Wednesday, September 29, 2010

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.


Monday, September 27, 2010

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.

Friday, September 24, 2010

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)


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.

Tuesday, September 21, 2010

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.

Sunday, September 19, 2010

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.

Thursday, September 16, 2010

Book View CafeNews: Breaking Waves

BVC has put out Breaking Waves, an anthology of stories centering around the gulf oil spill. The idea about Breaking Waves is that any money received will be distributed passed on to charities handling the gulf spill problems.

I've read a lot of it. It's damned good. You can buy it here.

Here are the authors.

Breaking Waves

Edited by Phyllis Irene Radford & Tiffany Trent

Stories by:
Ursula K. Le Guin
David D. Levine and Andrine de la Rocha
Vonda N. McIntyre
Laura Anne Gilman
David Gessner
Tiffany Trent
James Sallis
Elaine Isaak
Brenda Cooper
David B. Coe
Deborah J. Ross, writing as Deborah Wheeler
Sandra McDonald
Dayle A. Dermatis
Judith Tarr
Rachel Carson
Camille Alexa
Mario Milosevic
M.H. Bonham
Nancy Jane Moore
Sarah Monette
Jennifer Stevenson
Randy Tatano
Pati Nagle
Lyda Morehouse

Tuesday, September 14, 2010

In Our Time: BBC

Check out In Our Time on the BBC. All of their material is archived on the site.

Monday, September 13, 2010

Go To MIT, Free

Only MIT is cool enough to put up its classes on line for free. See here.

Sunday, September 12, 2010

Winter Preparation

Well, it's fall again. Up here in the Frozen North we have to view fall through the grim lens of impending winter.

Here's the stuff I have to get done before Columbus Day:
  1. Clear out the garage for the cars
  2. Set up the tractor for leaf collection
  3. Use the file cabinets I bought over the summer to make a work table
  4. Finish work on the overhead wood storage unit
  5. Fix the piping on the heater
  6. Close off the shop to the invading squirrels. (Kill them. Kill them all.)
  7. Bottle the summer wine I made
  8. Pull the shade cloth off the greenhouse
  9. Set up the new fish pond for use
  10. Fix the light over the greenhouse door
  11. Finish the alcove addition to the shop
  12. Move the wood and set up the wood pile canopy.
Columbus Day is a good stopping point for things that absolutely have to be done above freezing. Once they're done they enable work in the cold.

After Columbus Day there are a number of other jobs:
  1. Clean out the gutters after the leaves and pine needles fall.
  2. Repair the snow blower
  3. Test out the generators-- repair if necessary
Oh, yeah. "Enjoy the fall" is in there somewhere.

Saturday, September 11, 2010

More Why I Love the Internet

For all of those silly movies with silly endings:

Friday, September 10, 2010

The Academy of Khan

Sal Khan has put out a number of educational videos for free. Bill Gates like him. (See here.)

I listened to his lecture on evolution and it's a good introduction. So it's likely worth checking out for quick informational tutorials on something you might find interesting.

Thursday, September 9, 2010

Impending November Insanity

(Picture from here.)

I wonder if American elections would be less crazy if we just held them in the summer. I sometimes wonder if we all suffer from Seasonal Affective Disorder.

Probably not. We'd probably be just as crazy. Here we are two years after the 2008 election and Sarah Palin is still around, a fair amount of people think Obama's a Muslim and some nutcase (in Florida-- no surprise there) wants to have Burn a Koran Day.

I suppose that if Terry Jones thinks it's okay to burn a pile of Qurans, he would presumably think it's also alright for a Muslim to burn a pile of Bibles, right? After all, free speech is free speech? How much do you want to bet he'd give that great mantra of the offended: There ought to be a law!

As far as I'm concerned people can burn anything they want-- subject to fire codes, etc. Qurans, Bibles, Constitutions, Flags, leaves, buildings. I don't care. That's what free speech is about. I think burning pets is bad. And we fought wars over the burning of people. But paper? Doesn't bother me. Burning a book is merely symbolic of not liking something associated with the book-- in Terry Jones' case it's Muslims. He don't like 'em. And he's a camwhore so I'm not surprised he brought up the idea of burning a Quran.

Terry Jones is Florida's answer to the Fred Phelps.

Banning books-- making them inaccessible-- is a far more serious matter. You can download the Quran, Bible, etc. Unlike the Nazi book burnings, this does nothing to take the content out of circulation. It's just some jackass preacher in a podunk church in Gainesville pissing in the face of a religion he knows nothing about.

Hence, it's an empty symbolic gesture for the sole purpose of boosting the contemptible 50 member congregation church.

But, apparently, there are a lot of these gestures going around.

Acts of this kind are theater and the question for me is always who's the audience? Who's listening?

Who cares?

Tuesday, September 7, 2010

Why I Love the Internet

The Oatmeal. It's reason enough to keep on browsing.

See here.

Monday, September 6, 2010

About "Snow Tracks"

I didn't write about The Map Room when it went up on BVC. You can read it here. I'll write it up soon.

But Snow Tracks goes up today. (See here.)

There's no excuse for it, of course. I was very busy and then on vacation and now I'm very busy again. We'll see how we can manage this blog.

With The Map Room, and now Snow Tracks, I've started putting up material that has not been previously published.

Every writer has a collection of "trunk stories". These are stories that for one reason or another have not sold. Either the market isn't quite right, the timing is off or (God forbid) the story is a dog.

Certainly, I've written my share of dogs.

But I don't think that's the case for either The Map Room or Snow Tracks.

