Are the Na'vi Nazis?

Warning: Spoilers ahead. If you have not seen Avatar yet, go see it now. Twice. Or, if all this nonsense I noticed isn't coincidence, maybe don't see it at all, but it has to be a coincidence.

A lot of people have compared Avatar to Dances With Wolves and FernGully, due to the superficial resemblance of the plots of those movies. However, neither of those movies quite matches the plot of Avatar. Costner's character wasn't sent out to infiltrate the Native Americans; he was basically abandoned at an outpost and met the Native Americans out of boredom. And I never saw it (note to people my age and older who keep bringing this up: why did you see a cheesy not-even-Disney cartoon that came out in 1992??), but I don't think the logger guy in FernGully was sent to infiltrate the fairies, since IMDB says they live in a secret world (thus, presumably, nobody knows they're there). There is a much closer real-life analog to Jake Sully (the hero of Avatar): Hitler. Bear with me.

In Avatar, Jake Sully, a war vet who was wounded in combat, was sent by the RDA Corporation to infiltrate the Na'vi. In 1919, Hitler, a war vet who was wounded in combat, was sent by the Reichswehr to infiltrate the German Workers' Party. The Na'vi are an indigenous population that doesn't let anyone near them who doesn't look like them (thus the avatars). The German Workers' Party was later renamed the National Socialist (German: Nationalsozialismus, abbreviated Na'zi or Nazi) Party. We all know what the Nazis thought about people who didn't look like them.

It doesn't stop there, though. Despite not quite fitting the Na'vi ideal (he has too many fingers, he wasn't born there, his face is shaped wrong, and, of course, he's part human), Sully rises through the ranks of the Na'vi to lead them. Likewise, despite not fitting the Nazi ideal (born in Austria, not tall enough, black hair, rumors that he may have been part Jewish), Hitler rose through the ranks of the Nazis to become their leader.

Jake has a mentor, Dr. Grace Augustine. She runs the avatar program, and teaches Jake how to act and how to speak. SPOILER NOT IN THE COMMERCIALS: She is imprisoned with Sully, but dies shortly after that imprisonment (during an escape). Hitler also had a mentor, Dietrich Eckart. Eckart was one of the early founders of the German Workers' Party, and, according to Wikipedia, "Eckart became Hitler's mentor ... teaching him how to dress and speak, and introducing him to a wide range of people." Eckart participated in the Beer Hall Putsch with Hitler, and was arrested and jailed with him. Eckart was released due to illness, and died shortly thereafter. OK THE SPOILING IS OVER.

The code name for Avatar while filming was Project 880. Among Neo-Nazis, 88 is used as a code to identify one another (H is the 8th letter of the alphabet, so 88 means "Heil Hitler").

I have to be wrong about this, right? James Cameron didn't just make a 230-million-dollar Neo-Nazi movie, did he?

Today in Geek, 20091223

It's technology day among geeks today, apparently.

Technology

Video-stitched cellphone streams go widescreen. Microsoft has developed a system to stitch together cellphone videos of the same scene to create higher-resolution videos. I highly recommend the video. Neat idea!

Green

Body Heat Energy Generation. They say this is for "micropower devices," but I wonder how much power you could realistically harvest from non-intrusive devices. They say they can get about 100-600 microWatts for a wristwatch-sized generator. Is that getting close to something that could recharge my cellphone and/or run an mp3 player?

Awesome

Typing With Your Brain. Researchers presented a study at the 2009 annual meeting of the American Epilepsy Society in which they were able to consistently predict the desired letters of patients "at or near 100 percent accuracy." Other studies have had similar success, apparently, but this one promises much greater speed, more the "you think it, it happens" that we expect from mind-reading computers. Sure, it requires electrodes implanted in the brain, but that seems like a small price to pay.

Still Favorite Music from 1999

Everyone else is doing best-of-the-decade lists, but I'm going to try something different. Instead, I went back and gave a listen to some music from 1999 to see what I still like after a decade. Note: I think some of these songs might really be 1998 or 2000, but iTunes thought they were 1999, so I'm going with that.

10. "My Own Worst Enemy" by Lit
This song is just so fun. I don't have anything deep to say about it, which seems fitting for this song. Wait, is that deep?

9. "Camera One" by Josh Joplin Group

I don't think I ever heard anything else by this band, but this song was on the radio here in Austin all the time for a while, and I still love it.

8. "1000 Oceans" by Tori Amos

I'm a sap for Tori Amos songs, especially the ones that sound really depressing. "1000 Oceans" fits that bill.

7. "I Like Birds" by Eels

This one is cheating a bit. I don't know whether I ever heard this song until this year, but I fell in love with it. It just makes me so happy.

6. "The Saga Begins" by Weird Al Yankovic

Looking back, I kinda wish the prequels had just consisted of some trailers and this song/video. We could have been spared all trace of Jar-Jar.

5. "Across the Universe" by Fiona Apple

I like Fiona's version of this song (from the Pleasantville soundtrack) better than the Beatles version. Is that wrong? The video is pretty sweet, too.

4. "Rainbow Connection" by Me First and the Gimme Gimmes

Kermit was clearly punk at heart.

3. "Lucky Denver Mint" by Jimmy Eat World
I've loved Jimmy Eat World since I first heard them. Then I heard them live on SNL, and they were absolutely terrible. Their studio stuff is still pretty good, though, as long as I block out all memories of that performance.

2. "Babylon" by David Gray
This is the song that makes me really happy for having done this trek back to 1999. I'd forgotten all about this song, but I really love it.

1. "Porcelain" by Moby
If you'd asked me in 1999 or 2000 what I'd like best from 1999 when 2009 rolled around, I'd probably have to ask you to repeat that sentence a couple times so I could figure out what you're asking. But even if I made it through that sentence, I don't think I would have ever guessed this song. I wouldn't have even guessed it when I dug out my music from 1999 to compile this list. I honestly didn't like it very much at all when it came out, but it has really grown on me.

I'm sure I've forgotten something that I would love if I heard it again, perhaps something I never bought or otherwise acquired (and thus didn't have in my collection for my "Year=1999" search). Let me know what you think I missed in the comments.

Today in Geek, 20091222

I didn't see a lot of geekiness today, but some of what I saw was pretty awesome. These are the ones worth talking about.

Science
New DNA Analysis Method Drastically Cuts Time and Cost of Genome Sequencing. I think genetically tailored medicine is about to lead us to a medical revolution on the order of the discovery of vaccines or Lister's hand-washing campaign, and faster DNA sequencing will likely be useful for that.

Medicine Awesome
Robotic Knee Helps Perfectly Healthy Runners Run Even Better. Prosthetics aren't just for people who actually need them anymore. A Japanese team has developed a device that straps  to the leg and helps you run faster. Gentlereaders, we can rebuild us! We have the technology!

That's it for today. What did I miss? Certainly there's more out there!

Today in Geek, 20091221

Today we reaffirm that we are living in the future. Hurray!

