Dozois Year's Best on Sale Today

Today the 30th edition of the Year's Best SF edited by Gardner Dozois goes on sale.

The Table of Contents is here.

And my novella, Sudden, Broken and Unexpected is in it.

You can buy it here.

Consideration of Works Past: A Canticle for Leibowitz

(Picture from here.)

We can't effectively criticize Shakespeare or the Bible because they have so profoundly interpenetrated our culture and our language. People who have never read a word of the Bible know the meaning of the phrase "the patience of Job." People who would barely know the Bard's name know the meaning of the phrase "the green eyed monster." Such works have become the water in which we as fish swim. We read the Bible. We watch the plays. But we're seeing our own culture write large portrayed back to us.

These are big examples of how culture and literature reflect one another. It's the reason we should always have a literary canon. Not because these are the best we have to offer but because they are what inform our cultural milieu.

The process is dynamic and recursive. Some works are magnificent and immediately forgotten. Some distill a moment and continue to evoke that moment for decades after the moment is past. To Kill a Mockingbird shows a particular moment in the mid-20th century south and has become metaphorical in is depiction of American racism. 

Racism is timeless. The mid-20th century also experienced something particularly unique: the actual possibility of universal destruction of humanity by war. The prospect of such a holocaust has been around since the Revelation of Saint John but only until the 1950s did it become technically feasible. Humans were forced to confront not only their individual mortality but the mortality of their species. They confronted this prospect best (I think) in literature.

Nuclear holocaust and post nuclear holocaust novels were born.

We know of them as a staple these days. In film. In books. But modern post apocalyptic stories now are explorations of a trope. They don't arise out of impending doom. Those of us who learned to duck and cover are a dying breed and our children and grandchildren are products of a society that (I hope) outgrew such an immediate death. Instead, we'll have a slow chronic sickness of global warming and resource scarcity. Fertile literary ground to be sure but not the same as the quick flash and obliterating thunder.

Two books are still known today close to fifty years later: On the Beach and A Canticle for Leibowitz.

They're good bookends of one another On the Beach deals exclusively with death: there are no human beings alive anywhere on the planet by the end of the book. The work's complete focus is how people deal with the true and actual end of the world.

A Canticle for Leibowitz is almost exclusively about how humans (or human belief) survives the end of the world.

The plot is thoroughly discussed elsewhere and only needs a quick synopsis. Nuclear exchange happens. Most of humanity is killed either quickly or slowly by radiation. The living remainder turn first on those who they think did this, then the scientists and then anyone who can read. Isaac Leibowitz, a Jewish engineer, converts to Catholicism and founds an order that attempts to preserve knowledge in the face of this destruction. Six hundred years later, the order is still alive and has transformed from going out and getting knowledge to preserving what knowledge it has while being unable to understand it. They don't know if the works they are copying and recopying to preserve it is a laundry list or a prescription for paradise. It is at this six hundred year mark that Canticle begins.

The book is written in three parts: Fiat Homo ("Let there be man), Fiat Lux ("Let there be light"), Fiat Voluntus Tua ("Let thy will be done".) Part one begins with the discovery of an ancient (and important) cache of documents and ends with the canonization of Leibowitz into sainthood. It takes place during a dark ages where there are no states of any consequence. Part two involves the rediscovery of the importance and knowledge held within the documents and shows the rise of political states and conflicts. In part three the order is again gathering and preserving knowledge, this time in full understanding of the knowledge they have. The world is crumbling again between two mighty power blocs and on the verge of self destruction. The vast majority of the story takes place in the order's abbey.

Canticle asks some really big questions. What is the role of faith and religion over time? Miller suggests that the Church (and perhaps religion itself) is a means of stabilization over time. It serves as a repository for valuable things that are not currently treasured until that time they are once again revalued. The object in the story is the knowledge of the previous time. But Miller also points out the implications of faith are also held within the church and may never be properly valued in the secular world. This conflict between spiritual morality and secular practice occurs over and over again in the book both in the larger political macrocosm and the microcosm of the human interactions of the abbey. 

