Monday, August 31, 2009

Mad Science Monday, 8/31/2009

a record-breaking zombie hordeI 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.

Monday, August 24, 2009

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.

Tuesday, August 18, 2009

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!

Monday, August 17, 2009

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.

Friday, August 14, 2009

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.

Wednesday, August 12, 2009


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.

Monday, August 10, 2009

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.

Wednesday, August 05, 2009

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.

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.

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.

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.