Monday, December 29, 2008

Why I Gave Up on the Neanderthal Parallax

I recently read Robert J. Sawyer's Hominids, the first book in a trilogy about a quantum portal that opens between our world and a parallel universe in which humans went extinct and Neanderthals developed into an advanced technological culture. I enjoyed the first book, despite some glaring implausibilities, a bit of preachiness, and a distracting subplot involving a character being raped. And then I went on to start the next book in the series, Humans. But I only made it about halfway through before abandoning it. I really don't like giving up on books, especially ones that I've invested a fair amount of time in, but I just couldn't go on.

The flaws of the first book were accentuated in the second. In Hominids we find out that the Neanderthals never developed agriculture, and yet they found cities and develop advanced technology, such as AI implants called "companions" that assist them and record everything that happens around them. But how could a hunter-gatherer culture have the stability to settle down permanently and engage in the sort of division of labor necessary to advance technologically? Humans has an extended discussion of this, in an exchange with a Native American anthropologist, who manages to point out the arrogance and stupidity of "white people" while pointing out that it's perfectly plausible. The explanation rests on such a culture not growing beyond its available food supply by excessive breeding, and by not overexploiting their resources.

The Neanderthal visiting our world seems astonished that we would ever hunt another species to extinction. He also seems astonished that we would breed as much as we do. In our world there are over 6 billion people; in his world there are only a couple hundred million Neanderthals. I guess while they were developing advanced AI and physics, they didn't learn dick about ecology. No one should ever be surprised when a species exploits resources to the greatest extent possible and maximizes its reproductive potential. Evolution is a greedy algorithm. Individuals seek to maximize short-term gains; there is no foresight in evolution. A co-evolving population of predator and prey or bacterial infection and host population will typically oscillate. Fox populations increase as they prey on rabbits, but as the number of rabbits decreases, they are scarcer, so the fox population declines, which in turn allows the rabbit population to expand, and so on. If the foxes overexploit the rabbits and drive them to extinction, then the fox population will probably die out if that was their main source of food. What keeps this from happening is the reduction of the number of rabbits, not foresight by foxes, either individually or collectively. The foxes don't keep themselves from driving the rabbits to extinction. They do what they do. They hunt, eat, and reproduce as much as resources allow. This idea should not be surprising or shocking to a scientist.

We also get chided for polluting the environment (Neanderthals have sensitive noses, so all their locomotion is environmentally safe). They have no crime (because they have an Orwellian monitoring system and practice eugenics). However, the darker implications of the Neanderthal society are not really explored. Instead, human society is constantly portrayed as stupid and short-sighted.

However, it was Sawyer's ham-handed handling of a human character's rape that put the nail in the coffin for me. Being a geneticist, she collected the DNA from her rape instead of going to a hospital or the police. But the DNA samples are lost and she gets upset. Another woman in the area is raped, and this character blames herself for what happened. The Neanderthal tells her she needs to forgive herself, and so we get a scene where she goes to Catholic church and goes to confession. And that was enough for me. The rape subplot already seemed mildly exploitative, but its featured prominence in the second book and its awkward handling just drove me away from the story.

Which is a shame, because Sawyer's prose is incredibly crisp and readable. There are a lot of interesting ideas to explore in such a setup, but Sawyer instead writes a talky, polemical diatribe that's thin on story and stretches willing suspension of disbelief to the snapping point.

Sunday, December 28, 2008


In dire need of having our movie palette cleansed, we finally did manage to see Valkyrie yesterday, and it was quite good. Then again, it's been a long time since I've seen a decent movie, so maybe I was just starved for good acting, direction, and storytelling, and this one was just relatively good by comparison.

The movie is like others such as Apollo 13 where the broad strokes of the events are reasonably well-known, while the details are generally not. Some of the tension is sucked out of Valkyrie since we know that Hitler was not successfully assassinated. Thus, we know our protagonists are going to fail in their mission from the get-go. What we're interested in is how they fail, and how agonizingly close they get. That's where the tension comes from, and it's done well.

Several times in the film I was reminded of Alfred Hitchcock's "Bomb Theory":

There is a distinct difference between "suspense" and "surprise," and yet many pictures continually confuse the two. I'll explain what I mean.

We are now having a very innocent little chat. Let's suppose that there is a bomb underneath this table between us. Nothing happens, and then all of a sudden, "Boom!" There is an explosion. The public is surprised, but prior to this surprise, it has seen an absolutely ordinary scene, of no special consequence. Now, let us take a suspense situation. The bomb is underneath the table and the public knows it, probably because they have seen the anarchist place it there. The public is aware the bomb is going to explode at one o'clock and there is a clock in the decor. The public can see that it is a quarter to one. In these conditions, the same innocuous conversation becomes fascinating because the public is participating in the scene. The audience is longing to warn the characters on the screen: "You shouldn't be talking about such trivial matters. There is a bomb beneath you and it is about to explode!"

In the first case we have given the public fifteen seconds of surprise at the moment of the explosion. In the second we have provided them with fifteen minutes of suspense. The conclusion is that whenever possible the public must be informed. Except when the surprise is a twist, that is, when the unexpected ending is, in itself, the highlight of the story.

Valkyrie knows how to generate suspense, and it does it well. It also seems to have done a reasonable job remaining faithful to historical events (at least about as close as a Hollywood blockbuster is going to).

It's a depressing movie, though. You'd think it might be uplifting to think of the plotters as heroes, motivated to kill the monster Hitler by lofty notions. But they each had their own reasons, and they were guaranteed positions in the new power structure if they pulled it off, so it's likely that they were motivated by a mixture of base and noble reasons.

Still, I never found the movie boring. All in all it was a solid experience, and I'd recommend it.

The Spirit

It's been a long time since I walked out of a movie theater, but this one justified it. Laurie and I were in New Orleans for Christmas, and she won some movie passes in a White Elephant gift exchange. We wanted to go see Valkyrie, but it was sold out. Hey, I said, The Spirit opened as well. Big mistake. I hadn't seen the ratings on Rotten Tomatoes. I'll never make that mistake again.

Remember Derek's Movie Review Maxim: If most critics say it's good, they're sometimes right and sometimes wrong; if most critics say it's bad, they're almost always right.

Well, they were right about this one. It was a big, steaming pile of dookie. It was like someone took Sin City, sucked out all the good stuff (like interesting characters), and left a hollow, stupid movie with the same graphical style. You know you're in trouble in an early scene when the good guy and the bad guy whale on each other with toilet seats and punch each other dozens of times and neither one gets a scratch. Why the hell should I care about a fight in which no one has the capacity to get hurt?

Anyway, it was crap. Avoid at all cost.

Tuesday, December 23, 2008

Cake Wrecks

Via Boing Boing, here's a blog that posts pictures of horribly decorated cakes and then mocks them. Good fun.

The most recent post as of this writing was of an attempt to render a Texas Longhorn (from my alma mater):

They say:

It's impossible to say how this idea first entered the decorator's brain...

But now it will haunt us both day and night.

This cake makes a mockery of my horror, Chris L. It's also really icky. Tell me, do all University of Texas cakes look like week-old medical specimens?

Nice. Whoever made this cake should scribble "Deep in the Heart of Texas" on it. Or maybe "I Bleed Burnt Orange."

Anyway, they've got lots of holiday monstrosities, just in time for Christmas. Go check it out.

Monday, December 22, 2008

The Future of Computer Interfaces?

Check out this short video by Johnny Lee, a PhD student at Carnegie Mellon University. Using a Wii remote, a small LED array, and some reflective tape, he shows how you can have an interface which tracks the movement of your fingers.

Cool, huh? He talks about how the interface is similar to that used in Minority Report, though I was also thinking about the bit in Jurassic Park where the researchers manipulate virtual strands of DNA using their hands. Lee says that using your hands might not be practical because it's tiring. As the sole method of interacting with a computer, I'd think so. But as a peripheral to compliment existing means of interaction, or for certain special applications (e.g. computer-aided design), I think it would be extremely useful.

They should give this guy his PhD and someone should hire him so he can get this stuff to market.

Octopuses and Personality

This article from the Sydney Morning Herald talks about recent work with octopuses done by Macquarie University marine biology researcher Renata Pronk. The article describes two interesting things about the research.

One, it seems that experiments in which they displayed video to the octopuses were more successful with high-definition, 50 frames per second video than with the slower, lower-resolution 25 frames per second.

The second claim is just weird. She says they "have no personality."
"Octopuses," Miss Pronk said, "are very smart. I have seen my octopuses open Vegemite jars by unscrewing the lid. They can find their way through mazes to reach food rewards at the end.

"And they can learn simple puzzles", recognising that symbols, such as squares or circles, mean food is available.

"The definition of personality," she said, "is having repetition in your responses, for example, being consistently bold, or consistently shy, or consistently aggressive."