Politics

Mexico City Legalizes Same-Sex Marriage. Mexico City just legalized abortion two and a half years ago, but now they've jumped ahead 30 years to leapfrog over most of the United States. At least DC managed to pass it a few days before. Supporters of the Mexico City bill were chanting "Yes, we could!" That makes me smile a lot.

Entertainment

Focus on the Action to Avoid Headaches During 3D Movies. When you go see Avatar (if you haven't already), keep this in mind. Your brain really doesn't like stuff being 3D but out-of-focus, and trying to get around that gives bad headaches. Trust me on this one; I spent too much time on my second viewing looking at stuff in the background, and it played havoc on my head and stomach. I may have to go see it in non-3D so I can look for those extra little details (for example, that it takes place over several months leading up to August 24, 2154; Wikipedia says that's the anniversary of the patenting of the motion picture camera, I'm guessing that isn't a coincidence).

Astronomy

Video: The Asteroid That Will Almost Hit Earth. NASA produced a video of Apophis passing Earth on April 13, 2029. It'll pass just 18,300 miles above the planet's surface. Assuming we pass peak oil and civilization has fallen by then, I plan to remember that date to use it to secure a following in my post-apocalyptic cult; an asteroid passing that close should be interesting in the sky.

Medicine

Color-Shifting Contact Lenses Alert Diabetics to Glucose Levels. Soon diabetics will have a heads-up display of sorts, allowing them to see when they need a shot of insulin or a candy bar. Today diabetics, tomorrow killing machines sent back from the future!

Science

Groovy Teeth Suggest Dinosaur was Venomous. The story itself is cool, but it's also sort of an example of a (probably intentional) "crash blossom," a word I just learned this morning meaning "a headline that can be misconstrued." The New York Times claims that's a buzzword of 2009, but I think it's possible only the New York Times staff have heard that term.

Mad Science

Our of the Blue, DARPA Seeks Means to Manipulate Lightning. They all laughed when DARPA put giant red balloons all over the US, but DARPA's going to show them! It's going to show them all!! Muahahahaha!

Did I miss any geekery? Let me know in the comments.

Today in Geek, 20091218

This is the entirety of what geeks can think about today, rightfully so:

It was just so very, very beautiful. I loved everything about it. I could not possibly recommend it more. I've been trying to take it easy to avoid setting expectations too high, but I don't think expectations can be too high. I've often wondered what it would have been like to be an adult geek in 1977 when Star Wars came out. Now I know. Thank you, James Cameron.

Today in Geek, 20091217

Today was a good day to be a geek. There may have been a huge discovery in physics, there were at least two stories that seem too far fetched for science fiction but are actually happening, and I found a new hero. Let's start with the physics.

Science

Experiment Detects Particles of Dark Matter, Maybe. Researchers may have detected dark matter, the stuff that probably makes up about 80% of the universe, in a mine in Minnesota. The signal wasn't strong enough to say for sure yet, but the signal they got was the signal they expected if the stuff is real, so that's a good sign.

Medicine

First Commercial 3-D Bioprinter Fabricates Organs to Order. Ok, the printer is still in early testing, and the company that makes it says arteries and veins are five years off, with actual organs more like 10 (by their estimation), but if this thing works out, that'll simply be amazing. Theoretically, particularly combined with stem cell research, the printer could be used to print organs using your own cells, so they could build an organ that your body couldn't possibly reject. That's pretty darned awesome. Of course, I couldn't help thinking about how awesome the technology will be when combined with artificial meat. Mmmm, custom-designed meat.

Mad Engineering

Robotic Insects Could Pollinate Flowers and Find Disaster Victims. Some engineers want to design robobees to help pollinate flowers (since the real bees are still dying), and probably to find disaster victims, and, presumably, eventually to take over the world. I applaud your efforts, sirs.

Awesome

$300 Sci-Fi YouTube Video Lands $30m Movie Deal. The article originally put the amount at $300 million (and still mentions that amount as of right now, which would put the deal higher than the budget of Avatar). Regardless, the story is basically this: a guy made a 4-minute movies and posted it on YouTube, and Sam Raimi made a $30 million dollar deal with him to see what he can do with real money. I don't care if the resulting movie sucks, this guy is my hero. Here's the short that got him that contract:

Three days in a row. Wow. Maybe this is a thing again. As usual, let me know in the comments if I missed anything.

Today in Geek, 12/16/2009

Today's headlines were full of geeky medical news, but I have to start with the story that has me nearly giddy.

Awesome

Nearby "Super Earth" May Have Oceans, Thick Atmosphere. We found a planet that probably has a huge ocean of liquid water. It probably doesn't have life, but we're getting closer. As a researcher put it in another article on the subject, "This planet is a harbinger of what’s to come. It’s not just that we can study this one object in more detail. It’s the torch, telling us about this new thing that’s going to happen." This planet has astronomers talking about the likelihood that we'll find an inhabitable (and possibly inhabited) planet soon, and that's just awesome.

Astronomy

Dying Star Mimics Our Sun's Death. Have you ever wondered what our Sun will look like after it eats the inner Solar System? Ok, probably not, but I have, and now I know. Researchers with the Harvard-Smithsonian Center for Astrophysics have released a video of a pulsating nearby star going through its red giant phase, the same phase our Sun will go through in about 5 billion years. Keep in mind that, at its largest, that star is roughly the size of the orbit of Mars.

Medicine

Synthetic Nano-Platelets Added to Blood Cut Healing Time in Half and Artificial Red Blood Cells To Aid Drug Delivery, Imaging. Two independent teams released news today about advances in fake blood. The first team produced "artificial red blood cells," essentially tiny packets that could be used to deliver drugs, dyes, etc deep into tissues (because they're small enough to fit through capillaries). It doesn't look like they could be targeted yet, but just getting them to fit into such small spaces is a big jump. The second team produced synthetic platelets to help stop bleeding faster. The nanoparticles work pretty much the same as platelets, crosslinking to clot the blood. Treating wounds with the nanoparticles—or injecting them to help with internal bleeding—cut bleeding time in half in rats. Assuming they can be mass produced and pass testing, I can imagine these being very useful to EMTs.

Scientists Decode Entire Genetic Code of Cancer. I'm still trying to wrap my head around what this one means. Cancers are caused by combinations of many, many mutations. No individual cancer patient has the same set of mutations as any other cancer patient. So I'm not sure yet exactly what they mean by this story, but scientists have apparently mapped the 30,000 mutations associated with melanoma (skin cancer), and the 23,000 mutations associated ith lung cancer. I'll have to dig deeper to figure out what that means, exactly, but it sounds like it's probably a big deal.

Nanotechnology

Crowds of Bacteria Turn Gears a Million Times Their Size. I love this video. The bacteria aren't really doing anything "useful," they're just swimming around randomly... but the shapes of the gears translate those random motions into work (turning the gears in the desired way). I love the idea of future devices being powered by the random motions of bacteria.

Today was a pretty big day in geek. Did I miss anything? If so, let me know in the comments.

