Where It Comes From

I like to talk about science. however, Readercon is coming up and one of the panels I hope to be on is where you get your ideas. So this is my first stab at it.

First, I want to shift the concept of "ideas" to what I think is a better term, "material." In SF we tend to think of ideas as the basis of a story. Consider these three examples:

•  A Fire Upon the Deep, Vernor Vinge: Computation gets more efficient as you proceed away from the galactic core enabling higher order functions 
• Stranger in a Strange Land, Robert Heinlein: A human raised as a martian.
• A Canticle for Leibowitz, Walter M. Miller, Jr: After the apocalypse knowledge kept as part of a Catholic monastery

Certainly, these might describe a important idea for the work. However, nobody can say the idea comprises the work. I don't believe that a story accretes around an idea like the shell of a mollusc, as attractive as a pearl metaphor might be.

I think a writer brings everything he has to bear on a given story. Everything is material. Everything is material. The thoughts you had at your dead mother's funeral. The look of your puppy as it died in the street. The inappropriate thoughts you kept to yourself the first time you undressed at gym.

When I went to Clarion, Robin Scott Wilson said that writing was the only professions where you could drop your drawers, point to a big pimple on your butt and say look at that!


See? Everything is material.

So the problem with "ideas"-- or rather, material-- should be more what to leave out rather than what to put in. Material is everywhere. Looking at technology news today: "The Facebook Camera." Okay. Consider a world where every image is public. What does that mean? "Climate change allows once rare British butterfly to thrive." What is the state of Georgia going to do when the climate pushes animals currently living only in Florida north?

The point is not the material. The point is how you see the material.

Think of a black box. You want to know what's inside of it. What do you do? You pick it up. You feel its shape. You shake it. Stand it one one end and listen. Stand it on the other end and listen. What do you do when you get a new car? Take it out for a drive. Lean into the curves a bit. Check out the radio. What do you do when you get a new phone? Call somebody. Check the menus.

The first step of a writerly mind is to pick up a piece of material and examine it. Cuttlefish communicate by color. Interesting. How do they communicate? Flash pictures? Shapes? Maybe they use some sort of code.

The next step is sort of like how babies play with blocks. They fit them together and take them apart. They match them by color. By shape. By which ones fit with which other ones.

Back to the cuttlefish: What does a cuttlefish think about? Mating and eating probably. Do they play? Can a cuttlefish get bored? What does it mean for a cuttlefish to be bored-- what does it mean to play at all? If a cuttlefish was playing would we know it? Would we know it if it were bored? What would cuttlefish playing look like? Or cuttlefish boredom?

The writerly mind might try to answer these questions. Research is one answer-- put "bored cuttlefish" into Google and see what you get. Or you can imagine a bored cuttlefish. How? When I'm bored I might do something I know I like-- eat, maybe. Walk around. What would a cuttlefish do? Well, bored eating for a cuttlefish involves hunting. So it might go looking for a crab. That's a lot of work to alleviate boredom. The idea is to alleviate boredom without too much effort. Well, the cuttlefish has this color thing. Maybe it flashes at nothing-- doesn't sound satisfying, does it? Think like a cuttlefish. Hey! Look at this neat pattern. Where's Joe? Go find him. Hey, ,Joe! Check this out.

The idea is just there to catch interest. The material are the sticks from which you build the story. But what makes the story go is playing with the two.

Evolution, Embryogenesis and Science Fiction

(Picture from here.)

Here's a very good article on the evolution of the animal developmental process. It's not so good at explaining plant embryogenesis (wikipedia article here.) If you followed the articles conclusions, plants would be a form of degenerate animals since they also have embryogenesis. I'm not going to go into it in this post but I suggest reading it.

My own suspicion is that the process of multicellular organization that led to the evolution of development probably predated either plants or animals. The organizational principles might have been in play (see Volvox for example) but the actual process of developing embryogenesis likely have evolved separately between the plants and animals. When I read about it I see little similarity other than the fact that both higher plants and animals have a definable pattern of developing adult organisms from dissimilar embryonic precursors.

The evolution of fungal life cycles and that of slime molds likely also have evolved separately. Fungi look like they have evolved from animals or at least an animal precursor. (See here.) There is some genetic evidence that the gilled mushrooms and puffball fruiting bodies may have evolved fairly recently and may also have arisen separately as many as four times. (See here.) What's less clear is how fruiting mechanisms of fungi evolved at all.