To resolve the debate she collected 32 common Sydney, or gloomy, octopuses from Chowder Bay, near Mosman, and showed them a series of three-minute videos screened on a monitor in front of their tank.

One video featured a crab, an octopus delicacy.

A second starred another octopus, while a third had a "novel object" they would not have seen: a plastic bottle swinging on a string.

Miss Pronk then watched each octopus for any consistent response pattern, such as boldness or aggression.

When the crab movie was screened "they jetted straight over to the monitor and tried to attack it", she said, adding that was strong evidence they knew they were watching food.

When the octopus movie was screened some became aggressive while others changed their skin camouflage or "would go and hide in a corner, moving as far away as possible".

On viewing the swinging bottle, some puffed themselves up, just in case the object was a threat, while others paid no attention.

But significantly, when the experiment was repeated over several days, she found no consistent response from any octopus. Such random responses implied octopuses have no individual personalities.
So what we're supposed to believe is that the findings support behavioral variation within an individual, but not between individuals?

I'm sorry, but this just doesn't seem to make much sense. I'll grant her definition of personality for a moment. An organism in a population that has a personality would exhibit different patterns of behavior than some other members of the population. In other words, there would be individual differences in behavior among members of the population.

That's exactly what evolutionary theory would predict. In any population, while considering any trait, there will be some type of individual differences. The distribution of variation may be restricted or it may be broad, but it should be there. Variation is the engine which drives natural selection. In a population of bears, for example, some will have thicker fur than others, due to their genes, but also due to their specific developmental path (e.g., their specific diet, etc.). If a change in the regional temperature favors a particular subset of the population (e.g., it gets colder), those individuals better suited to the change will have an advantage, and will be more likely to survive and propagate their genes.

A population with no variation in a trait is evolutionarily stagnant with respect to that trait. I'm no evolutionary biologist, but I'm not even sure it's possible to have a population with absolutely no variation in a given trait. That would have to mean that the genes that encode for and mediate the trait are functionally identical and that any environmental influence on the trait has been exactly the same for all individuals. And with a trait as complex as behavior, I'm just not buying it.

I think Miss Pronk just needs to spend more time with her octopuses.

Saturday, December 20, 2008

A Conversation With Sam Harris and Rick Warren

In poking around the Wikipedia entry on Rick Warren, I came across this conversation between him and Sam Harris. The whole thing is worth a read, but I'll talk about a few of my favorite bits.

INTERVIEWER: Do you believe Creation happened in the way Genesis describes it?

WARREN: If you're asking me do I believe in evolution, the answer is no, I don't. I believe that God, at a moment, created man. I do believe Genesis is literal, but I do also know metaphorical terms are used. Did God come down and blow in man's nose? If you believe in God, you don't have a problem accepting miracles. So if God wants to do it that way, it's fine with me.

HARRIS: I'm doing my Ph.D. in neuroscience; I'm very close to the literature on evolutionary biology. And the basic point is that evolution by natural selection is random genetic mutation over millions of years in the context of environmental pressure that selects for fitness.

WARREN: Who's doing the selecting?

HARRIS: The environment. You don't have to invoke an intelligent designer to explain the complexity we see.

It's worse than that. If you invoke an intelligent designer, you've now got a whole lot of additional complexity to explain. How did the designer arise? Not only are you not explaining the existing complexity we see, you're adding a whole new heap of unexplained complexity.

But I like the silliness of Warren's answer about the literal interpretation of Genesis. He believes that "Genesis is literal" but that "metaphorical terms are used". Well, we sure didn't have to go very far in the conversation to find Warren saying things that contradicted each other. Maybe he doesn't understand what "literal" means. And I'd be interested to know if he literally believes in a talking snake and the rest of it.

WARREN: One of the great evidences of God is answered prayer. I have a friend, a Canadian friend, who has an immigration issue. He's an intern at this church, and so I said, "God, I need you to help me with this," as I went out for my evening walk. As I was walking I met a woman. She said, "I'm an immigration attorney; I'd be happy to take this case." Now, if that happened once in my life I'd say, "That is a coincidence." If it happened tens of thousands of times, that is not a coincidence.

INTERVIEWER: There must have been times in your ministry when you've prayed for someone to be delivered from disease who is not—say, a little girl with cancer.

WARREN: Oh, absolutely.

INTERVIEWER: So, parse that. God gave you an immigration attorney, but God killed a little girl.

WARREN: Well, I do believe in the goodness of God, and I do believe that he knows better than I do. God sometimes says yes, God sometimes says no and God sometimes says wait. I've had to learn the difference between no and not yet. The issue here really does come down to surrender. A lot of atheists hide behind rationalism; when you start probing, you find their reactions are quite emotional. In fact, I've never met an atheist who wasn't angry.

HARRIS: Let me be the first.

Hah! Nice. I'm guessing that not only is Harris the first non-angry atheist Warren has met, but that he's the first actual atheist Warren has gotten to know on any level. This is the sort of thing you learn in logic 101. It's called ad hominem, attacking the character of someone, rather than the legitimacy of their arguments. Oh sure, atheists make good arguments, but they're all bitter, angry, narcissistic little people who have daddy issues and just like to fling poop at joyful true believers since they're jealous because their own lives are so miserable.

Well, the atheists I've met are on the whole not angry and twisted. They're nice, gentle people who are decent and happy. They are often frustrated that they live in a society that's dominated by superstition and bronze age beliefs, but that doesn't make them fundamentally unpleasant people.

Anyway, go read the whole thing, if you can stand the annoying ads. They cover a lot of important ground in a relatively short space.

Christopher Hitchens on Rick Warren

So Obama has picked super-pastor Rick Warren as the guy to swear him in on inauguration day. Christopher Hitchens isn't happy about the choice, but his reasons are a bit silly. He apparently thinks that Warren is a bigot because he doesn't think Jews and Mormons are going to heaven. I would call that "being a denominational Christian". What Baptist thinks Jews have made the cut?

Here are Hitchens' three questions about Rick Warren's role in the inauguration:

  • Will Warren be invited to the solemn ceremony of inauguration without being asked to repudiate what he has directly said to deny salvation to Jews?
  • Will he be giving a national invocation without disowning what his mentor said about civil rights and what his leading supporter says about Mormons?
  • Will the American people be prayed into the next administration, which will be confronted by a possible nuclear Iran and an already nuclear Pakistan, by a half-educated pulpit-pounder raised in the belief that the Armageddon solution is one to be anticipated with positive glee?

That last point is a bit better than the other two. I don't think I've ever seen a poll question along the lines of "Would you support a nuclear war if you knew it would be closely followed by the return of Jesus to Earth?" I'd like to see some results from some variants of such a question.

Anyway, yes Warren opposed Proposition 8. According to Wikipedia he called removing Terry Schiavo's feeding tube "an atrocity worthy of Nazism". He's strongly against abortion rights. These are all consistent with his belief system.

Obama is obviously pandering to evangelicals. I think he's trying to show inclusiveness, but it's not a great symbolic start to the Obama Presidency.

Friday, December 19, 2008

Back From the Big Apple

I'm back from 5 days in New York City. It was kind of a vacation of opportunity. A friend was going up there and suggested I meet up there and hang out.

Here is a list of things I did while there:

1) Saw a real live New Yorker yell at our cab driver, who parked right in front of a bus stop just before the bus was pulling up.

2) Visited the American Museum of Natural History. We were there several hours, and barely put a dent in the place. Highlights: the human origins exhibit and the big-ass dinosaur bones in the rotunda.

3) After walking through Central Park we went to The Metropolitan Museum of Art. We'd just gotten in the day before, and I didn't get much sleep the night before, so I was pretty much dead on my feet at this point. And I felt bad only giving a few seconds to each Picasso or Dali I saw. I'd like to go back and spend some more time here.

4) Ate a Papaya Dog. I wasn't that impressed.

5) Went on a boat tour around Manhattan. Saw the Statue of Liberty while it snowed. That was cool. Saw the Empire State Building, the Chrysler Building, Yankee Stadium, and all sorts of other stuff.

6) Saw the musical In the Heights, which won the Tony for Best Musical last year. I'm not a big fan of musicals, but it was entertaining, if cheesy. It was free (my friend won tickets in a raffle), so I can't complain.

7) Saw a real live sewer rat while waiting for a subway.

8) Just before leaving town, I got to eat at a Yoshinoya, which took me back to my days in Japan. I used to eat at that place at least once a week when I lived in Japan.

New York is of course massively crowded, noisy, and expensive. If you're at all claustrophobic or mildly autistic, this isn't the place for you. I wouldn't want to live there for any length of time, but it's a pretty cool place to visit.

Friday, December 12, 2008

Falsifiability and Science

This blog entry over at NeuroLogica regarding SETI (the search for extra-terrestrial intelligence) brings up some interesting issues regarding the philosophy of science.

