Tuesday, October 31, 2006

Get your cell on

Who was I kidding. Midnight blogging rocks.

This animation of macromolecules, organelles, and cells is so beautiful that when I watched it I almost urinated streams of live bees out my tear ducts.

I found it on Scott Aaronson's blog, and in the comments to the same post I found this interesting Q&A:

Every male human is continually producing reproductive DNA in his testes. If the net DNA production of a single human male were unspooled as a single thread, the net linear rate of DNA production would most nearly be:

(a) a snail's pace
(b) human walking pace
(c) human running speed
(d) the speed of a car
(d) the speed of a jet fighter plane
(e) the orbital velocity of the space shuttle


Answer: human testes synthesize linear DNA at orbital velocity -- on the order of 100 terabytes of information is spooled out every second.

Yet on the other hand, this requires only that a few tens of nanograms of DNA be synthesized per second, which is easily handled by rather compact (air-cooled and paired for redundancy) organs.

No wonder we guys do so much of our thinking down there! Ba-dump-bump-ksssshhhhh.


A quick search revealed that the kickass music from that clip is by Matt Berky at Massive Productions. You can download the 8-minute MP3 for, uh, $25. Nice business model, dude. If you'd charged two or even three dollars I'd have gladly paid. As it is, I gotta beg my readers to send me the pirate version if any of them get a hold of it. Por favor.

Seriously. Has the lesson of iTunes been utterly lost on this guy?

Aaaaaaaaaaaaaaaaaah! [swipes hand dismissively like a crotchety old coot]

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Monday, October 30, 2006

Take that, falling sand game!

On the heels of MIT interactive sketchboard, check out this, which you can evidently download for free, and with which you can do some crazy stuff.

I haven't tried it yet, but as soon as I have two seconds to rub together, I intend to.

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Sunday, October 29, 2006

A missing term in the science of snark

I just coined a new term that characterizes lab-based genetic studies of limited scope or applicability: Drosophistry.

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Wednesday, October 25, 2006

More doggerel

I used to write poems. Most of them sucked, but they made me happy. I see from the time stamp that I composed this one 13 years ago to the day. Enjoy.



The other day I fought a duel
Against a very fearsome foe
He was ugly, mean, and cruel
I finally vowed to lay him low

He had killed most everyone
In the night he'd ambush them
At the rising of the sun
It was only me and him

We met upon a plain of war
With weapons ready at our sides
He let out a mighty roar
I swore right then I'd have his hide

We fought and yelled and kicked and screamed
Neither gaining the upper hand
I beat him with a wooden beam
He shoved my face into the sand

I could not put up with this
With a cry I drew my sword
I raised it back and swung and missed
So I crowned him with my board

In return he grabbed my arm
With a wrench he tore it free
The socket gaped, he'd done me harm
Time to take him seriously

I sank my teeth into his scalp
Against his awesome might I heaved
I heard a ripping and he yalped
Of his ears he'd been relieved

His skull gleamed in the dusty air
My missing arm sprayed jets of blood
We fought and tumbled without care
Our bleeding turned the dust to mud

He ripped my leg off with his claws
I shoved my sword into his gut
Deftly hopping 'round his jaws
I kicked him soundly on the butt

At last we both began to tire
Our bodies scattered round about
The situation now quite dire
My foe grunted, then passed out

Moving swiftly, no time wasted
I grabbed needle, thread, and leather
Cut and snipped and tied and pasted
Our many pieces back together

O, what a chore to reassemble
Cutting corners where I must
'Till I finally view a-tremble
Just what I had built of us

What is this? A revelation
Who could believe what I was seeing
I beheld with no elation
The beast and I were now one being

I ponder now this quandary:
Am I him, or is he me?

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New fossils from the Nerdocene

In the last post I mentioned this folder that I just found lurking in the bowels of my laptop, which just happens to contain a bunch of documents that I haven't seen in 13 years. This is another dispatch from that front (rear?).

For my first two years at OU, I roomed with Justin Lee, one of my best friends from high school. Just thinking about him brings back a load of stuff. Playing volleyball, the only athletic endeavor I was ever halfway good out or got much real enjoyment out of. (We called our team Athletes' Foot and our symbol was a volleyball globe standing on an upturned six-toed foot [one toe for each member of the team, of course]. We were the best team at the Oklahoma School of Science and Math in the fall of 1991, which is a bit like saying that you're the first to throw up at a party.) Playing X-Wing for the first time, which was mind-bending if you were part of the Atari 2600 generation. Playing Petra pretty much constantly for months on end. Mostly, lots of playing. Life and work had not yet arrived.

