Wednesday, January 30, 2008

Nothing today

Thinking today. No post.

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Links of Interest
The Hobbit really is a new species.
Can autism be prevented?
Does a woman's monthly euphemism contain stem cells?
Exercise helps your DNA.
Wash those hands!
Welcome to the Anthrocene.
Mercury, the latest frontier.
Wolves in Canada.

Science Fiction and the 2008 Race for President

My first introduction to race came when my family moved from California to Alabama in August of 1964. We were walking down the street to pick up a bottle of wine. My Dad had been out of work for a year. We were so very happy. I was practically dancing down the street. I turned into the package store ahead of my folks and stopped, confused.

The counter was in one side of the room. The rest of the room was open so people could line up to get whatever liquor they wanted. In the middle of the room, dividing the counter in two, was a metal railing. Blacks were on one side-- the side I had entered-- whites were on the other. Both sides were looking at me.

My Dad reached in and pulled me out. He pointed to the label on the doorway I had entered: Colored. I had reached the segregated South.

I've been trying to wrap my head around this ever since. Sometimes I've written about it explicitly as in my story, Stegosaurus Boy. Other times, aliens, gorillas and mystical beings have been stand-ins for aspects of this black and white conflict as I've tried to take it apart and understand it.

In science fiction and fantasy there is this recurring motif of a character who is destined to bridge gaps between peoples. Like the devil it goes by many names. In Star Wars, there is a prophecy of a Jedi who will bring balance to the force. In Fritz Lang's Metropolis, perhaps the greatest science fiction film ever made, Freder, the son of the ruler of Metropolis, is destined to bridge the gap between the elite and the low born workers. In LeGuin's The Dispossessed, Shevek, a physicist, spends his life trying to unbuild walls between the populations of Anarres and its moon Urras. In Cordwainer Smith's Norstrilia, a boy who manages to buy the earth also becomes a big part in the unification between humans and underpeople, though this happens generations later. Sometimes this destiny is foretold, such as in Metropolis. Sometimes it arises out of character, as in The Dispossessed. My own story, Stegosaurus Boy, takes place over the summer of 1964 when the Civil Rights workers were killed in Mississippi and its impact on a boy who loves fossils.

So, I'm driving in today and I'm listening to an NPR article on Barack Obama in Kansas, how he has departed from his normal stump speech there and instead is drawing a picture of his heritage. I was struck by the shape of his life-- born into a family where the father leaves at an early age and he's raised by a single mother. This is a leitmotif of the African American experience. But in this case, the single mother is white.

In the article he singled out his white cousins. Now, you have to understand that one idea that was drummed into me in Alabama is how one drop of black blood made you black. The power of black ancestry trumped all other considerations. People have been known to murder an unexpected black child or murder the mother. I had come to measure the level of integration within a community by observing how many mixed couples I saw.

Yet here is this seventy-one year old white woman enthusiastically claiming a relationship with this young black man.

Tavis Smiley, among others, have question whether Obama is "black enough". I think they have missed the point the way they misunderstood the idea that a white man pushing for Civil Rights (LBJ) might in any way tarnish the legacy of Martin Luther King. They way the Clintons misjudged their political moment and tried to paint Obama with the Reagan brush only to watch it detonate in front of them. The way that people have said the Obama candidacy isn't about race.

It's all about race but it's not about the divide. It's about uniting, as Americans, toward a common destiny.

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Now for something new: Links of Interest
Change in Climate Patterns: one of the last nails in the coffin
Sea Lions Slaughtered in the Galapagos: Environmental issues are political at the core
Goal Associated Neurons Demonstrated: This is your brain using a tool. This is your brain using a tool to do something.
Chameleon Color Change: Not necessarily just to blend in.
Internal Cell Clocks: Matching an organisms circadian rhythm to cellular rhythms.
Boosting African Soil: Managing the earth is more than just protecting whales.
Squirrels are Smarter Than You Think
Pouting Kills: Go out there and fight with your spouse.