What determines whether or not a researcher should spend time looking for a previously unobserved thing?

What's the difference between trying to observe the following unobserved things:

1) Bigfoot
2) Extraterrestrial intelligence
3) Subatomic particles
4) Leprechauns
5) Ghosts

Assuming we don't want to waste our time looking for something that has a very low chance of actually existing, how do we make that determination? Presumably, we should have some justification for thinking that a given thing might exist even though it has not yet been observed. In the case of extraterrestrial intelligence, we know that life and human-level intelligence arose at least once before. We don't understand well at all how either event happened, so our estimation of how likely either would be to happen again is very murky. But it's reasonably not zero.

I don't know physics very well, but presumably the people looking for unobserved subatomic particles have some justification for thinking that they might exist, based on some particular theory.

What about things like Bigfoot, leprechauns, and ghosts? Well, if we count eyewitnesses and other people's beliefs as evidence, then we have a decent amount of evidence for all of these. Here's a whole bunch of eyewitnesses saying they saw a leprechaun in Alabama:

They even have a sketch of the little guy! I guess when it comes to testimony, we have to actually have some way to assess credibility, yes?

And finally, I thought this comment on the original post was interesting:
One way you can think about the “falsifiability” objection is to turn it on its head.

If the hypothesis is: “There is intelligent life in the universe other than humans,” then no amount of evidence can prove this wrong.

But, if the hypothesis is: “There is NO intelligent life in the universe other than humans,” then you just need a single example to disprove the hypothesis.

It seems like SETI is assuming the latter, and doing their best to disprove it. That’s good science.
So a hypothesis instantly becomes scientific when you add a negative modifier?

According to that logic, the following hypothesis is unscientific: "Leprechauns exist."

While this one is scientifically sound: "Leprechauns don't exist." Because, after all, the observation of a single leprechaun would falsify it. And if a hypothesis is falsifiable, then it has to be scientific, right?

Uh. This is why I'm not an adherent to Karl Popper and the whole falsifiability criterion. A hypothesis is either good or bad depending on whether or not one can justify reasons for proposing it and the extent to which one can find evidence that either supports it, weakens it, or both.

Worst Defense of the Century

Carl and Raylene Worthington of Oregon had a 15-month-old daughter Ava who got sick with bacterial bronchial pneumonia and an infection, both of which could have been cured with common antibiotics. Her parents preferred treating her with prayer. Now she's dead. Here's their defense:
A Clackamas County, Ore., couple accused of letting their infant daughter die by relying on prayer, rather than medicine, today asked that the charges be dropped, arguing that they infringe on their freedom of religion and their right to raise their children in their own way.
Guess what, you loonballs? The state can't be infringing on your right to raise your child in your own way because your child is dead.

Why Waste Robotic Vaginal Sensors?

This story is kind of pathetic and disturbing at the same time. There's a 33 year-old Ontario computer programmer, Le Trung, who lives with his parents and has constructed Aiko:
Aiko is a 32-kilogram female android that Trung began building in August of last year.

She is just under five feet tall, has brown eyes that can distinguish 300 faces per second and speaks 13,000 English and Japanese phrases.

Her skin is made of silicone and her insides are made of an expensive collection of wires, motors and various sensors.

In total, Trung has spent more than $20,000 developing Aiko, maxing out three credit cards in the process.

So far it's not all that creepy (though her hands look pretty weird). Here's where it goes off the rails:
But for all the attention that Aiko has garnered, one topic area has elicited the most questions: Anything and everything to do with sex.

And Trung has answered every question that he has been asked.

"Does she have breasts? I will say yes. Does she have nipples? I will say yes. Does she have a vagina? I will say yes. Are there sensors there? I will say yes," he said.

"Do I sleep with her? No."
So...the guy builds this thing with nipples and a vagina, with sensors, but claims he isn't fooling around with it. Uh...right. What are the sensors for? To let you know when the toast is done? Or when the mail has been dropped off?

And then there's this bit of stupidity:
"If you talk dirty to her, she will talk dirty back," Trung said, admitting that an R-rated vocabulary was an unforeseen part of Aiko's development.
Right. We're supposed to believe that he's built an android that is learning vocabulary its builder didn't foresee. If you believe that, I've got a bridge to sell you.

This guys sounds like he needs professional therapy. I'm serious.

Reconstructing the Mind's Eye

That is supposedly what researchers at the ATR Computational Neuroscience Laboratories have done, at least on a limited basis.

I haven't read the source article, which is featured on the cover of the most recent issue of Neuron, but here's my rough understanding of what they did. Human subjects were shown 400 random 10 x 10 pixel black-and-white images for a period of 12 seconds each. During viewing, the blood flow in their primary visual cortex was recorded using fMRI. At some later point, the subjects were shown one of the 400 random images, the blood flow was monitored using fMRI, and a computer algorithm compared the previously recorded blood flow pattern to the current one to try to determine which image the subject was looking at.

Pretty nifty, huh? Here is another image showing the pattern the subject was viewing at the top and the reconstructed images based on the fMRI analysis:

I'm actually surprised that activity at such a coarse resolution, i.e. blood flow, is replicable enough between viewings of stimuli to allow for this kind of accuracy. Blood flow is an indirect measure of neuronal activity, and I wouldn't expect it to be very uniform from stimuli to stimuli, but apparently it is, at least in this sort of experimental setup, although I wonder how robust it is over time and with more complex stimuli.

And then there's the usual pop science silliness that usually comes with these sorts of stories:
According to the researchers, further development of the technology may soon make it possible to view other people’s dreams while they sleep.
I think it may be too soon to use words like "soon". Dreams are not a result of directly viewing visual stimuli, so it is unlikely that activity in the primary visual cortex will be the same when, for example, a subject is looking at a giraffe in a waking state as when they are dreaming of a giraffe. But who knows? Maybe in 10 years we'll be able to record our dreams and play them back for our friends.

Thursday, December 11, 2008

Jon Stewart and Mike Huckabee Clash Over Gay Marriage

This is an interesting exchange between Jon Stewart and Mike Huckabee on the issue of gay marriage.

I think Stewart comes out with the upper hand on this one, doing especially well at exposing the goofiness of the "one man, one woman" defense. From the transcript:
Governor Huckabee: Well, marriage still means one man one woman, life relationship. I think people have a right to live any way they want to. But even anatomically- let's face it, the only way that we can create the next generation is through a male female relationship. For 5000 years of recorded human history, that's what marriage has meant.


Stewart: But people got married in the interim and- then they went back and said you're not- I guess my question is...

You said, reaffirming the tradition of marriage over 5000 years, which takes it back to the Old Testament, where polygamy was the norm, not a heterosexual marriage between two couples [sic] that choose each other.

Marriage has evolved greatly over those 5000 years, from a property arrangement, polygamy... we've redefined it constantly. It used to be that people of different races could not... marry.

It strikes me as very convenient, to go back to the Bible and say, "Hey, man... we gotta look at the way they define marriage..." Why don't we look at the way they did slavery, in the Bible?

Huckabee: But if we change the definition, then we really do have to change it to accomodate all lifestyles. We have to say to the guy in West Texas, who had 27 wives, that's okay. And I'm not sure that I hear alot of people arguing that that's a great idea.
Huh? Huckabee wants to use biblical, historical tradition as a basis for defining marriage, but he doesn't want to endorse polygamy? Stewart is absolutely right calling him out on this silliness. The institution of marriage has changed throughout the centuries, depending on culture. "It's always been done this way" is a stupid and incorrect argument. One, because it hasn't always been done that way. And two, as I've pointed out before, incumbency doesn't make an idea a good one (see slavery, disallowing the female vote, and peeing in the same place you get your drinking water).

Tuesday, December 9, 2008

Gay Partner Rights

This rant against Proposition 8 (or "Proposition Hate", as the guy is calling it) is making the rounds on the internet. To briefly summarize the situation: A gay man, Jake, says he is living with his partner, and that they have taken in a mentally disabled 37 year-old named Thomas who was abandoned by his father and abused by his mother for the last 15 years. Thomas is Jake's partner's brother. Jake is railing against Proposition 8 because he says that if his partner died, Thomas' mother would have legal claim on co-ownership of their house. She could move in the next day and start abusing Thomas again. Presumably, Jake thinks that he and his partner should have the legal protection that marriage would bring.

A couple of aspects about the story seem very strange to me. First of all, Jake says that when he and his partner realized what was going on with Jake, they brought him to live with them. Apparently Thomas is his partner's brother. How did he not realize what was going on? Why did it take 15 years?

