Monday, May 31, 2010

About "The Ice"

Ah, The Ice. Which goes up on Book View Cafe today.

I don't have a lot of "favorite" stories. Each story pretty much is my favorite at the time of writing. Later, it has to take a back seat to the next favorite.

At the time I had discovered both ice hockey and Gordie Howe. My friend, David Smith, had taken me to a hockey game. At the time I was impressed by its speed and power but mostly because it was so beautiful. So, at age 41 I started to try to learn hockey. I never was very good but I enjoyed it.

Anybody who learns ice hockey eventually learns about Gordie Howe. Check the link. It says more than I could.

The Ice was published in 2003 and written in 2001. Dolly the Sheep was cloned in 1996. Human cloning was in the news all the time.

This was all churning in my mind so I ended up writing a Gordie Howe-Ice Hockey-Cloning story.

I sent the story to Gardner Dozois who was then editing Asimov's. He liked it and wanted to buy it but it was too long. I wrote a shorter version. Then, he wrote back he liked the earlier version and bought it-- bought it twice, for that matter, since he also picked it up for best of the year.

Go enjoy.

Sunday, May 30, 2010

Intelligence Outside Primates

(Picture from here.)

In the Will Farrel move, Land of the Lost, there's a set of scenes where the team is menaced by a T. Rex. Farrel keeps saying they don't have to worry about it because it's so stupid; it's got a brain the size of a walnut.

Later, there's a huge crash outside of the cave where they're hiding. The team comes out and sees this boulder sized object. "What is it?" says one. Says Farrel: "It's a walnut."

This describes the demise of the anthrocentric view of intelligence.

No one disputes the intelligence of us hairless monkeys. But we like to consider ourselves more than just smart apes. Wallace, Darwin's co-presenter at the initial offering of their papers on evolution, thought we were so special that we were outside of natural selection.

Well, over the years Jane Goodall and others have shown that we can find the roots of everything we do in our primate ancestors: tool using, proto-language communication, etc.

But we would expect that, wouldn't we? After all, we share more than 98% of the genetic material with chimpanzees. We only diverged a few million years ago. Jane Goodall thinks we should keep chimps in the same genus as human beings. Wouldn't our "specialness" just be redefined to be within our own little clade?

Well, it turns out: no.

Traits that are observed in animals are viewed as original or derived. Original traits are those that have arisen from the group under examination. Derived traits are those that come from the ancestral stem collection of which the examined group is a member. Hair, in mammals, is an original trait in that only mammals have it. The quality of having four limbs, however, is a derived trait that mammals inherited from their stem ancestors.

Birds derived from dinosaurs about 150 million years ago. Dinosaurs derived from reptiles about 230 million years ago. They synapsids (from which mammals originated) split from the sauropsids (from which the reptiles came) about 324 million years ago. I'd say it's a pretty safe bet that any intelligence showing up in birds came from a different ancestral origin than intelligence in, say, mammals.

Which brings us to Irene Pepperberger's work.

Doctor Pepperberg worked with the African gray parrot Alex for many years, teaching him a vocabulary and studying how he used it. Alex was able to understand and respond to a considerable range of questions, behavior, make demands and ask questions. These were not human responses. I was able to talk with Doctor Pepperberger some years ago at Boskone. The films she showed of Alex were truly remarkable. Not because of the symbolic reasoning and abstract perception that Alex was showing, but because how far from human they were. Alex was a wonderful bird. But his reasoning, from my quick observation of the films, was not a human reasoning. If you watch chimps and gorillas execute similar tasks the way they respond is eerily human.

Pepperberg's work is made even more interesting with the work done on crows. Crows have been shown to use tools to gather food in the file. Raves have been shown to use logic in solving problems. In this experiment, the ravens were given a complex task to complete. This is not the interesting part. Many animals can be trained to execute complex tasks. These ravens were given the task to figure out for the first time. They observed the situation and figured it out.

So: we see intelligence in birds. The next question is what are they using to execute intelligence?

Remember, mammals use the cerebral cortex for intellectual pursuits. But the cortex evolved in mammals after they split from reptiles. Therefore, intelligence in birds cannot use the same mechanism. Evolution of the brain is (roughly) in three parts: reptilian, paleomammalian and neomammalian structures. (See here.) The cortex is a neomammalian structure.

Therefore, birds cannot be using the same mechanism as humans. Which shouldn't surprise anyone. We have to use a big sweaty cortex to get things done. Birds do the same thing with something the size of your thumb.

Makes you think differently about dinosaur behavior, doesn't it?

I asked Doctor Pepperberg about this and she thought the structures of intelligence might be originating from the tectum. In non-mammalians it serves as the main visual area of the brain. The development of the mammalian cortex arises out of the embryonic tectum. Doctor Pepperberger also pointed out that the experiments required to demonstrate this sort of thing would be fatal to the subjects and so she wasn't interested in it.

The other component of human beings that people point to as "special" is empathy and altruism. Well, turns out birds might well be displaying these traits as well. (See here.) Research with ravens has shown that behavior remarkably like consolation between victims of aggression and the rest of the flock show up regularly.

There's a common discussion among scientists and science fiction writers about the likelihood of intelligence arising out in the universe. The word, "intelligence", here is a code word for "beings like us". Animals that build cities, engage in cooperative behavior, show up on television and litter the sky with satellites.

