the mermaid's brain exploded. The end."

"Okay, everybody! Anyone who hasn't eaten, put their arms in the air!... That's not YOUR arm! Stupid fucking zombies."

Tuesday, November 8, 2011

Fact Checked Rap

Baba Brinkman did rap on evolution here.

Monday, November 7, 2011

Politics and the Silly Season

A couple of articles have come across my desk recently.

From Gin and Tacos a nice analysis of why we might like some people pursuing their own self interests but not others.

From The Washington Post, an analysis of why the House of Representatives might decide to take time off of its busy schedule to reaffirm our motto is In God We Trust.

Some dynamite James Fallows (here and here) articles on how and why a majority in the Senate can't pass anything and how the party that is to blame (the Republicans) get off scott free.

Welcome to the Silly Season

Wednesday, November 2, 2011

News from the Book View Cafe

The Heiress Companion (regency romance)
Madeleine Robins
November 1, 2011 $3.99

ebook here.

Description: While Rowena Cherwood did not go around boasting of it, she had a tidy legacy from her parents. Free to choose the life she wanted, and unwilling to live with her overbearing aunt, she accepted a position as Lady Bradwell's companion.

A spinster of twenty-seven, Rowena gave little thought to marriage--until Lyn Bradwell, Lady Bradwell's long absent son, returned to England, their chemistry was immediate--and fiery.

Love was the last thing on Rowena's mind--or Lyn's. Lady Bradwell, impatient for her companion's happiness and her son's, wondered how long it would be before her companion and her son would open their eyes.

Bio: Madeleine Robins is the author of eleven novels, including five Regency romances; The Stone War; Point of Honour; Petty Treason; The Sleeping Partner; and The Salernitan Women. A native New Yorker, she lives in San Francisco

Copyright: 1981

Keywords: regency romance, historical romance

URL for the ebook:

BONUS: Madeleine Robins’ new Sarah Tolerance novel, The Sleeping Partner, is also available here.

Tuesday, November 1, 2011

Who Owns the GOP?

Expanded picture here.

Money. That's it, pure and simple.

James Fallows has a discussion here.

He's referencing Derek Thompson here, which is where the graph on the left comes from.

Rick Perry's graph is at left but the others are not much different.

You can see the tax advantage for millionaires is huge. That's the long blue line that makes all others invisible. No one else gets much or they pay more. Throw a pittance at the upper middle class because they vote and take money from the poor but make sure the rich get as much as possible.

Yeah. Of the people. Right.