Today in Geek, 12/15/2009

I have been terrible about blogging. Wow. Let's just put this shameful period behind us, shall we?

To do so, I'm going to start a new tradition by revising an old tradition. The title pretty much explains it. Here are the geekly stories that piqued my interest today:

Politics

D.C. Council Approves Gay Marriage. There's a good chance D.C.'s overlords in the US Congress will overturn this law, but the Washington, D.C., City Council passed a measure today to legalize same-sex marriage in the District. Strong work, D.C.

Medicine

Locked-in man controls speech synthesizer with thought. Locked-in syndrome is the condition where a person is completely paralyzed (unable to move any muscle and thus unable to communicate), but completely aware of their surroundings. I know I'd heard of it before they featured it on House, so I think at least two medical dramas showed how terrifying it would be. That might change soon, now that a locked-in man has controlled a speech synthesizer with thought. That's just unbelievably awesome. Such technology will also come in handy in the construction of my mecha, so that's good news, too.

Mad Science

Swiss Geologist On Trial For Causing Earthquakes. An experimental geothermal energy project triggered earthquakes in Switzerland, so now the guy in charge is being tried. Sure, they're spinning it more as an industrial responsibility kind of thing, but it sounds to me like they may have caught a real mad scientist (it was an experiment to see if this process would work for energy production, so he wasn't just a mad engineer).

Tech Tips

Create Instant Navigation Shortcuts from Android's Home Screen. Someone at Lifehacker noticed that we can create one-touch shortcuts for turn-by-turn navigation on our Android phones now. For example, I have a button on my home screen to navigate from wherever I am to my house. Neat.

Entertainment

The Lord of the Rings Trilogy Hits Blu-Ray April 6. Dammmmmit. I don't think I'll be able to hold out until they put out the extended editions months later (my guess: just before The Hobbit comes out in December 2011). How many times are they going to convince me to buy these movies???

That's it for today. Did I miss anything? Let me know in the comments.

An Open Letter to the Congress

Dear Politicians,

When I get money out of an ATM, I don't care what the serial numbers are on the twenties. It's completely irrelevant. All I care about is whether I get my cash. "Bipartisanship" as a goal is serial numbers.

We don't care whether a health care bill passes because Republicans vote for it, or because Blue Dog Democrats vote for it, or because a coalition of senior Congresspeople votes for it. We care that the bill fixes our health case system.

Please, I don't want to hear any more about bipartisanship being a goal. It isn't that we want you to become bipartisan intentionally. We want things to become bipartisan in that we want you to stop focusing so much on party. When you focus on bipartisanship, you continue to focus on party. Stop it.

Thank you,

Voters

Google Reader Send To Remember the Milk Lists

This isn't perfect yet, and that makes me angry. But it's getting there, and I'm hoping someone can help me finalize it in the comments.

What this trick will do: Allow you to send articles to specific Remember the Milk lists (I set up a Mad Science Monday list, and another one to add things to my Personal to-do on RTM, and one for food-related articles, and another for work-related articles) from Google Reader.

What you'll need:

• A bookmarklet from Twitlet (follow their instructions).
• An account on Remember the Milk. Set up any lists you want to use there. Your life will be easiest if you make these lists all one word (for example, I used "msm" for my Mad Science Monday list).
• A Twitter account.
• The Remember the Milk rtm Twitter trick.
• A list of things on Google Reader that you want to sort into to-do lists.
• At least a mild case of obsessive-compulsive disorder.

Do you have all of that set up? Ok, open up your Twitlet bookmarklet (right click and Edit it, most likely, depending on your browser), and copy that mass of confusion in the URL field. All you really want out of that is the part after ?a= and before &t=, which will be a jumbled mass of letters and numbers (that's your personal code for Twitlet).

Now go to Reader, and click Settings, and then Send To. Down at the bottom, click Create a custom link. Name it something to remember it by (for example, I used MSM and To-Do for mine). For the URL field, you want this:

http://www.twitlet.com/updates/?a=YOURCODE&t=d%20rtm%20${title}%20${short-url}%20%23LISTNAME

Obviously, swap in your code for YOURCODE and the name of your list for LISTNAME. If you have spaces in the name of your list, replace them with %20's.

For the Icon URL, enter this: http://www.rememberthemilk.com/favicon.ico (that'll put a RTM icon on it).

Now save it. Make more as necessary. Enjoy.

Oh, you'll have to tell your browser to allow popups from Reader (you need to do that for any Send To), and (here's the annoying part) the window that pops up is pointless; you can close it again after it loads. It just needs to load for this to work. I guess I might be able to kill it with a user script, but that's a bit overboard. Does anyone have any suggestions?

Mad Science Monday, 9/7/2009

I'm under the weather today, so I'm going to keep this week short. This week's article also isn't "mad science," per se, but simply "science" that makes me mad. It also happens to be about drug studies, so I thought it was fitting to give it a look while I'm sick.

What makes me mad isn't so much the study, but that it gets worse every time it's passed through another filter on the web. Today's "Placebos Are Getting More Effective" headline on Slashdot drove me over the edge.

Placebos are not getting more effective. Several factors are combining to make the placebo effect larger compared to the "real" drug in the same studies, but it isn't that something magical is happening with placebos.

First, the studies are getting better. For example, imagine if you were studying a drug in the 1930s (in a world where 1930s researchers knew to do placebo-controlled studies), and this drug was supposed to decrease the incidence of lung cancer. You would create two groups, a placebo control group and an experimental group, making sure to balance for factors you expected to affect the results--age, gender, etc. By chance you might end up with more smokers in your control group than in your experimental group (because why bother controlling for that, if you don't think it has anything to do with cancer?). After your study, you'd likely find that your experimental group had a lower incidence of lung cancer, and thus that your placebo had very little affect compared to your drug. Of course, if you did that same study today, you'd be able to balance your groups for all kinds of known factors, including genetic risks for lung cancer, not just for the smoking bit. More and more, any improvement in your experimental group vs the random improvement of your placebo-controlled group would decrease, which you could choose to see as your placebo magically getting stronger. That's not what it is, though; you're just doing better science. See this great article over at Mind Hacks for more on this side of the effect.

Second, we're getting better at making placebos. We know strange things about human psychology, such as the wondrous bits in the graphic about half-way down the page on Wired's version of this news. We can make the placebo green in an anti-anxiety study, for example, because green pills work better for anxiety medicine (or we can at least make the placebo and the real drug the same color). That doesn't mean something magical is happening, either; it means we know how to harness psychology to boost the effectiveness of the pills, even if the medicine doesn't actually do anything beyond what the placebo does.

Third, the medicines being tested are, very often, just marginal improvements (or potential improvements) on existing drugs. We don't see as much of an effect because there isn't much of an effect to see.

So, if you see the headline I'm expecting this to morph into, something about placebos proving that medicine is unnecessary or some other similar nonsense, be sure to take it with a grain of salt. The pharmaceutical industry is still making improvements to our health, it's just doing so with better scientific practices.