But "intelligence" is far broader than we first realized. Ravens, gorillas, chimpanzees, elephants, wolves, dolphins and even cephalopods have all shown themselves to solve problems, use tools and communicate in a sophisticated fashion. It seems to me that once you have a brain in place there's a selective advantage to use it that's limited only by the ability to keep it fed and full of oxygen.

That said, where humans are unique is the joining of intelligence with hands and a mysterious natural selection for more intelligence. Chimps have been chimps for a million years. Humans have advanced enormously just in the last few hundred thousand years.

Now that might be rare.

Lies about illegal immigrants
Anti-vaccine people
Dale Peterson

Russian local globes
Modern forms of life had single origin
29 cases of evidence for macroevolution
Economics meets reality: Krugman discovers human irrationality
Effects of CO2 in oceans: 55 million years ago
Honey badger
Group selection in evolution
Giant oarfish
Hacking quantum cryptography
Organ legging
Eco-friendly aircraft
Jupiter loses stripe

World's smallest houseboat
Kathi's Tiny House
Homemade globes
Soda bottles -> Polyhedra
Roast your own coffee
Altoid BBQ grill
Banana cake
Mobile veggie garden
Lifting fingerprints
Making biodiesel

Friday, May 28, 2010

True Cost of Oil

(Picture from here.)

There's an article over at Clean Technica that talks about the cost of oil vs. the cost of renewables. The article is good but it got me thinking-- never a good sign.

Anyway, I started looking for sites that analyzed the total cost of oil. Here was on that was interesting. Go look at the post. It is that author's contention that if all of the effort of protecting the oil, negotiating with the member states, etc., are factored in the yearly cost of depending on oil is 10 trillion dollars.

The US GDP is only 14 trillion and some change.

You can argue with many of the numbers. But it does seem clear that while you can't lay the Afghanistan war on the door of oil, you can and must lay the war in Iraq. We would never have gone in there had it not been for Iraq's oil, regardless of the tyranny of Hussein.

The true cost of oil is far and away much higher than the comparative cost of renewable power. And we don't end up hostage to bizarre thinking in the mid-east.

This is when it comes down to political posturing and hidden agendas. United States security is a conservative issue. They should be leading the charge.

Yet, somehow, the conservative agenda has been hijacked by strange economic forces. You would think that a technological path that points us away from being dependent on other countries would be central to a conservative ideology.

I've said it before. We need a true conservative movement with a positive ideology.
Wall of Idiots
GOP crowdsourcing experiment

Thursday, May 27, 2010

What is the "Top Kill" Method?

(Picture from here.)

BP is trying to use a "Top Kill" method of stopping the leak. It may have been successful. But what is it?

Well, here's a quick guide to what it is. Enjoy.
Also, here's the link to the live video feed at the well head.

Wall of Idiots
SWAT teams
Mitt Romney

Vito Fossellia
Vaccine haters foiled again
20 worst drinks in america
Peak water: 1970

Wednesday, May 26, 2010

Consideration of Works Past: Podkayne of Mars

(Picture from here.)

First, let's get a few things straight. Heinlein is not God. Heinlein was a good, if pedantic writer. Like Mark Twain, he liked to pontificate in his work. Like Mark Twain, the quality of his work suffered when he indulged that predilection. Unfortunately, Twain was nine times the writer Heinlein was. Heinlein's later work degenerated into long sermons punctuated by meaningless action and pointless sex.

Podkayne is the story about a young girl about fifteen who has been raised on Mars along with her brother, Clark. Podkayne is fairly intelligent and sophisticated by Mars standards but, Mars being a frontier society, her sophistication pretty much fails outside of Mars. Her twelve year old brother Clark is considerably brighter and much less trusting. They travel towards earth in the company of her Uncle Tom ostensibly for pleasure but later it's known that Tom is on an important political trip for Mars. Things get sticky on Venus. Clark gets kidnapped. Tom gets kidnapped. Podkayne gets kidnapped. Tom is released to do their bidding. Clark develops a plan to escape. Podkayne gets trapped inside the blast perimeter of Clark's bomb.

Podkayne was written in 1962 and published, also unfortunately, in March of 1963-- eight months before the Kennedy assassination. Podkayne, as a teenager, is a late fifties early sixties girl. She wants to be a space ship captain. The pill came out in 1960. Betty Friedan's book, The Feminine Mystique, came out in 1963-- the same year Second Wave Feminism started. Consequently, any radical notions of women working in a man's world (a subtext in the book) were outdated the moment it was published and possibly before.

For example, Podkayne starts out in the beginning of the book all fired up to be a space ship's captain. Later, she admits that it's not so clear she has what it takes since her educational opportunities are limited. She considers marrying a space ship captain as a legitimate alternative to doing it herself. After all, babies are important and fun, too. She doesn't consider bettering the alternatives-- getting help from her Uncle Tom, who is an important senator, or from her possible boyfriend, who is rich beyond belief. In short, there are only two alternatives: slugging it out with a man or sleeping with him. In this, she's a fifties teenager, not the incarnation of a teen at the moment the book is written.

The ending, as published, has Podkayne in the hospital and Clark waiting for her. Clark has some hope of redemption of his sneaky and selfish ways.