The characters in the novel grapple with these issues over and over again. At one point in the novel, when there is a nuclear strike near the abbey in part three, the government sets up medical triage tents where euthanasia drugs are handed out to those who have had a fatal radiation dose. The abbot fights this and protests it, not allowing the tent to be set up in the abbey.

The book continually shows intellect at war with itself, at war with morality, at war with passion. It is comprised with adults wrestling with some very big demons. This not the children's coming of age story that most post apocalyptic stories have become. These are adults who have made sacrifices for their beliefs. Who are trying to live to an impossible ideal (Christ) and failing and trying again while knowing all the while that such an ideal is, in fact, impossible.

I do not subscribe to much in the way of faith but Miller shows its nobility. Its intellectual and emotional rigor. The sorts of questions that a person of faith must ask and the integrity that person of faith must have to answer those questions honestly.

Usually, when SF deals with faith the religion is a construction to a purpose. (There's a good article on the subject here in wikipedia.) Often, the purpose is political. Sometimes it is a criticism of the concept of religion itself. Sometimes the religion is an allegory or a sacred mystery. Sometimes the issue is how to reconcile dogma with the physical world. I think, however, the consequences of faith are rarely dealt with head on. The Christian faith contains some hard nuts to crack: caring for your fellow man, the role of the secular leader, the issue of accountability and responsibility. These are not usually the stuff of SF.

There's a point in the book where the abbot of the monastery goes out to visit an old friend, a Jewish hermit named Ben. The implication is that Ben believes that he is Lazarus though it is not explicitly stated. In talking with Ben the abbot realizes that in Ben's madness he believes he is the last Jew and so bears the responsibility and accountability for the acts of every Jew that has ever been. The abbot thinks about this and considers his own role as abbot. What would it feel like to be accountable for the evil acts for every other abbot? This, by extension, is the role of Jesus: to be responsible and accountable before God for every evil act that has ever been committed by man, thereby accepting the punishment for those evil acts and absolving human beings from that crushing burden.

Heady stuff and not for the squeamish.

Canticle has not been out of print since its publication in 1959. It has a kinship with To Kill a Mockingbird. Harper Lee never published another work and has said it's because the popularity of her first novel was so great that any later work would inevitably be compared with it and found wanting. Walter M. Miller didn't publish anything else in his life time. He did work on a sort of sequel and got it a good way along but committed suicide after the death of his wife. I've read some conjecture that the difficulties of the book contributed to his death. Terry Bisson was in the process of completing the work when he died. (Here is Bisson's story of how that came to happen.) Saint Leibowitz and the Wild Horse Woman was published in 1997. I have not read it.

The book stands its ground now pretty much as well as it did when it was first published. We of the duck-and-cover generation still remember the deep, tidal fear of those times and it comes across in the book. But I think later readers will still appreciate it. Anyone born in the last hundred years will understand the apocalypse is always at hand, waiting for the moment when we might embrace it.

My Own Not-So-Private Writing Screed

(From here.)

I've been reading the entries over at the Aerogramme Writer's Studio. They have a lot of Rules of Writing by various writers. Many of these are very good. So I figured I should have some.

I came up with two.

1. Read intelligently.
2. Write honestly.

I am not saying the other rules for writing are bad. They are often very, very good. But to me they are refinements. They are methods by which you can made bad writing better or good writing great. They are not (again, to me) rules for writing in and of itself. 

Or, you could say that the usual rules for writing reflect what one should do once the state of writing has been achieved. What I'm talking about is the enabling principles to write at all.

At least for me.

Let me explain.

First, read. Read everything. Read bad fiction and good. Read science fiction, mystery, best seller, little known American authors of the thirties, translated Burmese poets. Read about the whisky rebellion, folk music of the nineteenth century, the care and feeding of llamas, the Teapot Dome Scandal and how steam engines work. Be Not Thou Narrow and Do Not Stop. I'm convinced when a writer stops reading he dies inside. William Goldman said it first in The Color of Light: It's all material. Every square bit of it. And you'll need every square bit of it.

Be voracious. Be eclectic. 