I'll talk about TMR in another entry. Snow Tracks is what is called a "linear story". It has few twists and turns and doesn't tend to surprise the reader. This is intentional. I was trying for a different sort of effect in the story.

David Smith said once I have this awful tendency to write origami stories: stories that are all folded up and neat and internally very complex. Stories, being sequential, you don't get a crane or a butterfly, you get a lot of folds, turns and crumples and suddenly find yourself holding crane or butterfly at the end.

When I wrote Snow Tracks I had that comment in the back of my head. So I decided to just write a straightforward, linear story. Step 1, Step 2, Step 3.

The purpose of a linear story is to not obscure what you want the reader to see by complex plot. The plot is the obvious component. Instead, the purpose is to show him the character and texture of the story. It's analogous to those gorgeous tapestries from the middle ages that all show the same thing: some knight fighting another night with some people looking on. Each image is exactly the same as a thousand other images. What you observe instead is the texture of the weave, the color of the thread and the fineness of the work. The image is a mechanism to show the quality of the work and not the purpose of the work.

Well, you can make your own decision if I succeeded. The editors have spoken-- it was a trunk story, after all.

But it's a story I'm fond of and so I put it up to be read.


Sunday, September 5, 2010

Shouldering the Load

(Picture from here.)

Fourth of July weekend I separated my shoulder. Consequently, shoulders have been on my mind somewhat.

Turns out human shoulders are remarkably interesting.

The human shoulder is composed of three bones: the humerus (upper arm bone), clavicle and scapula. A projection of the scapula, called the acromion, serves as the fourth point of the joint. Unlike, say, the hip joint where the femur sits solidly in a cup of the pelvis, the bones of the shoulder are not articulated directly but held together by a complex of muscles and ligaments. This is easy to see in the naked skeleton. In the hip joint (see here) the head of the femur fits snugly in the cup. The head of the humerus sits some distance from a join of the acromion, scapula and clavicle.

A better picture of the shoulder is shown at left. Here, while the articulation of the bones is obscured it's more easily understood that the shoulder, as a joint, is far more a result of the interaction between muscles, bones and ligaments than a bone to bone combination. While this is true of every joint I tend to it is especially obvious in the shoulder.

(My injury involves the ligaments between the acromion and the clavicle.)

The clavicle first appears in bony fishes and associated with the pectoral fins along with the cleithrum. The cleithrum ran vertically along the scapula and formed part of the gill cavity. This arrangement persisted in some of the early land animals but disappeared early in the evolution of reptiles. The scapula, too, was found in bony fishes and attached to the upper surface of the pectoral fin. In early land animals a bone called the procoracoid was paired with the scapula.

Amphibians became reptiles. These evolved into two branches that we find important: sauropsids and therapsids. Sauropsids evolved into all existing birds and reptiles as well as dinosaurs.

Therapsids evolved into mammals.

By the time therapsids came around a third bone, the coracoid, formed just behind the procoracoid. Monotremes (platypus and the like) kept this three boned structure but in mammals the procoracoid disappeared and the coracoid fused with the scapula. The scapula of modern mammals is the result of this fusion and isn't exactly congruent with the bone of the same name in earlier animals. Such is the world of comparative anatomy.

The humerus has remained the upper arm bone since primitive fossil amphibians.

The shoulder, bearing a quarter of the weight of a four legged animal, changes based on the evolutionary strategy. We would expect the shoulder joint of an elephant, cheetah and zebra to be different based on their body types and the lives they lead. However, in these cases the forelimb bears significant weight. These are four legged animals.

The shoulders of animals that have evolved a significant difference between forelimb and hindlimb activities have a different story. Monkeys, dinosaurs, birds, bats and kangaroos have all separated forelimb and hindlimb function. Consequently, much of the weight bearing utility of the forelimbs have been abandoned. Not completely, of course. Gorillas bear significant weight on the forelimb (and hence the shoulder) but they descended from arboreal monkeys that used their forelimbs more for other things.

Fast forward a few million years to chimps and humans-- and possibly human forebears.

The shoulders of chimps (and australopithecines) is more cranially oriented than humans.

On the left here we can see a human shoulder joint. On the right is a chimp. (See here for the root article for these pictures.) Notice how long the clavicle is and how straight it is compared to the chimp. Not how the acromion butts up in the chimp and it's laid down low on the human. What has occurred here is in the human the joint has opened up. The chimp joint is more constrained than the human joint. Stronger but with fewer degrees of movement.

A result of this is a measurement of humeral torsion, the twist between the head of the humerus and the other end. Different primates have different twists. (Greg Laden has a good discussion here.) It is one of the anatomical idiosyncrasies that enable both human and Neanderthal (and Homo floresiensis and Homo erectus) to better manipulate things in front of them.

But the modern human shoulder is even more open than its ancestors. It is much less adapted to hanging from a tree than the shoulder of any of our relatives-- a side effect of our extreme verticality. As soon as we committed to walking on two legs we freed up the shoulder to adapt to new uses. First it moved to allow manipulation in the front. Then, about two million years ago, it started to open up further.

The modern shoulder has an ability to move in almost any direction. It can, for example, reach all the way back and swing all the way around to the front easily and quickly. It can do that holding on to a rock.

We could throw things.

About 400,000 years ago we could throw things we built-- like spears.

All of a sudden our reach truly did exceed our grasp.

Additional links:
William H. Calvin, a professor in Seattle, has even ascribed this ability with shaping how our brains work. (See here for The Throwing Madonna.)
Katsuya Nobuhara's lovely discussion of the shoulder here.