Heinlein wanted the book to serve as a cautionary tale for parents that pursue their own goals at the expense of raising their children-- this is the reason for Uncle Tom's diatribe at the end of the book in the original, published ending. In his original, submitted, manuscript Podkayne died. Heinlein thought that having her die validated the rest of the book. The editors thought that killing Podkayne was a downer and had RAH change the ending. Hence, Tom's diatribe so that RAH can be sure we get the right message. RAH said that letting Podkayne live was like "revising Romeo and Juliet to let the young lovers live happily ever after." Which captures both what he thought of the required change and who he liked to compare himself at the same time.

From the tone above you can tell this isn't one of my favorite books.

First, the anti-parenting diatribe comes as a shock. There is no support for it in the book and since it's an add-on I need not respect it.

There are some interesting things going on, however. There's a racial subtext that apparently isn't obvious to a lot of people. I don't mean the obvious statements in the book. Tom is of Maori blood and is dark. Podkayne takes after the Norwegian side of the family and is blond. But there's a subtler, more interesting element. The very fact that Tom Fries is referred to as "Uncle Tom" cannot have been by accident. The scenes describing Pinhead the Venerian are reminiscent of southern white literature depicting black men as rampaging brutes. (See here.) There's also a scene where Podkayne reaches her limit and decides that she's going to plead with her Uncle Tom to do whatever it takes to save her. She's not proud but anything beats being tossed in the cage with Pinhead. RAH wasn't stupid. He knew what he was doing. It's not clear to me what he meant by this but it is clear he meant to something.

Finally, I'll weigh in on the ending controversy.

I read the 1995 version of Podkayne published in 1995. Apparently, there was an essay contest as to which ending was the best. The finalists were listed in the back of the book. Three versions of the ending were included in the book: the original, the first published version and an emended version combining the two.

Largely, the essays fell into "leave the original ending" camp. The biggest reasons seemed to be 1) because RAH wanted it that way and 2) reasons that RAH had given for wanting it that way. The pro essays were largely emotional of the "she's too nice to die" sort. The best essay was that Podkayne had to die because she was too stupid to live. RAH said

Which is close to what I would have said to RAH had he dropped Podkayne into our workshop.

Essentially, all of the essays, the editor and RAH himself were wrong though the "too stupid to live" essay was closest.

Consider the ending:
  1. Podkayne was out in the jungle with no hope of finding her way back.
  2. Clark gives her a tracker (essentially GPS) to help her find her way out. She loses it.
  3. Clark gives her a gun to take care of herself. She loses that, too.
  4. She doubles back to find a pet she'd left at the compound.
  5. She then gets lost and circles around in the blast area when Clark's bomb goes off. She dies/not dies depending on the version.
Yup. Too stupid to live.

But, like most problems in writing, the obvious solution (leave the original ending) is not the correct one.

It's not whether or not she dies that's the problem. It's the way the situation was set up. RAH set up a condition where her living or dying didn't matter. He had substituted sentimentality for pathos and by doing so made Podkayne pathetic regardless of what happened to her. It's a silly problem and both solutions are by their nature silly. The real solution is to change the problem.

Podkayne doesn't lose the tracker and doesn't lose the gun. She does turn around and goes after the pet. After all, how many pet owners have lost their lives returning to a burning building to save a cat or a dog? She gets the pet and runs outside but there wasn't time. She gets caught in the blast anyway. Perhaps she didn't figure the time well. Perhaps Clark's bomb went off early. Perhaps she bet poorly. Regardless, she was doing something she wanted to do and was caught by the blast doing it, not wandering in the wilderness like some lost and bawling calf.

Now, given that scenario her death (or life) has meaning. So, should she die?

I don't think so.

Forget all the issues of whether she's a role model or is too nice to die. That's all hogwash. What matters is artistic integrity.

For Podkayne to die is artistically sentimental. It's too easy. Podkayne doesn't get a chance to examine her life. (I submit that slogging through bog trying desperately to get away from a nuclear detonation isn't a good time for inner reflection.) She doesn't get a chance to open up her choices and decide her life. Nor does Clark. In either current version, neither gets an opportunity to look at themselves. RAH is giving us easy answers.

The last scene in the book would, of course, when Clark is there with Podkayne, her body burned and broken but with the possibility of recovery, and Podkayne wakes up.

I never liked Romeo and Juliet much, either.

Idiocy Level at Eleven

(Picture from here.)

Jesus. The idiocy level is exceptionally this week. Must be impending summer and mid-term elections.

I mean my Wall of Idiots list is huge.

I like a healthy debate. I like good arguments. I am not conservative myself by nature-- I've had too many opportunities in my life that came directly from the institutions derided by many conservatives to feel that way. But a good conservative opposition is absolutely essential to this country's well being. Any way forward out of this mess has got to be a blend of social responsibility and individual rights, intelligent investment and fiscal responsibility.

What we get is Sarah Palin: the intellectual rigor of overcooked spaghetti.

This week's crop must be led by the most egregious offenders: The Texas School Board, who voted to revise and dumb down history books.

More on it here, here, and here. Colbert was a hoot. But, of course, our greatest living journalist Jon Stewart was spot on.
Wall of Idiots
Lies about healthcare
Heartland Institute
Ocean heat increasing
Online education
American constituents
Newt Gingrich and here and here
Hawaiian Democrats
Rand Paul
John Boehner House, R-OH
Sarah Palin. As always. And here.

