Mad Science Monday, 2/21/2011

Sometime around the time it came out in 1996, I saw Project Grizzly, the documentary about Canadian inventor and awesomely crazy person Troy Hurtubise. Troy doesn't have a whole lot of scientific training, so he didn't immediately come to mind when I started Mad Science Monday... but I think he might really be a mad scientist (or at least a mad engineer with thoughts of mad science). I can't remember the exact quote, but he has a monologue in the doc about how his suit will let NASA study hibernating bears, which they can't do because the bears might wake up and rip the researchers to shreds. That argument made all of the madness he expresses in the rest of the doc, trying to build his bear-proof suit, seem worthwhile.

Today's research isn't as mad as Troy, but it enhances his madness (and has some mad applications of its own), so it fits the theme.

Mad Reference! "Hibernation in Black Bears: Independence of Metabolic Suppression from Body Temperature." Øivind Tøien, John Blake, Dale M. Edgar, Dennis A. Grahn, H. Craig Heller, and Brian M. Barnes. Science 18 February 2011: Vol. 331 no. 6019 pp. 906-909 (via National Geographic). That might not sound all that mad, but the National Geographic title made it more sensational: "Hibernating Bears Keep Weirdly Warm." Yes, that sounds deliciously mad indeed!

Mad Background and Observations! When most things hibernate, their bodies get cold, sometimes really cold. For example, when frogs hibernate in cold climates, parts of their bodies freeze solid under the snow. Even hibernating mammals allow their body temperatures to drop several degrees during their torpor.

Mad Hypothesis! Bears hibernate, so presumably they get chilly like everything else that hibernates, right?

Mad Experiment! This was the part that made me think of Troy. Surely to test this, the scientist had to suit up in a Mark V Anti-Bear Super Suit and get lowered by a crane into a hibernating bear's cave, ready to quickly read a well-placed thermometer and bolt, right?

It turns out it's much simpler than that. The researchers rescued four "nuisance" bears, which presumably had been stealing picnic baskets and/or making bad movies, and were slated to be euthanized. They rigged the bears up with various sensors to record their vital statistics, and placed them in artificial dens to hibernate. And that's all. I'm beginning to think maybe Troy was making up the whole "NASA would love this thing" explanation for his suit (or I guess it's possible nobody had thought to do things this way, since they didn't know until now how cool bears got while hibernating).

They All Laughed, But! This is one of the (many) cases where disproving the hypothesis is what makes things interesting. While hibernating, these black bears held their temperature between 30 °C and 36 °C (86 °F to 97 °F). To put that in perspective, normal human body temperature is 37 °C (99 °F, or, if you insist on too many sig figs, 98.6 °F). If you snuggled up against a hibernating black bear, it wouldn't feel particularly chilly. That's a big difference from the frogcicles hibernating near their dens.

Mad Engineering Applications! Troy wasn't completely wrong that NASA would likely be interested in better understanding hibernation. Hibernation for long space voyages is a staple of science fiction, because it's a good way to avoid many of the problems of long space flight. However, significantly cooling (or even freezing) tissues presents other challenges. If we can figure out how the black bears do it, we might not have to protect the astronauts' bodies from freezer burn (although we would, of course, have to spend a lot of energy keeping them warm in the coldness of space). To the terrestrial mad engineer, this could be even more useful. Cooling your clone armies for storage could be very expensive, particularly if your lair is hidden inside a volcano. Using the black bear hibernation techniques, you might be able to simply fatten them up for storage, and then let them hibernate at non-freezing temperatures.

Have you seen any other useful research for clone army construction and storage? Let me know in the comments.

Mad Science Monday, 2/14/2011

Happy Valentine's Day! I almost didn't get a post up today, but then I saw the perfect article to fit the holiday. Without further ado, I give you:

Mad Reference! "Extreme Aggression in Male Squid Induced by a β-MSP-like Pheromone." Hanlon RT, et al. Current Biology (online) February 10, 2011 (via National Geographic). Pheremones that induce aggression in a phallic animal during mating? Sounds like a Valentine's Day Mad Science Monday to me!

Mad Background and Observations! When longfin squid (Loligo pealeii) get together to breed, the females lay egg sacs. The males rush in and touch these sacs, and go into full-on pon farr rage.