Monday, January 28, 2008

The Intelligent Self Interest of Frogs

There's an old story about cooking a frog. If you put the frog in the water and heat it to boiling, the frog will placidly die. But if you drop the frog into boiling water, the frog will immediately jump out. I have no idea if this story is true or not or if that's even the best way to cook frogs or why one would want to cook a frog in the first place. But the metaphor is still valid: gradual changes are more difficult for humans to perceive than immediate changes. And, I submit, harder for humans to even acknowledge.

This is especially true in climate changes. Most of the world has decided that, oh, thirty years of science is probably correct. (See here and here, for example.) Recent events have put some interesting wrinkles into the whole process. For example, one of the impending problems of global warming is the raising of sea level as the world glaciers melt. The December Scientific American and the work from the NASA Earth Observatory program have pointed out the glaciers don't have to melt to cause the problem. If you take a glass of water and measure the water level in it, then drop an ice cube in the water, the water level rises. If you then mark the new water level and wait for the ice to melt, the risen water level remains the same. The ice displaces the same amount of water whether it's melted or not.

Similarly, if glaciers roll down hill into the water without melting, they raise the sea level the same as if they melted into water. The difference is that it takes an enormous amount of heat to melt the glacier and considerably less to get it sliding. Turns out that one of the brakes on glacier movement is the ice shelf in the ocean that the glacier piles into. All across the world, the ice shelves are breaking loose resulting in glaciers on the move. How this changes the model of global warming and the timing of sea level rise isn't clear. (What's the effect of cooling the ocean with a few billion cubic feet of ice?) But the Greenland glaciers and the East Antarctic Glaciers comprise together about 50 feet of sea level rise. The West Antarctic Glaciers comprise about 170 of sea level rise. (December Sciam article, here.)

My friend Erik makes the point that there have been previous, and potentially warmer) global warming events. This one is different in that we have control of the source but the others were not of human origin. Consequently, if we live on this planet long enough, we will have to deal with managing a global warming event. That means figuring out a way of sequestering the CO2 (or methane) that is in the atmosphere. He views the global warming we're causing as perhaps a good thing. We're not going to stop putting CO2 into the atmosphere. Therefore, when we finally become a boiling frog, we're going to have to get it out of the air somehow. I think he's overly optimistic but he does have a point.

There have been a lot of CO2 sequestration solutions put on the table in the last couple of years. Most of them involving pushing the CO2 into a new spot such as empty oil fields or other places or enhancing the uptake of CO2 by plants, such as forests or plankton. One interesting article suggested the "greenness" of ethanol, even in switchgrass plantations, might be suspect since it may involve the destruction of forests. Leveling a forest that takes up a few million tons of CO2 to create a plantation that takes up only a few hundred thousand tons of CO2 could be considered a bad deal.

A couple of bright notes have showed up, however. The big terrestrial CO2 uptake systems are equatorial since growth can happen all year long. Temperate forests are net CO2 sinks in the summer but when the forests go dormant they become net CO2 sources. Another NASA Earth Observatory article notes that one CO2 effect is to push off fall. This has the result of longer uptake of CO2 by temperate forests.

Another interesting idea is coming from outside climatology and instead comes from the continuing question of how to date sedimentary rocks. This article again comes from the NASA Earth Observatory. At issue is the rate of Calcium Carbonate crystallization. CaCO3 is a stable form of Carbon. In fact, it is stable enough that fossil CaCO3 is found all the time in the form of marine organism shells and is the most abundant single mineral on earth. Scientists studying the mineral in Yellowstone found that CaCO3 crystallization occurred twice as fast in the presence of microbes.

Now, to my thinking, this is a vastly superior method of sequestering carbon than pumping millions of gallons of carbonated water into used up oil fields. It does push off the problem (so do other methods) in that over geologic time carbon that is carried into the earth comes out again. But, as Erik said, we are going to have to deal with that eventually.

Go thou, scientists. Industrialize those microbes.

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Note from last post. My wife read about my two readers and asked who my other one was.
*sigh* I get no respect.

Tuesday, January 22, 2008

The Intelligent Self Interest of Evolution

Both of my readers have no doubt figured out that I strongly believe in evolution and have serious issues with creationists.

After the Dover decision one would think this would be a done deal, right? Not so. After all, defeat is not an option when you're working for a higher power. Florida is the current battleground, though Texas may not be far behind.