Mad Science Monday, 8/31/2009

I live in Austin, TX. Not only do we have confirmed record-setting zombie hordes, but we also have a populace ready to warn one another of outbreaks of zombiism. So of course I'm interested in knowing whether we (or anyone else) will be able to survive an actual bout with zombies. Thankfully, a group of certified mad scientists have figured this out for us.

Mad Reference: Philip Munz, Ioan Hudea, Joe Imad, and Robert J. Smith?. (2009) "When Zombies Attack!: Mathematical Modelling of an Outbreak of Zombie Infection." Infectious Disease Modelling Research Progress. (full text available free online [PDF])

Mad Background: First off, that isn't a typo in the name of the lead researcher. His last name is "Smith?" with a question mark. In addition, from his homepage at the University of Ottawa (emphasis added), "People kept asking if I'll be getting US citizenship next and I kept laughing at that. Somewhat hysterically, it must be said." Your last name is "Smith?", and you talk about your hysterical laughter on your homepage? You are an inspiration for all would-be mad scientists, Dr. Smith?!

As far as the science, the background you need is that mathematical models are used in fields like epidemiology to help predict the spread of diseases under various conditions, and thus to plan out the best way to combat those diseases. For example, mathematical models can help predict what will happen if only a limited number of vaccine doses are available for a disease, or what will happen if people infected with a disease are quarantined. But can they predict the outcome of a hypothetical disease that follows a pattern very different from known real-world diseases?

Mad Observations: Especially in modern movies and video games, zombiism spreads like a disease. If it spreads like a disease, it should be possible to model it the same way we model diseases.

Mad Hypothesis: If a zombie outbreak occurs, mankind can survive. At least, that's what they're pretending to test. What they're really testing is whether mathematical models can be put together for a "disease" as strange as zombiism, in particular the strain of zombiism in which the dead can become "infected" with the disease and come back to terrorize the living.

Mad Experiment: The researchers built five mathematical models for zombie outbreaks: a basic model, a model with an incubation period, a model in which the unaffected attempt to quarantine the infected, a model in which a treatment for zombiism is available, and a model in which humanity fights back. They then used each model to predict the equilibrium; in other words, to predict whether humanity would survive. Each model had some assumptions in common:

• The particular form of zombiism being modeled is the "slow zombie" style. "Fast zombies," like the things in 28 Days Later, were not studied. I'd be interested to see what would change in such a model, but, alas, that will require further research.
• As I mentioned in the Mad Hypothesis section, the strain of zombiism being modeled also infects the dead (including dead zombies), allowing the dead to join the population of zombies. The whole point was to model something far from known diseases to see how the models held up, so it made sense to include the truly undead in the model.

They All Laughed, But: We are all screwed. Unless we get infrastructure in place to quarantine zombies and zombies-to-be, or are able to quickly develop a cure when an outbreak occurs, or are able to successfully coordinate zombie-eradication attacks, zombies eventually wipe us all out. The eradication model was the only one in which we eventually won, and it seems likely to me that this would require military involvement. If you've ever seen a zombie movie, you know that involving the military is a terrible, terrible idea, so our best hope is also the one that, the "literature" shows us, is empirically shown to lead to a society in which the living envy the dead.

The treatment model was also unique in that, at equilibrium, a large zombie population survived in addition to a small human population. Note that this human population would remain at a certain size, but would not always contain the same individuals; you might become a zombie for a while, then get treated, then die, then rise as a zombie, then get treated again and rejoin the human population. This wouldn't necessarily be a fun existence, although it would definitely be interesting. This model is the only one in which pet zombies, like in Fido and Shaun of the Dead, are even slightly possible. And it looks far more likely that zombies would have pet humans (for a few minutes, before eating their brains and/or infecting them).

The quarantine model seems like our best bet, but, alas, assuming we don't have a massive infrastructure already in place for such quarantine, even then zombies eventually kill us all off.

Mad Engineering Applications: As it turns out, Dr. Smith?'s page indicates that a mad engineer has already expressed interest in this research, in that someone wrote to Dr. Smith? asking for help engineering a zombiism virus. Presumably that evil genius plans to control the treatment of his strain of zombiism, thus ensuring that he is (at least occasionally) a member of the small surviving human population. In case that nutjob is able to design such a virus, I guess the rest of us need to be ready to work with the military to make sure his plan isn't successful.

Of course, the other point of all of this was that the models seemed to work. The real application is to, essentially, not be afraid to try to model things that don't follow traditional disease models. The paper mentions the examples of allegiance to political parties or diseases with dormant infection, but there are definitely other things that can be modeled much like diseases.

It's hard to pick a favorite part of all of this, but, if you get a chance, I strongly recommend at least reading the last two pages of the PDF (the references). I couldn't stop laughing (maniacally, of course), seeing things like "Capcom, Shinji Mikami (creator), 1996-2007 Resident Evil" listed alongside "van den Driessche, P., Watmough, J. (2002) Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission. Math. Biosci. 180, 29-48."

If you'd like to continue to study zombie survival tips, I recommend my friend Jon's weekly Zombie Friday! You can probably guess on which day you should check his site for said column, unless, of course, you're already safe from zombies.

Mad Science Monday, 8/24/2009

Today I'm taking part in a blog hop to wish a happy birthday to UnderstandBlue. I met UnderstandBlue through my sister, Stampin Libby. We took part in the first ever "This Is What a Tweetup Is, Libby" tweetup at Phil's Icehouse (warning: that site makes annoying noises).

So, given that I met UnderstandBlue through Twitter, and I'm taking part in a blog hop, it seemed like a good day to look into the science behind how crap spreads around the internets.

Mad Reference: David Liben-Nowell and Jon Kleinberg. (2008) "Tracing information flow on a global scale using Internet chain-letter data." PNAS 105(12): 4633-4638. doi: 10.1073/pnas.0708471105 (full text available free online)

Mad Background: In 1976, Richard Dawkins introduced the word "meme" in his book The Selfish Gene as a way to describe the cultural equivalent of a gene. A meme is a a replicator, like a gene; it carries an idea, but must be copied to be transmitted. While genes copy through DNA replication, memes copy by being repeated. They still seem to evolve by natural selection, though; as they're copied, sometimes they change a little, and the ones that "work" better (from the meme's perspective, at least) spread.

Mad observations: The word "meme" is, itself, a meme, and has gotten a lot of use lately, specifically in the form of Internet memes. It seems entirely random, though, which things take off on the internet, and which fizzle. But science has a knack for finding patterns and explanations in the seemingly random. Maybe models developed for the spread of diseases will work.

Mad hypothesis: Perhaps internet memes spread "with a rapid, epidemic-style fan-out." If internet chain letters spread like disease epidemics, most people should spread it to several people, most of whom spread it to several people, etc.