Mad Hypothesis! A protein in the eggs acts as a pheremone, sending the males into this rage. Even without females present, this pheremone would set male longfin squid into gladiator mode.

Mad Experiment! The experiments are laid out really well in the apparently non-embeddable video at the top of the National Geographic article. They basically performed four trials (plus probably more trials with other proteins before they settled on the main candidate, but those aren't covered in this particular video and paper):

1. Trial with no stimulus (to establish baseline behavior of a group of male squid in their tank)
2. Trial with natural eggs (to establish what aggression looks like)
3. Trial with flask streaked with recombinant Loligo β-microseminoprotein (β-MSP, their candidate pheremone)
4. Trial with flask with no Loligo β-MSP (to make sure the pheremone matters in trial 3)

They All Laughed, But! β-MSP appears to be the thing that's necessary to piss off squid. The flask had eggs inside (to get the males to touch it), and I would've liked to see a trial without the eggs, but it'd be hard to isolate that it was the chemical doing the angering, not, say, poking them with a pheremone-tipped stick. The controls also established pretty well that β-MSP was the factor causing the aggression, although a sealed flask of eggs did produce a little more aggression than the stimulus-free control.

Mad Engineering Applications! This quote from the NatGeo article is what made me consider this research for Mad Science Monday: 

"We don't know of anything like this that exists in humans," Hanlon added. "But when we researched microseminoproteins in the literature, we found that they occur in mammal semen and, more importantly, that nobody has looked at what functional effect they have.

"We hope that our discovery stimulates research in that direction."

So they found a protein that turns male squid into gladiators, and a similar protein in humans... and they're hoping their research stimulates research. Clearly these guys are working on breeding their minion army.

Have any suggestions for Mad Science Monday (particularly articles published with full text in free online journals)? I'd love to read them in the comments!

Mad Science Monday, 2/7/2011

Ok, I really like writing these things. I think I'll try to do this weekly again.

Mad Reference: Josh Bongard. "Morphological change in machines accelerates the evolution of robust behavior." Proceedings of the National Academy of Science. January 25, 2011 vol. 108 no. 4 1234-1239. (abstract)

A lot of my random reads come from "cool" via Recommendations, a Google Reader list of things that other people have shared. As far as I can tell, this one mostly made that list because the title was cool, but the research is pretty neat.

Mad Background: Evolutionary algorithms are just about my very favoritest of things. Basically, computer scientists, inspired by the simplicity and elegance of biological evolution, have started using reproduction (of code fragments), mutation (of the specifics of the code), and selection (of the code fragments that are most successful at whatever task the programmers give them) to evolve programs. Such evolutionary algorithms often find solutions that the programmer might not have thought of, and do so faster than would occur if the programmer directly designed the solution. In other words, evolutionary algorithms flip the bird to intelligent design "theory" (which is only a theory in the colloquial sense of "guess;" there's no science there to actually make it a scientific theory).

Evolutionary algorithms are often used to design robots, both real and simulated (as shown in the video above).

Mad Observations: Real biological systems don't start out even crawling; they go through various body plans through their lifetime, and through the many lifetimes that take them from one species to another. For example, life has, multiple times, gone from a snakelike slithering form to legged walking form, both over many generations and within the lifetime of single organisms.

Mad Hypothesis: A robot that starts in a snakelike ("anguilliform") body plan before progressing to a four-legged walker can figure out how to walk faster and better than a robot that starts out up on four legs.

Mad Experiment: This experiment was mostly virtual. The experimenter set up digital "robots," some of which started out with legs, and some of which started out down on their belly. He then allowed them to search for a control mechanism for their four limbs that would get them from one corner of the simulation to the other. He also ran trials in which the belly-walkers gradually stood up on their legs (by slowly increasing the angle between the legs and the body), and then ran trials where robots pre-loaded with the slithering programs started out up on their legs. He even built Lego robots similar to his digital creatures, which just makes it all cooler.

They All Laughed, But: It worked. Robots that started out up on their legs took several hours to figure out how to walk, while the slitherers (and their progeny) figured it out in seconds. Even the Lego bots, which were slowly changed from slitherers to walkers, were able to figure out how to walk in the real world really fast, much faster than their always-walking cousins.