Secondly, in a later post, Jake details the steps he and his partner have gone through to try to make sure full ownership of the house goes to Jake:
The domestic partner and I went to what was promoted to us as the best gay attorney in Chicago to make sure we had all the legal protections of marriage. He drew up a thousand dollars in wills and powers of attorney and related documents, and we thought we were all set. But since then we've learned from our financial planner and some other attorney friends that mere wills—especially the wills of gay domestic partners—are easily contested by blood relatives and we need to fork over thousands more to have trusts and who knows what else drawn up to protect ourselves. So we're looking for a better attorney who will give us the legal protections we asked for in the first place.
I really want to know how true this is. Are wills that easily contested? If so, what good are they? I've always argued that the rights associated with marriage could be conferred without the legal institution of marriage. This makes that sound difficult, if not possible. I would think that a relatively competent lawyer could draw up documents that would grant the rights of marriage between a gay couple that would stand up in court. How hard should this be? A good will and power of attorney don't do it?

This follow-up post also tries to explain how nobody knew what was going on, and does so by saying that Thomas and his mother lived in a gated community and they rarely visited. Was the mother not abusive when the domestic partner was younger? And he notes that they're not pressing charges because it's a family decision, but some of the abuse they're attributing to this woman sounds horrific. Why should we necessarily believe Jake's story?

Anyway, I'm not calling the guy and out-and-out liar, but his posts are generating more questions for me than they answer.

Large-scale Thalamocortical Model

ResearchBlogging.orgA fellow student in my lab is basing some of his preliminary work on neuron models devised by Eugene Izhikevich, who published a book last year in which he described a system for modeling the diverse spiking behavior of many types of neurons with an elegant set of equations. In a paper co-authored with Gerald Edelman (of Neural Darwinism fame) they implement a model of the cortex and thalamus and their interconnectivity.

Here are some features of the model:

1) Simulates one million multi-compartmental neuron models of 22 basic types
2) Includes approximately half a billion synapses
3) Macroscopic connectivity is based on data derived from diffusion tensor imaging (DTI) of magnetic resonance image (MRI) scans of the thalamus and cortex
4) Microscopic connectivity is based on reconstruction studies of cat visual cortex
5) Synapses are modified through spike-timing dependent plasticity (STDP)

Now, the thalamus is the part of your brain through which almost all sensory input is routed before being sent to the cortex (the exception is olfactory input). This structure is about the size of the end of your thumb, and it is a place through which nearly all of your input from the world flows (visual, auditory, and tactile). But like most brain areas, exactly what it does is not very well understood. For example, we know that it does not function merely as a relay station. There is extensive feedback from the cortex back to the thalamus, creating a thalamocortical loop. Why would the cortex need to send information back to the thalamus if it's just a relay station? Some theorists have proposed that the thalamus is something like an active blackboard, maintaining a constantly updating sketch of the world. Others have proposed that the loop is a way of keeping recent events in a kind of short-term buffer.

Whatever the case, the Izhikevich and Edelman model does not simulate the stream of sensory input from the world. So how does anything happen in the model? Well, initially it is quiescent. The modelers get it going by causing random neurons to spike, which effectively jump-starts ripples of activity throughout the system.

One interesting finding is that the brain state is very sensitive, so much so that the alteration of the spiking activity of a single neuron radically alters the global firing patterns throughout the model within less than half a second. This seems a bit counterintuitive. We might expect that the brain is robust to small changes. After all, neurons can be fairly noisy (that is, they don't always fire reliably), and they also tend to die off. So either their model is overly sensitive to small perturbations (i.e. the butterfly effect) or this really is a reflection of the sensitivity of real neural systems. Either way, it's an interesting result.

One last comment...the authors state that they "started with the thalamocortical system because it is necessary for human consciousness." In discussing the paper with another student, I mused about the ethical ramifications of this kind of simulation. I seriously doubt that a simulation of a million neurons evoked anything like consciousness when randomly jump-started, but then, consciousness is a very poorly-understood phenomenon. I told the other student that I was reminded of Johnny Got His Gun, an anti-war novel in which a soldier is wounded such that he loses all senses but touch, all his limbs, and most of his face. He tries to communicate by banging out Morse code with his head on the hospital bed.

"But this thing doesn't even have a head to try to bang out Morse code," I joked, before I realized just how creepy that sounded. So like I said, I seriously doubt we have to worry about the ethics of simulating consciousness at this point. There are about 100 billion neurons in a human brain and about 20 billion in the cortex, while this model uses one million neurons. But it's something to at least ponder, and definitely something to consider more as models become more and more sophisticated.

E. M. Izhikevich, G. M. Edelman (2008). Large-scale model of mammalian thalamocortical systems Proceedings of the National Academy of Sciences, 105 (9), 3593-3598 DOI: 10.1073/pnas.0712231105

Monday, December 8, 2008

Living in 80 Billion Heavens at Once

Dinosaur Comics takes on Pascal's Wager.

Evolution of Mona Lisa

A guy named Roger Alsing whipped up a little program that encodes 2D images constructed of 50 semi-transparent polygons as artificial chromosomes. Each generation, candidate images were compared to a target image, the Mona Lisa, and those that were closer to the target were selected for reproduction.

He doesn't say what his algorithm or parameters are. Hopefully he'll share. Looks like he started with no polygons, and incrementally allowed them to mutate in, which is good evolutionary algorithm practice. Looks like it took just under a million generations to get something that's a pretty nice facsimile of the original.

Go check out the results.

Big Bang Theory at ComicCon

There was a panel for the producers and stars of Big Bang Theory at ComicCon and Phil Plait is posting chunks of his recording of it on his blog. Here's the first chunk.

It's a little lame so far, but one cool snippet is that there's a website called with links to buy the shirts that Sheldon and Leonard wear on the show. My favorite is probably the robot evolution tee:

They also sell belt buckles that Howard wears, such as:

Anyway, the show is pretty funny. If you haven't checked it out, you should.

Sunday, December 7, 2008

Keith Ward on Science and Truth

Keith Ward is an Oxford professor with "doctorates of divinity from Cambridge and Oxford Universities". One wasn't enough? Anyway, he writes at length here addressing the question of whether or not science is the only way to get at truth. He concludes that no, you can derive truth subjectively as well. Here are some excerpts:

What can justify the scientists’ faith that there is no event without a cause or at least without a good explanation? What can justify the faith that the laws of nature will operate in the future as they have in the past? What can justify the belief that human reason is adequate to understand the structure of reality? As the Cambridge quantum physicist Paul Dirac said, “It was a sort of act of faith with us that any equations which describe fundamental laws of Nature must have great mathematical beauty in them” (quoted in Longair 1984, 7).

This is the same tired-ass comparison of science to religion that has been around for decades, if not centuries. Seriously, he's asking what the justification for causality in the universe is? How about virtually every moment of waking life and every experiment ever carried out. We have overwhelming evidence that when we take our next step on a sidewalk we will not plunge through to the center of the earth. This is NOT faith. It is a belief borne out from extensive prior evidence.

Same with how we can work under the assumption that the laws of nature will act in the future as they did in the past. We can't know this with 100% certainty, but it is a strongly-justified belief based on prior evidence and experience. And again, we don't know that the human intellect will be sufficient to understand every intricacy of the universe, but we seem to be making good progress, and we should continue until we hit that wall, don't you think?

He then goes on at length about history and art, noting that both contain truth, but not the kind that is accessible by scientific methods. All right...I'd concede that point. I'd also concede the larger point that the truth is not always accessible to the scientific method per se. That doesn't mean that we abandon reason and standards of evidence. He takes the example of whether or not Caesar crossed the Rubicon. How do we decide whether to believe this is the case or not? Well, one perspective would be to say there's no real way of getting at the truth...that different people will have different perspectives, so I'll just believe whatever satisfies my personal tendencies. Or...we could ask what evidence there is that Caesar crossed the Rubicon and assess how reliable that evidence is. If the evidence is strong in either direction, we can make a judgment. If it's vague or incomplete, we'll have to be content to say we just don't know whether Caesar crossed the Rubicon.

His basic strategy is to try to lower the bar for what we should believe. See, he says, there are all sorts of things that we believe that science can't verify, so it's open season on believing without strong evidentiary standards. The problem with this kind of thinking is pretty clear. Once you lower the bar this far, anything goes. According to this way of thinking, belief in ghosts, witches, leprechauns, dragons, faeries, Santa Claus, Bigfoot, and on and on is just as valid as belief that the earth revolves around the sun. Basically, if you don't have any standards for belief, you can justify belief in anything. And that's not a very sensible position, is it?

Saturday, December 6, 2008

Atheism Sign in Olympia, Washington

The city of Olympia, Washington put up a nativity scene in the Legislative Building. The Freedom From Religion Foundation got permission to put up the following sign right next to it:

The atheist sign was then stolen, and later found in a ditch. I think the story as a whole is pretty silly.

