Wednesday, August 31, 2011


I haven't posted one of these in a while. These are cool projects from instructables:

Tuesday, August 30, 2011

Human History and Science

Truly terrific set of videos showing a representation of science and human history. By Uppruni Tegundanna.

Wednesday, August 24, 2011

How Lobbying Works

Who owns Rick Parry? Bank of America, that's who. See here.

Tuesday, August 23, 2011

Evolution as Fact and Theory

Here's a neat article on discussing the fact and theory of evolution. Everyone should read it.

Monday, August 22, 2011

Risk Benefit of Science

Theo Gray has a good lecture on risks and benefits of learning science here.

Sunday, August 21, 2011

A Case Study of Science in Science Fiction, Part 1

About mumbly-seven, Congdon and Weed published my first novel, Caliban Landing. It's still for sale as a used book and I'd like to bring it out as an e-book. Just as soon as I get up the nerve to cut up and scan the hard cover. Until then, you can get a copy here. Go ahead. I can wait.

I've been talking a lot about how science, evolution and fiction go together. So I'm going to talk about specifics by using Caliban as an example. Heck, maybe it will generate enough interest that somebody might want to read a mumbly years old book.

Caliban had a lot of science fiction elements in it: faster than light travel, several alien species, human/AI interconnection, cyborgs-- all sorts of things. I'm going to limit my discussion to the biology in the book.

Caliban was a first contact novel. Humans come to the planet Caliban to survey it for human exploitation and maybe stake a claim or two. The planet has ostensibly been cleared of sentient habitation. This turns out to be incorrect and the team accidentally kills one of the sentients. The legal situation being what it is, they decide to try and make first contact and in effect get absolution and stay out of a higher, and less forgiving, court. Things don't go as planned.

Given this was a first contact novel, what drove the book was the nature of the aliens. Since I was a biologist, the aliens had to be biologically derived. What drove the aliens were the plants.

Photosynthesis on earth uses only a small portion of the available spectrum of light. This derives from the heritage and limitations of chlorophyll, the primary pigment used to capture the energy of photons. Chlorophyll a has its absorption peaks in magenta and orange. Chlorophyll b has its absorption peaks more in the blue and yellow. The lighter blues and greens and the UV and IR regions are essentially areas of no absorption. One would expect that chlorophyll must be very efficient and conserved to remain so common across essentially all photosynthetic organisms.

Hm. I thought. Chlorophyll only responds in a fairly narrow set of ranges. Opsins, the pigment in the eye, have multiple absorption spectra. In humans, blue cones peak at 437 nm (blue), rods (night vision) peak about 498 nm (sort of blue to green), green cones 533 nm (green), red cones 564 nm (yellow). Rhodopsin, a common opsin in rods, is somewhat broader in absorption than the color opsins. In addition, there are variations in rhodopsins that have differing peaks. (A good description of how seeing works is here.) Rhodopsin is quite sensitive to light but fragile. It's why we have good night vision but also why that night vision can be easily destroyed. (See here.)

What if (an SF writer's favorite phrase) we had a pigment (or pigment system) that was tuneable. That is, its peak absorption spectra could be changed according to available light spectra. Possibly, it wouldn't be as efficient as chlorophyll but it might be adaptable to multiple conditions. An interesting side effect is how it would look to us. The close uniformity of green in the plant world is an effect of the narrow ranges of the pigments involved. There's variation in the other pigments but chlorophyll is pretty constant. A tuneable pigment would have different reflective properties depending on how it was tuned. The top of a forest canopy would be a different color than the interior. Shaded plants of the same species would change depending on light level. And most plants would change considerably with the seasons.

I took the idea and filed it away.

Later, I was reading an article on the biochemistry of photosynthesis. After all, the photon must be absorbed before its energy can be captured. That's got to be pretty interesting.

Photosynthesis is dependent on fluorescence. (See here and here.) Fluorescence is the process by which something that has absorbed energy by either light or other electromagnetic radiation emits it. Commonly, a photon strikes an electron of a substance and imparts energy. The electron emits a photon as the energy is released. Photosynthesis is a fluorescent reaction in that the energy is received from the photon by captured by biological systems rather than be re-emitted.

