DIY Friday

I haven't done one of these for a bit and this one won't be too long. But here are some fun hacks.

Skulladay: puts up or creates a skull image every day.
Jointmaker: a new kind of hand saw.
Springfield Middle School Tilapia Project
Jar Lights
Brass Rocking Horse
Famous Hacks from NASA
Garden Arbor
DIY Spectrophotometer
Growing Silver Crystals
Media stand furniture: looks a bit like some old Chinese furniture I saw in a museum once
1o1 Crafty Ideas
Blue Tooth Robot

and finally

DIY Fusion Reactor: I don't think he's kidding

Brass Ukuleles

Nice and interesting build of a brass ukulele here.

Were you thinking I was referring to something else?

Speaking Norwegian in Hell

Here is a comic from Russel's Teapot. (Link here but it no longer seems to work.)
Get more here, here and here.

Russel's Teapot is by Chaz Broman. As far as I can tell he as copyright. So if he chooses to contact me I'll take it down.

But just in case the site never returns:

Holiday Thoughts

I've been talking about how the evolution of things for a long time now. And it's very, very cool stuff. I've talked about shoulders, feet and hands. I've talked a little bit about Neanderthals. Animals. Cuttlefish.

But there's still a great deal of mystery out there. A lot about life in general and a whole bunch about us in particular.

These mysteries are still there. For one, our brains are seriously over-engineered for hunter-gatherers. Chimps are hunter-gatherers and don't have near the horse power under the hood we do. I know that comparing chimp hunting and gathering to what we do in the wild is a limited comparison-- we do a whole lot more. But, that said, why is the horsepower so necessary for what we clearly did in the past?

Why is there art, for example? And we've had art for a long time-- over twenty-thousand years if you judge by the cave paintings. Probably a lot longer. What is it about our evolutionary history that caused us to accrete an appreciation of beauty? Is it just that our surroundings were important to us? Then why do we view such blasted landscapes as the badlands or the Grand Canyon as beautiful? Why do we care?

Why is there music? How is it we can be transported by a Beethoven symphony or a Bach concerto? How is it we're transported at all?

Are these qualities side effects of the extraordinary brain or is there something more going on here? Something fundamental. Something interesting.

Let's be clear: I'm not saying there is any supernatural force here. We made ourselves by our reproductive choices over the last few hundred thousand years. There's nothing supernatural to it.

But I am saying that if there is such a thing as divinity in the universe, it's us and it would be a big improvement if we started acting like it.

The Creeptacious Era

Another Bioephemera winner. I give up. Just subscribe to her feed like I do.

Vas du Nacht Before Christmas

Bioephemera comes through again.

Werner Herzong's Night before Christmas.

Fox Viewers More Misinformed than Others

Here's the study.

Like any good evolutionary biologist, I know correlation is not causation. Are the viewers of Faux News misinformed because of Faux News or is it their innate stupidity that attracts them to Faux News and they are therefore more misinformed?

Relationships: They Do a Body for Good

Saturday Morning Breakfast Cereal presents the very finest in self-revelatory card games: Relationships!

Presentation of the Fourth Horseman Award

Another winner from Bioephemera and the United States Navy: The Return of Count Spirochete!

Statistics Visualization

One of the problems, I think, with science education is visualization. By this I mean the ability to take data and transform it into a good representative metaphorical representation so that it can be understood. The best scientists can do this with raw information. Many of us that are familiar with managing data can do it fairly well but stumble.

Those without the skills are forced to rely on anecdotal evidence-- which is no evidence at all. Personally, I think this is at the root of a lot of American problems including understanding evolution, climate change, vaccination and economics.

The BBC is doing a documentary on the joy of statistics. Part of the documentary directly involves visualization. (Terrific visualization here.) Brought to my attention by the , brought to my attention by Bioephemnera.

Visualization is the key to understanding and understanding science is the key to human survival.

Red Stimulus Forever

Interesting link between net government revenue recipients with social and economic conservatism.

I like living in a blue state.

BVC News

Holiday Cheer: Free reads from Book View Café.

BVC authors present their holiday-related fiction for your reading pleasure!

Go here.

Sex

Now that I have your attention...

The evolution of sex is one of the hardest problems in evolutionary biology. I'm defining here sex as the combination of genes between two individuals producing a new individual or set of individuals that is genetically novel from the parents. There are two pieces of it and I'm only going to talk about one of them. These are:

1. How did sex originate?
2. Why has it remained?

I'm just going to talk about why it's still around.

You would expect asexual reproduction to to win hands down at evolutionary roulette. After all, there's a fair cost to sexual reproduction. Regardless of how it's done, whether there are two organisms that find each other against all, subsequently losing their reproductive opportunity when their host ship strikes an iceberg or vast clouds of paired cell types mixing together in the restless sea, two different genetic patterns have to discover each other, meld and produce a new organism.

Cells reproduce non-sexually by means of mitosis: duplication of the DNA into two new cells. Reproductive cell division is different in that the result is a cells with half the original complement of DNA. Even worse, for the DNA to be meaningful it has to be a meaningful half-- a complete working copy of the mechanism. Which means each cell of a sexually reproducing organism has to have double the amount of necessary DNA for its operation. Otherwise, when it produced sex cells they would not have the necessary completeness for the next generation. More expense.

We have the expense of sexual delivery and the expense of duplicated material. In addition to that, given the increase of raw material there is the increase of the total amount of mutations in that raw material.

These are the basic costs of sex itself. But there is a second category of problems with it. The reproducing organism only gets to pass on 50% of its genes.

With all of this, nearly all of the multicellular organisms use sex. Multicellular organisms who reproduce exclusively asexually are often found to be evolutionarily recent and die out quickly. All this despite its cost and inefficiency.

You can't win. You can't break even. You can't get out of the game.

There are a lot of theories about sexual advantages, it being one of the central problems.

The oldest idea, proposed by August Weismann back in the nineteenth century, was that sex introduced dissimilarity in offspring thereby enabling variation. Variation is the necessary precondition to natural selection. A variable population is better able to respond to a changing environment. Asexually produced offspring and genetically identical to the parent. Whatever variation has to derive from beneficial mutations-- a rarity.

Another approach to variation tackles the issue of variation propagation. In an asexual species a beneficial mutation is limited to the bloodline of the parent. In effect, all bloodlines within a species are competing directly with each other as if each bloodline were a separate species. There is no mechanism to share possibilities with one another. In a sexual species a beneficial variation can spread through the species, sometimes very quickly. Such a propagation is called a selective sweep.

One of the more widely held concepts (and one that I particularly like) suggests that a variable population is better able to resist parasites and disease. Let's say you have a genetically identical population of animals. Like any other population, they have parasites that prey on them. If a parasite develops a novel and effective way of attacking the population it can strike them down to the last individual since they are all genetically identical. (This theory, by the way, was derived prior to the discovery of shifts in traits across generations by non-genetic means. As far as I know there is no modulation of the hypothesis from this recent discovery.) A genetically diverse population, and one that continues to propagate its diversity, presents a moving target to parasites.

This is something we've seen in both plant and animal husbandry in recent decades. Several plant disease, such as the potato blight, had as a precondition use of a monoculture of agricultural organisms.

It's also been seen in the wild recently. Potamopyrgus antipodarum is a common fresh water snail in New Zealand. There are sexual versions of this snail and asexual versions. The population dynamics of the two versions were studied over the ten years. (See here.) Initially, the clones had the numeric advantage. But over time they degraded and some bloodlines disappeared altogether. The sexual populations remained largely stable.