Mad experiment: The researchers used an online petition that spread mainly in 2002-2003. Each recipient of this petition was asked to add their name to the end of the petition, and then forward it on to their friends. They collected 637 copies of the petition from mailing-list archives, each representing a distinct chain of participants, totaling 18,119 distinct signatories. They repeated this procedure for another petition that circulated in 1995. They used the multiple copies of each petition to construct a tree diagram, tracing the routes that the letter traveled. This was complicated by "noise," such as rearrangements of the list of names, deletions, insertions, mutations (changing a name on the list to a political figure, for example), and even hybridization when a user apparently received two copies of the petition and merged them together (interestingly, these are all things that happen with genes). Both petitions resulted in similar structures. They then followed all of this up by computationally modeling different patterns of forwarding (including modelling different patterns of the information being posted in a form that they could evaluate, ie taking into account the fact that they couldn't see everything), and seeing which pattern matched the observed trees (if any).

They all laughed, but: The hypothesis that these internet memes would spread in a similar manner to disease epidemics was (at least for these two examples) disproven just from the initial tree constructions. The trees were much longer than they would be for disease epidemics (the average distance between a given individual and the "root" of the tree was much longer than for diseases), and more than 90% of the nodes had exactly one child (ie, most people only spread the meme to one person).

The modeling experiments showed that two parameters had to be added to the disease model in order to get results that matched the petitions. First, not all recipients respond in the same amount of time. Some respond right away, and some take months to respond. This would be similar to a disease with a very widely varying incubation period (the memes don't match real diseases because real diseases don't have such widely varying incubations). Second, some recipients would send the meme back to either the person they got it from or the people the original person sent it to. This also doesn't happen in quite the same way for real diseases, and thus doesn't match known disease spreading patterns.

Of course, this was just a model. It would take more research to determine if the model was correct.

Mad follow-up: Researchers in Spain did the additional research. They started a meme through the IBM company newsletter, and were able to more exactly track its spread, and they found that the spread matched the model's prediction. Moreover, given a small set of initial data on the spread, they were able to predict how far and fast the information would spread (by calculating the parameters used by the model).

Mad engineering applications: Combined with the Spanish research, this is getting close to a way to construct messages to spread far and wide (such as, for example, your Manifesto on Why Everyone Should Bow to Your Will). It definitely isn't there yet; they can predict how far it'll spread given initial information about its spread, but they can't predict it before it's released into the wild. But, given that ability, more experiments are now possible; they don't have to wait until the meme has spread to see how effective it is, they only have to know initial information, so now they can construct slight variants of memes and see what makes different ones spread. Perhaps soon we will know what to include in your Manifesto to get it out there.

BTW, if you want to see the rest of the UnderstandBlue Birthday Blog Hop, start here.

Awkward Praise [Updated 8/22]

If you asked me at any time in the last 25 years (including within the last week) what I wanted to be when I grew up, my answer would be uncertain. If, in any of that time, you asked me what my friend Jeffrey Dinsmore would be when he grew up, the answer would be easy and obvious: a writer.

I met Jeffrey in the back of Mr. Doolittle's band class in fifth grade. We were both drummers (aka the part of the band the conductor mostly ignores), so we got to know one another by yapping about various things while everyone else learned scales and such. No matter the topic, Jeffrey was always hilarious.

Over the years, I read many of Jeffrey's short stories, and they were always great. To this day, whenever I have writer's block, all I have to do is imagine how Jeffrey would say what I'm trying to say, and I can pseudoplagiarize my way out of the block.

So, of course, when he started a new independent publishing house (Awkward Press), and told me he'd have a story in their first anthology (appropriately entitled Awkward One), I knew I would have to buy it.

I just finished devouring his short story from the collection, "Little Deaths." This is where I need your help. I loved it, but I'm not certain if that's because it's as quirkyfunny as I think it is, or if it's just because I know Jeffrey. So, if at all possible, I need you guys to buy copies of Awkward One, and let me know what you think. Am I right?

Jeffrey has also always had a talent for recommending things I will love. He introduced me to The Hitchhiker's Guide to the Galaxy. He owned the Rocky Horror Picture Show on VHS before it was officially available in the US, and is to Blane for me being able to surprise friends with my knowledge of the appropriate lines for viewings. He got me hooked on They Might Be Giants. And, of course, apropos to the site of our first meeting, he introduced me to the album Doolittle by the Pixies, cementing a love of alternative music before we knew what to call the stuff.

My point in all of that is that Jeffrey wrote one story for Awkward One, but he also recommends the other authors, so they must also be awesome. I'm just saying.

PS: Have I mentioned that you should buy a copy of Awkward One?

Update: The rest of the stories are also great. Well, I didn't much care for one of them, but the others make up for it. And I'm too nice to say which one that was. Well, ok, maybe not "nice," per se, 'cuz now they'll all assume it was them. Muahahahaha!

Sad Science Monday

Sorry, I had to deal with my sister's dog dying today while I was dogsitting him, so no Mad Science Monday this week. We knew he was on borrowed time, but it was still far from fun to find him this morning. At least it looked like he went peacefully in his sleep.

I'll try to get next week's installment written ahead of time, so I don't have to worry about distractions.

Heavyweight Dropboxing

I love Dropbox. It's a simple tool that lets you synchronize files between multiple computers (such as a laptop and a desktop, or a work computer and a home computer), and it even lets you share files with friends or coworkers who also have it installed. It syncs files in the background, so you don't have to wait to open them once you actually need them; once they're synced, they're stored on that computer's hard drive (although they're also available through a handy web interface). Useful stuff all around.

But, back in February, Lifehacker had an article explaining how to sync folders outside of your Dropbox folder. I could tell that was potentially useful, but it took me a while to figure out the powerful way to use this: syncing things like settings folders for applications.

The Lifehacker article has details for other operating systems, so I'll only be covering the Windows Vista versions of the trick here (see their article if you need to figure out how to apply it to your non-Vista computer).

Syncing User Scripts Between Google Chrome Installations

I'm a big fan of Google Chrome, even moreso now that they support user scripts. User scripts are javascript tricks to add functionality to web pages. For example, I have a "Preview" button on each article in Google Reader (thanks to this script). I didn't want to have to remember to set new user scripts up both on my desktop and my laptop, though, so I made both of my user scripts folders point at a folder in Dropbox, like this:

mklink /D "C:\Users\USERNAME\Documents\My Dropbox\User Scripts" "C:\Users\USERNAME\AppData\Local\Google\Chrome\User Data\Default\User Scripts"

Note: Once you do this, the synced folder will already be there when you get to your other machine. You may have to turn off Dropbox, rename that folder, then do this, and then copy everything over from the renamed folder (if you leave Dropbox on while you do that, it might break your link on your other computer, and then you'll have to do the whole process again, etc).