Justin and I kept a list of words that we thought were awesome. We called this list the Heroic Dictionary, and it grew like this:

Justin: Are you going to that dance?

Matt: Dude, you know that dancing is anathema to me.

Justin: Anathema, eh? That's a great word.

Matt: Cool. Another entry in the Heroic Dictionary.

MAN we were weird (no offense, Justin). But it all worked out. We're both married, both have little carpet monsters that we adore, and Justin at least is gainfully employed. So again, armed with the knowledge that we turned out all right, here is a glimpse into the minds of two 18-year-old archgeeks.

Note that to be included a word did not have to be particulary exotic. If it was euphonious, that was usually good enough. Like maelstrom. I don't care who you are, that's a great word.


The Heroic Dictionary


































































































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Time capsule from the Dorkazoic

I just found a trove of files on my computer from 1993-1995. For reference, I graduated high school in May of 1993 and started my undergraduate work (term used loosely) at the University of Oklahoma that fall.

Something that I apparently kept up with from Christmas 1992 to February 1994 was a list of all the books that I read. I can tell you that in 1993 I read 69 books. In those 69 were two books I had to read for history class, one mystery, and two technothrillers. The other 64 were all science fiction and fantasy. I devoured that crap at that rate basically from the time I was 12 until I was 21. What changed in 1996 is that Rich Cifelli assigned me to an independent study to identify some dinosaur bones, and ever since paleontology has been taking a bigger slice of the pie and lurid escapism getting less and less. I don't regret that at all. As Rilstone says, if you think LOTR is the greatest work of the human imagination ever when you're 12, that's fine. If you still think that when you're 30, something has gone wrong with your life.

Actually, now that I think of it, Rilstone may be full of shit on that point.

But anyway, in the spirit of examining my 18-year-old self with 13-year-hindsight goggles, here is my newly exhumed reading list from Christmas 1992 to February 1994.


'92 Christmas Break (5) Favorite: The River of Time
Galapagos, Kurt Vonnegut
Swords Against Darkness, edited by Andrew Offut
The River of Time, David Brin
Dirk Gently's Holistic Detective Agency, by Douglas Adams
Han Solo at Star's End, by Brian Daley


January (5) Favorite: Eon
The Memory of Earth, Orson Scott Card
Prisoner of the Horned Helmet, James Silke
Wing Commander: Freedom Flight, Mercedes Lackey and Ellen Guon
Warriors of Mars, Michael Moorcock
Eon, Greg Bear

February (5) Favorite: The Mote in God's Eye
The Venom Trees of Sunga, L. Sprague de Camp
Blades of Mars, Michael Moorcock
The Mote in God's Eye, Larry Niven and Jerry Pournelle
Treason, Orson Scott Card
The Starwolves, Thorarinn Gunnarsson

March (9) Favorite: A Fire Upon the Deep
Falkenberg's Legion, Jerry Pournelle
Rising Sun, Michael Crichton
Starwolves: Battle of the Ring, Thorarinn Gunnarsson
Eternity, Greg Bear
Voyage of the Star Wolf, Peter Gerrold
A Fire Upon the Deep, Vernor Vinge
N-Space, Larry Niven
The Forge of God, Greg Bear
The Children's Hour, Jerry Pournelle and S.M. Stirling

April (2) Favorite: The Asteroid Queen
The Asteroid Queen, Jerry Pournelle and S.M. Stirling
In the Hall of the Mountain King, Jerry Pournelle and S.M. Stirling

May (5) Favorite: Anvil of Stars
Foucault's Pendulum, Umberto Eco
Anvil of Stars, Greg Bear
Dorsai, Gordon R. Dickson
Santiago, Mike Resnick
Han Solo and the Lost Legacy, Brian Daley

June (10) Favorite: The Quiet Pools
Jurassic Park, Michael Crichton
The Complete T-Rex, Jack Horner
Inferno, Larry Niven and Jerry Pournelle
Desperate Measures, Joe Clifford Faust
Precious Cargo, Joe Clifford Faust
The Essence of Evil, Joe Clifford Faust
The Quiet Pools, Michael P. Kube-McDowell
The California Voodoo Game, Larry Niven and Stephen Barnes
The Sum of All Fears, Tom Clancy
The Peace War, Vernor Vinge