There is strength in diversity.

BVC News

Book View Café Releases Katharine Eliska Kimbriel's HIDDEN FIRES

HIDDEN FIRES (Chronicles of Nuala 2)
Katharine Eliska Kimbriel
December 1, 2010 $4.99
ISBN: 978 1 61138 031 6

Nuala ... planet of deadly radiation levels, humans who heal by touch, and the rarest platinum group metal in the known galaxy.

Tribal leaders "Silver" Darame and her husband Sheel Atare have brought an uneasy peace to a world racked by sterility, intrigue, and unimaginable wealth. But two con artists ripe for mischief (and maybe murder) tangle with two misplaced quests, and political intrigue explodes into a conspiracy of death, treason, and abduction.

See here.

Not much today

I'm having a pretty busy time and can't do much more than my biweekly blog.

But I did find a couple of interesting things:

Periodic Table of Irrational Nonsense -- from Science Made Cool.
A vile condition in Florida here.
Epic Misney by T. Campbell.
Tom Tomorrow's take on The New Bipartisanship... It isn't pretty.

That's it for now.

Natural Selection in Homo sapiens alchemis

(Picture from here.)

This week we watched the new Harry Potter movie. Quite aside from the odd dreams it gave me (think Harry Potter vs. Stargate) the subculture of the wizards and witches, and their intrinsic abilities, suggested a subspecies of humans much like Homo sapiens neanderthalensis and our own Homo sapiens sapiens. I have named this subspecies Homo sapiens alchemis.

Consider the qualities of H. s. alchemis: There is limited reproductive communication with the neighboring subspecies, H. s. sapiens, as evidenced by the ferocious self-policing of the culture from outside contamination. It is not clear if a cross between alchemis and sapiens is fertile. We'll have to wait until part two to find out of there will be Weasley/Granger offspring. Fertility of the cross does not necessarily invalidate alchemis subspecies' status, however. There is evidence of cross-species fertility in other animals. Liger and tiglons, for example, though thought to be sterile have been shown to be fertile.

The dominate salient trait in alchemis is paranormal abilities. The trait is significantly variable in the population (note Harry Potter's aunt who did not inherit) and common in a distinct population. One would presume it is advantageous-- or is it?

Wizards have been documented as long as there has been documentation. Before written descriptions there are shamanistic artifacts from the neo- and mesolithic periods in human development. It would hardly be a stretch to mark the introduction of the genetic variation that led to alchemis according to these indicators. Therefore, we can estimate its appearance sometime in the last thirty thousand or so years. There's some evidence that sapiens and neanderthalensis coexisted for some time before extinction of the latter began. Possibly the introduction of the alchemis variation had something to do with it.

The actual age of the alchemis variation will remain speculation until DNA sequencing of an alchemis specimen.

Regardless, it is certain that the introduction of complex of genes that comprise the alchemis variation had some impact on the natural selection of the root population. A truly advantageous mutation would spread rapidly through the population in a selective sweep-- such as the duplication of salivary amylase genes in sapiens enhancing utilization of starches in the diet. However, the alchemis variation has only resulted in a relatively small population of magicians, powerful though they may be. Clearly, the situation is more complicated than it appears.

The genes responsible must be involved in brain development-- an hitherto unknown organ in other parts of the body being unlikely. Since speech appears to be involved even in very experienced wizards the speech centers may well be involved. We know the actual content of the words has little if anything to do with the effect since these "incantations" are in the form psuedo-latinesque gibberish and based on a language occuring long after the appearance of H. s. alchemis effects. One wonders on the variations of FOXP2, for example, in alchemis family trees.

Genes often have more than one effect and genes involved in brain development are no exception. It is entirely possible the traits under observation (i.e., wizardry) are concommitant with other traits that limit the spread of the alchemis variation in the general human population. While we don't have controlled scientific evidence of such limitations, we do have indirect observation of them as expressed in the way the culture uses the variations:

• The culture is hiearchically rigid and self-limits innovation. Use of magic is limited to repitition of earlier magical forms. There are few spells involving electricity or internal combustion and those that do use primitive forms.
• The culture is slow to adapt to innovation from the surrounding culture. Note extensive use of archaic technology in the schools. Candles, for example, instead of electric lights. Extensive use of hand written books in lieu of printed material. No computers or internet.
• The culture is violently xenophobic secretive and appears to barely be able to apprehend the existence of non-European cultures.
• The young are inculcated into this culture early and only dimly recognize the possibility of educational institutions past high school.

This latter point bears some investigation. Recent work on neanderthalensis suggest that their maturation process is considerably more rapid than that of sapiens. The extended childhood of sapiens may have an advantage in allowing more brain development. The cognitive impairment of alchemis coupled with their rapid maturation and localization to a European locale could indicate that alchemis was the result of a neanderthalensis/sapiens cross.

The xenophobia of alchemis is well documented to be self-destructive. In fact, I think this is the qualitiy that self-limits propagation of the alchemis variation. Alchemis qualities strongly favor in-breeding within the population. The vicious hiearchical nature of alchemis introduces culling as a means of limiting reproduction to the alpha wizards and their cohorts. Triumphant male lions kill the cubs of the previously dominant male. Wizards selectively kill the opponents of their dominant male. This has the effect of preserving the bloodline of the alpha wizards and destroying the bloodline of the opponent. That this effect is not the wizard's intention is immaterial.

This localizes the population in two directions. The xenophobia prevents outcrossing and the dominance slaughter prevents competition. The net effect is to isolate and reduce the population, limiting both the spread of the alchemis variation through the sapiens population and the size of the alchemis population itself.

In this case cultural isolation is a product of biological isolation rather than the reverse.

The future of Homo sapiens alchemis is in doubt. Though the population is influential it appears to be in decline. Sapiens is clearly outcompeting it on two levels: numerically, a few thousand alchemis versus billions of sapiens, and technologically. The rate of sapiens' technological innovation far surpasses the magical innovation of alchemis. Within a generation any advantage of alchemis magic will be overcome. Since this is the only advantage over sapiens possessed by alchemis, its future is in doubt.

This is a problem.

Alchemis is the only surviving subspeicies of genus Homo sapiens other than H. s. sapiens. Though the subspecies is difficult and unlovable, it is our kin and deserves our protection. It is also in our best interest to preserve the population. We have made great strides in antibiotics and medicines by examining the exotic plants and animals elsewhere in the world. Alchemis has also been studying the world's plants and animals and has made discoveries we would find beneficial. Not to mention that some magical technology can be used to accelerate our own understanding of the natural world.

Finally, like our studies of chimps and gorillas, examining our own neighboring subspecies can only benefit our own understanding of ourselves.

BVC News

Book View Café Releases Judith Tarr's Writing Horses, The Fine Art of Getting It Right.

WRITING HORSES, The Fine Art of Getting It Right (original non-fiction)
Release Date: November 15, 2010
Price: $4.99
ISBN: 978 1 61138 030 9
Formats: .pdf, .epub, .mobi, .prc

How far can a horse travel in a day? What does a horse eat? When is a brown horse really a sorrel (or a bay, or a dun)? What do 'tack' and 'withers' and 'canter' mean?

Author and horse breeder Judith Tarr answers these questions and many more in this long-awaited guide for writers, with insight into the world of the horse and the humans who both use and serve him.

Here.

Vladimir Putin Action Comics

The title says it all. Here.

Moral Evolution

Having dabbled last time in why some have difficulty with human evolution, I thought why not jump into the lake with both feet? Like Janet in Rocky Horror, "I've tasted blood/Now I want more." I'll have to make do without a chorus chanting, "More. More. More."