Second, read intelligently. By this I do not mean narrow the material. I mean that every writer has a point of view. Some defensible. Some not. Some you agree with. Some not so much. But they all have biases. So if you read somewhere that box turtles are vegetarians, be aware It Ain't Necessarily So and corroborate the author. Follow the material down to bedrock. Don't be satisfied until you have wrung your material dry. Tear it apart and build it anew in your mind.

Don't be worried that it won't prove useful. It will and in ways you cannot imagine when you're reading. Do it for fun. The love will follow.

I had a physiology professor in college who always answered questions with material that begged for more questions. Eventually, when the questions could not be answered, it was not because the professor had run out of knowledge; it was that we had run off the edge of the state of knowledge.

Cultivate such relationships.

Then, write. Write incessantly. Write about the sun, the moon, the darkness. Try your hand at plays, poems, stories, novels. But most of all write in your mind. Think about what you read, see, feel, experience. Frame it. Turn it inside out. Change points of view. Would that be the same if the person were a woman? Chinese? A squid? Compare it against what you've read-- bad and good. Compare it against things you know and things you don't. 

And write honestly. Don't be satisfied writing someone else's material. Every writer first has to discard the very writers that crystallized the desire to write in the first place. Don't worry. It's all material. It will come back to haunt you but when it does it will be in your voice. Write about people who work, play, have children. You don't have to talk about their work, play or children if it doesn't serve the story. But you will know them and through your knowledge so will the reader even if you never mention a whisper.

There is no character so minor that they don't have a back story.

Let characters come forward in your mind-- I like to think of writing as an exercise in multi-personality disorder. But for fun. You, as the writer, are in charge. But readers are like the audience at a magicians show. You can fool them for a while but if you do the same trick too many times you're just messing with them. They'll see through you and resent you. Treat not the reader with contempt. Treat them like the intelligent people they are and they'll give you their valuable attention. There's no sin in asking the reader to work with you. 

Treat not thy characters with contempt. It's a variation on treating readers with contempt. Simon Legree had a business to run. He had a wife and children to support. Yes, he was a cruel sadist that tortured slaves for fun and profit but that's not all he was.

I'll even give a great example of not treating your characters with contempt. In Huckleberry Finn, Huck's father, Pap, was one nasty piece of work. He was the worst kind of drunk. He abused Huck. He kidnapped him to get his money. Huck goes on down the river largely to get away from him and in fear of his life. Twain could have drawn him as a villain with no more depth than a playing card. He did not. The reader does not know how Pap came to this place, what sort of choices he made to get here, the nature of the people he came from and what formed him. But at no point in the novel are you ever in doubt there was a path Pap followed. There were decisions-- mostly wrong but likely looking good at the time-- that brought him to be the person Twain describes. That is writing honestly.

Writing honestly is doing the very best work you can do because you, of all people, know where the bodies are buried and which corners were cut. 

Writing honestly is doing your best when you know you will fail at it because you know where the bodies are buried and which corners were cut. 

Nobody's perfect. Suck it up and do it anyway. 

Consideration of Works "Past": Nausicaä of the Valley of the Wind

Usually I talk about works I read when I was younger now rediscovered. But in this case, I'm going to talk about something that I've read relatively recently-- not the film version of Nausicaä.The manga.

In a way, this is a cop out. I've been working on a set of posts involving regulation based on science and physics rather than on whim and appearance. I was going to attack gun regulation but it's more work than I anticipated. So I'm taking a break from that one and talking about Hayao Miyazaki.

Miyazaki is primarily a film director and animator and it's by his film work that he is best known. If you haven't seen a Miyazaki film, stop reading this blog right now and go rent one. Kiki's Delivery Service is a good one. Or Castle in the Sky. I have a weak spot for Porco Russo, since it's about seaplane pilots. Or you could go straight to the big guns and get Princess Mononoke or Spirited Away. Or, of course, you could also watch Nausicaä of the Valley of the Wind.

Oh, hell. They're all terrific. Go watch them.

The manga is in seven volumes. If you've seen Nausicaä the film, you'd be forgiven for thinking that the first couple of volumes are pretty much a recap of the film. There are more than one story about why Miyazaki did the manga. Miyazaki couldn't initially get funding for the film and so put out the mangas. Miyazaki couldn't get funding for a film that didn't have an associated manga. Etc. The mangas were written from 1982 to 1994. The film was made in 1984.