Syncing Digsby Chat Logs

While I love that Digsby stores my setup online (so it's all ready to go on whatever computer I use), it sometimes annoys me that the chat histories (other than Google Chat, which saves its own history) aren't always available; I have to remember which machine I was on when I talked to someone about something. Well, I used to. Not anymore.

mklink /D "C:\Users\USERNAME\Documents\My Dropbox\Digsby Logs" "C:\Users\USERNAME\Documents\Digsby Logs"

As with the Chrome syncing, you'll want to be careful about this, so you don't accidentally delete your other relative link. Also, you have to decide which set of logs you want to keep (or merge them manually, but that could be painful). I'm keeping my work logs, and copying them into the home folder (replacing duplicates).

I'm digging for more options like these. Let me know in the comments if you have other useful ideas.

Halleloumi!

On Iron Chef a few weeks ago, Michael Symon used something intriguing. Alton Brown explained that it was halloumi, a Cypriot cheese with a special distinction: it has a relatively high melting point, and can, therefore, be seared. You can throw this cheese (which, if authentic, is non-cow, so it's safe for people with casein allergies or light lactose intolerance) in a hot pan (or even on the grill), and the outside of it gets crispy and golden-brown, while the inside slightly softens. The result is a beautiful thing.

It took me a while to finally procure some halloumi; I think other people who saw the episode also made a run on Central Market to try it out. I finally got some last week, though, and got the chance to try it out today.

The halloumi that was left by the time I thought to take a photo of it.

OHMYGODTHATWASSOGODDAMGOOD. It's like a little grilled cheese sandwich, or maybe a cracker with cheese melted inside of it. Either way, it's yummy, and just so interesting.

If you track down some halloumi and decide to try it out yourself, I recommend this:

• Cut it into ~1 cm thick pieces. You should probably then cut those pieces diagonally (I didn't). Basically, make them roughly cracker-sized, but thicker (the thicker pieces had more gooey yummy cheese in the middle).
• Sear each side for a little under 2 minutes (about 1:45 seemed to be best, but I wasn't careful about it).

That's all. Top it with whatever you feel like topping it with. I used some leftover basil leaves and slivered almonds to make some pestoish stuff, which was good, but get creative. I think my next try will be to copy the Isaac Newton sandwich at B.D. Riley's, and top the cheese with bacon and green apple slices. I'll let you know how that goes, but I'm having a premonition that it'll be awesome.

Let me know in the comments if you try it out, or if you have any other ideas for what to do with it.

Mad Science Monday, 8/10/2009

Sorry that I missed last week's post. To make it up to you, I've found a paper just dripping with mad science (and bad puns!). Enjoy!

Mad Observations: Many organisms (ranging from apples to mammals) use chemicals called pheromones to communicate. As you'll see if you follow that link to Wikipedia, these signals are used to communicate many different things, from "follow me" to "look out!" The "look out!" class, better known as alarm signals, had been well-established in mammals. And humans are mammals...

Mad Reference: Mujica-Parodi LR, Strey HH, Frederick B, Savoy R, Cox D, et al. (2009) "Chemosensory Cues to Conspecific Emotional Stress Activate Amygdala in

Humans." PLoS ONE 4(7): e6415. doi:10.1371/journal.pone.0006415 (full text available online)

Mad Hypothesis: Humans, like other animals, have alarm pheremones. Those pheremones invoke an alarm response in humans (for example, the known responses associated with fear). In other words, humans produce something that makes other humans scared when they smell it (or at least makes other humans behave in ways that scared humans behave).

Mad Experiment: The researchers collected sweat from two groups: first-time tandem skydivers (the experimental group), and people exercising (the control group). They then had people smell this sweat to see if they could tell the difference (ie, they asked people which sample smelled worse), to rule out a noticeable difference in smells (the subjects couldn't tell the difference). They then had subjects breathe in this sweat (one sample or the other) while undergoing an fMRI (the test where they look at what part of your brain lights up in response to different stimuli). They also had the subjects identify whether faces looked frightened or not (we'll get into why they did that below).

They All Laughed, But: Actually, it turns out nobody was laughing. The most interesting thing I learned by reading this paper is that there had already been six studies published about a human alarm substance transmitted via sweat. In two, subjects were able to identify whether the sweat came from someone watching a scary movie or a "benign" film. Another study found that subjects were better able to complete a word-association task when they smelled scary-movie sweat (again vs "benign film" sweat). The remaining three found that stress sweat caused subjects to interpret expressions as more fearful, to be less likely to judge a face as positive, and to be more likely to be startled by "auditory stimuli" (that last one, which I like to think of as the "boo!" study, makes me laugh somewhat maniacally). If you're interested, all of those references are in the paper (linked above); I don't want to repeat them all here.

However, this new study did find two new things:

1. The previous studies had used scary movies or preparation for difficult exams to provoke the stress in the experimental groups. By using first-time skydivers, this one provides us a different variety of stress, broadening the range of where we can expect to find this signal.
2. The previous studies had looked at whether subjects could identify sweat from stressed people, or what subjects' psychological responses were to the fear sweat. This study showed a physical response to the fear sweat, specifically activation of the amygdala (the part of the brain associated with emotion), just as expected.

This new study also threw in an "is this face scared?" test, but that was just to confirm that those results agreed with the previous results (they did).

Mad Engineering Applications: This area of research positively screams to be implemented by mad engineers. You might not be able to make a fear gun, per se, but it just might be possible to make a fear bomb. And, combined with other research (including a piece in an upcoming Mad Science Monday), a good mad engineer could even use this to make his or her henchmen more effective (I mean, sure, your henchmen should already be afraid of you, but with this you could make sure they're working scared even when you aren't around). There simply have to be at least a few DARPA projects associated with this.

Do you have any other ideas for how to apply this? Let me know in the comments.

The Month In Geek: July 2009

July was an interesting month for all things geeky. Here are some of my favorite stories from the last month.

Astronomy:
Jupiter got smacked by something big, probably an asteroid (because we probably would have seen it if it were a nice, bright comet). That thing left a black spot on Jupiter roughly the size of the Earth. Wow. The Bad Astronomer has been keeping me up-to-date on exactly what happened.

Entertainment:
Information came out last month about three big geek movies. First, Disney released details and clips from Tron Legacy, the sequel to Tron. I'm sure it's going to be cheesy and terrible, but it may also be awesome.

Second, the announcement came out that Sam Raimi is set to direct a World of Warcraft movie. I will cringe when they make the obligatory Leeroy Jenkins joke (those non-funny bastards were on my server, and I hated them before they made the lame movie and somehow got famous for it), but the possibility of Raimi making a videogame movie is... intriguing.

As if that wasn't enough, at the end of July it came out that Ridley Scott has signed on to direct a prequel to Alien. Ridely Scott, not just some random schmoe. Wow.

Technology/Geek Culture:

A firm in Abu Dhabi has ponied up money to Virgin Galactic. Part of the deal is to build a spaceport in Abu Dhabi (in the UAE), making it the second commercial spaceport (after the Mojave Air & Space Port in Mojave, California). I'm guessing that one will get quite a bit of use. Note to science fiction authors: Arabic will likely be spoken in space roughly as much as English, at least in the early days of space tourism.