In reading the science blogs and articles this week, it came to me suddenly in a blinding flash of light, like unto riding towards Damascus, that the creationists did have one leg to stand on. Sure biologists can get an interesting take on the intelligence of whales by studying how all the evolutionary pieces fit together, but, really, of what earthly use is the knowlege of evolution? After all, at the end of the day the Creationist can bask in the Cosmic Background Radiation of God's creation but the evolutionary biologist has to trudge over to the next lizard/beetle/fern and reclassify it. Where's the emotional satisfaction? What can we use evolution for?

Well, one way is the prediction of disease propagation and the evolution of antibiotic resistance. But that's kid stuff. The creationists dismiss that as "microevolution". Macroevolution, the creation of new traits in higher orders of creatures, can only be the province of God.

Back in the 90's, it turns out, a term was coined by Nesse and Williams came up with the term Darwinian Medicine. This term is still in use but the term Evolutionary Medicine appears to have replaced it. This approach essentially takes the view that medical conditions have both a circumstance that is observed clinically and an evolutionary heritage that defines how it arose and how it behaves. In other words, we can't truly understand a condition without understanding how it arose.

A couple of diseases are already well known in the respect: sickle cell anemia where the red blood cells can't maintain their lovely circular shape and collapse into crescents that resemble sickles. SCA arises when an individual gets two copies (one from both parents) of a particular gene. However, when the individual gets one copy, resistance to malaria results. Therefore, there is a selective advantage to carry one of the genes but not both. Similarly, if you have both genes for phenylketonuria (PKU), you can suffer from mental retardation. Yet, if a baby has only one of the genes, it's less likely to be miscarried. (See here.)

Here are a collection of Darwinian (or Evolutionary) Medicine articles:
Evolutionary Explanations in Medical Courses
How is Darwinian Medicine Useful?
A New Germ Theory
Dr. Darwin
Evolutionary Medicine for Veterinarians
Evolutionary Medicine and Cancer

But (*sigh*), my whole argument is somewhat specious. The reason people don't like to believe in evolution has nothing to do with its use. Creationists are not stupid even though they are not using their intelligence. Not even Ben Stein is immune. As Larry Niven said in Protector: Intelligence is a tool that is not always used intelligently.

Which, given the evolutionary Rube Goldbergian genius that is humanity, should not be surprising.

Friday, January 18, 2008

Lady Liberty and the Seven Dweebs

I'm coming to the conclusion that Mitt Romney is the Republican version of Hillary Clinton and Hillary Clinton is the Democratic version of Mitt Romney. Both of them are going for the standard party image. Is Romney with his clean cut ways, purity of values, religious but not too religious and government for the sake of business, really so different from go for Labor, tough leadership, woman and gay powered Hillary. Neither of them is particularly trustworthy. Both of them are politicians to the core. If Detroit made candidates the way they made cars, both Romney and Clintion would be in the showroom.

Then, on comes Huckabee. We should not be enabling (i.e., forgiving) of those who went out and got bad loans. They have to live with their bad decision. One wonders if other people who made bad decisions, like marrying an abusive husband, should also be denied legislative relief. Of course, those decisions don't involve money.

For Obama: do you really one a guy with so little experience that close to the Big Red Button? The president has to do more than talk about hope and give out promises. He has to be willing to take the heat for good and bad decisions. I just don't see Obama with those kind of stones.

As far as Edwards is concerned, he's like Wal-Mart Hillary. He's going for a serious democratic base. Of 1945.

McCain has the stones. But there's the Big Red Button again. I have every faith that he would tell me in no uncertain turns why he had to push it. I trust his judgement. I just don't trust the values upon which that judgement is based. Not to mention he put his integrity in hock when he supported Bush back in 2004.

Guiliani. Will do for the country what he did to New York. That's the good news. The bad news is no other part of the country remotely resembles New York. And if I dont' trust Obama or McCain with the button, I'm sure not going to trust this git.

Who does that leave? Some dwarves in coats, I think. Can't remember their names.

Bad luck that one of them is going to get elected. Thank goodness for the separation of powers in the US Constitution.

