Friday, September 30, 2011

Climatology and the Inquisition

Skeptic magazine has a good analysis of science, politics, climatology and right wing nut jobs.

Thursday, September 29, 2011

Ruins of Empire

Gin and Tacos has a good opinion piece here on the crumbling infrastructure and how it relates/is engendered by the distrust of government.

Wednesday, September 28, 2011

Life in Liquid CO2

Man, some things will live anywhere. See here.

Tuesday, September 27, 2011

What if we had no moon?

Good article discusses that issue here.

Monday, September 19, 2011

Why We Have Regulations

Here is China. Here is China without regulation. Any questions?

Sunday, September 18, 2011

Dinosaur Thermoregulation

(Picture from here.)

I spoke about thermoregulation a while back. Well, now there's an interesting way to figure out if fossil animals were endotherms or ectotherms-- maybe.

Every element has a unique atomic number-- the number of protons in the nuclues. Carbon has 6 protons. Oxygen has 8. And so on. However, the number of neutrons are variable within each element, each numbered by the atomic weight-- the sum of neutrons and protons in the nucleus.

There are 15 known isotopes of Carbon and seventeen isotopes of Oxygen. Many of these isotopes are unstable: they undergo radioactive decay over time. Carbon-14 is a famous member of this dysfunctional family.

Carbon-13 is one of the stable ones. So is Oxygen-18.

Now, let's talk about bioapatite.

Apatitite is a collection of phosphate minerals. Bio-apatite are phosphate minerals that are produced and used in biological systems. Hydroxylapatite, found in bones and teeth, is hard-- Mohs 5 hard. It's why when you bite down on the European walnut, the walnut breaks and not your teeth. But it's only Mohs 5, which is why when you bite down on the black walnut your teeth break and not the walnut.

The chemical process by which bones and teeth are built in vertebrates is highly conserved and fairly similar across tetrapod classes. Hydroxylapatite is used pretty much across the board. Couple this with the fact the teeth are so hard that often they are the only component of a dead animal that escapes decomposition. Teeth have therefore been used to discern diet, behavior and physiology of extinct species.

Now, they can be used to tell body temperature.

Hydroxylapatite has a chemical formula of:


There's no carbon present: Calcium, Phosphorus, Oxygen and Hydrogen only.

However, bioapatite has a crystal structure that contains carbonate:


This is a Carbon atom connected to three Oxygens with a net charge of -2. It turns out that 13C and 18O have a natural affinity to one another that is related to temperature. This is called isotope clumping. The amount of clumping of 13C and 18O together is directly related to temperature. Could you use this to determine an animal's temperature?

This was determined in 2010 by a lab in University of California at San Diego in a wonderful paper in the Proceedings of the National Academy of Sciences. (See here for the abstract. Here for the full paper.)

First they calibrated the ratios for various animals: white rhinos, Indian elephants, Nile crocodile, alligator, sharks, etc. This gave them a good understanding on what the ratio meant.

Then, they looked at fossil mammoth tooth bioapatite. The average temperature found for the mammoth was 38.4 degrees. The temperature found for the Indian elephant was 36.9. The error bars on each measurement was about 2 degrees so the difference between these two values is well within error. Since mammoths are 1) mammals and 2) related to the elephants, the similarity further served as evidence that the technique worked.

Now, a year later, Eagle and Eiler have extended that research into determining the 13C/18O in species that have no real modern analogue: non-avian dinosaurs. (Abstract here.) They used two saurpods, Brachiosaurus and Camarasaurus. The data indicates that the body temperature of these two animals ranged between 36 to 38 degrees Centigrade. This is similar to most modern mammals but 4-7 degrees lower than some models that scaled for body mass.

So, what does it mean?

There are several possibilities:
  1. The sauropods investigated thermoregulated and kept the temperature lower than our models suggested.
  2. The sauropods did not truly thermoregulate but retained significant heat by sheer body mass. Tuna and other large mass ectotherms have been shown to do this.
If the animals thermoregulated at a lower temperature than expected it means that the animals used some mechanism to cool themselves or just operated at a lower "setpoint." This does not appear to be the favorite mechanism as I read the literature but I'm at a loss as to why. The operating temperature of an organism is important. Often, proteins cease to function outside specific ranges. These ranges dictate the require temperature range of the animal. There's a reason a high fever can be fatal.