Politics/Morality:

The UK Quakers are going to extend marriage services to same-sex couples. If that bleeds to the US Quakers, that would mean, when a state accepts one religious marriage ceremony as valid but not another, they are denying the religious freedom of that same-sex couple. I've often wondered what would happen if that tack were taken on the gay marriage issue. We might get to find out. Of course, the consequences could be dire.

I'm sure there were a number of geek stories that I didn't cover here. Let me know in the comments if I skipped any big ones.

Blog Squishiness

Update: Fixed!

I picked a new template to reset some things that were broken... but that means my blog is so narrow now that some of my photos don't fit. I'll fix it soon... ish...

If you're reading this on RSS, you shouldn't notice any effect.

Multi-Parameter Firefox Keywords and Chrome Search Engines

By far, my most popular post is my guide on Firefox Keywords and Chrome Search Engines. I recommend reading that one to get caught up if you don't know what Firefox Keywords and/or Chrome Search Engines are.

Shortly after I wrote that, I found this post on Lifehacker explaining how to combine bookmarklets and keywords for some very clever and useful tricks, but it didn't work on Chrome as written, and I never got around to figuring it out. Tonight I finally took the time to figure it out.

The problem (besides the Lifehacker example being overly complicated) is that Chrome doesn't like {}'s in keywords. Those aren't really necessary unless your keywords are very complicated, though, so I got it to work. This is the code we'll be working with:

javascript:
var s='%s';
url='YOUR URL, WITH %s's FOR EACH TERM';
query='';
urlchunks=url.split('%s');
schunks=s.split(';');
for(i=0; i<schunks.length; i++)query+=urlchunks[i]+schunks[i];
location.replace(query);

As it says in the code, all you need to do is insert the url you want to use, with the usual %s's anywhere you want to insert a search term. You then set it up like any other keyword or search engine (see the other post for how to do that; note: you can just copy/paste the multi-line code into Chrome or Firefox, they don't require that you condense it down to one line first). To use it, just separate your search terms with ;'s.

This fairly simple code can let you do some very cool things. Here's an example for mapping between any two points in Google Maps:

javascript:
var s='%s';
url='http://maps.google.com/maps?saddr=%s&daddr=%s';
query='';
urlchunks=url.split('%s');
schunks=s.split(';');
for(i=0; i<schunks.length; i++)query+=urlchunks[i]+schunks[i];
location.replace(query);

I set this up as a Chrome search engine with keyword "mapp" (although something like "directions" might be easier to remember). If I type "mapp NYC; DC", I get a google map between New York City and Washington, DC.

A warning: if you include a space after the ; like I did in that example, you technically get a space before your second search term. I could probably over-complicate the code and clean that out, but it works fine for Google, and I can learn to avoid it once I set up ones that don't tolerate it. Oh, and if you include more ;'s than the keyword has %s's, the extra stuff will just be tacked onto the end (for example, "mapp NYC;DC;Other" tries to generate a map between "NYC" and "DC Other"

If you use this, please let me know in the comments if you come up with any clever ones. Remember: this works for any url that you want to insert something into, not just searches, so there are definitely some interesting possibilities out there waiting to be discovered.

Mad Science Monday, 7/27/2009

If you've been reading this blog, you might have found yourself wondering, "What exactly makes science mad?" Even if you haven't, I have quite a bit recently. I've been reading papers, searching for things that are suitably mad, and nothing seems to be up to snuff. So, both to let you know my process and to work it out a bit for myself, I decided this week I'd present:

Meta Mad Science Monday: Defining Madness

There's one definite requirement for a paper to make the cut for Mad Science Monday: it has to clearly be science, not engineering. The researchers have to be testing a hypothesis using controlled experiments, not piloting new technology.

Beyond that stipulation, there are a lot of signs that a study might be mad. Here are some of them.

1) Use of Mad Engineering as a Research Tool

When I saw a study involving implanting lasers in rat's brains, I knew there was a strong possibility that I was reading about mad science. Frikkin' laser beams are often mad engineering, and implanting them in rat's brains (and using viruses to alter those rat brains) cements that definition. Robots also often fit this rule. If the researchers are using mad engineering, there's a good chance they're doing mad science.

2) Mergers of Man and Beast

A lot of biological research involves human genes, or cognates of human genes, being tested in non-human models. But when researchers implant human genes into mice to test something unquestionably human—speech, in this case—there's a good chance we're looking at mad science. That particular paper also has another defining characteristic of mad science, which is why it launched this project.

3) Mad Quotations from the Researchers

If I see a story about some research in which they say, for example, "We will speak to the mouse," I know there's a good chance I'm looking at mad science. If you can imagine lightning flashing as the researcher shouts the quote, it's probably something I need to write about.

4) Quantum Entanglement

Any paper about quantum entanglement is mad science. Some of them are too thick to boil down into something fun to write about, but they're still mad science. That shit is just weird.

5) Research Involving Fear, Pain, Etc.

If the subjects of the research have to be scared, or pain has to be inflicted upon them, or otherwise the research sounds like it's on questionable moral standing when I first hear about it (before, inevitably, reading about the very humane protocols used in the research), it's probably mad science. This even works if the subjects aren't human, but the research has potential human applications. That borders on the next requirement.

6) Research with Clear Mad Engineering Applications

Clear applications usually aren't present in my favorite research, but if they're mad applications, they can make me take notice. If the research is aimed at, say, finding the formula for taking over the world, that's probably mad science. Research on weather control, giant weapons, doomsday devices, etc would also qualify as mad science, but I have yet to find anything good in this arena.

Those are the criteria I use right now. Right now I have a Rule 5 and a potential Rule 1 on deck, but they both look like weak applications of those rules. If you notice anything else fitting these criteria, or notice a criterion I missed, let me know in the comments.

Mad Science Monday, 7/20/2009

Are you a mad engineer looking to take over the world (or even a small section of it)? Do you also have a powerful, supervillainous ability to extend a simple example into a general principle? If so, this research is for you.

Mad Observations: In widely varying areas, animals follow leaders. This behavior ranges from ants seeking food, through birds and butterflies migrating long distances, to human politics. In all of these cases, the followers have a strong tendency (and motivation) to keep following the established leaders; if they didn't, particularly in the non-human examples, things would quickly be very bad for them.

Mad Reference: Note: This is a not-yet-published letter, not a peer-reviewed paper. It's basically raw presentation of research, which is what arxiv.org is for. "Effective leadership in competition." Hai-Tao Zhang, Ning Wang, Michael Z. Q. Chen, Tao Zhou, and Changsong Zhou. Full text available from arxiv.org.

Mad Hypothesis: As the authors state it, "is it possible for the minority later-coming leaders to defeat the dominating majority ones and how?" In other words, the hypothesis they're attempting to disprove is "It is impossible for minority later-coming leaders to defeat the majority leaders." If they manage to disprove that, they'll also have the how covered.