Oh, yeah. Bush destroyed that.

Romney Rhetoric

Every election cycle we see two kinds of rhetoric reappear: 1) Let's run government like a business and 2) Don't elect Tax and Spend liberals/democrats whatever. Both of these statements are demonstrably false and, depending on how they're phrased, range from the misleading to the deceptive.

The most recent foray of this sort have been the Mitt Romney ads. My state, Massachusetts, had the silly stupidity to elect this clown to office. Romney is on the same wavelength as Reagan was when he was governor of California and the only reason he didn't cut the same sort of swathe of destruction here was a very democratic and powerful legislature. Now, he's taking that show on the road. One thing's pretty clear: it's very unlikely he'll manage to carry his own state in the primaries which shows how bankrupt his ideas are up here.

The first idea, that you can run government like a business, is absurd. Government is, in part, the catchall of all necessary society activities that business doesn't want. Pony up for roads and bridges? Well, business is ready to take your money to do it but it's not about to pay for it on its own.

Government's job is infrastructure: the water in which we swim. It is intended to maintain the environment in which we all operate. Schools, hospitals, financial mechanisms, transport-- all of these have a base infrastructure upon which they operate. Many corporate systems have an investment in people not understanding this. Big Pharma, for example, likes to publicize how much money is spent bringing a drug to market. This is one way they can justify the high cost of drugs in the US. What they don't publicize is the science behind the drug they choose to bring to market is often funded by the NSF or NIH and that a sizable portion of that process is preparing the market for penetration in the form of advertising and physician junkets. Not that clinical trials are cheap. They aren't. However, many of them are administered in other countries where either regulation is less or the health system is publicly subsidized.

When infrastructure is put in the service of profit, bad things happen. My own particularly favorite example of this is for profit hospitals and public health.

Any system, be it an engine or an institution, must have enough capacity to manage the range of its required activities. If you need a car to be able to drive at eighty miles an hour, you have to build in that capacity. Even if most of the time you don't use it and putter around grocery store parking lots. A hospital is no different. If you require a hospital to be in a position to manage, say, epidemics, you have to maintain spare capacity. Spare capacity is expensive-- it means empty beds. Empty beds means less revenue-- anathema to a for-profit institution. For-profit hospitals, then, either downsize the hospital capacity to be in line with revenue or increase the available services to bring the hospital up to capacity. The result, as we've seen in the last couple of decades, is that even minor epidemics of flu or other viruses swamp the hospital system.

Private enterprise isn't going to pick up an activity just because it's societally good. Capitalism is amoral and expecting moral behavior from it is a lost cause. That's where government comes in and creates an environment where the morally blind engine of capitalism operates in a moral environment. So: in point one, running government as a business means no government at all.

The next, closely related aspect of anti-government rhetoric is the tax and spend fallacy-- closely related to the big government, bad, little government, good, fallacy.

First, let's remember what government actually does: not much. There are very few agencies that don't operate through government contractors. The SEC, FDA and FAA are all independent agencies but even here significant private contractors contribute heavily. Consequently, the expense of government is, in part, the responsibility of those contractors.

The federal government is more efficient than you might imagine. The first line item in the federal budget is servicing the national debt. The second one is the defense department. These two are followed by the special appropriations for the war in Iraq. The first line item that pokes up after these are entitlements such as Medicare, etc. DHS is down in that area. Everything else the government does must use what's left. When I did this exercise about eight years ago, the entire meaningful budget of the US government was about 300 billion dollars out of a 1 trillion dollar budget. To get some perspective, Citigroups assets as of 12/31 this year was reported to be 2.2 trillion dollars. I defy any corporation to do what the federal government does on that kind of money.

There is a true tax and spend problem but it is not what is being referred to in the rhetoric. It is best exemplified by Mitt Romney's term here in Massachusetts. It goes like this:

Step 1: Get elected on reducing taxes and downsizing government. Usually, this involves pointing at some financially trivial but emotionally disturbing waste of money.
Step 2: Downsize those portions of infrastructure support over which you have control. This often includes, as in Romney's case, roads and bridges repair or other unnecessary governmental activities.
Step 3: Move on to higher office or the private sector and use your time of Step 2 as a symbol of your success.
Step 4: Vilify your successor (or other similar successors) for "taxing and spending" when they attempt to repair what you've left undone.