A thousand years before the story starts there was a terrible war fought, in part, by God Warriors: giant mechanisms with horrific weapons. Vast areas of the world are now filled with poisonous forests inhabited by giant insects. The forests appear to be fungal in nature and spread by spores, often carried by insects or unwary travelers. However, the poison is everywhere and people eventually die of it.

Nausicaä is a princess of the Valley of the Wind-- the royalty component of the story seems to not have a direct connection to rule. Her father did rule the valley but there are hints toward the end that there may be other paths to being a sovereign than heredity. Regardless, she is looked up to and admired by the folk of the valley.

War breaks out and there are treaty obligations that the Valley send troops. Nausicaä goes with them. The war was between the Torumekeans and the Doroks. As she proceeds through the different convolutions of the war, encountering spiritual battle, biological warfare and enormous cruelty, she becomes more and more important, a force for good in an amoral conflict. Eventually, her influence, the power of the insects and the suffocating horror of the war all come together and she prevails.

I'm not going to get more detailed than that. The plot is intricate and clever but I think is actually a side note to the issues Miyazaki is handling.

Miyazaki has always had environmental concerns. Pretty much every movie has some sort of component that can be construed to be environmental. Even Porco Russo, a story about a seaplane pilot who's become a pig, has a continuing discussion of the balance between selfishness and selflessness-- which, I think, is a stand in for Miyazaki's issues with the environment.

In Nausicaä these issues are front and center. Humans have to live on a poisoned planet-- poison that is of their own making. The poison is killing them. Yet they still war. Religion is a political means to an end. The personal and selfish pursuit of power is the source of the world's evil.

But it's not a screed. It's a story where these bits come out as important plot details. Nausicaä never says "If only humans will somehow sees the immorality of their ways and learn to help one another. Ah, Atlantis." She does lament human behavior more than once but it's more in the vein of "Come on, guys. Stop hitting yourselves."

The film handles some of this but much of the rich and detailed tapestry of Myazaki's world is given only token treatment. The God Warrior is just a prop. The sword master Yupa a part of the chorus. This is the cost of making it into a film. The manga is much more detailed.

One of the interesting things in Nausicaä's character is her continuing avoidance of killing-- not because she's a pacifist. But because she finds out early one the killing rage she has in her own heart and how easily it can be released. She decides that this is something to struggle against and from then on she keeps trying to find different ways to make things better. Not easy in the middle of a war.

This continuing attempt to not kill anybody and to stop people from killing one another, coupled with her own forceful personality, begins to have knock on effects. People start to take her seriously and, by doing so, take her point of view seriously.

Nausicaä is, no doubt, some sort of Christ figure in this. But it's a Christ figure that we're not used to. Nausicaä is not passive. She's not going to volunteer for the cross. If she goes down she's going down trying to save everyone around her whether they want it or not.

I've read this series twice now and this aspect of Nausicaä's character is what stays with me. She's like the members of Doctors without Borders, going out there and working until they drop to save people's lives.

The work has its limitations. There is little introspection regarding motive-- people just do, knowing what they must do instinctively. In my experience there's just a little consideration of what must be done. The ending is a bit abrupt. It feels wrongly shaped-- I think everything happens that has to happen but it seems clunky in execution. Miyazaki did all of the drawing in pencil and the artwork is wonderful. But you want to just see the precise definition of ink in some of the action sequences.

But these are quibbles. It's a terrific read rendered by a master story teller at the height of his powers.

The Snowden Perspectives

Here are some articles that have interesting perspectives on the whole surveillance state.

Edward Snowden probably didn't commit treason
500k contractors have access to top-secret stuff
Booz Allen Hamilton
Five ways to stop the NSA from spying on you
Is a democratic surveillance state possible?
Has the US become a nation from which you must seek asylum?
Will PRISM damage tech companies' reputations for privacy?
Obama is wrong about NSA oversight
NSA asked Verizon for records of all calls in the US

And just to make sure other things are discussed:
The people have taken over American politics and they hate it
Infrastructure Hawk vs Deficit Hawk

Webcomics Of Interest

(Picture from here.)