Slime molds (Myxomycetes) are interesting in that they have a single celled form and a multicelled form. When they mate they form a plasmodium, a large structure consisting of nuclei without any intervening cell membranes. The plasmodium then extends itself (and sometimes appears to actually move) by cytoplasmic stream and consumes the food source. When the food source wanes, it forms a fruiting body that looks mushroom like and develops spores.

These sorts of strategies are important in Science Fiction. SF aliens even in their most extreme form are usually animal in nature. There are a few exceptions: the living planet in Stanislaw Lem's  Solaris. And the microbial gods of of Ken MacLeod's Engines of Light trilogy. SF Plant intelligences are essentially animals in plant suits. (See here.) Which is only marginally better than humans in alien suits.

It doesn't have to be that way.

I'm a big fan of using the strange and wonderful biological world of earth as inspiration for alien worlds. And, certainly, the animal kingdom is filled with the truly strange and completely non-human. But I'm also among the first to admit that this is animal chauvinism.

We have no idea of the shape of life on other worlds. I think we can suggest that if there are the ingredients and opportunity for a carbon based origin of life that life will in fact arise. And we can further speculate with evidence that the result will go as far as  a similar metabolic path as earth's: using light to fix CO2 into carbon polymers and thereby releasing oxygen and metabolizing the resulting organic compounds in the presence of the resulting oxygen.Note the caveats: it says nothing about non-carbon life. We can't even say that life has to take a cellular path-- there are some very interesting experiments involving organic compounds unconstrained by chemical cells but constrained by physical components such as the cavities in lava rock. Or that individual cells are the preferred path. The slime mold plasmodium mentioned above is fairly large-- sometimes meters across-- and has no cell membraines. It is, in effect, a single cell.

We have no idea what things are like out there.We know only a little more about what things are right here.

The stories we want to tell are about human beings. Aliens are one wrench in the tool chest writers can use to tinker with the human experience and see how it works.This is, in my opinion, one of the distinctions between SF and fantasy. SF has at least the toe of one foot in the world we live in, the world of thermodynamics and the Cretaceous. Fantasy does not need that toe. In a fantasy world we can have creatures that pursue evil for no reason except they're evil. In the SF world, evil villains at least have to pursue evil because it makes them look cool. This is a technical evaluation not a judgement of quality. It's just a distinction. A work of fantasy does not have to conform to physics though it may choose to. A work of SF is informed by physics even if the physics are ignored.

I've been talking about biology for a bit now. My intention is not just to say Look at that! Isn't it cool? though that is certainly true. Instead, I'm saying that the biological world can serve as a tremendous well of metaphorical construction. Along with history, anthropology and archaeology, biology can help determine motivations, develop character and make stories.

Even with slime molds.

Changing Human Paleobiology

(Picture from here.)

One of the things that changes over time is our perspective on our ancestors. It wasn't so long ago that we thought of Neanderthals as stupid, shambling brutes. Now we know they may have had brains that rivaled ours, speech and red hair. Our perspective of our ancient ancestors is also undergoing a revision.

Lucy is one of our earliest relatives. She's a representative of Australopithecus afarensis from about 3.2 million yers ago.  Two years ago a new species of Australopithecus, A. sediba, was discovered also in Africa. A. sediba has a brain that is more organized like a human's than others.(See here.) She also has a tool maker's hand-- a hand much more capable of using tools than other members of her genus. However, she also has a foot that is more primitive than Lucy. (See here.) A. sediba is dated to about 2 million years ago.

Human beings belong to genus Homo. Home first appears with Homo habilis 2.33 to 1.8 million years ago.Which make one wonder if there was an overlap between the origin of Homo and the existence of A. sediba. It certainly makes the origin of genus Homo more interesting. Possibly, we'll discover another member of Australopithecus that will join the bipdal gait of Lucy with genus Homo.

The rhino in the room for this discussion is what traits are derived traits that humans inherited from non-human ancestors and what humans evolved on their own.Traits that we identify as hallmarks of our humanity include bipedal gate and the human brain. A. afarensis was fully bipedal but didn't have a human brain. A. sediba had, organizationally at least, something that might have evolved into a human brain but didn't have a human foot to back it up.

Adding to that is a recent find of another Australopithecus, a contemporary of Lucy, that had more of a tree dwelling foot than Lucy did. (See here.)

Questions about. Did Lucy or another Lucy-like relative serve as the ancestor of Homo habilis and the brain organization derive separately from A. sediba? Or did A. sediba, or something like her, serve as an ancestor to Homo habilis and the foot derive separately? Or, is there a third Australopithecus species waiting to be found?