It's a great system.

Wednesday, January 16, 2008

Martin Luther King, LBJ and Revisionist History

I couldn't quite believe the flap over what Hillary said the other day about LBJ and the Civil Rights Act. It all felt like some strange and lumbering dream. You know the kind: you're being chased by an ice cream truck filled with killer clowns brandishing deadly pistachio cones and you can only run away in slow motion.

You haven't had that dream? Maybe it's just me.

An in-depth picture of Martin Luther King, Jr., is here. An in-depth picture of LBJ is here.

What Hillary said was: "Dr. King's dream began to be realized when President Johnson passed the Civil Rights Act. It took a president to get it done." (See here.)

MLK was inspirational. He was a civil rights leader. He was an activist in the Mahatma Ghandi tradition. No question there. And, like Ghandi, he relied on the conscience of the oppressors to be pricked by his actions. MLK first really started to show up in the national news during the Montgomery Bus Boycott of 1955 which led to the Supreme Court upholding the lower court decision that Alabama's segregation laws for buses were unconstitutional.

LBJ was an old school politician from Texas. Who had, it turns out, been working within his party for civil rights legislation long before he became president. As majority leader, LBJ was responsible for the passage of the 1957 Civil Rights Act. He brokered a compromise that weakened the bill but ended a filibuster. To say that LBJ came to civil rights de novo as president only after MLK's inspiration denigrates what LBJ did. It's possible the boycott had some influence but since Eisenhower proposed the bill Southern Senate Democrats opposed it, I'd say the MLK influence was minimal though the influence of the boycott might have been present. MLK just wasn't that big a blip on the national radar screen at that time.

The response to Hillary's statement clearly has nothing to do with historical accuracy and everything to do with code words and mythic perception.

I'm not a fan of Hillary for lots of different reasons. And I tend to like Obama but mistrust his judgment on a national stage.

But I do feel that when we engage in debate we discuss things honestly. The implication Hillary makes is that she's Johnson and Obama's King. Well, Hillary is no LBJ and Obama is no Martin Luther King. That should be obvious to anybody not blinded by rhetoric.

Did Hillary put down King's role? I don't think so but then I'm an aging white guy. I'm not going to be terribly sensitive to it if she did. Was it a terribly stupid statement? It sure was and is just another feather in a achingly heavy pile of items weighing against her.

But I think the problem is deeper and bespeaks a misunderstanding of the nature of power.

A few demographics. In 1965, the census document 10.8% of the USA was Black. While many of the deep south states had majority African American populations after the Civil War over the first part of the 20th century, much of the population moved north. In Mississippi, for example, the percentage that moved was enough to take the African American population from majority to minority.

My point here is the demographics did not favor African Americans in an oppressed country by the 1950's. First, they were a minority across the national stage. Second, they were a minority within state boundaries. Third, the money, weapons and political power were controlled by the white majority.

King knew this. He realized that there was no way of winning a war of power between whites and blacks: whites held all the cards. There was no way African Americans could win power from the white majority without the cooperation of the white majority. This was not South Africa where the whites were outnumbered 10 to 1 and held power by terror and force of arms. Whites here used terror and force of arms, too. But the biggest weapon they had-- and still have-- is numbers.

King also understood the odd idealism of the US. It's not sufficient to rule by majority. Both the demographic and power majority and the demographic and power minority must come under the same laws. He used Ghandi's technique to bring this hypocrisy to the white majority's attention. Both King and Ghandi realized that while force of arms could not prevail, conscience could provided the cause was just.

This, then, becomes the calculus of the civil rights era: King, triggering the conscience of the oppressors, who could not be dislodged without their cooperation. LBJ, acting from his own conscience and utilizing that triggered national conscience, enacting that change. Neither could have acted without the other.

LBJ was a southern politician all his life. He lived and breathed politics. I think it's probable there has been no other single individual that understood the American process any better. LBJ is rumored to have said when he signed the 1964 Civil Rights Act, "We [the democrats] have lost the south for a generation."