I follow about four hundred web comics. A bunch of them can be seen here.

Fortunately, the update schedule for most of these brings it down to about fifty or so a day. Is that a lot? Not sure. It takes me about forty-five minutes or less to get through them. Maybe I just read fast. Or, at least, read comics fast.

At any rate, I'm going to start a new subthread on this blog. I'm going to talk about certain webcomics that I follow.

One of the problems of webcomics is that there's not a good mechanism to pay the authors for their time and trouble. (In my example, if I paid a dime to each webcomic I read every day it would costs me $5/day or $1800/year. I can't afford that.) While this can mean that webcomics creators are free from deadlines, publishing oversight, etc., it also means it's a labor of love unless and until they make some money on it. There are some definite success stories in webcomics (PVP and Sluggy Freelance leap to mind) but many webcomics just last until the life pressures on the creator consume them.

Another scenario is that a given webcomic starts, goes for a period and then is actually ended. (My God! A comic that actually has an ending!) A terrific example of this is Anders Loves Maria by Renee Engstrom, a wonderful story that has an actual beginning, middle and end. You know. Like a story. Another is Ursula Vernon who wrote Digger. Digger won the Hugo in 2012.

Often, webcomics have support mechanisms embedded on their site. This can be print versions or donations or other means.

So. Here is today's list and discussion. Go read them. If you like them, figure out a way to support them.

Since Science Fiction webcomics are relatively rare, I'll talk about them today.

Cleopatra in Space: Take Queen Cleopatra from Egypt. Put her in space cadet school. Send her out for adventures. That's pretty much it. The bad news is it doesn't update enough.

Darths and Droids: Imagine Star Wars as a D and D game. You remember them, right? You play in your living room and all sorts of things happen? Some of them within the game like killing rebels or something. But personalities come out. Marriages come and go. Little sisters grow up. Now imagine that using as illustration actual pictures from the Star Wars movies.

Blue Milk Special: Same Star Wars venue in that the same rough plots are followed. But Leia is a rough girl who smokes and is tougher, much tougher, than Han. Han, for his part, bumbles. Think of it as an orthogonal reimagining of Star Wars. Man, I never thought I'd get to say "orthogonal" quite that way.

Decrypting Rita: This comic is, in part, science fiction. It's the life of a woman over several planes of simultaneous existence. In one she's a robot. In another she works in a store. You get the idea. The comic is drawn with these pieces of her "life" crossing over themselves. The character doesn't seem to interact with her other selves but the art does.

Dresden Codak: A terrific comic that doesn't update enough. It's fringe SF rather than true SF. Aaron Diaz plays with scientific concepts and art at the same time. He had one long arc, the Hob story, that is closer to true SF than most of the arcs.

The End: This is straight SF. Aliens have a humanitarian mission. When they see the end coming they save some of the species. Our number is up.

Freakangels: One of the ended strips This one is by Warren Ellis who's done a lot of other things in the entertainment industry. Remember Village of the Damned or The Midwich Cuckoos? TMC was  a story about psychic kids that resulted from alien intervention. VOTD was the film version. At the end of both the kids are killed. Now imagine they lived and grew up. That's Freakangels.

Freefall: Freefall has been around forever. It's basically about a larcenous squid starship captain and is first mate an AI housed in a humanized wolf body. It's very funny. It also usually gets the science spot on.

Galaxion: This one is a more traditional SF story. Woman is an admiral. Her husband was captain of a crew testing a new star drive. They disappear. She finagles an appointment to a new star ship to go after him. She finds them. Sort of.

Jump Leads: Parallel universes abound. We have trading relations with many of them. We're always looking for new ones. The explorers are called Jump Leads. Two of them (a sort of Lister/Rimmer pair from Red Dwarf) get lost and try to find their way home. Think Sliders done right.

Moon Town: This one is new and I don't know how it's going to be yet. It's about miners on the moon. One if them is always bring in more material than the others. So a second miner decides to find out how he does it.

Carpe Chaos: Strange little strip about all sorts of alien races. Each race has its own mythology and cultural history. Inevitably there are conflicts. Beautifully drawn.