First of all, the message on that sign is horrible. It categorically states that things like gods, angels, and demons don't exist, rather than accurately stating that such things are very unlikely to exist. That's a subtle, but important distinction. And the last sentence is just provocative, and again, about as subtle as a smack to the head with a shovel. It completely ignores the very real positive benefits of religion. I happen to think that the net effects of religion are negative, but I'd never categorically assert that religion turns people into mindless assholes. This thing was designed to piss people off.

Secondly, as with the gay marriage issue, what I want to see is exclusion, not greater inclusion. On the street corner or on your private property, exert your First Amendment rights to the fullest. But in a government building? Let them carry out their intended function. If we adopt a policy of inclusion, pretty soon the halls of government buildings are going to be choked with whatever wackaloon shows of religious speech every sect in the world wants to put up. That's dumb.

Instead of letting the atheists put up a sign in the Legislative Building, they should just prohibit any such fixtures.

So, to summarize:

The people who put up a religious display in a government building are dumb.
The atheists who put up this sign are dumb.
The idiots who stole the sign and threw it in a ditch are dumb.
Oh, and so is Bill O'Reilly.

Thursday, December 4, 2008

What Americans Really Believe

My first two years of undergrad work were done at Baylor University. As a result, I still get Baylor Magazine in my mailbox every time it comes out. I rarely read it, but the Winter issue for this year has an article about the Institute for Studies of Religion at Baylor.

Here are some excerpts:
The co-directors of the Institute for Studies of Religion (ISR) were surprised when more than half of those responding to their latest survey on religious belief said that a guardian angel protected them. Fifty-five percent of Americans surveyed--not just evangelicals, but the entire United States--agreed with the statement, "I was protected from harm by a guardian angel." Dr. Rodney Stark describes the result as "extraordinary" in a new book detailing the findings called What Americans Really Believe. "I would have believed 10 percent or less would have had an experience with a guardian angel."
I find the result "extraordinary" myself. And where's he getting his prior presumption? From some guardian angel run-in index? We then get anecdotes from people who contacted Stark via email to tell them about how an angel saved them from falling down and another where an angel pulled a man from a burning car.

Which makes me guardian angels look out for lowly atheists like me, or just for true believers. Actually, I'm probably fucked. I doubt a guardian angel is going to save me from being mugged. I'll probably just have to rely on other people. Bah.

On atheists:
Generally, the snapshots reveal some surprises--the guardian angel statistic, for example--and some expected results. In the latter category, responses show that just 4 percent of the population is atheist--a result that might not be expected by those who have seen book after book on atheism hit the bestseller lists in recent years, but one "that doesn't surprise us," Johnson says. "It has been that way for decades. If it were 8 percent, we would be stunned."
Of course, the most recent report by the Pew Forum on Religion and Public Life found that 92% of Americans claimed to believe in some kind of god or spirit, so go figure. I think the numbers probably vary pretty wildly depending on the phrasing, but I wouldn't think Johnson should be knocked out of his chair if they had found 8% of Americans claiming to be atheists.

Finally, I liked this bit too:
The researchers are finding that faith undergirds prosocial behavior, Johnson says. "Typically, scholars don't write about this."
I wonder if their survey included people in the prison system, and asked what their religious beliefs were at the time they committed their crimes. I don't doubt that in many cases religious belief compels people to act nice. But I do quibble with the idea that it's the only way to get people not to shit on each other. I blogged about this not too long ago in reference to Phil Zuckerman's book about the Danes and the Swedes.

Anyway, I do think it's important to try to figure out what people believe, because those beliefs have a profound impact on society. Here's hoping that the next time the ISR takes a survey, they are shocked by the rising number of atheists.


I spent half the day today trying to get rid of a trojan my computer somehow got infected with, but dammit I scourged that thing from my hard drive.

It was ugly, too. It was actually a little program by the name of xtgoj6119471.exe that launched itself upon startup and generated a fake warning from Windows security alert in both my operating system and browser that my machine was infected with a trojan that captures my screen shots and keystrokes. The warnings come with links to a website that sells a fake security program called Perfect Defender 2009. So these shitbirds actually infect your computer with a program that makes you think it's infected with a completely different program, in order to scare you into buying a fake product. Nice, huh? If I ever met one of the assholes responsible for this, I'd break his kneecaps.

It took me a while to figure it out because none of the anti-spyware software I used detected it. I finally found a post by a guy on a malware forum who had posted a profile listing a log if his active processes. I compared it with mine and found that we had little ol' xtgoj6119471.exe in common. It wouldn't let me delete it, until after I disabled it from starting up automatically and rebooted. Then I was able to delete it, and the problem was solved.

Wednesday, December 3, 2008

Can You Be an Atheist and a Conservative?

Via Andrew Sullivan, John Derbyshire answers in the affirmative:

There are many people like us: people who cherish limited government, fiscal restraint, personal liberty, free enterprise, self-support, patriotic defense of the homeland and its borders, love of the Constitution, respect for established ways of doing things, pride in Western Civilization, etc., and yet who cannot swallow stories about the Sky Father and the Afterlife, miraculous births and revivifications. What does the one set of things have to do with the other? We are secular conservatives. What else are we? Figments of our own imaginations?

Sullivan comments that there's no conceptual reason why secularism and conservatism couldn't go together, but points out that in America conservatism and religion have become more and more entwined over the years, to the point where Christianity is very nearly an integral part of the Republican party.

I smiled at one value Derbyshire lists: respect for established ways of doing things. Why necessarily respect a way of doing things simply because it's been done that way for a long time? Either it's a useful, sensible law/method, or it's an inferior one. "We've always done it this way" isn't a good argument for continuing to do it that way, especially if the world around you is changing. But that sort of unquestioning respect for ideas based on longevity is very much in line with religious thinking. Derbyshire asks what these values have to do with religion, and there's his answer.

Monday, December 1, 2008

Cincinnati Zoo Cuddles Up To Creationists

Via Pharyngula, it looks like the people running the Cincinnati Zoo have lost their damn minds:

This holiday season, save more by visiting two of the areas fantastic attractions. Cincinnati Zoo and the Creation Museum. Ticket is valid for one day regular admission to each attraction plus the holiday events PNC Festival of Lights (Nov. 28-Jan.4) and Bethlehems Blessings featuring a live Nativity scene(Dec 12 Jan. 4)

Save more with our new Combination Attraction Ticket:
Cincinnati Zoo & Botanical Garden and Creation Museum The Creation Museum, located seven miles west of the Cincinnati Airport, presents a walk through history. Designed by a former Universal Studios exhibit director, this state-of-the-art 70,000 square foot museum brings the pages of the Bible to life.

As PZ Meyers points out, it might be a good idea to shoot off an email to the zoo to remind them that they're crapping all over their mandate.

I wonder if the same ticket agency will bundle together a trip to the Holocaust Museum and an Iranian-sponsored holocaust denial conference?

Friday, November 28, 2008

Pecanless Butter Pecan Ice Cream

I once ordered a blueberry muffin at Corner Bakery in Dallas, got to work, and found a blueberry muffin with no blueberries in it. I once ordered chile relleno in a restaurant in Lafayette, Louisiana that didn't have a chile in it.

But last week I got some butter pecan ice cream at Maggie Moo's. When I got it home, I opened it to find butter pecan flavored ice cream, with absolutely no pecans in it. I think Maggie Moo's is one of those places where if you want anything other than smooth ice cream you have to order the nuts/chocolate chips/whatever kneaded into the ice cream. That includes pecans in your butter pecan ice cream. I guess if they did Rocky Road, it would be nut and marshmallow flavored. Bah.

Anyway, I hope everyone had a good Thanksgiving. I'm in Texas for the holidays, and I'll be back in the cockpit on Sunday.

Tuesday, November 25, 2008

What are Car Horns For?

There's a weird article in Slate today about car horns, and I'm not sure what the point is. The tagline says "the car horn is bleeping useless," but the author starts out the article talking about his mother and wishing she'd use her horn more.

My mom is not much of a honker. You know what I mean when I say that: If a driver in front of her fails to hit the gas when the light turns, she simply waits. Time passes, and the green light glows. Eventually, the driver notices the signal change, or the cars behind begin to lay on their horns. Traffic proceeds. But no thanks to my mom; she's just not much of a honker.

For years I've been telling my mom that she ought to learn to honk a little more.

Then he goes on and on about how the horn isn't really a safety device. He talks about studies that show that honking is linked to aggression and gender, and that in most accidents, when it is used, it's too late.

Well, no crap. I've never viewed the horn primarily as a safety device. It's a crude communication device. Sometimes it's useful in exactly the situation the author talks about with his mother. If someone is not aware that a light has changed, beeping at them is fine. Other times it's useful to express dissatisfaction, e.g. when someone does something dangerous or rude on the roadway.