One of the defining characteristics of human beings is an inherent disposition to morality.

For my purposes I'm going to define morality as a set of principles that are intended to apply to human behavior. I want to differentiate morality from sentiment-- where one might do the right thing just because it makes us feel good. Moral codes are defined not by what feels good but by how we make hard decisions. A moral decision without cost is no moral decision at all.

What's interesting about human beings is how various we are. Even with that broad diversity there are some features that appear to be present in some for in all human societies: gender roles, rules regarding pair bonding, religion, parentage, music, morality and dogs. I think we can be on fairly safe ground that when we find a feature common to all groups of human beings we can define it as a part of our common biological heritage.

Note that I did not specify the nature of the different rules regarding pair bonding, etc. Just their presence.

Franz De Waal, one of my personal heroes, has spent a great deal of time finding common ground between humans and chimps. The first book of his I read, Chimpanzee Politics: Power and Sex among Apes, was a brilliant case study of the rise to power of an alpha male, his fall before a rival, the building of his supporting coalition and his return to power. If chimps are that close to us in one arena, why should they be so far from us elsewhere?

De Wall goes on to discuss the presence of empathy across the animal landscape. (See here.) But empathy and sentiment are not morality. While the underpinnings of morality, the recognition of fairness, the ability to sympathize, altruism, appear to be present in several disparate species (not all of them primates) other animals do not appear to codify these qualities into morality. Moral thinking requires being able to abstract from personal judgment to judgment for the group-- to go from "this is good or bad for me" to "this is good or bad for all of us". It's not at all clear that other animals have been able to make that jump.

Not to mention that humans often follow moral rules when there is no one present to observe. Morality works when nobody is around. As Emilio Lizardo said, "Character is what you are in the dark."

Darwin thought that a moral sense was inevitable given the right circumstances. He thought that any social animal "...would inevitably acquire a moral sense or conscience as soon as its intellectual powers had become as well developed... as in a man." While I think this is probably true as far as it goes, I think it doesn't recognize any role morality might have played in the animal developing those intellectual powers.

One of the interesting facets about evolution how it self-modifies over time. Humans developed upright posture long ago. But the act of beginning to develop our upright posture also had effects on our diet, our gait, our ability to run from predators, etc. These changes then also modified our bodies regarding our upright posture. A selection for one trait doesn't just work on that one trait. It works on the rest of the organism-- which has a knock on effect on that one trait. Everything is connected.

Human brains are difficult to figure out. Not only because they are so complex but because they are difficult to take apart. How a femur fits into a hip is fairly straightforward. Teasing apart the musculature that makes it work is somewhat more difficult but not terribly so. But when you open up the skull of a mammal you find some jiggly misshapen structures that appear to be made of a stiff gray good. When you cut it open you get more gray goo. It takes a fairly sophisticated technology just to be able to see all of the cells at all much less how they talk to one another. The technology is barely a hundred years old. (And is the discipline two of my heroes: Ramon y Cajal and Sir Charles Scott Sherrington.)

However, we know it took quite a while to transform monkey to man in terms of upright posture, hands, feet, shoulder and size of brain. It seems unreasonable to me to then suggest that the brain organization, which surely must be the basis for our moral sense, took any less time for an equally significant change. While we must recognize that our ancestors from a million years ago were not us, we must also recognize that they did become us, with all our foibles including our moral sense. It must have evolved, feeding back into the rest of our evolution, just as the growth of our thumbs, the reduction of the shoulder and the lengthening of our femur. And with all of the wrinkles, warts and discolorations that are the hallmark of the ad hoc nature of evolution.

So, given that assumption, we are pushed into the corner of an evolving moral sense that at worst was benign and at best aided our formation.

We are left, then, with wondering why we would have need of a moral sense and how it could possibly be selectively advantageous.

Most of the speculations I've read have to do with the invention of altruism, concern and action for the welfare of others that do not directly benefit the self.

Robert Axelrod wrote a book, The Evolution of Cooperation, suggesting that altruism came about in part as a mechanism to defeat the Prisoner's Dilemma. The game is boiled down to a situation where you and your partner execute a crime and your caught. The police grill you separately. Here's the deal. They don't have enough to convict you both outright but they have enough to send you both up for one year. However, if one of you turns on the other then they can free the defector and put the other one up for ten years. The best outcome for both is neither of you squeal and the two of you do your time. However, there is a significant advantage in defecting for the one to do it first. Remember, the two of you have been separated so it can't be discussed. If you're both "moral" (adhering to a code) and neither sticks it to the other guy, both of you have a better outcome together. But if you cheat you might get a better outcome alone.

To reframe it, you and your partner civil rights worker are caught in marching in Selma. Bull Conner takes you to jail and puts you in two cells so neither of you can communicate. Bull goes to each of you and says he wants a confession. First one who confesses gets out free and he'll beat the other one to death. And he'll keep beating on you until he gets tired. The rational, non-altruistic person gives in immediately, signs the confession and walks out of jail. The altruist takes a deep breath and hopes like hell there's a higher power that recognizes such sacrifice. There's no other possible gain.

How could such behavior possibly evolve?

Darwin invented the idea of group selection, where inherited traits are selected for and spread through a population such that the entire group of individuals benefits. There are some significant problems with this since it doesn't seem to account for the time between when the trait first appears and when it has saturated the group. The trait must not only benefit the individuals with the trait so it can spread, it must also benefit the individuals of the group without the trait so the group can be selected for. Some traits might work this way-- immunity to disease, for example. It benefits the individual that doesn't get sick and it also benefits the group in that the disease is deprived of a vector. It's hard, though, to see how altruism would work in this way.

Another idea is reciprocal altruism, the I-scratch-your-back-if-you-scratch-mine. This has some credence as evidenced in a variation of the Prisoner's Dilemma when the game is repeated. As the game proceed (or life) proceeds and the behavior and reliability of the other person is discovered, the partners can rely more on a verified prediction of their partner's behavior. One would also presume, as described above, that if you see your partner civil rights worker standing fast it would be more likely you will stand fast, too.

Computer simulations (and actual PD tournaments) have suggested that the best strategy for long term victory to be nice:

• Cooperate: never be the first to defect
• Return defection for defection, cooperation for cooperation
• Be fair with your partner
• Don't game the system

One wonders about the last point. I expect gaming the system works only so long as cheating detection and punishment are effective. "If we reward Wall Street, they will do it again" sort of thing.

But I think these altruistic approaches solve only half the problem. Yes, we do good things. It's good that the fig wasp doesn't lay so many eggs it kills the fig tree. It's good the cleaner wrasse isn't eaten by the shark it's cleaning. But while not all sharks are human beings, some human beings are sharks. We have to accept that the species that likes puppies and pats the heads of small children is the same species that tortures and eats those children and puts their parents into gas chambers.

Let's go back.

Humans likely lived early on in groups similar to that of chimpanzees. These are called fission-fusion groups. These sorts of groups range around 50 individuals and sleep together even if they range in small groups during the day. One could argue that humans live in elaborate fission-fusion groups today if one changes the word "sleep" to "work". But that's another blog entry. But we have a singular difference that happened very early on. We were essentially omnivorous scavenging prey species for a long time. Somewhere between Homo habilis and Homo erectus we became hunters.