July (11) Favorite: The Last Command
Flight of the Old Dog, Dale Brown
The Hitchhiker's Guide to the Galaxy, Douglas Adams
Indiana Jones and the Peril at Delphi, Rob MacGregor
The Restuarant at the End of the Universe, Douglas Adams
Life, the Universe, and Everything, Douglas Adams
Indiana Jones and the Dance of the Giants, Rob MacGregor
This Present Darkness, Frank Peretti
Miss Pollifax on the China Station, Dorothy Gilman
Dark Force Rising, Timothy Zahn
The Last Command, Timothy Zahn
Indiana Jones and the Seven Veils, Rob MacGregor

August (5) Favorite: The Player of Games
Indiana Jones and the Genesis Deluge, Rob MacGregor
The Player of Games, Ian M. Banks
Naked Came the Sasquatch, John Boston
The Lost King, Margaret Weis
The Boys From Brazil, Ira Levin

September (4) Favorite: Bread Givers
Black Elk Speaks, Neihardt
Bread Givers, Anna Yezierska
Robotech I: Genesis, Jack McKinney
Robotech II: Battle Cry, Jack McKinney

October (5) Favorite: Oath of Fealty
Robotech III: Homecoming, Jack McKinney
Robotech IV: Battlehymn, Jack McKinney
Sentinels I: The Devil's Hand, Jack McKinney
Oath of Fealty, Larry Niven and Jerry Pournelle
World of Ptaavs, Larry Niven

November (5) Favorite: The Forever War
The Practice Effect, David Brin
A World Out of Time, Larry Niven
Lords of Destruction, James Silke
The Forever War, Joe Haldemann
The Wind From a Burning Woman, Greg Bear

December (3) Favorite: Truce at Bakura
Bio of a Space Tyrant I: Refugee, Piers Anthony
Bio of a Space Tyrant II: Mercenary, Piers Anthony
Star Wars: Truce at Bakura, Kathy Tyers


January (6) Favorite: The Ringworld Engineers
Swords of Mars, Edgar Rice Burroughs
No Frills Science Fiction, Anonymous
Playgrounds of the Mind, Larry Niven
Afrikorps: White Rhino, Bill Dolan
The Stainless Steel Rat Wants You, Harry Harrison
The Ringworld Engineers, Larry Niven

February ( ) Favorite: Jedi Search
The Integral Trees, Larry Niven
Tunnel in the Sky, Robert Heinlein
The Number of the Beast, Robert Heinlein
The Mucker, Edgar Rice Burroughs
Jedi Search, Kevin J. Anderson

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Monday, October 23, 2006

...and life beyond

Okay, belying what I just wrote, I always have time for highly evolved posthumans (the image above is borrowed from the link target). And while you're at it, go look up one of the greats in this weird, awesome field, Wayne Douglas Barlowe.

Update: Woah. The guy who painted the thing above goes by the handle Nemo Ramjet, and he has a lot more cool, weird stuff on his site. Freak out with your geek out.

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I have always despised blogs that are nothing but online journals in which boring people recount the boring incidents of their pathetic, pointless lives. And yet from time to time I find myself dipping into that form. This is one such time.

I have so many things to do in the next few months that I have absolutely no idea how or if I will prevail. These tasks include, but are not limited to:

1. Being a dad
2. Being a husband
3. Writing my dissertation chapters (without which I will have no more papers)
4. Submitting for publication said papers (without which my chances of employment are greatly diminished)
5. Sending out job and postdoc applications (without which I have nowhere to go once the dissertation is done)
6. Teaching
7. Dealing with all of the administrativa bullshit that goes along with being a student, a teacher, and a human being with a car, an apartment, paychecks, insurance, taxes, etc.

The first, second, sixth, and seventh tasks are common to most of humanity, so I get no relief bitching about them. It's 3-5 that are stressing me out. I've been writing papers for eight years now, but mostly this has been at my own pace and without any immediate consequences. Now I have to write the equivalent of several years' output at once, and that output will set the pace for the formative years of my career. Simultaneously, big swaths of time are given over to applying for jobs and postdocs. It's a total catch-22. Without the dissertation I can't get any jobs, and without the job there's no point in finishing the dissertation.

Never mind the other problem, which is that my research costs basically nothing to do, so I have no experience applying for big external grants, and most employers want to see someone who can develop and externally-funded research program. So I have to figure out how to do that with very little experience and at the same time as I'm writing the diss, getting the papers out the door, and applying for positions.