The only time it really works as a safety device is at speeds less than 10 mph, such as in a parking lot. Someone is pulling out of a spot and they don't see you. A beep let's them know you're there, and can avoid a fender bender. But when you're going much faster than that, of course the horn isn't going to help. If you're about to hit someone in an intersection, your attention and motor control is best spent with your hands on the wheel, trying to actually avoid the collision or minimize the damage, rather than moving one of your hands off the wheel in order to honk the horn.

The car horn is the pedestrian equivalent to "Hey!", which is used for a variety of situations, not all of which involve safety.

I sometimes wonder if we had easy car-to-car communication, making car travel more analogous to walking on the street, whether it would in general make driving a more safe and humane enterprise. I think there is an impersonal effect to sitting in a hunk of metal and glass without the ability to talk directly to those around us, and that it makes people inherently view those in other cars as competitors or obstacles, rather than as people. Until then we're stuck with the horn. And the wave and the finger.

Saturday, November 22, 2008

I Am a Nielsen Family

I got randomly chosen to be a Nielsen family, which means the Nielsen TV Ratings people mailed me a diary to keep track of my viewing habits. Filling out the diary should be fairly simple, since I don't actually watch any TV on my television. I use it for watching DVDs. What little TV I do watch is on my computer.

They also mailed me five shiny new dollar bills. It was like getting a birthday card from my grandpa. These people need to get with the times.

Sexual Harassment Training

Via Instapundit, here's an editorial from a professor at UC Irvine who refuses to take state-mandated sexual harassment training and is losing funding and resources because of it.

Four years ago, the governor signed Assembly Bill 1825 into law, requiring all California employers with more than 50 people to provide sexual harassment training for each of their employees. The University of California raised no objection and submitted to its authority.

But I didn't. I am a professor of molecular biology and biochemistry at UC Irvine, and I have consistently refused, on principle, to participate in the sexual harassment training that the state and my employers seem to think is so important.

He then recounts that his continued refusal to take the training resulted in the university turning his lab and assistants over to someone else. Then he says that he told the university he would take the course if they provided a signed statement absolving him of any implication that he had harassed students in the past, which they refused to provide.

So what are his big problems with the training?

First of all, I believe the training is a disgraceful sham. As far as I can tell from my colleagues, it is worthless, a childish piece of theater, an insult to anyone with a respectable IQ, primarily designed to relieve the university of liability in the case of lawsuits. I have not been shown any evidence that this training will discourage a harasser or aid in alerting the faculty to the presence of harassment.

So his first big gripe is that he thinks the training is silly and hasn't been demonstrated to be effective.

Now before I returned to graduate school I actually worked in a department that administered sexual harassment training. As part of my job, I reviewed some existing programs, most of which consisted of videotapes and questionnaires. Most were relatively short (you could finish within half an hour). As you might expect, some had poor production values, while others were more polished. And the better ones actually relayed good information regarding existing laws, while acting out scenarios that could be considered harassment.

Now I haven't seen studies regarding the effectiveness of such training, but I would be surprised if a simple informational video drawing attention to the details of existing laws would not have some positive effect in terms of reducing incidents of sexual harassment. And even if it didn't, what actual harm would it do?

Again, from Dr. McPherson:

What's more, the state, acting through the university, is trying to coerce and bully me into doing something I find repugnant and offensive. I find it offensive not only because of the insinuations it carries and the potential stigma it implies, but also because I am being required to do it for political reasons. The fact is that there is a vocal political/cultural interest group promoting this silliness as part of a politically correct agenda that I don't particularly agree with.

Uh, this guy thinks he's part of some kind of witch hunt. Could it possibly be that sexual harassment is an actual continuing problem, and that the state has enacted the law in order to help with the problem? Nah...gotta be a witch hunt of some kind. And how exactly does training carry a stigma if everyone is taking it. That's moronic.

The imposition of training that has a political cast violates my academic freedom and my rights as a tenured professor. The university has already nullified my right to supervise my laboratory and the students I teach. It has threatened my livelihood and, ultimately, my position at the university. This for failing to submit to mock training in sexual harassment, a requirement that was never a condition of my employment at the University of California 30 years ago, nor when I came to UCI 11 years ago.

Uh, dude...I'm afraid it's you who are threatening your livelihood by not agreeing to take an innocuous, probably helpful little piece of training. This paragraph smacks of a sense of entitlement. He acts like he shouldn't have to take the course because he's tenured, because it wasn't a requirement when he joined the university. Guess what? Laws change, man. Thirty years ago your university probably turned a blind eye to incidents of professors screwing their students for grades. Tenure doesn't make you immune to the laws of your state. If you don't like it, write your representatives and get out and vote. If a law passes that you don't like, that's just tough shit, man.

I could possibly understand a principled stance against a training program, but this guy just seems like a whiny ass.

Friday, November 21, 2008

The Tyranny of the Discontinuous Mind

I finally finished Richard Dawkins' The Ancestor's Tale. I'd give it a B.

One bit I thought was especially interesting was a section where he commented negatively on what he calls "the tyranny of the discontinuous mind," a subject that he's also written about elsewhere. What he's talking about is people who are only able to think of things in discrete, black-and-white terms. The issue where the rubber most often hits the road is the concept of personhood. You can view the concept of personhood as an all-or-nothing affair, and determine the criteria by which something meets that definition (e.g. when an egg becomes fertilized by a sperm, that single cell is a person, and before that it's not). Or you can view personhood as a gradient (e.g. a 5 year-old is more of a person than a fetus, which is more of a person than a fertilized egg), with a sliding scale based on various criteria such as level of development, brain activity, etc.

I'd provisionally agree with Dawkins that discontinuous thinking, in the absence of continuous thinking, is a bane. But I'd make two points to qualify that.

One, discontinuous thinking is often desirable and necessary, especially when enacting laws. When is a person considered legally drunk? Currently, as far as I know, we have a threshold for blood alcohol levels. If you're beyond that you're considered legally inebriated; below it and you're not. We could enact a spectrum of various offenses depending on the exact blood alcohol level, but how fine do we slice it? Do we have 10 categories of inebriation? If we're doing any slicing at all, we're dividing a continuous variable into discrete chunks, so we really can't avoid it. And here's the thing...if you zoom in far enough, the continuous becomes the discontinuous, and if you pull far enough back, the reverse occurs, the discontinuous blurs into a continuum. The fact is, we simply cannot avoid legal categories if we want to have a system that's not bewilderingly complex to the point where it cannot function. So we have to define cut-off points.

This is what Roe v. Wade did with the abortion issue, by creating categories by trimester. Some abortion rights advocates would be in favor of advocating abortion at any time up until birth, while many pro-lifers want protection from abortion upon conception. They're both exhibiting discontinuous thinking, defining personhood in binary terms around a strictly-defined point in time: birth in one case, and conception in the other. Roe v. Wade affords incrementally more rights as the individual develops in the womb.

The last main point I'd want to make is that Dawkins is ignoring the reverse phenomenon, what I'd call the ineptitude of the continuous mind. It's important to be able to view the world from either perspective, as the situation calls for it. If you view everything as continuous, then you would essentially be unable to every make category distinctions or decisions. Many times we need to define hard boundaries and thresholds. Many times we need to sharpen distinctions between groups. In his own field of biology, Dawkins notes the slippery, continuous notion of many concepts, such as species and life. Populations may not always fall neatly into categories, but at the end of the day biologists must use category labels if they're going to be able to study, communicate, and attempt to make sense of it all. To apply purely continuous thinking would be to do away with boundary distinctions altogether, to say that life is just a spectrum of life forms that vary continuously along a spectrum. And that kind of fuzzy thinking is just as problematic as strictly discontinuous thought.

The obvious answer is that we need both, and we need to develop the judgment to determine in which cases each type of thinking most appropriately applies.

Wednesday, November 19, 2008

I Passed

So...I passed my proposal defense. I'm officially ABD now.


The Mentalist Jumps the Shark

Actually, during last night's episode, The Mentalist didn't just jump the shark. No, it strapped on some rocket boots and a jetpack and motherfucking blasted its way over the shark, scorching everything and everyone below. The episode was appropriately named "Seeing Red," because anyone who actually admired the show for taking a skeptical perspective on astrologers, TV psychics, and other flim-flam hucksters would actually be seeing red after the end of the show.

Normally people call giving plot points away "spoilers," but that implies that the show or movie might actually be ruined by knowing the story ahead of time. Trust me, there was no way to make it any worse.

Here's what happened: There was a lame story about a rich woman who was run over by a car in the opening segment. She was leaving an appointment with her psychic, Kristina, who warned her that she was in danger. The cops show up to investigate, and we learn the major characters: the dead woman's son and daughter and her lover, a flaky, womanizing photographer.