Now, this is interesting. Band size was on the increase. We had meat-- brain food if ever there was one. We went in to being Homo erectus already social and fairly smart-- brain size was similar, though somewhat larger, than modern chimpanzees. By the time we were Homo erectus, brain size was 850 cc and rising. We started smart and we got smarter in about a million years. More interestingly, we went from being prey to being predators. But I suspect our brains, while bigger, weren't organized all that differently. After all, we had more or less the same body as before with some significant improvements. It's likely the brain was also more or less the same as before, with some significant improvements.

Let's think about that for a minute. You're a chimp out there in the veldt. You worry at night about leopards and hyenas. You worry in the daytime about lions and hyenas. You're always looking over your shoulder. Within the group you're always worried about your place in the group-- getting cast out means pretty close to certain death. Worry, worry, worry.

Then, in a blink of an eye, you're out there killing some of these guys. Maybe not leopards, hyenas and lions, but those animals that were pushing you away from the carcass you were eating yesterday? They're the carcass today and you're eating them. Your brain gets bigger. You can see lots more ways to do this killing thing better.

Back in the olden days, you were Long-Nose-McGrunt, not much smarter than a chimp. When Og-Hefty-Balls came down and beat the crap out of you because you were trying to get it on with his favorite female, Big Bumps, there wasn't much you could do.

Nowadays, you have a much bigger brain. You look at Og-Hefty-Balls over there and you think, Hm. You know, if I took this sharp bit of flint and sliced the tendons over his ankles he wouldn't be able to walk. Sure worked that way on the buck we killed last week. Probably work on him just as well. Then, Big Bumps would be available.

Or Big Bumps might be saying you know? Og-Hefty-Balls is okay as a hunter but he doesn't treat me so well. Long-Nose is always nice. I bet if I cozy up to Long-Nose over there he might just solve this problem for me. Or, I could just borrow a knife from Long-Nose and do it myself. What's to stop me?

That scenario wasn't so adaptive. They found the remains of that particular group all over the cliffs at Olduvai.

But the other group across the hill thought, well, I could slit Og-Hefty-Balls crotch to sternum and have my way with Big Bumps. I just don't want to.

They did all right.

Links of Interest:
Science of Morality
Moral Thinking from The Economist
Evolutionary Origin of Religion
Richard Joyce's The Evolution of Morality

Not much today. Read the links.

I read a lot. So here is today's sampling of sites.
Enjoy.

• Five Books: An expert chooses five books on their special subjects and recommends it to the lay reader.
• Carnival of Evolution #29
• A NYT article on the Great Plague of Europe. (Not to be confused with Randy Newman's song, the "Great Nations of Europe." Or maybe it should.)
• Wilmot Baptist Church Judgment House.
• The suicide of Zach Harrington.
• Physics of Mind and the Limits of AI
• The Politicians We Deserve
• You Tube Videos of the International Atheist Conference
• Politics of Global Warming Denialism
• Web of Stories
• Hitchens vs. Hitchens: Civilization with/without God
• NYT: Morals without God by Frans De Waal
• Good analysis of the 2010 election (with some ranting) here. Also here.
• Alaskan politics
• Brain development in Neanderthals
• The Oatmeal on Toilets

Athiests Have Their Own Hymn

...courtesy of Steve Martin. Here.

An Event Sociological

Jon and Al Kaplan have made several parodies that are fun to watch. Including, Spartacus: The Music Video, 24 Season Two: The Musical, and Conan the Barbarian: The Musical.

But they've outdone themselves with Silence! The Musical, based on The Silence of the Lambs.

Mel Brooks would be proud.

Wikipedia entry here.

Check out some videos on YouTube by entering Silence! The Musical for the search.

BVC News

Four new ebooks will debut at Book View Café this month. Two are backlist fiction (GALVESTON by P.G. Nagle and HIDDEN FIRES by Katharine Eliska Kimbriel), one is original fiction (THE HANDS OF GOD by Gerald M. Weinberg), and one is original non-fiction (the long-awaited WRITING HORSES by Judith Tarr). The books range in price from $2.99 to $4.99 for DRM-free ebooks. Full details here.

A Tiny Island of Blue Sanity

I could have written this on Wednesday but I wanted to digest the election news.

First the bad news.

Unless you've been living under a rock you know that the Republicans (or as I like to call them Satan's Little Helpers) took the House and made serious inroads into the Senate. Reid won in Nevada. Bennet won in Colorado. The solid blue states remained fairly blue-- California, Washington, Oregon. O'Donnell lost in Deleware-- a victory for the forces of right if there ever was one.

The "Enthusiasm Gap" (See here.) seemed to account for a lot of it. The Tea Party seemed to make the Republicans more enthusiastic about voting. Democrats, not so much. And, as one would expect, the groups that get out more votes tend to win elections.

My own opinions are well known. (See here.) So we gave to keys of the House car to the drunken teenager that ran it into the ditch in the first place. What's worse, given the rhetoric, we've found out the drunken teen's favorite idol is Lindsay Lohan. Here's an interesting blog entry about the election in a microcosm: the eighth Minnesota district.

Oooooooooooookay.

So: what's the good news?

It was a completely democratic sweep in Massachusetts.

The Scott Brown election earlier this year seemed to act as a wake up call for the state. By and large, the entire state said screw the Tea Party. We'll do what we think is best, thank you very much. If the Massachusetts GOP had fielded better candidates things might have been different. But if the Mass. Dems had fielded better candidates in the special election Scott Brown would never have won.

It was all local politics here (See this analysis.) and the national lunacy didn't quite penetrate.

Sometimes it's good to live in Massachusetts.

(PS: Addendum: One problem with the election are the Rasmussen polls. Check here.)

The Minimum Liberal Hope

While there's not much silver lining in today's election prospect for a liberal such as myself, there are a few interesting wrinkles.

The Rally to Restore Sanity was fairly successful-- 200,000 people, regardless what some conservative pundits are saying. Hopefully it will help to, well, restore sanity.

There are some very curious biases built into the anti-democratic polls. 538 talks about them here.

BTW: 538 is Nate Silver's political analysis blog. I heartily recommend it to every one.

Evolution as Fact Addendums

I cross posted my fairly mild (for me) discussion of evolution over at Book View Cafe Blog. You can see it here.

There was one predictably difficult comment about issues people had with evolution as a fact.

I responded and here are my responses.

Paraphrased: What are the foundations of evolution as the origin of speciation?

A “species” has at its heart effective reproductive isolation such that selection can act upon a group without being compromised by outside genetic input. There was a frog I learned about in college (whose species name I do not recall) that lived in two locations, at the canyon rim of the site and in the canyon valley. The two animals appeared to be physically identical. However, upon close examination the they did not appear to interbreed. Even in the laboratory. Investigation revealed that one of the groups (I forget which) was making its call at twice the rate of the other. This effectively reproductively isolated it. Subsequent investigation showed that the “quick” frog group had undergone chromosome doubling– rare in vertebrates but it does happen. Consequently, it was now reproductively isolated from the parent group. The discussion at that time was whether this was a new species or a sub-species, since it appeared to be physically identical. I would argue that the intransigent nature of the reproductive isolation (it’s pretty unheard of to un-double a chromosome) made it a species. Regardless, now the new group could be selected against without the effect being diluted by influence from the parent group.

There’s an interesting faq about speciation here:
http://www.talkorigins.org/faqs/faq-speciation.html

The NSF also has a good evolution section and here are some articles about it:
http://www.nationalacademies.org/evolution/Reports.html

Paraphrased: I'm having trouble with an explanation of how everything go there by accident, especially us. Scientifically speaking, I've see no significant evidence of it.