Mad Engineering Applications: When you're building your robot death army, don't start them out as bipedal killing machines. Sure, give them arms and a desire to rip things to shreds, but start out forcing them to use those arms to slither, then walk, and then finally they can stand erect and use those arms for their intended purpose.

This would probably also be useful for less destruction-focused robots, but that wouldn't be nearly as Mad.

Mad Science Monday, 1/31/2011

It's been a long time since I've written one of these, but this story is too mad sciencey to pass up.

Mad Reference: "Can Our DNA Electromagnetically 'Teleport' Itself? One Researcher Thinks So" by Clay Dillow at Popular Science, about work by Nobel Prize winner Luc Montagnier. Uh-oh, the work hasn't been published yet, and apparently first appeared in New Scientist. Going to the press first is a bad sign. Going to New Scientist first (the magazine that reported that SETI had found concrete evidence of alien intelligence, causing SETI scientists to reply "We did what now?") just might mean even you know what you're peddling is nonsense.

Mad Background: Quantum teleportation is a real phenomenon, and it's really interesting to read about. But it has nothing to do with what happened here, so I'm not going to go into detail about it. If you're interested, I recommend the Wikipedia article I linked as a good primer.

The more interesting (and relevant) background is that of Luc Montagnier, the scientists whose lab is reporting this finding. I was first introduced to Dr. Montagnier through the excellent 1993 HBO movie And the Band Played On. And the Band Played On tells the story of the discovery and characterization of AIDS and HIV, and the political nonsense that slowed down the progress of those discoveries. I changed my major to biology shortly after first seeing that movie, in part inspired by it. In the movie, Luc Montagnier (played by Patrick Bauchau) is one of the good guys, fighting against the egomaniacal American biologist Dr. Robert Gallo (played by Alan Alda). The film shows how Gallo pretty clearly (in the movie, not in reality) stole a sample of HIV from Montagnier's lab, and used the sample to fake results showing that he had discovered HIV.

However, around the same time the movie first aired on HBO, a group looking into those allegations published their report. They found that a sample sent by Montagnier's lab to Gallo's had been accidentally contaminated with the sample, and then Gallo legitimately used that sample in his studies. Evidently, Montagnier's lab still has issues with contamination.

Mad Observation: DNA is complicated. People understand very well how it gets copied in cells, but maybe they're wrong. Also, quantum teleportation is really cool (honestly, that's the best set of observations I can come up with to explain what Montagnier did).

Mad Hypothesis: Maybe DNA undergoes quantum teleportation in cells! We have no reason to think this, but let's devise an experiment to test it anyway!

Mad Experiment: Montagnier's lab put two test tubes, one containing a known DNA sequence and the other believed to contain pure water, in a straight-up mad scientist contraption meant to "mute the earth’s natural electromagnetic field to keep it from muddying the results," according to the Popular Science article. They then subjected these tubes to a weak electromagnetic field, because, hey, why not? After several hours, they performed PCR on the pure water tube to see if it contained any DNA.

They All Laughed, But: Holy crap, the tube of pure water totally contained DNA! It must be that quantum stuff! We're geniuses!

We're Still Laughing: From every report I've read, Montagnier's lab didn't do the control experiment, in which both test tubes contained "pure" water. Chances are very good they'd still get the same result.

PCR amplifies any trace of your target DNA. Modern PCR can amplify as little as a single strand of the target DNA. Add to that the fact that DNA is very stable, and thus easy to contaminate your lab with.

I often cook with jalapeños. After slicing them up, I'm careful to wash my hands. But sometimes, even after washing my hands, I touch my eye, and it starts to burn. Were I in Dr. Montagnier's lab, I guess I'd assume those muddying effects from Earth's natural magnetic field were causing bits of the jalapeños on the counter to quantum teleport into my eyes. Since I don't work in Dr. Montagnier's lab, I just assume there was a trace contaminant (jalapeños) left on my fingers, and that got into my eye.

Mad Engineering Applications: Since this research is nonsense, there aren't any. However, were it correct,  there would be all kinds of applications. We'd probably have to stop working on all of the antiviral agents that block them from entering cells; surely viruses could just quantum teleport their DNA into our cells, skipping all the bother of physically entering cells. I'm sure other people could also find uses for this research.