Monday, May 24, 2010

News from BVC

(Picture from here.)

Book View Café will be attending two major SF Cons this weekend. Lori Devoti, Nancy Jane Moore, Madeleine Robins, and Jennifer Stevenson will be present at Wiscon, held in Madison Wisconsin Friday, May 28 through Monday, May 31. Panels include: “My Big Fat Paranormal Wedding,” “Internet Publishing: The Graduate Seminar,” “A Path to Ending Women’s Fear of Men,” “The Colonialization of (Middle Class) Children,” “Research: ur doin it rong,” “Let’s Create an Online Business Model That Works,” and “Does Media SF Get a Free Pass for Scientific Illiteracy.” In addition to the panels, BVC members will be reading from their work at the all-BVC reading as well as signing books on Monday’s big Sign Out. Details and schedule here.

Also this weekend, Maya Bohnhoff will be at Baycon, Friday, May 28 through Monday, May 31 at the Hyatt Regency in Santa Clara, CA. She will be holding a writers workshop on Saturday. On Sunday she’ll be reading and signing her books as well as performing music. On Monday she will be on the Media Tie-in Fiction panel. Information on Baycon here.
Wall of Idiots
Environmental toxins linked to ADHD
More to worry about than global warming
Breaking climate science
BP oil enters Loop Current
House GOP stops science bill

Links of Interest
Good news: Malaria may not get worse from global warming
Resveratrol and SIRT1
Musk turtle breathes through its tongue

Bamboo bike frame
Flower bike spoking

The Oilpacoplypse Will Be Televised

(Picture from here.)

Here is a live video feed of the oilpacolypse.

A discussion of the events is here.
Growing deep water oil plums here.

It's enough to make you sick. In all senses of the word.

Wall of Idiots
Plastic soup in the Atlantic
Using fossil water

Links of Interest
Jupiter's stripes
Fish extinction allowed modern animals to arise
Scientists resurrect mammoth hemoglobin
The end of the ozone hole
New evidence that meteorites from Mars have fossils
How we make memories.
Eurotrash for power; US lags
Exoplanets eccentric orbits
Estimation of Earth like planets
Reinventing the internal combustion engine and here
New US chemical laws
Local brown dwarf
Magnesium for power

Saturday, May 22, 2010

Sim-Life... For Real

(Picture from here.)

The Second Big Thing that happened this week is the creation of an synthetic bacteria.

No, I don't mean fiddling around with an existing bacterial. I mean a fully functional artificial bacterial genome.

Craig Venter has been working on this problem for some time. His approach to artificial life is to create a synthetic bacterial genome and implant it in a host cell where the original DNA has been removed. The cell machinery itself is not synthetic.

Once the DNA was placed in the host cell, the cell behaved as it had been programmed to do by the synthetic DNA and not according to the DNA of the original host cell. The cell has replicated successfully.

This approach to synthetic life solves a piece of the problem: creation and transfer of a working synthetic genome.

The genome in question, though created in the lab, derives from a living system: Mycoplasma capricolum. The target cellular host is also a Mycoplasm. It is not a genome created from scratch to a particular purpose.

There is corresponding research into the smallest possible genome: the bare essential genome that can be used as a pattern for true synthetic life. Carsonella, for example, has only 182 genes and 160,000 DNA base pairs. The artificial chromosome used by Venter's team was a million base pairs. Carsonella, however, is a parasite. A recent nanoorganism, dubbed ARMAN, has been discovered in northern California. (See also here.) Its genome has about a million base pairs-- more comparable to Venter's chromosome.

It could be that Venter's team is pushing down towards the lower limit of a viable genome.

Articles on the work:
Nobel Intent
Jerry Coyne
Wall of Idiots
James David Manning. And here.
Gleeeen Beeeeck
Lies about Kagan.
Brit Hume
Rand Paul and here
National Republican Congressional Committee
Sue Lowden
House GOP
Douglas Hughes, R candidate for CA governor
Andrew Brown

Links of Interest
Solar ovens
Earthworms don't just eat dead things
Japan launches Akatsuki probe to venus
Sexual deceit in antelopes
Birds don't like organic seeds
BP tries again
Crane locomotives

Solar Homesteading Videos
Satay peanut butter sandwich
Terracotta home composter
Your First Robot
Garden rain barrels
Resin cast parts
5 minute bottle brush
Bucket bee hive
Solar cooking

Tuesday, May 18, 2010

You'll Wonder Where the Anti-Matter Went

(Picture from here.)

Two Really Big Things happened recently in science. One in physics. The other in biology. We'll talk physics here today.

The physics Big Thing has to do with the composition of the universe.

Anti-matter is the opposite of normal matter. Electrons have a negative charge. Their opposite number, positrons, have a positive charge. Protons have a positive charge and anti-protons have a negative charge, etc. Anti-hydrogen would be an anti-proton with a positron shell.

When anti-matter and normal matter come into contact they annihilate one another into photons.

However, there appears to be no other difference between anti-matter and matter. The particles are of the same mass. They interact with one another in the same way. Antihydrogen and antihelium have been created and appear to be identical to their normal counterparts.

So, in the big bang why weren't there equal amounts of matter and anti-matter created? (Other than we wouldn't be here to talk about it because we would be... annihilated.)

This has been an ongoing question for a long time and is referred to as asymmetry and is considered one of the big unsolved questions in physics.