Hm. I thought again. I remembered my tuneable pigment. Let's say our pigment can absorb terrifically in its narrow tuned range but it can't retain the photon as easily such that the photon is re-emitted. That's what happens in fluorescent paints. Of course, if the photon comes in as blue and emits as green that's not much of an energy gain. To make this worth it as many of the photons would have to be absorbed as possible and then re-emitted at as low an energy as possible.

Visible light is just what we see. It's not magic. It's the visible part of the electromagnetic spectrum. The spectrum goes up into gamma rays and down into microwaves. So I thought, let's make them re-emit radio waves.

Cool, I thought. And put it away again.

Time passed and I was reading Hubel's work on visual systems. The eye captures photonic data but it's the brain that makes sense of it. I wondered what it would be like to have a visual system that didn't operate on the rules of optics. Radio waves, for example.


I dusted off the plants I'd thought up and then derived an alien biology that would take advantage of it. There are drawings of these guys in my notes, skulls that were laced with radio detecting proteins (likely with metallic cores). Opsins chemically resemble chlorophyll.

All opsins have a common heritage (see here) that is different from the evolution of chlorophyll. (See here.) But both chemical families harvest available light. I made the presumption that if radio waves were as present and as ubiquitous as light then biochemical systems would evolve to take advantage of them. I also made the presumption that animals who could detect their environment using radio waves would be selected for over animals who could merely detect visible light. Neither of these assumptions were provable but they made great aliens.

Okay. I had an alien biology and an alien ecology. Now I needed intelligence. Culture. Communication.

I was reading a lot about dolphins in those days and one article I read (which I cannot find, unfortunately) noted that dolphin sonar (like the sonar of bats) created the medium of perception rather than used one that was available. The article suggested that if dolphins were intelligent, they could communicate by actually producing an "image" of an object to show a receiver.

Oh, this was too cool to leave on the floor. I modified my Caliban aliens to be able to manipulate the radio waves they were receiving and seeing by-- sort of like modern metamaterials, though I certainly didn't think of them.

I now had an alien biology. But I still had to create an alien culture.

Stay tuned for Part 2.

Saturday, August 20, 2011

Google's Ad Sense

I signed up for ad sense on this blog. It's an experiment. Maybe I'll make some money. We'll see.

However, what's incredibly interesting is what has been chosen to present for the ads. Of course, these ads are local to the computer being used to view the blog.

So: why would a set of ads involving Summer's Eve Douche show up on my computer?

Well, I was viewing articles involving facing off on evolution, the selfish gene becomes a musical, metropolitan undergrounds, smart elephants, risk in science education and an article on vaginal pH entitled, "Don't douche, she declares acidly."

Should I be surprised at which one was chosen as an ad to grace my pages?

The selection mechanism for these ads is interesting. On one end you have to match the ad to the viewer's interests. (I almost said "tastes.") But on the other you have to match a advertisement to that interest. I'd expect a sliding scale of matching based on how much the advertiser has paid for the placement for the ad. An inexpensive but precise connection to Scientific American subscriptions (most of the above were SciAm blogs) might well lose out to an expensive ad that has only a marginal probability of connection.

How those connections are made might also be interesting. If it's word oriented, what's the probability that the word "douche" might be indicative of interest in a feminine hygiene product or just being used as a pejorative, as in, "Rick Parry is a douche."

Also, how is the content of the article viewed joined with the title of the article viewed. In this case the word "douche" is used several times in the article along with the words "vagina", "pH" and, lo and behold, "Summer's Eve". This could, for a fairly simple machine, indicate strong interest. It also argues for that simplicity of algorithm since one could, by examining the site and references to the article, determine that this is an article mostly about science. One wonders if I had been viewing an article about vaginal pH of baboons in Science magazine would I have gotten the same result.

The number and frequency of the ads are also interesting. There was space for 3 ads in the window for the blog. Consistently, for several minutes, the ads for douches were present. I looked at that article once. I looked at many other articles over an hour. But those adverts resolutely stayed douche.

Either douche is a major interest point or Summer's Eve is really pouring on the money.

Heh. With this entry I'll probably have douche articles for the rest of the summer's eve.