Just some small additional points: evolution is the model for how organisms changed over time from the point at which natural selection could occur– once life began, for example. No one has a good model of how life began and until that occurs no one can say what role natural selection played. The natural selection model applies extremely well– to the point of “scientific theory”– once life occurred.

Second, no reputable scientist will ever say that a given organism got here “by accident”. Evolution is not an accident. Evolution results from circumstances presenting an opportunity for the natural variability of organisms to make a difference in reproduction. If there is an advantage to being fast in the animal’s circumstances that animal is going to breed more effectively and pass on that trait to its offspring. There is *nothing* accidental about that.

There is chance and circumstance at two ends of the selection process. The variability present in animal populations is one arena where changes that have a random character to them occur. Even this over time can have less randomness than one might first think. Cuttlefish, for example, have a variability within their reproductive strategy. One subgroup has a battle for dominance approach to win over a female. Another sneaks in and makes itself look like a female until it can present itself for mating. *Both* strategies occur in the same population. That sort of variability has been preserved.

The other area that is more truly random is the nature of the surrounding circumstances– the ecology and physical surroundings of the organism. But here, too, animals can adapt to each other as well as to the physical environment, thereby altering odds in their favor.

But the randomness of the physical geography over time also has an influence. One of my professors said that you only really know an organism if you can observe it over a few tens of thousands of years. Because the organism that is presented to you isn’t just the organism that succeeded in the environment you’re observing it in, it’s the organism that survived all of the droughts, rains, ice ages and meteor strikes prior to the environment you’re observing it in.

Finally, I think the crux of the problem isn’t other animals; it’s our own evolution that matters to us. The descent of man is pretty well worked out now in that the basic sequence of species is known. What we don’t know (at least I don’t think we know. Others probably know more) are the selective pressures that caused the changes.

And then *Something Happened* about fifty-to-eighty thousand years ago that put us on the trail to where we are now. We don’t know what that was. Whatever it was it hasn’t seemed fossilize.

But that species fifty thousand years ago did become us. Not through any set of random events but by winnowing out those who *weren’t* us and mating with those who became us. Again, the selective pressures are obscure though there is some interesting work coming out of South Africa suggesting we started eating fish.

For reasons that are difficult for me to understand it is hard for a lot of people to accept “Man still bears in his bodily frame the indelible stamp of his lowly origin.” We are tremendous beings. And that magnificent heritage is the result of thousands of decisions of people over thousands of years. How could we possibly expect those decisions not to help form who we are? And if those decisions are pushed back far enough how could we not expect those that made them would not be human?

Personally, I find this a wonderful idea. It says, concretely, we came from somewhere through the actions of those much like ourselves. It says we’re going somewhere; that our actions and decisions bear long term consequences not in some hereafter but here, now, and in the future. It gives heft and meaning to what we do right now in the physical world around us. We are responsible for what we do and what we do matters. As did the actions of Ogg, fifty thousand years ago, sitting out in front of a cave in South Africa, watching the fish jump and wondering if they were good to eat.

Evolution as Fact

(Picture from here.)

Mostly I think evolution speaks for itself.

But I'd be remiss if I didn't talk at least a little about people's difficulty with it.

Personally, I think evolution has sufficiently proved itself to move from the scientific concept of theory to the scientific concept of fact. No scientist of any integrity disputes the fact that we got here by a natural mechanism that we call evolution. The component parts of the mechanism are in dispute, argument and enthusiastic debate. But no one disputes that evolution happened.

It's the same way the no one disputes the facts explained by Maxwell's Equations or Newton's Laws of Motion. Maxwell's equations explain the phenomenon he observed regarding electricity and Newton's equations explain the operation of the phenomenon of motion. That neither model is complete does not refute the fact that there is electricity or the fact there is motion.

Natural selection is the model. Evolution is the fact.

But unlike electricity and motion, evolution strikes at the heart of human exceptionalism-- not too terribly different from American exceptionalism which I spoke about here. Human exceptionalism is the belief that we are special beyond our natural endowments. It usually takes the form that humans are endowed of their abilities by God.

This should not be surprising.

A species by its definition must distinguish between like and not like, otherwise propagation is impossible. Arising from that, reproductive groups distinguish between mine and not mine-- horses, cows, lions and gorillas all make that distinction. Chimpanzees make war against other bands, showing that they have made the leap from reproductive group to societal abstraction. From mine to my people.

One of the human abilities we so prize is the ability to abstract-- the ability to simplify and categorize like things together. The ironclad concept of species itself is a human invention. Reproductive isolation in the wild is much more complex and interesting. (What's the nature of the species boundary between dog and wolf, for example?)

Abstraction is an enormously powerful tool. From it we have deduced cosmology, Euclidean geometry and evolution.

We apply this ability to ourselves and derive nations, states, political ideology and religion which, I submit, are all examples of human exceptionalism. Democrats are better than Republicans. Americans are better than Canadians. Southerners are better than Yankees. Christians are better than Moslems. On and on and on.

I wonder sometimes if we would benefit as a species if we would just stop thinking about ourselves all the time. We're a tiny piece of life on the world that through bizarre happenstance developed abilities that give us inordinate power.

We've been to the moon, cracked the atom and moved machinery with only the circuits of our brain. We've also not managed to make it back in thirty years, burn the atom like it was coal and are figuring out how to better manipulate our brain to make us buy more things from China.

Our view of our exceptional selves was advantageous for the last several thousand years. (For a fun view of this, see Milo Manara's Man. NSFW.) But at some point in the recent past we reached a tipping point, a point beyond which considering ourselves as the sole important group on the planet, made things worse instead of better. I'm not sure when it began but it is unmistakably true now.

The philosophical worth of human beings has been paramount throughout our history. The corollary of that is the worth of human effort has been valued over the natural world. James Watt said in an interview I heard years ago that it wasn't that he didn't value wildlife; it was that he valued human beings more. By extension, he valued human property as symbolic of human worth since he had no trouble developing public land for private interest. Humans, as exceptional creatures, have decided they have the moral right to exploit the living world as they see fit.

I think it's time to change that outlook. And I think it begins by not thinking of ourselves as a special creation outside the operations of nature but as something that evolved directly by the operations of nature.

I don't mean that we are part of everything in the world in some subjective spiritual way. I mean it in an objective mechanism. As Tom Lehrer sang in Pollution:

The breakfast garbage that you throw in to the bay,
They drink at lunch in san jose.

Or perhaps we should quote Benjamin Franklin:

We must all hang together, or assuredly we shall all hang separately.

Vote with your Brain

There is so much disinformation and misinformation out there.

The current conservative talk about deficit presumes as if the deficit sprung full grown from the head of Democrats in January 2008. Look at the graph at left. This is a flat out bald faced lie. (Picture from here.)

There's another lie circulating around. That the debt is exclusively the problem of the Democrats and the Republicans have nothing to do with it.


See graphs at left. (From here. Another one here.)

The pink (Republican) and blue (Democrat) background colors indicate what presidential administration is in power. Two things should be immediately apparent to anyone whose brain is still consuming oxygen. 1) Debt slope crosses administration boundaries and 2) it accelerated the most under Republican administrations.

This is not, most emphatically not, a defense of Obama. You can make all sorts of arguments against what he's been doing in the last couple of years. But the current rhetoric about deficits and debt by Republicans is at best disingenuous abut more likely an outright lie.

Remember that when Clinton wanted to reduce the deficit and pay down the debt the Republicans lined up and voted against it. (See here.)