Well, some new clues came out of Fermilab recently that sheds a few photons on the problem. It turns out that there are a set of particles called B-mesons that decay into matter and anti-matter. The neutral form of these particles oscillate between a matter and anti-matter form. Depending on the point of oscillation, the particle decay into muons or anti-muons. (A muon is an elementary particle similar to an electron. It has a negative electric charge. See here.)

The B-mesons preferentially decay into muons rather than anti-muons-- a preference of about 1%. Here's another demonstrable pre-disposition towards normal matter.

It's not much. But it is interesting.

The preferences that have been described are small-- 1% isn't very much since the universe is overwhelmingly normal matter. This causes me to have the following questions:
Is this tiny preference constant? Or was there a greater preference at the moment of the big bang?
If the preference is the same, and since normal matter is overwhelmingly present, this argues there was considerably more mass at the time of the Big Bang that was subsequently annihilated. Can that energy be accounted for?
Where is dark matter in all of this? Is there a normal/anti- form of dark matter or does it not have this sort of interaction?

Isn't physics fun?

Further links:
Nobel Intent
Wall of Idiots
Wall Street Banks
Glenn Beck
Teacher, Center High School, Alabama

Links of Interest
Mechanical swallowtail butterfly
Solar sails
Artificial life. And here. And here.
V: Human industrial palace in action
Llyn Foulkes: One Man's Band
Billboard stop action animation

PVC didgeridoos
Upside down tomato planter
Old window greenhouse
Pringles wind turbine
Solar thermal collector
Saving energy
Sun jar
Solar panels
Bike generator
Water flow sensor
Eco-friendly living room lamp
Power generating wind turbine
Solar PV tracker
Pulse oximeter

Monday, May 17, 2010

About "Two Boys"

My story Two Boys goes up on Book View Cafe today. I chose that one to put up this time in celebration of the sequencing of the Neanderthal genome. I spoke about that here and here.

The story came about in an odd way. I was approached by an editor to write something for his anthology. The idea of the anthology was to take a bunch of SF writers and have us write upbeat stories that solved the world's problems. The anthology never materialized.

I thought for a long time about this and came up with absolutely nothing. What did I know about curbing global warming? Stop emitting CO2, I suppose. Or world hunger? I guess one could feed people contingent on not having more children-- since that was the root of the problem. Clean up the environment? Hm.

The more I looked at these as "problems" the technical solutions were manifest. We know how to solve these problems. It's not a technical problem. It's a managerial problem.

I came up with two stories for the anthology. Two Boys is one.

Sunday, May 16, 2010

Neanderthal Speculations

(Picture from here.)

I spoke in my blog (see here) about the recent Neanderthal sequence effort and the resulting evidence that Neanderthals and humans interbred.

Now, mitochondrial DNA of Neanderthals was sequenced some time ago. (2008: See here.) What's interesting about that is there is no evidence in that DNA of interbreeding. This new information is about nuclear DNA and has several common points. I suggest you go to the previous blog mentioned above sequences to get the original information.

The high points, then:
  1. Homo neanderthalis is 99.7% identical to humans. (Chimps are 98.8% identical to humans.)
  2. Neanderthals and humans split about 400,000 years ago.
  3. Interbreeding could have occurred as recently as 80,000 years ago, when modern humans migrated out of Africa, but more likely about 60, 000 years ago.
  4. Approximately 2% of the genomes of present-day humans living in Europe to Asia comes from Neanderthals.
  5. No appreciable DNA in present-day humans in Africa appear to have derived from Neanderthals.
  6. There is evidence of selective sweeps: DNA that was found to be sufficiently selectively advantageous to move through the population.
From this point on we're indulging in pure speculation. No data to support any of this and the sample size is too small for prediction. We're just gonna' have fun.

The first interesting thing is the differential inheritance between nucleic and mitochondrial DNA. Mitochondria derive solely from the mother. Now this cannot mean that human men would not mate with Neanderthal females. Humans will copulate with anything: dogs, cats, trees, garbage cans. If it can be done, human males will do it.

It can mean Neanderthal females would not accept human male advances. There's some evidence that sexual dimorphism between males and females were not as pronounced as between human males and females. Neanderthals were incredibly strong in comparison with humans. It's fairly likely that a single Neanderhal woman could easily take care of herself against human men. This doesn't preclude gang rape or possible infanticide of the offspring. But we have to start building some pretty high air castles to account for no interbreeding.

Although there is one interesting scenario. At some point in human history we started hiding estrus. We don't know when that happened-- none of the characteristics of an animal being "in heat" fossilize. But it did and it did long before recorded history. Chimps, our closest living relatives, have the standard primate estrus cycle. The female is not particularly receptive to sex when she's not ovulating. The males are excited by the physiological signals she puts out when she is. Humans don't do any of that.

It's not a far speculation to think that Neanderthals were like chimps in this respect rather than human. Like other primate species, males are always producing viable sperm even when no available female is in the vicinity. It's not too far off to think that Neanderthal women, even if willing, would not necessarily be viable outside of estrus periods. And it's also not so far off to think of this being the point when they would be most vigorously defended by Neanderthal men.

Another possibility is the differential representation is biological. Possibly the cross of male Neanderthal and female human was viable but the cross of male human and female Neanderthal was not. Perhaps female Neanderthal reproductive systems rejected human embryos as non-viable or irretrievably damaged and female human reproductive systems were not so selective.