Friday, August 19, 2011

Koch Brothers Exposed

Here is an interesting site. More links here. Money talks.

Sunday, August 7, 2011

Bill Morrissey: 1951-2011

Way back in the early eighties, my friend Steve Caine introduced me to the local folk scene and, specifically, to the work of Bill Morrissey.

Bill died on Sunday, 7/23. There are obituaries and appreciations on his home page here.

He left behind a phenomenal body of musical work, one well respected novel and a second due out this year.

I've read a lot of obits about him in the last week and found them somewhat wanting. Most of them were of "he was really good and we'll miss him" or "here is his considerable work. He was really good and we'll miss him." But that's sort of like saying the Beatles were good a pop songs and that's why we missed them when they broke up. So I want to dwell on him. Why he's really good. Why we'll miss him.

We'll start with an example from Barstow on his first album.

Barstow is about a bunch of transients (possibly bums) huddled around a campfire in the desert town of Barstow, California, cold, half drunk and not sure where they're going to go next. The chorus goes:
Don't the freight yards sound like a drunk in a metal shop
I can't believe it gets this cold in Barstow
I can't believe I pissed my 20's away
Baby if you take me back I promise you I'll stay
There's a lot of power in these words. Like nearly all of Morrissey's work, the song tells a story. Not a big story of break up or pursuit of power but a moment, sitting around the campfire drinking a found bottle of wine:
It ain't much. It ain't good. But it'll get us through till dawn
What struck me first about his work was its tremendous precision. Not just his words-- though they're precise enough-- but his timing and voice as well. Morrissey referred to his his voice as a "dulcet front loader" and, like Dylan, it wasn't what would normally be called a singing voice. But his sense of music and timing was second to no one's. If you think about that Barstow chorous, how the hell can you make something like that scan? But he does and without any mush mouthed slurring the words together.

I can't really discuss Morrissey's singing. That's something you have to hear. Every note is placed exactly where he wants it in a strange timing and tone that he understands. It's right but I can't say I always understand it. You can disagree with the timing-- and on the albums I often do-- but this is still the result of his painstaking and careful effort.

I can talk about his lyrics.

Morrissey was not hobbled by consistency in his work, either. In other, lesser, artists changing voice, point of view or even character in a song might be a problem. But Morrissey brought them together. For example, on the Night Train album the first stanza of the song Time to Go Home reads:

Well, she looks so small
She looks so frail
It was like the world forgot her
As she stood outside the jail
They sit and stare
They rarely speak
She comes to see him
The same time every week
Later in the song we have:
Well, your T shirt's clean
like your dungarees
and in two days you will be
on your way overseas
sit on the bed
with a warm six pack
It's not like how they said
but it's too late now to take it back
There's no explanation of the change in tense, point of view or other "inconsistencies". The listener, or reader, is left to make his own judgement. The three stanzas involve a jail visitation, a man trying to figure out if he should cash out his fishing boat in Alaska and a man about to leave to some indeterminate location. Is the main character in the three stanzas the same person at different times? Are the three stanzas connected except in the Morrissey's mind? You get to decide.

Many of these are dark stories but not all. From Grizzly Bear:
I could tell by how she high stepped
she learned to dance uptown
where I come from we just kind of get drunk
and slam bodies all around
You have to hear Bill's singing to understand how that all gets sung together right.

Or , from Car and Driver:
I've got a Mercedes Benz with MD plates
I have no trouble finding dates
I've got a 1980 Subaru
One more semester then I'm through
My slant six Dodge is no big thrill
But it's a car no atom bomb can kill
I make a lot of dough in a high tech job
Yeah you bet I drive a turbo Saab
Or, from She's Your Baby Now
You're the one who stole my baby
You took her with such ease
But now I feel just like Atlas
saying so long Hercules
She's your baby now
Morrissey had an eye for stories and they came up in the songs continuously. He liked stories about people who were on the fringe and often not likeable.

Consider the song Pantherville from North, which as far as I can tell is a song about an incestuous father. The song begins talking about how the roads to Pantherville disappear in the snow and there's no way out:
When it snows like this, the state man don't come around
When it snows like this, the state man don't come around
I wake up a happy man when the snow is falling down
The song later says:
The state man says he won't rest until I'm up in Thomaston.
(Thomaston is where the prison is.) Then, the song closes with
Put down those dishes daughter
Come watch these clouds above
Sit here right beside me, girl
Tell me who you love
Definitely creepy.