What we've been calling late derived traits are being pushed back all the time. Baboons had been shown to be able to distinguish gibberish from actual words-- an astonishing feat for a species that doesn't talk. (See here also.) Clearly, they are not determining this by the meaning of the words. Instead, they must be using some sort of statistical mechanism to detect patterns. Humans probably do the same thing. However, the lineage from which humans arose split from the baboon line thirty million years ago. Baboons

My point is the the dividing line between what an ancient genus Homo and an ancient genus Australopithecus may not have been all that great.

A new study that came out in the last few weeks looks at the number of large predators over time. These days there are only a few predators over 70 kg. But as recently as three million years ago there were many more. About two million years ago the number of large predators crashed. The study ruled out climate change or other more typical "natural" disasters. But it couldn't rule out that humans, or equivalents, might have done it.

The granularity of the time domain is broad-- 500k years. Which is problematic since if the actual date moves one way or the other genus Homo might not be responsible. If it's too early, Homo wasn't around to do the job. If it's too late then Homo was around for quite a while without making any impact.

But as I read the article, I kept remembering A. sediba. Baboons. Chimps. And all the other animals we've arrogantly claimed couldn't use tools, communicate or think.

If humans didn't do the deed there might still be other candidates.

Higgs Boson and the LHC

PhD Comics has a quick tutorial movie on the Higgs Boson here. It's very good and explains a great deal.

I do quibble with one comment in the film. The narrator says there cannot be repulsive gravity. Some models (notably relativistic models) actually predict repulsive gravity as a product of negative mass. (See here. A good discussion of gravitational interaction with anti-matter is here.) The Standard Model doesn't have negative gravitons. But there are some models of dark matter that suggest it.

Harry Potter, Revisited

A few years ago I wrote this Harry Potter story.

Voldemort stole into Harry's room, invisible. He paused to make sure the boy was sleeping. Carefully, he deposited his gift, Introduction to Nuclear Physics, complete with a note "From a Friend." He left immediately he had miles to go before dawn. 

He saw the flash all the way from London.

I find the Harry Potter stories fundamentally uninteresting except for enjoying spectacle-- which the movies provide nicely. 

Enter Eliezer Yudkowsky and her fanfic in progress: Harry Potter and the Methods of Rationality.

I have not finished this yet but I am enjoying it hugely. Go thou and do likewise.

Neurology of Molluscs

Quick follow up on Neurozoans. This is a brief discussion on the neurology of molluscs. It didn't fit with the larger discussion but I thought it was interesting.

There are seven rough groups within molluscs-- I say "rough" because there's a lot of discussion over who belongs with whom. (See here.) These are:

• Bivalvia: scallops and the like
• Monoplacophora: limpet like shelled molluscs
• Gastropoda: snails/slugs
• Cephalopoda: squids and their relatives
• Scaphopoda: tusk shells
• Aplacophora: worm like animals
• Polyplacophora: chitons

Bivalves don't have a CNS. Neither do monoplacophora. Gastropoda and Scaphopoda have similar central nervous systems in that they have ganglia that interconnect. These are not usually considered a brain as such though some complexity can be achieved. Aplacophora look simpler than snails in that they have a cerebral ganglion but it's not terribly complex. Polyplacophora (chitons) have no true ganglia but there is a ring of neural tissue around the esophagus. The Cephalopoda have highly developed brains.

Are bivalves the primitive state and the other two classes evolved brains on their own? Or did the primitive mollusc have a brain and lost it in bivalves?

Mollusc clades suggest the that there are two great divisions within the mollusc phylum. One side leads to both bivalves and cephalopods. The other leads to chitons and Aplacophora. Neither chitons or aplacophorans have brains but they do have central ganglia. Over on the other side while bivalves don't have any CNS, gastropods, cephalopods and scaphopods do. Since both sides of the same phyla have at least central ganglia, we can presume that the primitive ancestor of molluscs had one, too, and that bivalves lost theirs.

This is supported by a paper in 2001 by Reichert and Simeone. By analyzing small rRNA sequences, they were able to redraw phylogenetic relationships between phyla and push back the origin of the central nervous system to the very first bilaterally symmetric animals. They further speculate that the original ur-bilateral animal might have had significantly complex brains and that subsequent simplifications of the brain (such as in clams) is just the complexity of the brain degenerating.

Biological Revolutions: Neurozoans Part Deux

(Picture from here.)

Last time we discussed the evolution of neurons. We are now deep in the world of metazoans.

The "most primitive" organisms of which we know all use neurons as part of a system. A nervous system allows stimulus/response complexity and adaptation by system organization. That means that to introduce new capacities to the organism can be done by reorganizing existing tissue types. You can reuse that hand for both holding a spoon and playing the piano; you don't need to grow a new one.