So we have back in the past two human groups cohabiting the same landscape where males from both species are competing for females of one species. An interesting dynamic.

Of course, it could all just be the result of genetic drift. That's the basis for the mitochondrial eve hypothesis.

Another curious feature of the research is the differential between African and non-African human groups. The answer is obvious: the humans that moved north didn't move back south. Consequently, any genetic sweep that occurred stayed north of the Sahara.

The two questions that immediately leap to mind are 1) What were the selective advantages of the genes in the sweep? and 2) Do they have any bearing on the world now?

Now this is the sort of thing a blogger might say: "here be dragons." After all, it doesn't take very much to get a good racist attitude going. The Eugenics Movement started with less.

Still, where we came from is an indicator of where we're going. So, let's dive in.

Some of the genes implicated as "sweep" genes are DYRK1A, CADPS2 and AUTS2. RUNX2 is also implicate. It's already known that Neanderthals share the FOXP2 gene, though it is thought that this is more an artifact of common heritage than interbreeding. DYRK1A is implicated in Down Syndrome. CADPS2 has to do with managing the vesicles in neurons and has been implicated in autism. AUTS2 is also one of the candidates for autism. RUNX2 is one of the regulatory genes for skeletal development. FOXP2 mutations have been associated with speech and language disorders.

So: we have two regulatory genes (DYRK1A, regulating cell proliferation and possibly brain development, RUNX2, skeletal development) and two genes strongly correlated with neurological development (CADPS2 and AUTS2).

Why would they sweep?

It can't have much to do with intelligence-- Africans show little difference from Europeans when corrected for test deficiencies. It's also an unlikely candidate since intelligence is highly selected among human beings. Any thing that swept on basic intelligence would be driven strongly towards maximum. I.e., we'd see a huge difference.

The skeletal development gene might be interesting. Are there cold adaptations in skeletal development between African and Eurasians? Hard to say.

It must also be remembered that whatever selected for the sweep of these genes through the population may no longer be active. We could easily be seeing an artifact of a past sweep and the relic has no present bearing at all. Or, it could be that the group that moved north had some disadvantages that were remedied by the introduction of Neanderthal DNA and the net effect is zero.

But I'm a science fiction writer. I like to play with dangerous things.

I've read Jared Diamond's two books: Collapse and Guns, Germs and Steel. When I read both books, I kept coming back to the idea of the Tragedy of the Commons, Garret Hardin's article from 1968. To encapsulate a very interesting idea: private gain trumps common good. This is something I see as an American all the time. (Of course, America is the encapsulation of the world, right?)

When I read about other cultures I see it considerably less than I see it in Euro-centric cultures. In many other cultures, tribe and/or family trump individual gain. What if this was something we gained from the Neanderthals, a change in the boundary condition between tribe and extended family versus local family and individual? A minor reduction in the ability of the individual to defer gratification based on inhibitory cultural patterns? A tiny reduction in the ability to sensing tribal/familial place? Something that might have served us back when we had to fight mammoths and glaciers but which has little place now?

Now, let me say on record that I think any genetic differences between races, genotypes and gender are completely overwhelmed by the noise of cultural adaptation. Whatever we use in our heads to navigate the internet or solve differential equations is not derived from any tiny differences accumulated from 80,000 years ago when one small group of humans moved away from another small groups of humans.

I expect there are differences between peoples based on genetic heritage. I also expect that they rarely manifest themselves as conveniently as simple differences in abilities. Do Kenyans have an innate genetic ability to win the Boston Marathon? Or are Kenyans predisposed by their upbringing and geography to win the Boston Marathon? My money is on the latter more than the former. But the former has more juice for a science fiction story than the latter.

To paraphrase Randy Newman, "I'd sell my soul and your soul for a story idea".

That said, genetic sweeps don't just happen; they're the result of something useful propagating through the biology of the population. They are evidence that different subgroups of the human population have, historically, evolved differently from one another.

They are relics of where we came from.
Wall of Idiots
V: Bleeding Gulf and here and here
Kagan and the American "Heartland"
Identity politics and the right
Tea Party Woodstock
Senator Kit Bond (R-MO) and here
Laura Ingraham
Republican lies about Bobby Bright

Links of Interest
DNA Robots
Bared teeth in archaeological artifacts
Possible new Homo species and here

Friday, May 14, 2010

Pet Trade Logistics

(Picture from here.)

We have pet turtles. The majority of them are captive bred and we like that for a reason: the terrible logistics of the pet trade. Most imported reptiles (or any exotic) come from the third world. This makes sense given that the developed world has largely depleted its own stock of reptiles or didn't have much to begin with. The path goes like this:
  1. capture
  2. holding in the source country
  3. shipping
  4. holding in the target country
  5. distribution to point of retail
  6. retail sale
  7. home husbandry
There have been some estimates that each step can take as many as 50-80% of the animals. But, even if only 10% are lost at each step, a hundred animals in the wild drop to forty-eight in the home. If 30% are lost at each step that forty-eight drops to eight.