I believe the word for what's going on here is clusterfuck.

I know that many of you are current or former grad students and you have been or are in the same boat and I'm bitching to the choir. Feel free to bitch back. And don't be surprised if I post further updates at long and irregular intervals.

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Monday, October 16, 2006

Interactive computer sketchboard

I smell....the future! Check it out.

Thanks to Rodster for the tip.

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Saturday, October 14, 2006

Suck on that, Harvard!

The editors of the Harvard Crimson published this annoyingly self-congratulatory and breathtakingly ill-informed attack on open-access publishing on Oct. 5.

One week later, Berkeley's Michael Eisen handed them their asses.


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Friday, October 13, 2006

Hot tyrannosaur action

I've been watching the dinosaur scenes in Peter Jackson's King Kong with London these last few evenings. Those being the brontosaur stampede and the scene with King Kong fighting the three tyrannosaurs. It's all very, very good. No other dinosaur footage in any movie or documentary even comes close. The "brontosaurs" are not convincing as Apatosaurus--nor are they intended to be--but they look about right for Cetiosaurus or Jobaria, especially the size of the latter. They've got big rows of hooves on their front feet, like all movie sauropods and most from children's books. In truth, the forefeet of most neosauropods--your favorites like Apatosaurus, Diplodocus, and Brachiosaurus--were vertical tubes of bone wrapped in skin, and only had thumb claws, which faced inward and backward. This is probably the hardest aspect of sauropod anatomy for artists. If you draw sauropod forefeet correctly, they look goofy. But that's what the morphology shows; Darren had a great post on it a while back. However, more basal sauropods like the mamenchisaurids had claws--not hooves, claws--on all five toes. Cetiosaurus at least consistently comes out down the tree with those guys, so the King Kong sauropods are credible cetiosaurs.

But the sauropods are merely cool. The tyrannosaurs are mind-blowing. I really think that except for perhaps being a bit less athletic, real tyrannosaurs probably looked like that and moved like that.

Here's a question for discussion: given that T. rex had the strongest bite of any animal every by a very wide margin, thousands of pounds of pressure and all that, would even King Kong be able to pull a tyrannosaur's mouth open against its will?

My one wish about that fight scene is that the deaths of the first two tyrannosaurs ought to have been gorier and more graphic. The first gets its head crushed with a boulder and the second get its noggin pulped against a cliff wall, but in both cases the camera shows the moment of impact and then cuts or glides away. I want to see those heads bust wide open till the white meat shows!

In the annals of dinosaur battles that are not nearly as famous as they ought to be, check out The Valley of Gwangi (cowboys versus dinosaurs in the Old West!) to see an Allosaurus fight a circus elephant. That movie climaxes with the protagonist fighting the marauding carnosaur inside a burning church, in a scene that involves such a collision of evolutionary, religious, American, and cinematic artifacts that it about made my head bust open.

Also, in the annals of scenes I want to see in a movie but haven't yet and probably never will, it would be awesome to see a tyrannosaur take a shoulder-fired antitank missile right in its open mouth. I want a blood-tinged fireball of flying teeth and bloody chunks of head, along the lines of some of the exploding nasties from Starship Troopers.

Finally, and waaay off topic, could the Men In Black movies have possibly sucked any more balls? No? I didn't think so. G'night.

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Tuesday, October 10, 2006

Dream bomb

I have always been obsessed with nuclear weapons. Maybe that was externally inevitable: I grew up under the twin shadows of Reagan-era Mutually Assured Destruction and the Alvarez impact winter. As soon as I knew what nukes were, I wanted to know everything about them. How many there were, where they were going to fall, how far away I needed to be, whether I wanted to survive a total exchange....

I can only remember dreaming about A-bombs once. It was when we were living in Norman. I dreamed that I was driving on Highway 9, which runs southeast from Norman and Oklahoma City. In my dream the road was elevated so I could see the whole OKC metro area spread out before me to the horizon. It was sunset. A warhead came in, burned a white line down through the atmosphere, and hit in the middle of the city. But it didn't detonate, it plowed right into the ground and threw up a huge fountain of earth. Like, miles high. Then, nothing. After a few seconds, a bone-deep rumble. Then more geysers of soil and rock, forming a circle more than 30 miles across*, like Satan's own cookie-cutter had punched through the landscape from below. Clearly, this was outgassing from a subterranean detonation. Then that 30-mile-wide pancake of land, containing the entire city and all 500,000 people within, lifted up in the air, ballooning, as if inflated from below, and cracks appeared and light shined through and I could finally see that the whole city was being blown upward by a nuclear fireball, and as the city-pancake cracked and broke apart the individual pieces fell into the fire, just like stone blocks sinking into lava.

