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.

Tuesday, August 30, 2011

Human History and Science

Truly terrific set of videos showing a representation of science and human history. By Uppruni Tegundanna.

Wednesday, August 24, 2011

How Lobbying Works

Who owns Rick Parry? Bank of America, that's who. See here.

Tuesday, August 23, 2011

Evolution as Fact and Theory

Here's a neat article on discussing the fact and theory of evolution. Everyone should read it.

Monday, August 22, 2011

Risk Benefit of Science

Theo Gray has a good lecture on risks and benefits of learning science here.

Sunday, August 21, 2011

A Case Study of Science in Science Fiction, Part 1

About mumbly-seven, Congdon and Weed published my first novel, Caliban Landing. It's still for sale as a used book and I'd like to bring it out as an e-book. Just as soon as I get up the nerve to cut up and scan the hard cover. Until then, you can get a copy here. Go ahead. I can wait.

I've been talking a lot about how science, evolution and fiction go together. So I'm going to talk about specifics by using Caliban as an example. Heck, maybe it will generate enough interest that somebody might want to read a mumbly years old book.

Caliban had a lot of science fiction elements in it: faster than light travel, several alien species, human/AI interconnection, cyborgs-- all sorts of things. I'm going to limit my discussion to the biology in the book.

Caliban was a first contact novel. Humans come to the planet Caliban to survey it for human exploitation and maybe stake a claim or two. The planet has ostensibly been cleared of sentient habitation. This turns out to be incorrect and the team accidentally kills one of the sentients. The legal situation being what it is, they decide to try and make first contact and in effect get absolution and stay out of a higher, and less forgiving, court. Things don't go as planned.

Given this was a first contact novel, what drove the book was the nature of the aliens. Since I was a biologist, the aliens had to be biologically derived. What drove the aliens were the plants.

Photosynthesis on earth uses only a small portion of the available spectrum of light. This derives from the heritage and limitations of chlorophyll, the primary pigment used to capture the energy of photons. Chlorophyll a has its absorption peaks in magenta and orange. Chlorophyll b has its absorption peaks more in the blue and yellow. The lighter blues and greens and the UV and IR regions are essentially areas of no absorption. One would expect that chlorophyll must be very efficient and conserved to remain so common across essentially all photosynthetic organisms.

Hm. I thought. Chlorophyll only responds in a fairly narrow set of ranges. Opsins, the pigment in the eye, have multiple absorption spectra. In humans, blue cones peak at 437 nm (blue), rods (night vision) peak about 498 nm (sort of blue to green), green cones 533 nm (green), red cones 564 nm (yellow). Rhodopsin, a common opsin in rods, is somewhat broader in absorption than the color opsins. In addition, there are variations in rhodopsins that have differing peaks. (A good description of how seeing works is here.) Rhodopsin is quite sensitive to light but fragile. It's why we have good night vision but also why that night vision can be easily destroyed. (See here.)

What if (an SF writer's favorite phrase) we had a pigment (or pigment system) that was tuneable. That is, its peak absorption spectra could be changed according to available light spectra. Possibly, it wouldn't be as efficient as chlorophyll but it might be adaptable to multiple conditions. An interesting side effect is how it would look to us. The close uniformity of green in the plant world is an effect of the narrow ranges of the pigments involved. There's variation in the other pigments but chlorophyll is pretty constant. A tuneable pigment would have different reflective properties depending on how it was tuned. The top of a forest canopy would be a different color than the interior. Shaded plants of the same species would change depending on light level. And most plants would change considerably with the seasons.

I took the idea and filed it away.

Later, I was reading an article on the biochemistry of photosynthesis. After all, the photon must be absorbed before its energy can be captured. That's got to be pretty interesting.

Photosynthesis is dependent on fluorescence. (See here and here.) Fluorescence is the process by which something that has absorbed energy by either light or other electromagnetic radiation emits it. Commonly, a photon strikes an electron of a substance and imparts energy. The electron emits a photon as the energy is released. Photosynthesis is a fluorescent reaction in that the energy is received from the photon by captured by biological systems rather than be re-emitted.

Hm. I thought again. I remembered my tuneable pigment. Let's say our pigment can absorb terrifically in its narrow tuned range but it can't retain the photon as easily such that the photon is re-emitted. That's what happens in fluorescent paints. Of course, if the photon comes in as blue and emits as green that's not much of an energy gain. To make this worth it as many of the photons would have to be absorbed as possible and then re-emitted at as low an energy as possible.

Visible light is just what we see. It's not magic. It's the visible part of the electromagnetic spectrum. The spectrum goes up into gamma rays and down into microwaves. So I thought, let's make them re-emit radio waves.

Cool, I thought. And put it away again.

Time passed and I was reading Hubel's work on visual systems. The eye captures photonic data but it's the brain that makes sense of it. I wondered what it would be like to have a visual system that didn't operate on the rules of optics. Radio waves, for example.

Ping!

I dusted off the plants I'd thought up and then derived an alien biology that would take advantage of it. There are drawings of these guys in my notes, skulls that were laced with radio detecting proteins (likely with metallic cores). Opsins chemically resemble chlorophyll.

All opsins have a common heritage (see here) that is different from the evolution of chlorophyll. (See here.) But both chemical families harvest available light. I made the presumption that if radio waves were as present and as ubiquitous as light then biochemical systems would evolve to take advantage of them. I also made the presumption that animals who could detect their environment using radio waves would be selected for over animals who could merely detect visible light. Neither of these assumptions were provable but they made great aliens.

Okay. I had an alien biology and an alien ecology. Now I needed intelligence. Culture. Communication.

I was reading a lot about dolphins in those days and one article I read (which I cannot find, unfortunately) noted that dolphin sonar (like the sonar of bats) created the medium of perception rather than used one that was available. The article suggested that if dolphins were intelligent, they could communicate by actually producing an "image" of an object to show a receiver.

Oh, this was too cool to leave on the floor. I modified my Caliban aliens to be able to manipulate the radio waves they were receiving and seeing by-- sort of like modern metamaterials, though I certainly didn't think of them.

I now had an alien biology. But I still had to create an alien culture.

Stay tuned for Part 2.