We reasoned that reversing that logic, by competing with wild caught animals, any captive bred animal in the pet trade saved at a minimum forty-eight animals. Breeders lower demand on the retail end. It's not at all clear that this might have any effect. We'll see.
Wall of Idiots
Lies from the Pennsylvania special election
More birther nonsense
More bad climate news
Bogus anti-net-neutrality campaign
Cage match: Adobe vs Apple
Facebook: Creeping up the evil scale
Minerals Management Service
More crap about Kagan
Louisiana house

Links of Interest
Tracing light in paper
More on the new Eurasian human
More on the Burgess Shale
V: Clustershag at 10 Downing Street
Hermes Private Spaceship
Does immigration cost jobs?
Criticisms of Obama's space plan
Diabolically admirable evil: Paul Hubbert
Archaeopteryx biochemistry

Rok-Bak Chair and here
French toast
Nomad furniture
V: Solar cooking
Wall mounted barbecue
Inventions of Prisoners
Chicken house in a box
Database of electrical components

Monday, May 10, 2010

BVC Steampunk Photo Contest

(Steam Punk Iron Man from here.)

Book View Café’s Extraordinary Steampunk Photo Contest

In celebration of Book View Press’ upcoming release of The Shadow Conspiracy Volume II (SCII), Book View Café is holding a steampunk photo contest. The winning photo will be used on the cover of SC II which is scheduled for publication in December of this year. Prizes for the winning entry will include a copy of The Shadow Conspiracy Vol. I and The Shadow Conspiracy Vol. II, as well as assorted ebooks from BVC authors. Additional photos may be chosen for illustrations in SCII.

Details and rules for the Shadow Conspiracy Extraordinary Steampunk Photo Contest can be found here.

Wall of Idiots
Fox News
Pubic lice for sale
Don Benton, Washington state candidate
Blamethrowing: oil executives and the spill
V: Bradley Byrne, runnning for Governator of Alabama and here
Brad Goehring, R candidate for Congress
God smacking

Links of Interest
Language of evolution
Best optical illusion of the year
The ice in the oil slick: clathrates
Blackbird SR-71 flight manual
Status on the BP oil spill
Making government work: handling the oil spill
Black hole hurled from galaxy
Belgian recumbent bicycles
Tea-tards conquer Maine
Hexapod dance off

V: Stuck in Vermont: Tiny Houses
V: Overhead projector music
V: Jarton: The Robot
6 month solar duration images
Backyard fire pit
Twig trellis
Concertina disassembly
Spice jars
Tiny house in Pacific Grove
V: Tiny Yellow House
Soda can Stirling engine
Stirling engine videos: Here. Here. Here. Here.
V: Taking apart a Stirling engine

The Great Neighborhood Oil Spill

It's hard to put things in perspective when you hear it on the news. Paul Rademacher has managed to give us a tool to do just this with the Gulf Oil Spill.

If you go to his google maps site here, the site will take your given location and take the current extent of the spill and place it over the location.

I live up here near Boston. It covers from Boston to Worcester and a good portion of the harbor. I got the site from Jessica Palmers Bioephemera, which I highly recommend. Another site gives the perspective of the size of the really big oil spills: here and here. Current status here, here and here. Here's a discussion on how oil chemically breaks down in water.

Other places I've lived:
Columbia, MO: All of Boone County. Jefferson City. Booneville.
St. Louis, MO: All of St. Louis. Most or all of St. Louis county. St. Charles and much of nearby Illinois.
Seattle, WA: All of the Sea-Tac area. All of the inland sound. Bellevue. Snoqualamie. The nearer cascades. Mt. Rainier is missed. Barely.
Thousand Oaks, CA: Oxnard. Santa Clarita. Anacapa Island and a good deal of the Pilgrim Banks.
Huntsville, AL: All of Madison County. A good portion of north central Alabama with a tongue half way to Burmingham.
Albuquerque, NM: West nearly to Mesita. Santa Fe. Las Vegas, NM. Pena Blanca.
Wall of Idiots
Senator John Barrasso (R-WY)
NJ Judge Kenneth Del Vecchio and here
GW Bush US Minerals [Mis-] Management Service
People's impression of "just a theory"
Economic loss from nature loss
Senator john Cornyn (R-TX)
Losing coral snake antivenin

Links of Interest
Solar in a shipping container
Water colors as response to heart condition: Lorianne Parker
State budgets unwind. And here.
3 best optical illusions of the year
Footprints of nonsentient design in the human genome and here
Granny pods
Losing Voyager 2
World's tiniest cannon

Upside down tomato planters
Kid cabin
Vegetable oil heater
V: Bottle island
V: Peltier cooled cloud chamber
Biltong maker
Webcam -> Microscope and here
Molasses cookies
Sugar infused apple-cinnamon ice cream thingee
Wood lathe-sander-grinder/sharpener
Garden fountain
Coke can Stirling engine
Hybrid photovoltaic/thermal solar panel
Model hovercraft
Seasoning small section timber

Saturday, May 8, 2010

Neanderthal Hanky Panky with Humans

(Picture from here.)

I've had a love affair with Neanderthals since I was a kid.

From Brian Aldiss' Neanderthal Planet to Neanderthal references in Sover and Harrison's Apeman, Spaceman, I've been a junkie pretty much forever.

It's not an accident my first short story sale (A Capella Blues) was about the end of Neanderthals. I revisited them last year with a story, Two Boys, about Neanderthal resurrection.

For a long time it's been the position that Neanderthals and Homo sapiens never interbred. This has been, I think, resoundingly disproved by analysis of the recently sequenced Neanderthal genome.