The last time I wrote one of these, the mad scientist I wrote about had a clear claim to that title, but only tongue-in-cheek. Sadly, I think this week the scientist in question may really be mad.

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, 8/10/2009

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.

Mad Science Monday, 7/6/2009

It's Monday again (already!), so that means it's time for some mad science. It might not be immediately obvious how this week's article fits the theme, but I have one mad science stereotype stuck in my head now about this one, so hopefully I can get you there, too.

Mad Observations: Despite portrayals in media, scientists are human beings. Sometimes decisions made by human beings are clouded by emotion.

Mad Reference: "Large-Scale Assessment of the Effect of Popularity on the Reliability of Research." Thomas Pfeiffer, Robert Hoffman. PLoS ONE 4(6); e5996. 2009 June 24.

Mad Hypothesis: Research is not impacted by the trendiness of the subject of that research. Yes, I know; this is one of those hypotheses that is pretty much obviously untrue once you say it, but it's something nobody had said scientifically (and followed up with experimentation), and thus it was tacitly accepted as truth.

Mad Experiment: This is what's known as a meta-analysis paper. The researchers didn't perform experiments, per se. Instead, they analyzed over 60,000 published statements about 30,000 unique interactions between yeast proteins. This data set was drawn from papers focusing on specific interactions; each paper from which the 60,000 statements were drawn focuses on one or a few interactions, investigated using small-scale, focused experiments. They evaluated the "popularity" of the proteins involved in these interactions by how many times those proteins were mentioned (ie, more mentions = more popular).

They then compared that first data set to a second data set, gathered using high-throughput, mostly automated techniques. These high-throughput techniques don't focus on one or a few interactions, but instead test pretty much everything simultaneously. In other words, these techniques don't focus on anything in particular, so they don't "care" whether the interactions they're looking at are "popular" or "interesting."

They All Laughed, But: The reason this research seems mad sciency to me is that I keep imagining these researchers giving their speech about the popular researchers laughing at them. Well, who's laughing now?? It turns out, when you compare the results from the specific data with the results from the high-throughput data, popular proteins seem to get by on their looks. Specifically, interactions involving unpopular proteins tend to agree in the data sets more often than interactions involving popular proteins. Popular proteins have a higher proportion of likely incorrect interactions published than do unpopular proteins.

When I first read the summary of the research, I thought this might be an example of damned lies; I figured it wasn't necessarily that the unpopular protein research was correct more often, it was just that nobody bothered disproving statements about those losers. But the methodology here seems sound; it looks like the popular proteins really are getting treated differently. This points out a possible large flaw in current research, and a need to put more safeguards in place to prevent this stuff from getting through. Strong work, mad scientists. You have successfully exposed the flaws in the work of your enemies.

Mad Science Monday, 6/29/2009

I'm a little late today (which is to say, I didn't write this over the weekend and schedule it to release at a seemingly random time during the day), so, to make up for it, I'm offering a twofer; one experiment that tested two hypotheses. They even threw in a little mad engineering to spice things up even more.

I first mentioned this story back in April, but it deserves a closer look. I really think it's going to end up being the biggest science story of the year.

Mad Observations: With things like the Human Genome Project and the other genome projects that preceded and followed it, we are gathering reams of data, more than we'll be able to fully investigate any time soon. At least, more than we can investigate by hand. But hey, computers are pretty advanced these days...

Mad Reference: "The automation of science." King RD, Rowland J, Oliver SG, Young M, Aubrey W, Byrne E, Liakata M, Markham M, Pir P, Soldatova LN, Sparkes A, Whelan KE, Clare A. Science. 2009 Apr 3; 324(5923): 85-9. I also recommend the excellent write-up on the research in Wired.

Mad Hypotheses: The first hypothesis was chosen by the researchers (who were bordering a bit on mad engineering, so the hypothesis is pretty close to "Let's see if we can do this"). It's along the lines of "It is possible for a properly programmed robot to investigate data, make a hypothesis, and test that hypothesis."