This ability to crawl into someone else's skin, talk about something from their point of view, thereby removing judgement, is a wonderful talent. Again, Morrissey lets the listener decide what to think about the song. Morrissey's the reporter and reciting the story. It's up to you to react. The character in the song has the moral integrity of a shark: he's not going to judge himself. That's up to you.

Another example of this ability is The Driver's Song from Standing Eight.

Back in the eighties there were firms that would take toxic waste from Massachusetts, fill up tanker trucks with it and, at night, drive over the dirt roads of New Hampshire with the spigots open. Morressey wrote about one of those drivers in The Driver Song. A happy man doing a job he likes:
I stop my truck in the middle of the road
The same stop each time on this familiar route
I open the side valve then climb back to the cab
and I drive these woods till that big tank empties out
then, later,
I love these back roads of New Hampshire
They twist and wind like a rolling sea
I feel like a Captain who knows no fear
Everybody goes to sleep so early up here
Again, the moral judgement is left to the listener.

I think of Bill Morrissey as the folk singer equivalent of James Joyce. Joyce was a sponge. It seems like everything Joyce saw in Dublin he kept and then contorted it onto the page for us to read. Bill grew up in the northeast and did the same. (As a side note, Bill once said he was working on putting Ulysses to music one long dark winter. It was a waltz.) While he often put himself in his music he was also smart and deft enough to slip out of the way when he wanted to.

Morrissey was at his best in performance. I'm hoping some live performance recordings will find their way onto CD or mp3. Morrissey was at his best by himself and shorn of instrumentation other than his voice and his guitar. The albums are good but not as good as he was by himself.

I'm not a big fan of most poetry. I think the word is overused and poetry is overrepresented. Poetry, if it is worthy of the word, ought to stun you right between the eyes. It should in a single moment transform you so that you can bear witness to being one way at point A and being a new way at point B. Such things are necessarily individual and subjective. But Morrissey transformed the way I looked at lyrics and music. He was poetry for me. One song especially, These Cold Fingers:
It's four o'clock and the sun's gone down the drain.
It's still late winter but they say it's early spring.
Louis reads the gas pump. Rossi counts the oils.
But me I'm done so punch the clock and see you in the morning.
There's nothing back at home that ain't gone greasy from the stove.
I never laughed so hard as when that typewriter broke.
Think I'll stop along the river road for a half pint and some beer.
Everything would be okay of those old dreams would disappear.
Morrissey had trouble with alcohol. He smoked and abused his body. I saw him last winter and it was clear he was not as strong as he was. But he was game and trying. It didn't surprise me to hear that he died.

But it struck me just the same. He'd gone through rehab. He'd gotten clean. He'd been given a second chance and was grabbing on and not giving up without a fight. These sorts of things happen, I know. It's not the years; it's the mileage. Still, I hate to see someone taken down in the middle of taking on a second chance.

Greg Brown said this about Bill in his song Fishing with Bill on the album Friend of Mine
Sittin' in a bar in Brattleboro
Thinkin' about one of his songs.
The rain was pourin' down, and I was pourin' it down,
And all I could do was hum along.
We've talked about goin' fishin' so often
At some party when the gig was done.
Well, life slips by like a little dry fly
Sliding down a deep slick run,
So let us stand steady like an old mill.
Oh I, I'm goin' fishin' with Bill.
Sad to say: not any more.

Thursday, August 4, 2011

Debt Bill: Not completely ludicrous

Some parts might actually be useful to democrats. See here.

Team iLuminate

Check out these dancers. Here. Here. Here.

Monday, August 1, 2011

Obama: Cave Dweller

Okay. I'm gonna say it. Obama's caved. He's caved over and over again whenever the Republicans get hard line. He caved again over the weekend.

James Fallows has some things to say about the debt here.

Here's his take on the cave here and here.

Read Gin and Tacos for a lovely fairy tale about it.

Godzilla won't you please come home

Good article on the speculative biology of kaiju here and here.