Okay, people are pissed. The economy is in the tank. A whole f*load of jobs have been sent overseas to the point that most of what we buy is made in China. It's not clear how we're going to get free of this mess-- especially since a lot of the jobs we exported to China were jobs that helped bring us out of past recessions. If you want to say that thirty years of crap didn't happen and Obama is responsible for it since he's right there now for the last 18 months, you can do so. It's a free country. You can vote with your adrenal glands if you want to.

Me, I'll vote with my brain.

Glenn Beck vs. Donald Duck

Here.

RIP Benoit Mandlebrot

I have nothing sufficiently pithy to say about it. But here is a great good-bye.

Baby Speculations

(Picture from here.)

There have been a lot of media attention on what makes us human. Alan Alda hosted The Human Spark. Nova did a series on it as well. I figure I'm at least as uninformed and ignorant as Fox (or as I like to say Faux) News. I'm going out on a limb today and put my oar in the water.

Much of the attention to where we came from is based on what we are now.

I'm not so sure this is a good way to think about it.

While that is interesting-- not many other primates blog, for example-- it's often putting the cart before the horse. I've seen a lot of shows, articles, books, that push who we are now back to what we were. Certainly, what we were was the enabling animal that became what we are. But we always have to remember in evolution a few things:

1. Selection is against individuals, not traits. The traits can enable successful selection but the whole organism has to reproduce.
2. What enabled successful selection in the ancestor may or may not be the same thing enabling successful selection in the descendant.
3. The ancestor was also a successful product of evolution.
4. Anything to be selected against had to be in place prior to the act of selection.

These are fairly critical points to make. For example, we have big brains. It's important to us. They have made us what we are. It's very easy to say that brains are what make us human so bigger brains four million years ago are a selective advantage to Hairy Joe the Australopithecus. Not necessarily. Brains are big and expensive and our big lump between the ears didn't happen overnight. Therefore, for a larger brain to be useful to Hairy Joe it had to be a enough bigger to be useful but not so big as to be unaffordable.

We know Hairy Joe was successful-- we're his descendants after all. But we need to remember that what made him successful isn't likely to be what has made us so successful.

So, what was it about Hairy Joe that was successful (or at least neutral) in its own right at the time that enabled him to evolve into us?

Well, there were a bunch of things: shoulders, hips, thumb, etc. But, because we like our brains let's dwell on that.

One of the characteristics of human development is how bloody long it takes. Human infants are born after a gestation period not too dissimilar to chimps (8 months to 9 months) . A chimp infant learns to hold on to the mother soon after birth. Humans can't even turn over prior to two months of age. We can safely presume that modern humans are born more immature than our closest relative.

Add in to the fact that human brains keep growing long after birth-- much longer than chimps. From one of the above shows I learned that chimp skulls fuse solidly before age five. Humans don't fuse solidly until they're thirty. Humans retain immature characteristics long after birth.

This is called neoteny.

About 6-11% of human births are preterm-- prior to 37 weeks. I looked for statistics for other mammals but didn't find them. But I suspect that the human rate is higher. It makes sense. Unlike most other mammals humans are in a position to accommodate a variability in gestation period. After all, what's the difference between a baby born at 36 weeks and a baby born at 37 weeks? Both are pretty helpless. Apply the same logic to a pig or a cow where the animal be able to walk, follow the mother, etc., from birth. There's no way a cow can look after a helpless infant. Herbivores have to go where the food is and can't bring it back to the cave and give it back.

There's a significant advantage to neoteny-- birds do it all the time. The hatchlings aren't a lot more capable than a new baby. Predator babies (think kittens and puppies) can afford to be born a little helpless. The mother can bring food to the baby-- the same way birds do. If an animal is set up for it, neoteny is great. Smaller infants. More of them.

Not too small and helpless and not for too long. The mother is tied to the den where those puppies are and she can't wait forever. The cost of predation is high and most predators don't have a big support group.

Our long legged ancestors had a capability possessed by neither lion nor lamb: hands. Like chimps, our ancestors could carry an infant with them. They could carry their offspring to the food source. Gorillas do that now. When Hairy Joe went out on the savannah, he was already capable of rearing a less mature offspring than a lot of his neighbors.

Remember what I said about trains that can be selected against having to be in place before selection occurs. Hairy Joe had to have those traits available for selection. This meant a lot of those components we think are peculiarly human had to be present or latent.

There are a lot of things that helped us along: duplication of the genes for salivary amylase, modifications of the shoulder, the shift to upright posture (which also gave us our thumbs), several genes involved in brain development. But I think while these have aided in our evolution since we started on our path I'm not so convinced they started us on our path.

But I think neoteny is key.

Variability in birth timing is something that shows up in chimps as well as humans. We know we needed it to get here since selection for immature infants can't happen without it. The same social paradigms we share with chimps allows for some variability in infant maturity. An increase in this variability could be tolerated if it favors selection-- which it did in our ancestors.

I am not saying we didn't need the other things that have brought us where we are. Variability in brain size, enabling brain size to be selected for, was pretty nice to have. Nor am I saying that preterm birth is always good thing-- it isn't. Our species tolerates a variability in gestation that I don't think other species do. And it's not just because we have better technology. I think it's part of who we were and who we are. It's an evolutionary opportunity like any other pattern of variation.

I'm saying that out in the veldt Hairy Jolene gave birth to a child a little bit earlier than her sister and she cared for it just fine.

It took a little longer to mature than the other kids but when it was all grown up, it happened to be a little bit smarter.

Krugman on Rupert Murdoch

Krugman takes on Murdoch here. Finally.

Murdoch is pretty close to 10 on the Evil Scale as far as I'm concerned.

News from BVC

Book View Café Publishes K. E. Kimbriel’s Fires of Nuala.

Book View Café has published Fires of Nuala from Campbell Award-nominated Katharine Eliska Kimbriel. Fires of Nuala concerns the people of the planet Nuala, a world cursed by radiation...and riches. Mutant microbes and high ground radiation make it a deceptive paradise, but wealthy planets always attract predators. This time, one predator may be Nuala's salvation. Originally published by Warner Books in 1988, Fires of Nuala garnered much praise and recommendations for reading from such entities as Locus Magazine. BVC is releasing the ebook version of the book in epub, mobi, pdf, and prc formats.

Read chapter 1 of FIRES OF NUALA for free here.

Buy the ebook for $4.99 here.

Chili Peppers Forever

More video on the New Mexico State Chile Pepper Institute here.

Spiderpunk

(Picture from here.)

I am not a steam punk writer. I enjoy it immensely. But it is a fantasy arena in which I do not participate. Partly this comes from my love of eighteenth and nineteenth century science and engineering, much of which is ignored or used as mere furniture in steampunk romances. My limitation, I suppose.

I work a great deal in systems and instrument control which is largely accomplished these days by the use of software and electronic mechanisms. The big advantage of software is you're instructing systems how to be have in a language.

In the nineteenth century this was done by mechanical means using hydraulic systems, and comprises the field of fluid mechanics and hydraulic engineering. This means that steam-- the nineteenth century's nuclear power-- was tamed and controlled by valves and whistles. The physical world was controlled by physical laws and physical mechanisms, not minute bits housed in silicon. Very different from what I do and, of course, therefore fascinating.

Hydrodynamics, from the view point of nineteenth engineering, was formalized by Blaise Pascal and canonized in Pascal's Law:

What this says is the hydrostatic pressure (the difference in pressure between two points in a fluid column: delta-P) is a function of the fluid density (p), the acceleration due to gravity (g) times the difference in height between the two points in the fluid column (delta-h). To reframe it, if you take a garden hose and hook it to a piece of four inch PVC pipe and fill them with water the difference in height of the two water columns is a function of the weight of the water between them.