But then we get into the first experiment, and get the cooler hypothesis. The researchers programmed a robot, named Adam, to perform science. Without help, just looking at the data from the Saccharomyces cerevisiae (brewer's yeast) genome project and other genetic databases (plus a model of S. cerevisiae metabolism), Adam hypothesized that certain genes in the yeast genome coded for an enzyme that had a certain function in metabolism. These genes were there in the data, but had not yet been characterized. So Adam set out to characterize those genes, hypothesizing that they would produce an enzyme that would catalyze a certain reaction in yeast metabolism.

Mad Experiment: Unfortunately, I don't have full access to the article, and both the abstract and the Wired article are sketchy on the details here. I'll lay out a couple possibilities, though, for people interested in how a researcher (including a robotic researcher) might figure something like this out.

Put simply (but close enough to give the idea), Adam knew that yeast used an enzyme to turn compound A into compound B, and another to turn B into C, and yet another to turn C into D, etc. He just didn't know for sure what those enzymes were. Let's say he was hypothesizing that the enzyme he was looking at turns A into B.

One way to figure out if he's right would be to create a yeast cell that lacked the genes he was looking at (likely one at a time plus all three); the yeast cell would be exactly like a normal yeast cell, just missing the one gene he was looking at. If he fed normal yeast cells A, they'd grow and produce B, C, D, etc. If he fed his modified yeast cells A, if he was right, they wouldn't produce B, C, D, etc. He could then feed his modified cells B, and they'd then be able to produce C, D, etc. If any step of that didn't work as expected, his hypothesis would be false.

The other possibility would be that he directly characterized the genes, creating copies of the genes he was looking at in a test tube, supplying them with the components necessary to translate those genes into proteins, and seeing what happened when he put A into those test tubes. That sort of research is less reliable, though (if it doesn't work, it could be because you're missing some factor necessary to make the protein, not because the proteins are important in what you're looking at), so I think it's more likely that he used the first approach.

All this time, all the researchers did was supplied him with the chemicals he needed, and emptied out wastes. He did all the rest, designing and performing over a thousand new experiments a day.

They all laughed, but: Since I'm writing about it here, you've probably already figured out that it worked. He was able to identify that three previously uncharacterized genes in the yeast genome code for an enzyme that catalyzes a certain step in yeast metabolism.

The particular discovery made by Adam wasn't particularly Earth-shattering; he found something that would have otherwise have been assumed to be true, but he verified it. The next step is the cool part. Robots like Adam can now dig through the genomes that we've sequenced, making similar hypotheses and performing similar experiments. Now that we know that they work, the interesting part comes when they fail to verify what they're looking at. On top of verifying and adding to the body of science, they would then find something for us to look at more closely.

Mad Engineering Applications: Since this all started with a dose of mad engineering—specifically, making robots to analyze data, make hypotheses, perform experiments, and analyze their results—there isn't much left in this particular area for mad engineers to do. For a while now, this one's pure mad science. Hopefully they'll make us some more robots capable of performing other experiments, but, once they give us our army, it's scientists that will utilize that army. And hopefully more scientists (mad or not) will come up with more ways to apply this research, potentially dramatically increasing the rate of increase of the sum of human knowledge. "What we know" already increases dramatically every year, as does the rate of discovery of new information (so if it doubled last year, it's likely to more than double this year). If robot science catches on, the rate of increase is likely to go way, way up.

Have any ideas for what tasks we should set our army of robot scientists on? Let me know in the comments.

Mad Science Monday, 6/1/2009

Several weeks ago (even before my last post!), I saw this comic, which points out that so-called "mad scientists" are really more like mad engineers; they aren't trying to test anything, they just want to blow stuff up. That got me to start looking for actual mad science. Since then, to my surprise and delight, I've seen quite a bit.

Assuming the world of science continues to be beautifully strange, I'm going to try to bring you news of mad science every Monday. This week, I give you talking mice.

Mad Observation: People in a certain family had "difficulties with articulation and grammar." The people in that family who had those issues all had a certain version of the gene Foxp2. The gene Foxp2 is present in many (all?) mammals, including both humans and mice.

Mad Hypothesis: Perhaps the two mutations present in human copies of that gene but missing in the mouse version are important to human speech. We have the complete genomes of people and mice (and chimps, and rhesus macaques, and a growing number of organisms), and we know that gene is different in humans than it is in other mammals. There's some evidence that gene is important to speech. Is it?