There are two rough categories of nervous systems we've discovered on this planet. A Nerve Net System (NNS) where organization is regionalized rather than centralized and a Central Nervous System (CNS) where there neurons collect centrally. In the NNS data is received through an input system and the response is distributed through an output system. There is no central switch board but there are regional differences allowing alterations in behavior based on input stimulus.

Jellyfish, comb jellies, starfish, sea cucumbers are NNS animals. Humans, squids, crabs and planaria have something resembling a CNS. Note that an actual brain (as opposed to something called a central ganglion) is a further refinement of a CNS. Having a CNS does not require it.

NNSs can be fairly complex. Often NNSs connect up in something called a nerve ring-- sea stars do this. They have a nerve net in each arm that connect to all of the other arms in a nerve ring. They hunt their prey. Box jellies also hunt prey and can perceive visual patterns. There's some evidence for sleep patterns.

However, on this planet, the full range of nervous system complexity really only arose in those animals with central nervous systems. And, curiously enough, the most complex of those arose in vertebrates although the cephalopods give some vertebrates a run for their money. I'd stack up cuttlefish against lampreys for intelligence any day of the week.

The nerve ring approach seems to appear in those animals that are radially symmetrical (Radiata.) The animals that bilateral (Bilateria) tend more towards a central ganglion and a central nervous system. It's not at all clear why this is so. There is now some evidence (See here.) that at least one group, the Ctenophores, show a bilateral plane in their gene expression during development. Another study (See here.) suggests that the radial symmetry is actually a derived form from animals that were originally bilaterally symmetrical. If that's the case then it could be that the NNS/CNS division is an evolved response to a change in body plan: a radial body plan drives the creation of a radially oriented nervous system.

A 2003 paper by Alain Ghysen (See here.) uses that as a reason to neglect radial organisms entirely in describing the evolution of nervous systems. I'm not sure that's as far as I would go since he leaps pretty much directly into brain evolution neglecting the organization of the Radiata. Personally, I think if you haven't explained nerve nets in some way you haven't really addressed the problem. Finding an excuse to throw them under the bus doesn't really solve things.

(Ghysen's paper is a lot of fun to read. It harkens back to the playfulness I used to read in the early papers of neurology, say in the late 19th and early 20th century. Here's an example:

"In this context it is interesting to note that when the chordate Amphioxus is swimming it has its neural side up, as decent chordates do, but when it lies buried in the sand it has its neural side down, much as a legitimate protostomian would, whereby its mouth opens in free water."

Maybe it's an acquired taste.)

Regardless of that, Ghysen makes a strong case that the CNS of the different phyla such as crabs, molluscs and kittens have a common ancestor. The reference to dorsal and ventral nervous system organization in the quote above is key to this. Chordates (the phylum to which we belong) have their nerve cord on their up side (dorsal) and other invertebrates have their nerve cord on their down (ventral) side. Amphioxus is a tiny worm that shares the phylum with us vertebrates. The current thinking is that the chordate nerve cord is flipped upwards during development. In effect, we are all ventral nerve cord animals. Some of us just hide it.

This is supported by a paper in 2001 by Reichert and Simeone. By analyzing small rRNA sequences, they were able to redraw phylogenetic relationships between phyla and push back the origin of the central nervous system to the very first bilaterally symmetric animals. They further speculate that the original ur-bilateral animal might have had significantly complex brains and that subsequent simplifications of the brain (such as in clams) is just the complexity of the brain degenerating.

So, what's a brain? What's a central ganglion?

The ancient urbilaterian is thought to be a sort of segmented tube worm. The nerve cord proceeds through each segment from the anus towards the mouth. Each segment has a ganglion (a collection of neurons and neuron bodies) on the nerve cord and the ganglion in the "head" segment has a larger central ganglion.

Many call the central ganglion a "brain". I don't think that's appropriate. There's a significant difference between the computation potential of the central ganglion of a tube worm or planaria and the computation potential of a spider or a mink. It's not one of merely quantity. Below a certain level of computability complex responses and perceptions aren't possible. For example, the recognition system male spiders have to present to female spiders to make sure the males are not taken as prey requires a filtration and evaluation of incoming data that simply isn't possible by a central ganglion.