He was wrong. The democrats lost it for far longer.

Monday, January 7, 2008

Rube Goldberg Uber Alles

One of the continuing staples in the Creationist/Evolution debate is the Watchmaker Hypothesis. Briefly put, it says whatever is under examination at the moment (species, biology, stars, the universe, etc.) is far too complex not to have been designed. I'm not discuss the fallacy of this argument but instead go into its symbolism.

Back when I was in college, one of my professors suggested that God is the black box in which you put your lack of understanding of the universe. His thesis was as human beings understand more, the size of the black box decreases and, therefore, the role of God in the universe decreases. Daniel F. Galouye even wrote a book, The Infinite Man, that dealt with a similar concept where God starts out pushing every photon in the universe at c and just starts getting tired.

The point I'm getting at is the concept of a simple universe versus a complex universe is a human construction. Since we have difficulty handling complex tasks we presume that a complex universe must derive from something higher. A self-organizing complex universe is difficult for us to comprehend.

A good example of simple thinking versus complex thinking is how we look at the greenness of biofuels. Matt Ford, over at my favorite blog, Nobel Intent, talks about some recent evaluations of biofuels and how they are not as green as you might think. Another is brain function. We think we know what the brain is doing. Hey, it's a computer, right? But we really don't know that much at all, as Chris Lee points out here.

Often in engineering we talk about the KISS principle: Keep It Simple, Stupid. Systems that are more complex than they need to be for the task at hand are referred to as "Rube Goldberg" systems, after a cartoonist that created bizarre solutions to simple problems.

This is not because "simple" is the best solution but because "simple" is often either easier for us to understand or cheaper to implement, or both. Simplicity is often considered a virtue: "Tis a gift to be simple", as in the Shaker hymn, or "The Simple Life". We glorify simplicity as a virtue in and of itself rather then as an artificial means of managing ourselves. Simplicity, in these contexts, is really a realization of our difficulty and limitation, not a goal by itself.

One of the problems people have with science in general and biology in particular is that the closer you look at things the less simple things are. We used to think of atoms as indivisible. But now we know they are. Then, we had a simple proton/neutron/electron model. But it didn't take too long for that model to fall apart. Then we had the Standard Model of quantum physics-- what drives most particle physics. Of course, that falls apart when gravity is introduced.

Similarly, we had all sorts of nice models of biology until Darwin came along. Some of them had God driving the works from afar, some had him pushing every animal behavior everywhere. But we were, of course, on top and the only divine creation with free will. Like most things in the world, things became less simple. Darwin came along and created a model where God didn't have to be there: things could self-organize.

Prior to Einstein and other early 20th century physicists, light was considered a wave. It certainly behaves like a wave: it obeys the inverse square law, it reflects, there are angles of refraction, etc. All of which can be modeled in a wave tank with water ripples. But physicists couldn't imagine a wave propagating without a medium to propagate within. So they invented the aether: an undetectable medium in which light propagated. There were some experimental problems with this model. Einstein came along and presented a model in which light needed no medium in which to propagate. Aether may or may not exists but it was no longer needed to describe light propagation.

Darwin did something similar in biology fifty years previously: God may or may not exist but we certainly don't need Him in order to explain biology. Or geology. Or other things. The modern view of living things is that they are self-organized mechanisms that have no internal mechanisms that are intrinsically different from non-living things. We came from the dust and to the dust we shall return and, by the way, the same mechanisms that operate in dust operate in us, too.

To accept this, however, requires an understanding that living systems (or any other natural system we look at) is a complex system and not simple. Living systems operate by the same chemical laws governing non-living systems but those chemical laws are functioning together in a vastly more complex way. And, since they evolved, they show relics of ad hoc, roundabout solutions that are far more reminiscent of Mister Goldberg than an elegant God.

So: to understand the universe we have to give up simplicity. Or, at least, recognize that any simple representation of any part of the universe must be an abstracted and flawed view.

I submit that the view of systems, be they biological, physical or political, as complex must become a world view. Simple solutions are suspect. Complex solutions must be proven. Rigor in thinking must be preserved. And Rube Goldberg must be recognized as contributing engineer.