Mad Experiment: Introduce the mutations in the mouse version of Foxp2, and see what happens. If there aren't any significant changes in the mice, the mutations must not be important (at least not alone) for human speech. If something significant occurs (like, say, a slight change in brain development), the gene might really be important to speech.

Mad Quotation: At the beginning of the project, Svante Paabo, one of the lead investigators, said, "We will speak to the mouse." I'm sure he worded it that way on purpose (he never said anything about the mouse speaking back), but, if spoken with the proper flair, it's a great mad scientist quote to set the scene.

They All Laughed, But: The lab really did only expect the mice to have slightly different brain development. Certainly far too many genes are involved in speech for this to have any significant effect, right? Except, when they made the mice, they found more differences than just brain development. Sure, the mutant mice had interesting developments in the part of the brain associated with speech, probably moreso than the researchers expected. But, in addition, there were actual changes in their communication.

When a baby mouse is away from the nest, it emits chirps to let its mom know where it is. The chirps of the mutant mice were significantly different in several characteristics, including pitch and rhythm.

The mice can't speak, of course, but holy crap. This change of two amino acids in one protein had a significant effect on the way the mice communicate.

Mad Caveat: The changes in the mouse vocalizations are actually within the range of normal variation among mice. It's probably an effect of the gene, since the differences were statistically significant between the mutant pups and their non-mutant littermates, but it's possible it's just random chance. Further tests will be necessary to further characterize the effects of Foxp2, but this is an interesting step.

Now to go find more science news sources to follow, to make sure I can keep this up next week. If you have any suggestions, let me know in the comments.

Today's Shared Google Reader Items, 12/9

Holy crap, I haven't done this since last Thursday. These are my favorite Google Reader shared items in that timespan.

Zombies:

• My friend Jon found two cool zombie movies. And I created a "zombies" tag, because I realized it was missing from my blog.

Politics:

• The new New Deal is starting. Woot.
• I don't have anything against David Gregory for Meet the Press, per se, but I was pulling for Chuck Todd. Then again, I've never seen Chuck Todd interview anyone, and that's what's required. It's big shoes to fill in any case, and I'm not sure anyone can pull it off.
• The first challenge of Obama's citizenship has been rejected by the Supreme Court. There's another one coming, but it's a good start. He was born in Hawaii, you idiots. That's all it takes, as long as he hasn't rejected his citizenship... and if it's possible for a little kid to reject their US citizenship, the system is insane.
• Holy crap, the Governor of Illinois is super corrupt, and was trying to sell Obama's Senate seat. It may take a while now to get that seat filled. Chances are good the Senate will reject anyone Blagojevich picks, and it takes time to spin up an impeachment and/or special election.
• Bill O'Reilly, in describing how terrible Seattle is from a war-on-Christmas perspective, makes me want to move there.

Science:

• This article was entitled "Scientists Achive Mental Body-Swapping," but it's about getting people to essentially think as if they're in another body. It's not nearly as sci-fi cool as I thought it must not possibly be.

Technology:

• The summary of this article about Hawaii's plan for a state-wide electric car network on Slashdot annoyed me. An electric car grid encourages/allows more efficient power generation; it takes the power generation step out of the car, so you can do whatever it takes to make the power generation clean on a statewide basis. It doesn't rule out wind and solar, it just puts that step in a centralized place.
• I'm very annoyed that I didn't hear about/see the 3D NFL broadcast.

Biology:

• There's some evidence that the herpes simplex virus (the virus that causes cold sores, among other things) causes Alzheimer's. It would be awesome if this pans out and leads to treatment and/or a cure.

Atheism:

• Techskeptic (via Pharyngula) has a list of Atheist/secular charities. I've often wanted something like this myself, so it's nice that someone else compiled it for me.

The Internets and other Computeriness:

• A nearly full-featured, browser-based, image-editing program is available. It's very cool, and I love the pic they made in their demo video.

Programming (but the first one is awesome, Libby):

• This evolutionary algorithm to create the Mona Lisa is stunningly amazingly awesome. It dovetails with something I've wanted to do, and might inspire me to finally get that project moving.
• Google has announced Google native client, which promises to put code written for x86 processors onto the web. That's very, very cool, and opens up all kinds of possibilities.