Essentially, I call it a "brain" when it's able to evaluate incoming random data against a standard model. A male fiddler crab waving that big claw in front of her is trying to get her to evaluate his action against her model of an acceptable mate. That's a brain. A planaria evaluating different chemical concentrations to choose a direction in which to crawl is using a central ganglion. One has an abstract model to work against and the other is a difference engine. The fact that the model a mate in, say, a crab is a matter of fixed neurons and the model of a mate in, say, a human male is a matter of acquired video images of red heads, isn't relevant. Both systems retain an abstract model of acceptable mate criteria against which the prospective mate is compared.

The evolutionary history of animals has a definite trend towards higher complexity from a central ganglion to simple brains to extremely sophisticated brains. The term for this is is cephalization. (See also here.) "Cephalum" is latin for head. Cephalization is the trend to move nervous system organization centrally-- which, in earth animals, is usually oriented around the mouth as the origin of the head.

A side note: humans are extremely cephalized. Our brains have taken over many functions that in other animals are mediated by the spine. A good example of this is spinal walking which is well known in dogs. Parapalegic dogs often still have enough spine neural tissue remaining that if one leg is stimulated it will cause a walking reflex without any interaction with the brain. In humans the same stimulus rarely results in more than muscular spasms-- which isn't surprising. Walking erect requires a great deal of coordination between the balance system and the muscular system. The only common meeting point for those two systems is in the brain.

A Central Nervous System implies a division between the CNS and other less central neurons: the Peripheral Nervous System (PNS). The PNS serves up data and effects change. CNS tends to operate on data served up by the PNS.

Central processing of data has a couple of not-so-obvious advantages over decentralized processing. For one thing, having a central processor served by peripheral processors allows natural selection to operate on them separately. The PNS can proliferate sensors, interact with muscles, all of which can have different selective pressures. The CNS can then be driven by data incoming and outgoing to the PNS. (See here.) Humans are a good example of this. Our PNS isn't all that different from our chimp relatives but what's between the ears is significantly different.

One example of this is nervous system convergence. Convergence is the evolutionary development of similar structures from unrelated ancestors. The human eye and the octopus eye have similar construction. Yet the cephalapod eye and vertebrate eye evolved long after the two groups diverged. The reason they look similar is because the functional requirements for an eye are dictated by the physics of light and the biology of excitable cells. Any two organisms that need to see visible light and have similar cell physiology can produce a similar eye. They don't have to-- consider insects. But they can. (There's a really good paper by Kiisa Nishikawa on nervous system convergence here.)

Once, about 500 million years ago, the CNS and PNS were in place evolution brought forward all manner of creeping, crawling, swimming and whining things.

At some point in vertebrate evolution the animals became experiential beings. By this, I mean that pain and pleasure were felt by an entity. Do ants feel such things? I suspect not. Do squids? Maybe. Do dogs? You bet.

But if you unwind us and look back to where we came from, all of the fundamental mechanisms of that original urbilateria are still there, influencing us every day.

Post Script

The set of posts on biological revolutions was a lot of fun. But, as with anything, they have come to an end.

In retrospect they were woefully incomplete. For example, when I was thinking up this series I considered talking about the life's invasion of the land. Naah. It's just a new venue for life. It's not really a revolution.

Then I thought about it. Really thought about it. There was a profound revolution when life invaded the land-- or, rather, invaded the atmosphere. A whole series of mechanisms evolved to handle gaseous oxygen. In our current atmosphere, O2 is about 18%. Over time it has ranged between x and y. In water, the solubility of O2 is a function of temperature. Near freezing it gets up to about 15%. This falls sharply as the temperature rises. By 72F or so it's about 9%. By body temperature (37C) it's closer to 7 %. All of the mechanisms to handle toxic O2 concentrations evolved when life invaded the air. Gaseous oxygen promotes aerobic metabolism and discourages anaerobic metabolism-- this is why we have to limit oxygen in fermentation. Plants, fungi and animals all had to evolve new mechanisms.

And how could I have missed the evolution of embryonic development? That is crucial to all modern multicellular organisms. A much bigger revolution than nervous systems.

Maybe I'll revisit them again in the future.

But or this set of posts, so long and thanks for evolving all the fish.

Additional reading:

Developmental genetic evidence for a monophyletic origin of the bilaterian brain, Reichert, Simeone

Evolutionary origins of the [human] nervous system, Mo

Evolution of the Nervous System, slide show

Expression of ctenophore Brain Factor 1, Yamada, Martindale

Axis establishment and microtubule-mediated waves prior to first cleavage in Beroe ovata, Houliston, and others

The origin and evolution of the nervous system, Alain Ghysen

Without Miracles, Brain Evolution and Development

Evolutionary Convergence in Nervous Systems: Insights from Comparative Phylogenetic Studies, Nishikawa