Note that no additional pressure has to be attributed to get the difference in pressure. Therefore, one interpretation of Pascal's law is that any change in pressure applied to a point in a fluid is transmitted undiminished through the fluid. Similarly, since pressure is a function of the mass of the fluid (the pg part of the equation), if you apply pressure across a wide area it will be increased when the area is reduced. Like a lever where the mechanical advantage is a function of the difference between the lengths of the lever on either side of the fulcrum, you can achieve mechanical advantage by a difference between the difference in areas where pressure is being applied. (See here and here.) Area increases as a square function (πr² in the case of a circle) where length increases linearly. A consequence of Pascal's law was the Age of Steam.

Pascal's law, like a lot of physical laws discovered by human beings, was already exploited in biological organisms. The vertebrate heart and circulatory system exploit Pascal's law in reverse; by increasing the total cross sectional area of the carrying tubes (arteries->arterioles->capillaries) they reduce the pressure in the blood vessels. Once blood reaches the actual cells the pressure is quite low.

But vertebrate circulatory physiology is a topic for another time. Now I want to talk about something more steampunk-ish.

Spiders.

Vertebrates and a large number of invertebrates have flexor muscles and extensor muscles. Flexors reduce the angle of a joint (flexion) and extensors increase it (extension.) Your biceps is a flexor and your triceps is an extensor. (See here.)

Spiders do not have extensor muscles.

This was discovered back in the early twentieth century but the thought was that there was resistance in the joint such that spider locomotion was a sort of pull-relax-pull mechanism. The relaxation of the flexors would allow the resistance to straighten the joint. Then, someone noticed that dead spiders curled up. If there had been a passive straightening force dead spiders would have spread out.

In 1959, Parry and Brown published The Hydraulic Mechanism of the Spider Leg, a lovely paper where they put house spiders in tiny harnesses and measured how much actual pressure was being created by the spiders. They came up with some fairly impressive numbers for such a tiny creature-- as much as 50 mm Hg-- about .06 atmospheres. Not bad for a creature that's about the weight of a paper clip, if that.

Spiders share the same phylum as insects and pillbugs: Arthropoda. They belong to the subphylum Chelicerata, which they share with horseshoe crabs and sea spiders. The class Arachnida contains scorpions, ticks and mites as well as spiders, which fill the order Araneae. The line that evolved into spiders began at least 400 million years ago. The first true spiders seem to appear about 300 million years ago.

Fluid pressures are generated by muscles in the abdomen and transmitted to the legs. It's likely a primitive condition since a similar mechanism has been shown in whip scorpions which diverged from true spiders prior to the Carboniferous period. (See here.) The heartbeat, however, does appear to have something to do with it since the heart rate changes under forced exercise. (See here.)

There are evolutionary problems with a hydraulic based system. An injury can reduce the effectiveness of the pressure by fluid loss. The animal can be prone to desiccation reducing the ability to move. In addition, use of a hydraulic system for locomotion and for the circulation of oxygen and food puts the two systems in competition. (Anderson and Prestwich discuss this at length in a paper here.) Not to mention there is the additional complexity of managing two separate systems for locomotion. But spiders are very successful. How come?

Wilson (mentioned in the Anderson and Prestwich paper) noticed that the spider mechanisms of predation using webs and poison were extremely efficient. He suggested that these mechanism were so successful that they were able to overcome the problems inherent in their design. Anderson and Prestwich suggested additionally and advantage to the hydraulic system itself. By using a power mechanism whose source resides in the abdomen rather than the legs, the legs were freed up to add more muscles for purposes of flexion, increasing power.

Spiderpunks, indeed.

More on spiders:
Space system based on spider locomotion and here
Ed Nieuwenhuys great articles on spiders of Europe and his microbook, The Spider
AMNH's World Spider Catalog
Wikipedia's Evolution of Spiders
Energy Storage in the Pedipalpal Joints

New Mexico Chili Institute

(Picture from here.)





I follow the PhD comics. Jorge, the man behind PhD, put up this video about visiting the Chili Pepper Institute.

Enjoy.

Book View Cafe News

(Picture from here.)

It’s Banned Books Week and Book View Cafe is getting in on the action. Join our crack blogging team all week as we celebrate banned books and how they’ve impacted our lives. Banned book bloggers include Sherwood Smith, Brenda Clough, Nancy Jane Moore, Amy Sterling, Judith Tarr, Sarah Zettel, Jerry Weinberg, Deborah J. Ross, and more. Grab your can of lighter fluid and join us at the Book View Cafe blog.

Physiology of the Apocalypse

John Joseph Adams' anthology, Living Dead 2, just came out. The contributor's copy is on my desk. It contains my story, The Crocodiles. I wrote a blog entry for it and Tor's zombie week but it didn't make any sense to people who haven't read the story.

That never stopped me in this venue.

So here it is. And, just for fun, here is The Oatmeal's take.

A New Species of Toxoplasmid Worm

Otto Weber, Josef Mengele, Otmar von Verschuer, Maxwell Schmidt
Kaiser-Wilhelm-Institut für Hirnforschung, Buchenwald
Zeitschrift für Immunitätsforschung und experimentelle Therapie, 129 (1939)

Abstract

A new species of worm, Toxoplasma brasilia, has been demonstrated to cause behavioral changes in Homo sapiens.

Suitable human hosts were acquired as subjects. T. brasilia was shown to preferentially infect human hosts over cat, dog and Rhesus monkey specimens. Cat and dog showed marginal infection rates when inoculated. Rhesus monkeys showed approximately 35% infection rate compared to 100% human infection rate subsequent to inoculation.

Inoculum was derived from centrifuged samples of Cerebral Spinal Fluid from an infected subject. Five types of inoculum were used experimentally: distilled water as control, an unfiltered centrifuged sample, a solution derived from the sample using a 100 micron filter, a solution derived from the sample using a 50 micron filter and a solution derived from the sample using a Chamberland filter. Subjects inoculated with both the centrifuged sample and the 100 micron filter showed full disease presentation. Subjects inoculated with a solution prepared from 50 micron filtered residue caused cerebral hemorrhage and stroke. Subjects inoculated with the result of the Chamberland wash showed symptoms consonant with rabies. In all cases when full presentation of symptoms was not demonstrated, incubation was prolonged. However, when full presentation was demonstrated, incubation was markedly shortened. No infection was shown using distilled water. Subsequent inoculation of the distilled water subjects using a combination of the result of the Chamberland wash and the residue of the 50 micron filter wash showed full disease presentation.

T. brasilia was identified via microscopic examination of the residue from the 50 micron filter wash.

Cat and dog specimens infected with centrifuged samples showed no behavioral abnormalities with disease presentation. Similarly infected Rhesus monkeys showed only lethargia and fever. Humans showed significant initial behavioral changes including euphoria and expressed affection, followed by coma. Coma persisted three to five days and was accompanied by substantial drop in body temperature approximating 20 ℃. Upon arousal, the low body temperature was retained and subjects exhibited increased aggression accompanied by aphasia. Post mortem examinations showed marked lesions in the cerebrum and cerebellum as well as in the amygdala and hypothalamus. Stereotaxic analysis is shown.

It is concluded that T. brasilia either hosts or cultivates a form of the rabies virus. In return, the virus facilitates infection. T. brasilia acting alone or T. brasilia acting in concert with the virus is responsible for the physiological and behavioral changes.