Finally, uncategorized, I shared this old video of "Keeping the Dream Alive" by Munchener Freiheit (huh, I always thought the band was just "Freiheit"), because I missed it and randomly searched to see if it was on YouTube... and it was. Enjoy. Or, ya know, don't, if you don't like cheesy music. In any case, comment below.

Today's Shared Google Reader Items, 12/1

I'm going to try to get back up to daily (or more) posts, at least 'til Newtonmas or so. So, without further ado, here are today's shared Google Reader items.

Life:

• Lifehacker has a guide to pronouncing names correctly. If you're bad at this, read it now. I'll personally be using the other links in that article, about how to find out a name you've forgotten and how to remember names in the first place.

The Internets:

• In case you didn't see it, Cartoon Network Rick Roll'd the Macy's Thanksgiving Day Parade. Good stuff. In case you haven't been exposed to it, "Rick Rolling" is the internet meme of sending a link to the Rick Astley video "Never Gonna Give You Up" and telling the recipient it's something else, like a movie trailer.
• The FCC is considering a plan to provide free wireless internet for the US. I hope this works out.
• Woot, Chrome's about to get extensions. I love its stability and javascript speed. Making it extensible would keep me permanently off Firefox (except for work, where I need Firefox for some things, and even IE for a few things. Grrrr).

Biology:

• A diet of fat, sugar, and cholesterol may increase the risk of ALzheimer's. I had something witty to say about this, but I can't remember what it was.
• This quote from Creationist Ray Comfort is dumbfoundingly idiotic. It's even more moronic than his banana argument, in which he merely didn't understand that bananas had been selected by humans. This new one is just... wow.
  
• Geologists are finding evidence that the early Earth cooled long before we used to think it did. That makes some things make more sense; chemical evolution would have more time to ramp up from simple chemistry to life. But, darnit, it means we can't say "Life showed up on Earth just about at the moment that it was possible for it to do so" as an argument for why finding water on another planet would be super, super awesome.

Shared Items through morning of 11/29

I haven't had much to share lately. Here are a few:

• A Wal-Mart employee was trampled to death in New York. I've never understood why people would want to go out shopping on a day that's so crazy that it's generally known as Black Friday, just to save a few bucks. It just isn't worth it. This has me even more dumbfounded than usual.
• Scientists have found the mechanism for how resveratrol slows aging, and have demonstrated that it also works in mice. This could be huge. In the meantime, drink some wine and/or grape juice. Wow, we really loved run-on sentences when we wrote that thing (I can't remember whether I wrote it or edited it, but it was one of the first things I worked on at my current job).
• Foundation movies are coming! It'll be interesting to see if they pull them off. If I'm remembering the right book in the series, Foundation spans hundreds of years (the series certainly does). That's a tricky series to make.

Hopefully that's enough to let everyone know that I'm still alive.

Today's Shared Google Reader Items, 11/19

Hey, it's tomorrow already! That means it's time for more of my shared Google Reader items:

• Us hardcore Obama supporters are feeling kinda lost. As we vamp waiting for Bush to get the heck out of Obama's chair, we don't have much to do. But someone came up with something for us to do while we wait: the Yes We Cans! food drive. It's a cheesy pun and Obama-related, and it's for charity! Perfection!
• A European group used stem cells to reline a transplanted trachea, so the recipient's body would see it as self and not reject it. That's awesome. Of course it happened in Paris, though; US stem cell research took a hit in 2001. To be fair, these weren't embryonic stem cells, but the research as a whole is hampered here.
• Monty Python has an official channel on YouTube. Whoot.
• Tom Daschle will be the next Secretary of Health and Human Services. Somehow I missed it back in June when he basically said he was aiming for HHS, so I wasn't expecting this announcement. There's certainly nothing wrong with it, I just didn't know it was pretty much sewn up already.
• A US-Russian team has pieced together most of the genome of a woolly mammoth! Mammoths very likely went extinct at least in part due to the actions of humans. It'd be so awesomely awesome if we could bring them back.
• There's now a service to passive-aggressively teach your friends to answer their own damn questions. If it worked on cell phones, I imagine I'd be texting the results around quite a bit.

That's it for now. As always, comment on these or any other shared items below. Or, ya know, really anything. I'm not picky.