O Human Star: From the comic's self-description: "Alastair Sterling was the inventor who sparked the robot revolution. And because of his sudden death, he didn’t see any of it. Until he wakes up 16 years later in an advanced robotic body that matches his old one exactly." He looks up his old business partner and lover, thinking he did it, and finds out that there is mystery here.

Quantum Vibe: This is also straight SF. Several hundred years in the future the planets are colonized. There are L5s everywhere. Space transportation is easier than flying shuttle between Boston and New York. Nicole Oresme gets a job with scientist Seamus O'Murchadha and they have adventures across the solar system. It bears a strong resemblance to John Varley's work but is in no way a rip off.

Space Mullet: Another one that's a bit new. So we'll see. Jonah is a washed up space marine who's ended up with an alien partner Alphius. They do the odd jobs and then get hammered by the unexpected. We'll see how it goes. Think of Firefly meets the Bob Hope/Bing Crosby on the road movies.

Space Trawler: Oh this lovely comic. This work is by Christopher Baldwin who did Bruno a while back. I had issues with Bruno but those issues are in the past and more than made up for with the deft touch he's brought to Space Trawler. Essentially, a group of humans are shangied into serving the galactic community with hilarious and poignant results. Come to think of it, a cup of tea does sound good.

Whither Came We?

I apologize for not putting up a post last week. Without getting too deep into the personal space, life intervened.

Anyway: Back to Science!

At least one of my two readers may remember the series I did on Biological Revolutions. You may recall one I did on the transition of proto-life-as-we-know-it to the prokaryotes (See here.) and the rise of the eukaryotes. (See here.) From there I talked about when multicellularity occurred. (See here.) I made a leap then to neurozoans: animals who had differentiated a system of "perception" of the world that allowed integrated responses.  (See here.)

Now I left out many other Biological Revolutions in that series. One of which was the development of, well, development.

Organism development is the process by which a proto-organism, such as a zygote, develops into a larva and eventually into an adult. The core of this process is the development of an embryo, termed embryogenesis. Since an embryo is a proto-organism that is pre-directed towards developing into a larva, this is clearly the first step.

Most embryos begin as a zygote: an egg fertilized by sperm. Some embryos begin via parthenogenesis, in animals this starts asexual development from an unfertilized egg. The egg spontaneously doubles so that it resembles a zygote and development proceeds from there. This is called psuedogamy. There is a similar process in plants where pollination is required to get the ball rolling but the DNA of the pollen has no role in the developing embryo.

Regardless, once we have the moral equivalent of a zygote the process proceeds with the "goal" of a target embryo that can then continue to a larval or adult form.

When you think about it, embryogenesis is really, really strange. It starts with a single cell that looks not much different from a single celled organism. But it is programmed very differently. The zygote is packed with special proteins that are intended to shepherd the first few divisions of the cell into a multicellular collection of cells. There's a terrific experiment that one can do with frog eggs (I did this in college.) where you wait for the egg to do its first division and then carefully separate those two cells. Each of the two cells will then develop independently into a separate (and largely identical) frog.

This can occur for multiple divisions. Depending on the species and technique one can divide two, four, eight, etc., cells and get viable larval forms that grow into identical adult frogs. These cells are totipotent.. Any one of these cells can become any cell in the developed body. At some point, totipotency is lost and the cell becomes pluripotent. In animals, this means the cell can be become any cell in any of the three germ layers. Think of germ layers as the next step. They are also called primary tissue layers. At this point the embryo has formed a hollow sphere called a gastrula. (Before this it was called a blastula. I skipped that step.) The "layers" refer to the placement of the cells in the sphere. In animals, they are:

• Endoderm: Forms the organs of the animal's internal tube such as the stomach, colon, liver, bladder, etc.
• Mesoderm: Forms organs not associated with either the internal tube or external skin such as the circulatory system, kidneys, gonads, etc.
• Ectoderm: Forms the organs associated with the outside skin. The skin itself, central nervous system, peripheral nervous system.

These pluripotent cells are the stem cells that everybody talks about.