Mad Experiment: The researchers used a "generic model of collective behavior, the Vicsek model." As far as I can find, this is a widely used model for motion. Specifically, in this model individual motions are aligned to the average of their neighbors. In other words, if you want to think of this research in a more global context than just motion, you have to make the assumption that the individuals you're targeting will tend to follow along with whatever the people near them are doing. However, "near them" could mean "politically near them," for example, so it's not necessarily a bad assumption. Remember that translation of "near them" when pondering the rest of the findings, though.

In this model, the researchers introduced "leaders," which were simply individuals that did not simply align themselves to their neighbors. The followers obeyed the "follow your neighbor" rule, but the leaders were set to either move right (the established leaders) or left (the newcomer leaders).

After establishing the model with the right-leaders + followers, the researchers introduced late-coming left-leaders in various patterns and with various distributions. They measured how well these patterns of left-leaders were able to overcome the movement direction established by right-leaders.

They All Laughed, But: The researchers found that the late-comers were able to change the direction of the group, but that their ability to do so could be predicted based on two factors: the spatial distribution of the leaders (how far apart groups of leaders were) and the clumping of the leaders (how close together the members of a group of leaders were). Higher values for either of those factors increased the chance that the left-leaders could overtake control of the group. And, of course, it helped if the right-leaders had lower values for those factors.

Mad Engineering Applications: What these researchers found is that two factors help in taking over control of a group: wide distribution of the individuals working to change the group, but tight clumping of change-introducing individuals. In other words, it's good to spread out your leaders, but give them allies to work with locally.

It's easy to accidentally keep too much of the geographic part of this model, though. For example, if you translate the findings to politics, you should translate all of the model to politics. If you want to spread an idea throughout a group, you need people idealogically clumped to help each other influence others who are close to them idealogically, but it helps to also have such groups spread out to different places on the idealogical scale.

I'd be interesting to see other ways mad engineers could find to adapt this model to other scenarios. If you think of any, let me know in the comments.

Have a Horrible Day!

Today is the one-year anniversary of the release of Dr. Horrible's Sing-Along Blog. If you have not yet seen it, watch it now. If you have seen it and love it like I do, show them some love in return.

Remember: It's not about making money, it's about taking money.

Mad Science Monday, 7/13/2009

Dammit. Dammit dammit dammit.

You might think from that intro that I'm writing about one of the more widely talked about science stories from this week. I may get to that one eventually, but the actual source of my frustration is the realization this morning that I had gotten the wrong paper for this week's entry. Sure, the one I got is mad, but I didn't get the one by the same group that involves rats with frikkin' laser beams attached to their heads. I'm going to try to give as much of an overview of all of that group's research as I can, but I can't for the life of me figure out how they made the stuff work in the laser rat story.

Update: I got the other paper in the middle of writing this, but I'm still focusing mostly on the newer paper; the one with the actual laser beams appears to use many of the same techniques, and I haven't had as much time to digest it, so I'll stick to the one I'm mostly grokking.

But I'm getting ahead of myself. First you're going to need some...

Mad Observations: A lot of observations are necessary to culminate in this level of mad science. There's too much to cover it completely, but let's see what I can get.

First, there's an archaebacterium, Natronomonas pharaonis, that makes a protein that pumps ions across the cell's membrane in response to light (specifically certain wavelengths of orange light). This pump is called the Natronomonas pharaonis halorhodopsin chloride pump, or NpHR. This pump has been adapted to be expressed in mammalian cells.

Next, there's the known mechanism of epileptic seizures, namely that the'rey caused by cascades of electrical potentials; basically, one cell has more positive charge inside than outside, and that causes it to induce the next cell to switch to the same condition, etc down a line.

Mad Reference: "Optogenetic control of epileptiform activity." Jan Tønnesen, Andreas T. Sørensen, Karl Deisseroth, Cecilia Lundberg, and Merab Kokaia. PNAS, published online before print July 6, 2009.

Mad Hypothesis: This paper even included a direct reference to the hypothesis they were testing: "Therefore, we tested a hypothesis that epileptiform activity can be optically controlled by selective expression of NpHR in principal cells." In other words, they thought screwing with the potential differences across membranes (by pumping chloride ions into those cells) would stop the epileptic cascade, and they figured they could induce that change with light by putting those pumps into the right cells. They also tested whether putting in the pumps (but not inducing them with light) caused any changes in the behavior of brain cells, and whether turning on the pumps caused any other problems (like sucking up too many chloride ions, stopping other things that need them from functioning properly).

Just to make sure that's clear, what they were testing is whether shining a laser beam inside a brain would work to stop seizures. Obviously.

Mad Experiment: It just keeps getting better. To test whether shining a laser on brains might be useful for treating epilepsy, they infected rats with a virus. Ok, this sounds all kinds of mad scientist, but it's actually a fairly well-established technique. This virus, technically a lentivirus, was modified to incorporate the gene for NpHR into cells that it infected. That gene was put under control of the calcium/calmodulin-dependent protein kinase IIa (CaMKIIa) promoter, meaning that, no matter what cells the gene might get inserted into, the protein would only be expressed in certain cells--namely, brain cells. They also put the enhanced yellow fluorescent protein (EYFP) in the same virus, also under control of that promoter. That let them cut up some of the rat brains (and other rat bits) and confirm that the technique had worked to get the protein expressed in the right place, and not in the wrong places (because it'd be bad for light-sensitive proteins to be expressed on, say, the skin, where they'd be doing their thing all the time, not just in response to a frikkin' laser beam).

Most of the research, unfortunately, was done in cultured rat brain cells, using that same basic technique as I described above. But they showed that they could get the protein expressed in rat brains. That's important, since they'd already done other research with implanting frikkin' laser beams in rat brains, to stop Parkinson's tremors.

Yes, that's a photo of a rat having light beamed into its brain through a fiber optic cable attached to a laser. We truly live in amazing times.

So anyway, they got their protein into cells (both in rat brains and in cultured cells), and then they tested the cultured cells using established epilepsy tests. They did these tests on unaltered cells, altered cells without light, and altered cells with the correct wavelength of light shining on them.

They All Laughed, But: It worked. When they shined lasers on the altered cells, their idea worked; the seizures (well, technically simulated seizures, since it was just a plate full of cells) stopped. It looks like this would actually work. But the whole time I was reading it, I was thinking, "Um, so. You need a frikkin' laser beam implanted in your brain." But then I found out I was missing half the story, since they'd already implanted frikkin' laser beams in rat brains. So this whole thing would totally work, and all it takes is:

• infection by a virus to put an archaebacterial protein into your brain,
• glowing proteins engineered from jellyfish thrown in to make sure it worked,
• surgery to implant a laser (or lasers) in your head, and
• potentially a fiber optic system following you around (although I guess we're bigger than rats, so maybe the lasers could be worn directly).

I say this all jokingly, but apparently that's way better than the current system of curing intense seizures, namely cutting the hell out of the affected area, hoping you don't get too much that's useful.

Mad engineers: This one's all yours now. We scientists have shown it would work. Implementing this is all you.