* I know that it was 35 miles across because the A-bomb article in the World Book Encyclopedia set Mom and Dad had showed the footprint of a 15 megaton bomb, the largest we ever detonated, and the "light damage" area was 35 miles across.

That's it. That was the whole dream. It stuck with me because it all unfolded in slow motion, and because it was so big. I had plenty of time to think "that's impossible" and to watch in horror as entire neighborhoods cracked off from the fragmenting city and fell into the inferno, until the last fragments of the city were overtaken by rising fireball. It was wildly unrealistic--subsurface detonations just don't do that--but you know how dreams are: most of the time you don't have any choice about believing what you see.

I hadn't thought about that dream in years, but then tonight I came across this. Part of me shudders, and part of me thinks, "Freakin' cool, man."

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Sunday, October 08, 2006


File this under "Dissertation-related nerdosity".

Sauropods have big pneumatic vertebrae and I have been curious for a long time about the ratio of bone tissue to air in the skeletons of sauropods and other vertebrates. I made a stab at quantifying this with the Air Space Proportion (ASP), which is the volume of air in an element divided by the total volume of the element. A bone with an ASP of 0.60 is 60% air, by volume. Actually measuring volumes is a bitch, and for my current purposes no great precision is necessary, so I've been happy to take the area of air vs. bone in a two-dimensional slice (or, ideally, a series of slices) as an approximation of the volume. You can get 2D slices of bones with a CT scanner, which I've done, but you can also get them by photographing broken bones. That's nice because the world has a lot more broken fossils than it does CT scanners.

One problem with computing ASPs for sauropod vertebrae is that the air spaces that are actually enclosed by bone are a very small part of the total. The largest air spaces lay alongside the vertebrae, so they are only constrained by bone on one side. We don't know whether those air spaces were big and fat like balloons, or whether they just formed a thin skin of air over the surface of the bone, or what. So ASP is nice, but it only gets you so far.

About two years after I came up with ASP, I realized that if you have a stack of 2D slices through a bone, and if you know the density of bony tissue, you can easily compute the mass of a bone. In retrospect, that's really obvious, but it didn't occur to me until seven years after I first CT scanned a sauropod vertebra. So I guess it pays to keep thinking about some things, because you never know when you're going to spot something obvious.

Anyway, just knowing the masses of the vertebrae might tell you different things than you would find out by looking at ASP alone. For one thing, once you know the volume of a bone or a neck or a whole vertebral column, you can plug in whatever density you like and see how the mass changes. If you want to know how much the cervical column of Brachiosaurus would weigh if Brachiosaurus was a big giraffe, just switch the densities. (As it happens, giraffe vertebrae are a bit more than twice as dense as Brachiosaurus vertebrae, so the hypothetical Giraffasaurus would be screwed.)

It turns out that the 8.5-meter cervical series of Brachiosaurus only massed about 600 kg. That's really surprisingly light. The bones of that 28-foot neck weighed about as much as a small cow. In fact, the humeri of Brachiosaurus, each 2 meters long, weighed about as much together as the cervical series. That's because they are really dense, with a density of 1.8 or 1.9 g/cm^3. By comparison, the cervical vertebrae were about 70% air by volume, which would give them a density of 0.6 g/cm^3.

All of that is simple junior high math. But it's still a surprising result. Hence the title of this post. I've been over the numbers and it all checks out, but it still blows my mind.

Here's a graphical representation, which is going into my SVP poster. Comments welcome.

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Tuesday, October 03, 2006

I'm back, baby!

By which I mean, yeah, I'm back from the East Coast, but more importantly, I'm back ON. Which is good, because SVP is coming up in two weeks and I have a presentation to prepare. And after that, nontrivially, a dissertation to write.

So don't be surprised if you don't hear much outta me for a while.

In the meantime, you can get a quick gloss on the trouble with string theory here. For a more in-depth look, go to Shtetl-Optimized (link to your right) and from there to Not Even Wrong, Smoit's blog. Sounds pretty fishy to me. The Bogdanov brothers rock!

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