This is the process for animals. Plant embryogenesis is somewhat different (See here.) but the overarching process is the same. A single cell proceeds to a larval form (i.e., a seed) which under the proper circumstances grows into an adult. (See here.) But I have to say I know animals better than plants so I'm going to stick to animals for the time being.

The critical feature here is the process by which the original single cell is programmed and the subsequent cells dance to each other's tune until the target stage is created. Remember, that there is no plan written into the genes. There are very few genes that are only used during development. Most of them are used throughout the organism's life. However, the choreography of development is exquisitely precise. I like to think of the genes as individual notes in a symphony where each note determines which other collection of notes is played.

Embryogenesis is the first step of a life cycle. Once you have an organism that can generate a life stage that can then act as a precursor to another life stage, changes can be introduced at one point that have knock on consequences down stream. The bones of the middle ear are called the auditory ossicles. There are three bones: the malleus, incus and stapes. Of the three, only one is used in the ear in reptiles. In reptiles it's called the columella. In mammals the columella is referred to as the stapes. The malleus derives from the lower jaw bone of earlier forms and is still there in reptiles and birds. The incus derives from the upper jaw bone.

In this case, "derives" means that if you take careful not of the process of jaw development in reptiles and follow the migratory path of the cells, you'll be able to identify the cells that form the articular and quadrate bones of the reptile jaw. If you follow the same cells in a mammal embryo, those same cells eventually become the incus and malleus. If you follow the cells that create the columella in reptiles you'll seem them form the stapes in mammals.

Where it can, evolutionary pressure ruthlessly forces efficiency. It is far, far cheaper to derive a structure from the embryologic development of an existing structure than create something new. Most vertebrate eyes derive from exactly the same tissue. One exception is the eyes of snakes (See here.)

The evolution of embryological development appears way back in the Cambrian (600 MYears ago.) The first clear fossil record we're familiar with is, in fact, a mark of embryogenesis. Of course, it happened earlier than the Cambrian since when we see Cambrian fossils it's already in full swing. (See here.) The article referenced talks about a bunch of circumstance that might have enabled or selected for embryogenesis but they do not address how these mechanisms might have happened in the first place.

Okay. Now I'm going to link this discussion back to the evolution of the prokaryotes and eukaryotes I mentioned in the beginning.

One of the interesting mechanisms that might have occurred to cause the creation of both groups is the creation of viruses. I mentioned in the prokaryote post that the majority of the DNA in the virus families has little similarity to the DNA the viruses target. Patrick Forterre has suggested that the viruses were instrumental in catalyzing the creation of the prokaryotes and may have been instrumental in the creation of the eukarotes. A virus happily floats around using cells to make other viruses and something breaks. It gets stuck in the cell. The virus DNA machinery becomes incorporated into the host cell and a new, hybrid, group is formed. His argument is the current viruses are those that didn't get incorporated into modern cell machinery and the modern cell machinery reflects viruses that did.

There is a type of virus that is abundant across the genome of various animals. These are endogenous retroviruses. "Endogenous" meaning part of the current genome. "Retroviruses" are those that are RNA based and then transcript into DNA. So the DNA that represents the ERV is the resulting DNA from an RNA virus. Some very interesting research has been published in the last couple of years showing that in humans, HERV (human  ERV) is a precise marker of pluripotency. (See here. And here. And here.) In fact, it is so active that there's evidence that HERV is, if not necessary, extremely important in stem cells. (See here. And here.)

HERV has been implicated in carcinogenesis, immunity and the creation of the placenta. (See here.)

This relationship to pluipotency is not limited to humans. It's been shown for other mammals as well (See here.) to the point that several scientists are wondering if the ERVs drove mammalian evolution. (See here.)

We don't have to stop at mammals. Two active endogenous retroviruses have been found in fruit flies: gypsy and tirant, though it's not clear if they're related to pluripotency. The research is still new.

But that never stops me from speculating.

What if the embryonic development derives from viral interaction with early eukaryotic cells? What if the reasons the phyla are so different from one another derives from the original root viral material that triggered their embryology?

What if we're really viruses underneath?
 
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By the way, if anybody is interested in how we did in the solar vote last time: we won. Hard fought but we did better than the Senate with over a 2/3 majority.

Rationality triumphant.