More on Breaking Waves

Here's the official Book View Cafe press release for Breaking Waves.

Book View Café Publishes Benefit Anthology for Gulf Relief

Book View Café has launched their benefit anthology, Breaking Waves. All proceeds from the sale of this book will go to the Gulf Coast Oil Spill Relief Fund of the Greater New Orleans Foundation.

The collection features over thirty stories by a wide range of best-selling and award-winning authors, including a previously-unpublished poem from Nebula and Hugo award-winner Ursula K. Le Guin, as well as a chapter from Rachel Carson’s groundbreaking book The Sea Around Us. Authors contributing stories of environmental rescue and recovery include Vonda N. McIntyre, Judith Tarr, Deborah Ross, Sarah Monette, David D. Levine, David Gessner, and Lyda Morehouse among others. Tiffany Trent and Phyllis Irene Radford edited the collection.

The book is available in epub, pdf, mobi, and prc formats in the Book View Café bookstore and will be coming to the Kindle store soon.

See here for the previous blog entry which contains linked list of authors.

Tapping Our Inner Dog

Three qualities are usually discussed when we talk about ourselves as different from other animals: tool making, symbolic behavior/language and the domestication of plants and animals. (I paraphrased Pat Shipman. See here.)

Tool making we clearly share with other hominids and even crows. However, it is also clear that what we do even as far back as the Homo erectus hand axe is different from our animal cousins. There is indirect evidence for symbolic behavior in the paleolithic grave sites.

And, 14,000 years ago, buried next to a human was the jawbone of a dog.

Dogs have been with us for a long time. There is a fair amount of dispute as to when this long friendship began. A 1997 paper (see here) puts it at 100,000 years ago based on genetic analysis. That is, the shift from wolf to dog began that far back. Whether they had thrown their lot in with us or we accepted it is still questionable. A complete fossil dog skull has been found dated to over 30,000 years ago.

But the site in Germany dated 14,000 years ago is pretty clear. By that time, at least, we had joined up.

There are a couple of interesting things about this. First, there is the curious nature of the relationship itself. Long before we had horses or goats, we had dogs. It's hard to believe that Og woke up outside the cave and saw this proto-dog looking back and said: "Hm. Bet that would be a good colleague in the hunting biz." It's equally hard to believe the proto-dog looked back and thought wouldn't I like him for a master. Evolution only works on traits that are already in existence.

So, first we needed the proto-dog.

We like to think we domesticated wolves into dogs. That doesn't make a lot of sense. Who had the time and resources? I believe paleolithic man had the intelligence to be able to do that; I just don't think he could afford it.

Raymond Coppinger has suggested what I think is the most plausible path to the proto-dog. He suggests that humans had dumps where there was enough leftover material to be scavenged that wolves would visit it. The wolves that were most successful at the scavenging had a selective advantage over wolves that weren't. The trait he believes is the object of the selection is the ability of the individual wolf to tolerate the close presence of the human being.

Coppinger bases his ideas, in part, on the Dmitri Belyaev's work on foxes. Belyaev attempted to make the foxes easier to work with-- to tame them using selective breeding. He succeeded extremely well in only a few generations. In fact, along with the tamed animals he got floppy ears and coat variations that matched quite well what we see in dogs. "Tameness" involves interactions between the hypothalamus and the pituitary gland, which, in turn, manages the production of adrenaline. This happened extremely quickly-- the current population of "domesticated" foxes is only 30-35 generations old. Further, the changes brought on by tameness may well not be limited to canids. (See here.) Using the same techniques, river otters and rats, taken from the wild, have been "domesticated" with similar results.

I don't believe Belyaev's work precisely mimics what happened in the wild. What I do suspect is that our hunter gatherer ancestors were very successful. So successful we had middens and the wolves, then proto-dogs, visited the middens. This is what Coppinger suggests.

But I don't think the proto-dogs were enough in and of themselves.

Anybody who's lived in an urban environment has seen the same sort of "domesticated" results in the urban ecology: rats, raccoons, etc. These animals are not particularly afraid of human beings and do quite nicely in our modern middens. The proto-dog could have survived quite without any particular love of human beings. At some point the bond had to form.

Humans are hard wired to like animals with big heads and big eyes-- the cute factor. Human beings are smart enough to figure out that bashing the kid until he stops crying is going to get some peace and we're ornery enough to do it more than once. But we tend to melt a little when those big eyes turn on us. Hey, it's kept us going for the last couple of million years.

I suspect at one point puppies came into the tent. One of the interesting thing about mammals is how some species can adapt to a human environment once they've been brought in as an infant. Consider the puppy of a proto-dog. Once it comes into the tent, it can adapt. Individual variation involving tameness can then be acted on-- I wouldn't put it past some paleolithic dog breeder to keep take the puppies he liked and have the one the bit him on the thumb for dinner. Belyaev's principle at work. And, once in the tribe, the dog can transform from animal that keeps junior occupied to help mate fairly easily. Dogs are anything if not adaptable.

But what of the other side? We can see the evolutionary effect of this on dogs. What happened to humans?

Enter Pat Shipman.

Shipman goes Coppinger one better. She suggests that we already had a connection to animals as evidenced in our cave art and artifacts. Paleolithic man often wore necklaces of canid teeth. Perhaps they were dog teeth for tribes that had already domesticated them. It's her contention that our connection to animals were one of the things that made us human. (See also here and here.)

So, if we domesticated dogs 32,000 years ago (as she suggests), did it stop there? It sure didn't for the dog. Why should we be any different?

Consider the dog working for the human. It's in the best interest for the human to care for the dog since the working dog benefits the human. But the dog can't communicate directly back to the human-- no language and only fairly gross body movements. The human has to infer what's going on in the dog in order to care for it. Humans do this for each other all the time. We have mirror neuron systems that are designed to represent internally the state of another organism, be it dog or human. (See here.) We evolved it so that it works between human beings. But we also use it to manage dogs. And other animals. Wouldn't that select for humans to be able to model the states of other organisms?

Remember also that we're not the cold calculating machines we like to believe. Compassion and empathy are selected for just as much as cognition. Not surprisingly, dogs get to be more like people. They automatically imitate humans when humans are trying to communicate to them. (See here.) They infer conclusions based on a model of human beings better than chimps. (See here, here and here.)

I suspect that while we were changing dogs they were changing us. We've spent somewhere between 14,000 and 32,000 years with dogs. (700 to 1,600 human generations.) We didn't spend them with chimps. Of course dogs would better understand us. And, of course, we'd better understand dogs.

We made each other.

Addendum for cat lovers:
I didn't talk about cats in this essay for a couple of reasons. For one, the time difference is considerable. The evidence is that humans have been associated with dogs for at least 14,000 and as much as 32,000. With possible evidence that dogs have been following us around for a lot longer than that. There's just been a lot more time for dogs and humans to influence each other than there has been for cats and humans.

For another, I think that the relationship between dogs and humans is an enabling factor for other animal relationships. By the time cats and cattle came along, dogs had domesticated us sufficiently we could take advantage of them.

There's something unique about the relationships between dogs and humans. Unlike our other animal relationships, dogs threw in with us for life and death. It is not unheard of, nor particularly rare, for dogs to throw themselves into situations where they sacrifice themselves for human beings. And I don't think that they are so stupid or unmindful that they don't recognize the danger.

That said, the relationship between humans and cats is a long and loving one. It's no accident that when they when the 9500 year old grave of a man in Cyprus was opened, nestled next to him was a kitten.