Non-avian dinosaurs have no close living relative so we don't have a biochemical analogue, such as birds or crocodiles, with which to compare them. We also no that somewhere in dinosaur evolution some dinosaurs developed thermoregulation-- they became birds. So that presumes at some point the animals did not thermoregulate. Mammals and dinosaurs share a common heritage but it's generally accepted at the point they separated they were ectotherms. Consequently, thermoregulation evolved in the two groups independently. It does not strike me as unreasonable that the biochemistry of those dinosaurs that have no modern analogue required a different temperature than predicted by models of those animals with which we are familiar.

On the other hand, it is common for large mass ectotherms to be able to maintain a body temperature higher than ambient. Tuna do it. Large crocodiles do it. The earth was warmer back then so the temperature difference would be less. And these were incredibly large animals-- there is no modern equivalent to a sauropod. Whales are not a good comparison tool since live in such a different environment. Who is to say that once an animal's mass increases past a certain point that metabolic heat alone is enough to sustain temperature. We know it is possible. We don't know if it happened that way. It's distinctly possible that sauropods essentially got higher body temperatures for free.

There are profound differences in behavior depending on which is true. What is the nature of the thermoregulation of sauropod young? They don't have the mass to support it. But if they have endothermy, then they would need to temper it as they grow to retain that lower temperature. Could the temperature of the young and temperature of the adult sauropod be different? Could endothermy be a product of development? Young sauropods have it; older sauropods don't need it.

If they have endothermy as adults, would they have to have elaborate mechanisms for cooling to keep from overheating because of their gigantic size? If they are essentially ectothermic as adults, how would they manage in some of the antarctic sites. Antarctica was warmer then but it still had winter. And how did this relate to smaller sauropods? Ones that had significantly lower thermal mass?

It's like a really elaborate mystery novel. I can't wait for the end.

Saturday, September 17, 2011

Friday, September 16, 2011

New Pictures Show Faked Moon Landing Site

NASA has just released pictures of the Apollo moon landing sites. (See here.) Since the landing was faked in the sixties, clearly they must have gone up there and built the sites and then took pictures of them. Or, maybe Halliburton contracted it to one of Bush Lite's alien buddies.

Thursday, September 15, 2011

Remembering 9/13

Remembering the day we forgot that we were most intending to remember. Here.

Friday, September 9, 2011

Wednesday, September 7, 2011

Watching the Republican Beast

Well, 2012 is in gear and it's going to be an... interesting year. I have no love for the Republican Party and only grudging commitments to the Democrats.

I've been reading a lot of James Fallows recently and I suggest you read these entries to his blog:

But before you read them, I suggest you first read Mike Lofgren's article on his leaving the congressional staff. (See here.) Lofgren was a professional staffer in congress until he retired this year.

This is going to be an important election.

Sunday, September 4, 2011

A Case Study of Science in Science Fiction, Part 2

Previously, I talked about how I created the aliens in my first novel, Caliban Landing. If you didn't read that, look here.

To summarize, the aliens of Caliban were blind to normal light but saw by the emitted radio waves from the photosynthesis of Caliban's plants. Animals that saw in visible light were limited to nocturnal organisms that were active when photosynthesis, or similar reactions, were not active.

I wanted to give the natives of Caliban some interesting differences and similarities from humans. Humans have sex. But, then so do pretty much all vertebrates. For that matter, so do most multicellular organisms. Any nearly universal property of organisms bespeaks strong selective advantage.

The evolution of sex has been discussed and theorized in biology pretty much since Darwin. It's advantage is to mix possible gene combinations more quickly than waiting around for some mutation. It broadens the opportunity for selection across many gene combinations simultaneously, since each member of a generation is significantly different from any other generation even when springing from the same parents. They mystery is not how beneficial sex is-- that is obvious. It's how it got started. Which I will discuss at another time.

I also made the Calabi vertebrates of a sort. They have hair, a head, mouth something resembling vocal cords, etc. I did this on purpose since it would have been difficult to get into the head of or sympathize with a walking, oozing jellyfish. Similarities breed common ground.