Throughout the show, Kristina the psychic spars with Thomas Jane, and she also continually provides information that she shouldn't otherwise know, like that the car used in the murder was ditched in the town's reservoir. Now Jane thinks this implicates her as a suspect...and rightly so. But it turns out that she had nothing to do with the murder. It was the woman's daughter, who was mad at her for threatening to cut her brother out of the will and snapped when her mom didn't answer her phone call, so she ran her down in the street with the car. Okay.

Anyway, the show repeatedly insinuates that Kristina the psychic knows things that she shouldn't, she is not implicated in the murder, and she is not exposed as a fraud by the skeptical Jane. And then we come to the stomach-turning final scene.

Kristina asks to speak privately with Jane. He grudgingly accepts. When alone, Kristina says that she spoke with Jane's dead wife, and that there is a question that's been haunting him since their death at the hands of a serial killer. "Your daughter never woke up," Kristina tells him, and then leaves the room.

Jane starts to cry.

And then Derek starts to vomit.

Either Jane is allowing himself to be emotionally manipulated by Kristina, or more likely the show is suggesting that her powers are real, which is repulsive kick in the nuts to anyone who started watching the show because it was a rare little beacon of skeptical perspective in a media landscape filled with sympathetic treatments of supernatural hogwash.

Thanks for completely destroying a promising show before it even really got started, you monkey-humping asshats.

Supercomputer Hyperbole

Wired has an article about the latest iteration of supercomputers breaking the petaflop barrier. That means they can carry out just over a quadrillion (1,000,000,000,000,000) floating-point calculations per second. That's a lot. And it's a significant milestone. But this seems like a bit much:

"The scientific method has changed for the first time since Galileo invented the telescope (in 1509)," said computer scientist Mark Seager of Lawrence Livermore National Laboratory.

Look, this is a quantitative, not a qualitative, change. Some are making the claim that the ability to model and simulate at greater and greater levels of detail will allow for qualitatively different ways of doing science. But I don't think so.

Breaking the petaflop barrier is more like building a bigger and better telescope that allows us to see farther and clearer, and to see things we've never seen before, but it's not like the invention of the telescope in the first place.

Tuesday, November 18, 2008

Defending My Proposal

So tomorrow I'm defending my proposal, which is basically a review of the area I'm interested in and a road map for my dissertation work. If I pass, then I'll be ABD (All But Dissertation), and then I'll actually have to do all the stuff I've said I'm going to be doing.

The basic theory driving my work isn't really all that complicated, though I can easily get bogged down in the details, an urge I'll have to try to resist tomorrow.

In a nutshell, I'm proposing a model of how we learn and process sequences. Virtually everything you do is a result of either learning new sequences, recognizing ones you've already learned, or generating them. So it's crucial that we try to understand how this works. I was inspired a great deal by Jeff Hawkins' ideas, but I saw a large gap between his theory and how it might actually be implemented based on what we know about the brain. My model is an attempt to try to fill in some of that gap.

First of all, the brain is hierarchical, which just means that some areas are "above" others, while others are "below". So broadly speaking there are three kinds of connectivity:

  • Feedforward: from lower to higher areas
  • Lateral: between neighbors in the same area
  • Feedback: from higher to lower areas

I'm proposing that each of these types of connectivity plays a distinct role in learning and processing sequences.

Feedforward connectivity allows you to "chunk" sequential information. For example, when you learn a phone number, you typically learn it as a chunk of 3 numbers combined with a chunk of 4 numbers. If the whole system is arranged hierarchically, then we can group smaller chunks into larger chunks, up and up the hierarchy, so that we can efficiently store very long sequences.

Lateral connectivity allows you to learn pairwise sequences, for example, what comes after "g" in the alphabet. I'm hypothesizing that the type of learning that occurs between neighbors allows for a kind of domino effect. You hear "a" and it's like knocking over the domino for "b" and then "c" and so on, in a cascading effect. This type of representation is directional (i.e. it's difficult to say the alphabet backwards) and content-addressable (which means that you can reproduce the sequence simply by being given some small part of it, like the first few notes of a song).

You can see how these two types of representations might complement one another. The first is efficient and scalable, but isn't content-addressable. The second is content-addressable, but doesn't scale well.

Finally, feedback connectivity has been hypothesized to push predictions back down the hierarchy, which helps when we're confronted with input that is noisy (e.g. a cell phone conversation). If there is noise or gaps in what we're sensing, the higher level nodes are transmitting via the feedback connectivity what they expect to experience next, and that helps fill in the missing pieces, making the whole system very robust and reliable.

My plan is to implement the model incrementally, and I've already got a preliminary model using feedforward connectivity. It learns by associating the immediate past with the present. Let's say you're learning the alphabet for the first time. You hear "a", then "b". The way the model works is, it stores "a" in a kind of short-term memory, and when "b" is presented, the system binds them together, the delayed "a" and the current "b". It chunks together "ab" and "c" in the same way, storing progressively larger chunks. And it does so using spiking neuron models and learning mechanisms that have been experimentally confirmed in animals and humans.

So that's it in a nutshell. There a many more details I'm leaving out, but that's the gist. Hopefully everything will go smoothly, and by tomorrow evening I'll only have one more hurdle to jump before getting my PhD.

Monday, November 17, 2008

The Ancestor's Tale

I'm just finishing up The Ancestor's Tale by Richard Dawkins, which is basically a description of the evolution of life on earth treated as a journey back through time to meet up with common ancestors.

It's been all right, filled with lots of interesting tidbits about various animals, but many times it just feels like Dawkins is riffing about whatever he wants to talk about at the moment. I blogged previously about his lengthy digression about race. In that section, he distinguished the concept of race from that of species by claiming that there was an objective scientific criteria for species. Namely, if individuals mate and reproduce under natural conditions, they're considered to be in the same species.

"Wait...what about asexual species?" I thought. Later in the book Dawkins brings up species that reproduce asexually, and admits that their designation to species is based on similarity judgments by scientists. In other words, the concept of species doesn't really have any firmer ground to stand on than any other classification in biology.

Another thing that bothered me was when he talked about why wheels haven't evolved, another topic I blogged about not too long ago. He pointed out that wheels aren't all that useful without roads. But then he goes on to point out what he says is probably the only example of wheels having evolved: the bacterial flagellum, which is a wheel-axle mechanism that freely rotates, whipping around a tail-like appendage that propels the bacteria forward. Well, if this is considered a true wheel, then we don't necessarily need to think about wheels purely as means of locomotion on land, do we? Why haven't they evolved in aquatic animals? In other words, why don't fish have rotors?

Anyway, it's been a pretty good read, but I'm glad it's nearly over.

Which is Smarter: Cats or Dogs?

The Straight Dope question for today is a classic one, asking which is smarter between cats and dogs.

Cecil takes the political route and gives the following answer:

Judging the relative intelligence of cats and dogs is like deciding which is better looking — there's just not much basis for comparison. Psychologists have a tough enough time coming up with a culture-blind IQ test for humans, who all belong to the same species; designing a species-blind test for dogs and cats is just about impossible. What people take to be signs of intelligence in their pets usually are just specialized survival skills that say nothing about innate brainpower. A cat, for instance, is much more dexterous with its paws than a dog. This dexterity fascinates cat lovers, who also cite the cat's legendary standoffishness as proof of its mental superiority. The dog, on the other hand, is much more of a social animal; dog advocates claim this proves the dog is more civilized, ergo, more intelligent.

This reminds me of Howard Gardner's theory of multiple intelligences. Nobody's really smarter than anybody else. Some people are good and some things, like music and swimming, and others are good at writing poems and solving geometric proofs.

That is to say, there are some people who consider intelligence a wholly subjective concept, and others, such as myself, who consider it an objective concept, amenable to defining and measuring without regard to value judgment.

Instead of talking about two individuals or species that are relatively close in their cognitive capacities, let's take an extreme example to illustrate the point and ask:

Which is more intelligent, an earthworm or a chimpanzee?

There are two broad ways to answer this question. The first is to do so as Cecil did, under the idea that intelligence is subjective and relative to the individual or species. In that case, we would say that the question is nonsensical. An earthworm is good at burrowing and detecting various nutrients in soil. A chimpanzee is good an living a semi-arboreal lifestyle and all that that entails. I personally think this is a silly response. That particular answer negates the concept of intelligence as relating to cognitive capacities, and instead more closely associates it with the concept of evolutionary fitness.

The more sensible answer is the one that I think most scientists and laypeople would give if pressed for an answer, the obvious one: the chimp. And why? Well, those same people might be hard pressed to justify their answer, and as I've blogged about before, there's a paucity of good theory relating to intelligence, especially across species and systems.