Today's Shared Google Reader Items, 11/18, part II

Holy crap, I cleared my Google Reader list! I shared another half dozen or so stories in doing so, though, so let's go ahead and get those ones posted, too:

• Wired has a piece on why Apple won't ever allow Flash on the iPhone, and their reasoning is sound. In short: allowing Flash would remove Apple's control of apps, since there are already a bazillion apps in Flash and more could easily follow, posted out there on the "real internet" for iPhone users to access without downloading them from the store.
• I've wanted a Roomba for a while, mostly because I want to own a robot, and it couldn't hurt. But now, apparently, I also need a cat:
• Burnt Orange Report dug up Obama's announcement from 1/16/2007 that he was going to form an exploratory committee and think about maybe running for President. That got me wondering, so I dug up the text of Bush's announcement on 3/7/1999. It's interesting to compare what Bush said back then to how things turned out. I'll have to remember to virtuablog or whatever we're calling it in 8 years, comparing Obama's speech to how things turned out. He's done a good job so far of sticking with the same message, but who knows what might happen over the next 8 years. I mean, who other than James Dobson.
• Indecision 2008 over at Comedy Central has discovered Time magazine's pressing question for this year: Who will be Time Magazine's Barack Obama of the Year?
• Finally, this photo that PZ Myers found at Scientific American is simply stunning. Number 15 is also pretty cool, but I share PZ's enthusiasm for #4.

Comment here or back at the first part of tonight's shared items.

Edited to add: This was my 42nd post this year. Arrrrrr!

Today's Shared Google Reader Items, 11/18

I'm back in Austin. Well, I technically have been for over 24 hours now, but now I'm back and nearly settled back in. I still have 103 105 107 unread items in my Google Reader (which gives me an idea what those of you who are on my shared list go through), but I'm catching up. I think. Anyhoo, here are the shared items from the last few days:

• I haven't had a chance to use Lifehacker's Complete Guide to Speeding Up Your PC's Startup yet, but I'm looking forward to doing so. Mmmm, fast boots.
• Barack released his first YouTube weekly address. Just about everything about that sentence makes me smile.
• According to a study linked on Slashdot, unhappy people watch more TV. I've been happier overlapping with the time that I've watched less TV, but I can't figure out which came first.
• I can't wait to try my hand at making gummy candies. If that turns out well, I might cut out TV entirely.
• I grabbed this guide to liberating yourself from old email addresses mostly for McCarron (Yahoo mail as a primary? Seriously?? Do you like spam??), but I think I'll also use it to get rid of my own extras.
• This story about antimatter creation made me smile a lot. In a science fiction novel I just finished, a major plot point involved production of anti-matter. I'm pretty sure this discovery puts us ahead of where the author saw us in 2020.
• This video of the development of sand dollars linked at Pharyngula is amazing.
• Lieberman is still a "Democrat." Dammit. I almost would have prefered us having no chance at a filibuster-proof Senate. Now Lieberman gets to continue being more important than he should be.
• Speaking of filibuster-proof Senate chances, Ted "Series of Tubes" Stevens has lost. Alaska didn't quite elect a convicted felon to the Senate. They just came very close. Of course, some of the outrage of that is silly. John Ashcroft lost a Senate race to a dead man, which I'm pretty sure makes you even more clearly inelligible for the Senate than being a convicted felon. I'm hoping at least some of the people voting for Stevens in Alaska were really voting for "whoever Caribou Barbie appoints to replace Stevens." Hmm, wait. I guess voting for the felon on purpose might be better.
• Microsoft is going to offer free anti-virus software starting late next year. This should be interesting. I agree with the idea in principle; having antivirus software on all PCs would cut down drastically on the spread of viruses. On the other hand, this pretty much spells the end of other antivirus program makers, and I can't imagine MS's free system will be very good without competition. My solution: people should start programming more viruses for Mac, to keep those other companies active.
• Firefox 3.1 is going to have tab tearing, a feature that I love on Google Chrome. I never noticed that it was missing in Firefox until I got in the habit of tearing off tabs in Chrome whenever I need to see things side-by-side, such as when I'm copying links from my shared items to my blog. If they can make 3.1 run for a whole afternoon without crashing, I might finally switch back.

That'll do it for today. Now off to work on some more of those unread items. As always, comment below so I know you're there!