Now, I knew there was no reason for there to be common ground between life that arose on earth and life that arose somewhere else. We have highly conserved life forms here. They all use essentially the same systems of DNA/RNA encoding and production of proteins. Proteins are used similarly. Oxygen based metabolism (the TCA cycle) and non-oxygen based metabolism (glycolysis) are essentially the same. Cellular organization falls into two basic camps: a prokaryotic approach which has a fluid approach to exposing operational DNA and the eukaryotic where DNA is systematically turned off or on in different tissues. Even across these basic differences between prokaryotes and eukaryotes the process is one of how to exercise the basic mechanisms, not the mechanisms themselves.

How those mechanisms are applied to organism varies highly between species-- jellyfish versus coyotes, for example.

Whatever preceded the life forms that we now have is gone and left no relic as far as we can tell. (Though Peter Watts has played in this arena with his Rift novels.)

With only a sample size of one, we have no idea how life might originate on other planets or even if it has.

That said, I decided with Caliban that the Calabi would have genes, chromosomes and cells, something like an internal skeleton and other common characteristics with our world. I even made them tetrapods for which I had no basis in fact whatsoever. Why not make them six limbed? There are a lot of advantages in hexapod robots. Why not use that?

Because who wants to sympathize with an alien that looks like a spider. That's why.

So, I made them essentially human: tetrapod, skin, hair, feet and the ability to think.

But aliens have to be, well, alien. Don't they?

I had made their sensory systems alien enough. After all, radio waves pass through flesh with only a faint muddling. It wanders around corners. The Calabi had a very strong sense of texture in the same way humans have a very strong sense of surface. They understand warmth and seasons but have no understanding of stars or planets. They sense the sun as this light from the sky that is largely outshone by the plants. Cloud formations that are radio transparent are invisible to them but those containing rain are clear. They have a much better local weather sense than we do.

This is a lot to make them different. And I wanted to set at least part of the novel from a native's point of view.

But it wasn't enough.

All biological systems are driven by the need to reproduce. This should not be surprising: those that didn't were outcompeted by those that did.

Humans are no different. Our reproduction, as exemplified by our obsession with the act of sex, drives our fashion, conversational interactions, sports competitions and entertainment. Now, humans are different from most other species in that we don't have a particular time for reproductive activities. Most species cycle the opportunity for reproduction so that the opportunity to actually reproduce is maximized. In vertebrates this is driven by the female. Female dogs, chimps, opossums, cats and mice come into heat. That is, the urge for the sex act coincides with ovulation. Not so humans. Human beings have separated the sex act from the reproductive act.

Most terrestrial vertebrates have males and females of similar lifespan and function. This is not true universally across the kingdom of life. Anglerfish females are the fish people see. Male anglerfish are tiny little animals that attach to the female, parasitizing her for food and with the sole purpose of producing sperm for her. Spoonworm males live inside the spoonworm female, eating food the female provides and supplying her with sperm.

There are interesting evolutionary consequences to these models. When you have males and females of similar lifespan and function, selection can operate on males and females separately. It is to the male's advantage to reproduce with as many females as possible. It is to the female's advantage to be selective. Think cats. That's one strategy. Another strategy is to hold onto a single female and rear offspring with her. Think geese.

I decided that Calabi would have separate species with separate lifespans. But in this case, the females were long lived and mated with multiple males. However, the males were weak and fragile and died shortly after mating. This pushed the females to select multiple partners and put a strong bias in the males to pick the right female. This gave me the added drama to have the humans on Caliban accidentally kill the male being courted by the female.

Funeral rites are uniquely human. I postulate that Calabi would also have elaborate funeral rites. Here, however, I departed from science and wandered into mysticism.

I have always been fascinated by how religion depends on there not being a demonstrative deity. If a deity shows itself, there's no longer any point to the religion since all can see what the deity is and what the deity wants. Religion depends completely upon the deity being an unknown quantity.

I've played in this area by creating situations where something serving a deity equivalent is real and knowable and how that affects the situation.

In Caliban, I had the Calabi take their dead and apply them with ointments and preparations to the roots of a particular species of tree. The tree absorbs the chemical nature of the corpse and the personality and memory of the dead individual lives again within the tree. Since the tree is emitting radio waves and the Calabi speak by radio waves, the living can therefore communicate with the dead. I had fun with that.

And, no, I didn't steal it from Avatar. Caliban Landing was published in 1987. My wife has a strong opinion on the relationship between Avatar and Caliban Landing.

That's it for the Calabi. There are other aliens in the book and maybe I'll talk about them another time.