Personally, I'd say that intelligence is the collective capacity of a system to recognize patterns (temporal and spatiotemporal), generate patterns, and in some cases learn patterns. An individual's ability to do so is dependent upon the number and quality of their sensory modalities (vision, hearing, touch, etc.) and the range and complexity of their behavioral repertoire. We can measure an individual's ability to recognize, generate, and learn patterns, both in naturalistic and controlled settings by observing four main metrics:

  • breadth: how many different kinds of patterns can they recognize/generate/learn?
  • depth: how many patterns within a given class can they recognize/generate/learn?
  • speed: how fast can they recognize/generate/learn patterns?
  • accuracy: how well can they recognize/generate/learn patterns?

In terms of its ability to perceive and process its environment, a chimpanzee has far more powerful and numerous sensory systems than an earthworm. Also, the range of behaviors that a chimpanzee can perform vastly outnumbers those of an earthworm. Even without any quantitative assessment, it's very easy to see that by these criteria a chimpanzee is more intelligent than an earthworm.

I think an answer exists to questions like: Is person A more intelligent than person B? and Which is more intelligent: cats or dogs?

In the case of species with numerous breeds, the answer may be complex. But I believe there is a practical way to determine whether or not the mean intelligence of a given species is greater or less than that of another. What is needed first is a strong theoretical framework, followed by the development of rigorous tools and methods to make those determinations, and right now we are sorely lacking in both.

Saturday, November 15, 2008

Atheist Advertising

A couple of atheist ad campaigns have made it into the news recently. The most famous is a campaign in Washington DC with ads appearing on buses saying "Why believe in a god? Just be good for goodness' sake".

And my sister just sent me a link to this story about a similar campaign in Denver, featuring billboards that read "Don't believe in God? You're not alone."

Now, both of these seem like decent campaigns to me. The spokesperson for the group that sponsored the first ad says the motivation is to increase awareness for non-religious people in the community that they are not alone, and secondarily to try to help dispel the mistaken notion that morality is necessarily tied to supernatural beliefs. The second campaign very obviously shares the first reason as well, to indicate to the non-religious that even though their views may be in the minority, they are not alone.

Obviously, not everyone thinks its a great idea. From the Fox story:
The humanists' entry into the marketplace of ideas did not impress AFA president Tim Wildmon.

"It's a stupid ad," he said. "How do we define 'good' if we don't believe in God? God in his word, the Bible, tells us what's good and bad and right and wrong. If we are each ourselves defining what's good, it's going to be a crazy world."
Well, Tim, we don't individually decide what's good. We can still collectively reach consensus on how we want to treat each other. That's called a society, with laws and mores. As I've pointed out before, many of the rights put forth in the US Constitution are not dictated by god, but are secular ideals. The very first amendment insures freedom of religion, the personal right to worship whatever you want. In contrast, the first commandment of the Old Testament strictly forbids worshipping anything but the Old Testament deity. One is a secular value, the other is a religious one, handed down from on high. How did we get the idea that religious pluralism is good? The founding fathers used their brains.

There are some gems in the Denver story as well:
Pastor Willard Johnson of Denver's Macedonia Baptist Church called the billboards a desperate effort to discredit Christianity.

"The Bible is being fulfilled. It says that in latter days, you have all these kinds of things coming up, trying to disrupt the validity of Christianity," Johnson said. "If they don't believe in God, how do they believe they came about? We denounce what they are doing. But we do it with love, with gentleness, with decency and with compassion."
Glad the atheists could help fulfill prophecy. Now think for a moment about inventing your own religion. What would be a good feature to implement that would be self-reinforcing against any kind of criticism? How about adding something about how there will be people who will try to tear down your beliefs and discredit them? That might be a good psychological mechanism from keeping your followers from ever actually listening to criticisms of their religious beliefs.

And I very much like the idea that you can denounce something gently.

Also from the same story:
Bob Enyart, a Christian radio host and spokesman for American Right to Life, said it's hard to ignore the evidence.

"The Bible says that faith is the evidence of things not seen. Evidence. If we ignore the evidence for gravity or the Creator, that's really dangerous," said Enyart. "Income tax doesn't not exist because somebody doesn't believe in it. And the same is true with our Creator."
Holy crap...I can't argue with that logic, mostly because there is no logic there. Whew.

Anyway, I applaud the efforts of the non-religious to increase awareness of our presence in society and make an effort to communicate to like-minded others that they are not alone. It's a small step toward community building, although as I've argued in the past, ultimately such a community will need to be build on a foundation of positive principles, things we do believe in such as human rights and scientific inquiry, rather than simply the absence of belief in the supernatural.

A World With No Nukes?

Wired has a feature called Danger Room, with advice from experts to President-elect Obama on issues related to national security. The latest installment is about nuclear weaponry by Joseph Cirincione. His credentials?
He's the president of the Ploughshares Fund, and the author of Bomb Scare: The History and Future of Nuclear Weapons. During the election, Cirincione was an informal advisor to the Obama campaign. Previously, he served as director for nonproliferation at the Carnegie Endowment for International Peace.
Okay, what's his advice?
On nuclear weaponry, the United States must lead by example. Expect President-elect Barack Obama to call for a nuclear summit of leading nations on practical steps that all can take towards a world without nuclear weapons. Their ultimate elimination should be a core principle of his national security strategy. Look for early talks with Russia on mutual reductions to show we are serious. There are dozens of other steps to take, but cleaning out our own nuclear house would be an important early move.

Stopping new nuclear states and preventing nuclear terrorism will also be at the core of Obama's new, more effective nuclear security policy. Fortunately, Obama developed during the campaign the most comprehensive nuclear policy program any candidate has ever detailed. He now must implement it, beginning with a multi-level effort to prevent nuclear terrorism, then quickly pivoting to preventing new nuclear states and eliminating the 26,000 weapons in global arsenals.

The key to is stop terrorists from getting the stuff for the bomb core—highly enriched uranium or plutonium. No material, no bomb, no nuclear terrorism. Obama pledged to lead a global effort to secure all the weapons materials at vulnerable sites within four years, destroying as much as possible. Look for him to appoint a deputy national security advisor to coordinate the work.

The more countries with weapons, the greater the risk, so expect also a quick start on tough, direct diplomacy to roll back the North Korean nuclear program and preventing a nuclear Iran. He will gain leverage by dealing with our weapons. If we cling to our thousands of hydrogen bombs, how can we convince others that they cannot have one?
There's a key problem with this line of reasoning. It assumes that if current nuclear powers eliminate their nuclear weaponry this will "lead by example" and no other states will have motivation to develop or acquire nuclear weaponry. This type of thinking would be nice, if it actually had some kind of basis in reality. In fact, it's incredibly foolish with a moment's reflection.

Imagine a world in the near future where the US, UK, Russia, France, Israel, China, Pakistan, and India (and whoever I might be leaving out) all agree to a pact completely eliminating all of their stores of nuclear weapons. What does the world look like now? If anything, the US has actually increased its military standing, because it still retains the most powerful conventional force by far, but there are no nuclear trump cards to keep it in check.

The equalizing power of nukes is patently clear; they enable a military with weaker conventional forces to provide a clear deterrent to a military with far stronger conventional forces.

This is the simple strategic argument for why it would probably be impossible to get countries like Russia and China to ever give up nuclear weapons. On the practical side, how could we ever enforce such an agreement? We have seen how difficult verification is even in relatively small countries such as North Korea and Iraq. A case in point: In 1972 162 states signed the Biological Weapons Convention (BWC), including the Soviet Union. The treaty banned the development and production of biological weapons. However, we now know from former researchers in the USSR's biological research program that they continued development on biological weapons, despite the treaty, including attempts to weaponize smallpox, a scourge that humanity had declared eradicated.

If a given country does not want to cooperate with a given arms agreement, especially if that country has sufficient resources, there is simply no practical way to ensure cooperation. So even if all the current nuclear powers all agreed to get rid of their weapons, there would be no way to make sure that everyone was abiding by the agreement, and there would be little motivation to cooperate, especially for those with weaker conventional forces.

Finally, in a fantasy world where all the current nuclear powers gave up their stockpiles and we were actually able to verify complete cooperation, why would small states necessarily give up on development of nuclear programs of their own? The naive perspective of Cirincione is that if no one has nukes, no one will want nukes. The implication is that nukes are only ever strategically defensive. But imagine a world where no other power has nukes, but North Korea has secretly developed them. A dictator who was the sole possessor of nuclear weaponry would have carte blanche in annexing neighboring states. They would be able to conquer their neighbors without firing a shot with a nuclear trump card.

No, I'm afraid you can't put the toothpaste back in the tube. For both strategic and practical reasons, nuclear weapons simply will not be expunged from the world stage. I would like to live in such a world, but then, I also entertain a number of other utopian fantasies. I do agree that we need to try to reduce the stores to the lowest possible levels, and implement better controls and tracking for existing nukes. But getting rid of them altogether? That's a silly pipe dream.