Neanderthals co-existed with European humans for thousands of years. For a species (ourselves) that's been known to copulate with goats and dogs, I've always thought that it was impossible for humans not to have copulated with Neanderthals. I speculated on this in A Capella Blues, thinking that one significant difference between Neanderthals and Homo sapiens was the open ended sexual nature of humans as opposed to a closed estrous cycle of other primates.

The delirious humping mentality of Homo sapiens aside, the question of offspring was always curious. Hence, the research.

The Neanderthal sequences were first reported back in 2006. (Incidentally, inspiring Two Boys.) The work had to be redone because of Homo sapiens contamination. That work was completed and reported in this week's Science magazine gave evidence of interbreeding in several ways.

First, it was noted that the Neanderthal genome was pretty uniformly distinct across much of its range as evidenced by the difference between the samples sequenced and known human sequences. Even so, Neanderthal genetic difference from human appears to be pretty minor. There were only 78 differences in the sequences that "encode proteins that are uniformly present in humans but absent in Neanderthals." (See here.)

The similarity between the species is more than skin deep, much of it in the regulation of other genes. Neanderthals had the human form of many regulatory genes 90% of the time. There were still several changes in the Human Accelerated Regions (HARs) that humans had picked up since the original divergence from Neanderthals.

So far, this does not constitute evidence of interbreeding.

The authors looked for what is called a "selective sweep": a mutation that proves useful and migrates through the population since its selective advantageous.

They found 200, many involving neural development. One of which shows evidence of sweeping through humans after we picket up the Neanderthal copy. We've got the Neanderthal copy of the gene.

To push this further, the copy of the gene that is Neanderthal isn't uniformly spread through the human population. It shows up in European and Asian populations much more uniformly than it shows up in African populations. Neanderthals were restricted to Europe and Asia when the human invasion began.

This brings up very interesting ideas. For example, if the genes involved were advantageous enough to spread through one population (Europe and Asia) but not through another (African), what does that mean in modern times? Were they advantageous only in the areas where the Neanderthal was prevalent? Are they advantageous or disadvantageous today? The nature of the sweep says the genes were important enough to sweep through the populations at the time but that says nothing of the nature of the advantage.

Not all the Neanderthal DNA was sequenced: there's not a complete genome available. So we're not going to see my characters from Two Boys any time soon.

But we might some day.

Original Science Articles
Nobel Intent
Science News: Here, here, here, here.
Gordon's Notes
John Hawks
Jerry Coyne and here
Signs of the Upcoming Apocalypse
Glenn Beck more reasonable than John McCain

Wall of Idiots
Neil Cavuto
Reverend George Rekers and here
Bobby Jindal
Technology fail in the Gulf Spill and here
Rupert Murdoch
Chris Cates
Blanche Lincoln
AB32 Implementation Group
Rush Limbaugh Listeners
Drill, Baby, Drill
94% fish stock fall since 1889
People magazine

Links of Interest
Naked Mole Rats!
Star creation
Back to the moon
Found objects and Jean Shin
Giraffe-necked tortoises
Ian McEwan's Solar reviewed
System regulation: E. coli vs. Linux
You are your microbes
White House to host science fair
US CO2 emissions drop
Google Energy
Invention among primitive people

Friday, May 7, 2010

Deep Idiocy

Okay. This one is such an idiotic idea, just placing it in the Wall of Idiots section was too little.

Representative Charles Dent (R-PA) and Senator Joe Lieberman (I-CT) have proposed a plan to "revoke the citizenship of Americans who side with terrorists". (See here.)

Note: It doesn't say plan to prosecute Americans or try them. It's to revoke their citizenship.

Hell, even baby rapers and mass murderers, people who have poisoned their aging mothers, people who eaten their fellow man, have not had their citizenship revoked. They've had their voting rights revoked. They've had their property confiscated. But they have remained citizens.

Of course, there would have to be a "complete investigation" and "convincing evidence".

No. "The burden of proof would have to be on the State Department." I don't care. Citizenship is not something the government should be able to take away. When did we give our government ex cathedra power?

You! Over there! I don't like you. You don't deserve to be a citizen. You are hereby excommunicated from being an American.

Fox News is, of course, right there to help.

This is bad ju-ju. A reprehensibly stupid idea. In a similar (but nowhere near as egregious) show of governmental idiocy Senator Orrin Hatch (R-UT) slammed the FBI for Mirandizing Faisal Shahzad, an American citizen.

Is it not remarkable that those that claim to distrust Big Government are the very first to give that government Big Power?
Wall of Idiots
Washington Times
Mike Pence
Bill Kristol
Jon Scott
Louisiana State Rep Henry Burns (R)
RNC Chairman Michael Steele
Michael Brown/Fox News and here and (incredibly) here
John McCain
The search for Noah's Ark

Links of Interest
Real time natural selection
Aphids steal genes from fungus
Douglas Adams on endangered life
Early electric trucks
Mirror Man
Facade printer
Pakistani vehicle painting
Weaponizing Wall-E: Peter Clute
Box jellyfish
Element photography
Honda's Segway

Soccer ball from found materials
Simple workbench
Multitasking workshops
Office crossbow
Fab@Home acrylic body
Anaerobic digester for methane
Folding guitar stand by
Workshop organization ideas
World smallest car