April 07, 2016 at 11:10PM

Today I Learned: Today's TIL brought to you by a special talk by representatives from Industrial Light and Magic. 1) You know that really cool remote-control BB-8 robot that J. J. Abrams took onstage with himself a while back? That model was, sadly, built after the movie was finished. What you see on screen is mostly a puppeteered model, mixed in with a wheelable "trike" model, a stationary wobbleable model, and CGI. 2) One of the novel features of Star Wars: The Force Awakens' CGI was their shader palette. Usually shader palattes, which determine the color and spectral response of materials on a CGI model, are designed by an artist. ILM made theirs by actually measuring spectral responses of reference materials in the field. So if you ever caught yourself thinking "huh, the Millennium Falcon's hull has awfully realistic specular reflection", now you know why. 3) Speaking of the Millennium Falcon, the CGI model of the Millennium Falcon is technically a character. In fact, all (most?) of the CGI ships in The Force Awakens were designed using the same software and animation model as their CGI aliens and characters. Bonus fact: Tentales are apparently notoriously difficult to animate. In particular, the longer the tentacles, the more difficult they are to animate realistically (and the more likely they are to accidentally clip through each other).

April 07, 2016 at 01:59AM

Tody I Learned: 1) Today I have some super cool facts about B. subtilis, a commonly-studied sporulating bacteria. B. subtilis (or B. sub, as it is affectionately known) grows into colonies on surfaces, just like most studied bacteria. The colony displays an interesting growth pattern. It grows quickly at first, but slows down as it becomes too big for nutrients to diffuse easily into the middle of the colony. Then, at somewhere around 50 or 100 microns, the colony starts growing in regular pulses. Apparently what happens is that bacteria near the center of the colony become nutrient limited by gluatamate, which is the primary nitrogen source for B. sub (and therefore more or less absolutely required for growth). When the colony gets big enough that glutamate can't diffuse easily to the center past the mass of growing bacteria on the perimeter, the whole colony will periodically stop growing for a bit to let glutamate through. This lets the colony keep growing while keeping the cells in the interior alive. Now, how does a population of bacteria communicate their pulse across a colony that could be hundreds of microns across? The answer's a doozy -- they use propagating electrochemical signals that are functionally reminiscent of (and possibly the ancestral basis for) neuronal communication. Here's how it works. B. sub, like pretty much all cells, keeps a ton of (positively charged) potassium ions in its interior. This potassium, among other things, maintains an electrical potential of about -150 mV across the cell membrane. B. sub has a membrane channel that, when activated, lets out potassium ions, depolarizing the cell and causing the electrical potential to go away, and spewing tons of potassium into the surrounding environment. The channel is thought to be held closed by glutamate. When intracellular glutamate is low, the channels open. B. sub also has membrane channels that actively pump glutamate into the cell, BUT these channels rely on the membrane potential to function. So when a neighboring cell fires, the efflux of potassium ions depolarizes a B. sub's membrane, turning off its glutamate channels. The cell pretty quickly runs out of glutamate, which triggers its potassium channels, spewing out more potassium to trigger the next cell to fire. Using this active firing mechanism, B. sub can communicate across a hundreds-of-micron-diameter colony in a few minutes, which is *way* faster than it could communicate by diffusion. These spikes also look uncannily like neuronal firing, and honestly, the mechanism is rather similar. 2) When bacterial biofilms reach a certain size, they undergo complex patterns of (programmed?) cell death. This causes the biofilm to buckle*, forming ridge-like "veins", like you can see in this colony of Pseudomonas aeruginosa: http://ift.tt/1RQqWdV. Apparently scientists have recently observed fluid movement through these channels, suggesting that they *may* serve to move nutrients around the colony, which at this point has a lot of difficulty getting nutrients to its center. * This is because the whole surface of the colony is under a lot of physical strain -- it's full of bacteria that are actively growing and pushing on their neighbors. When a hole opens up, the whole thing expands into it, which causes things like buckling. 3) ...how to calculate Ct in qPCR (the cycle at which an amplified sample crosses a threshold, which is used to back-calculate the starting concentration of the sample). In particular, I learned that the threshold value is basically arbitrary, as long as it isn't in the noise range or the plateau. The rest is just linear interpolation.

April 05, 2016 at 11:49PM

Tody I Learned: 1) There is a scientific definition of a pebble, as a shape -- it's a 3D solid for which the curvature* of points around the surface has a normal (Gaussian) distribution. That is, if you sample random points on the outside of a pebble and measure the curvature of each point, and make a histogram of those curvatures, you get a normal distribution (bell curve). *Also, today I learned the definition of curvature, at least on a plane. The curvature of a point on a plane is one divided by the radius of a circle you could make that would snugly hug the plane at that point. The idea is that as the radius of the circle gets bigger (and the curvature gets smaller), the edge of the circle gets flatter and flatter. Credit for these two facts goes to Mengsha Gong. Thanks Mengsha! 2) Ants get their pheromonal boquets from the queen, especially in a young colony. The ants that attend to the queen pick up her scent, and as they share food and grooming, they spread it around the colony. This means that you can take pupae from another colony, and if you can get them to survive and be groomed in the nest for long enough, they pick up the queen's scent and are treated as members of the colony. Conversely, if you take those ants and reintroduce them to their mothers' colony, they will be rejected as foreign. This suggests a somewhat risky tactic for supplementing young queens' retinues if you have a breeding hive of the same species. Getting new workers in a young colony is critical for the colony's stability. I'm not sure if any special treatment would be required to keep the larvae safe, but it seems worth a try. 3) Polytetrafluoroethylene (PTFE, also known by the brand names Teflon and Goretex) is ridiculously safe stuff. Item 1: PTFE is used to coat stents, and is not obviously toxic or dangerous (http://ift.tt/1V8eBra and http://ift.tt/1SOGQYA for a couple of different perspectives -- it's not clear whether or not they're better than bare-metal stents, but they're ceratinly not overtly toxic). Item 2: Rats fed a diet of 25% PTFE for 90 days showed no signs of toxicity or damage (http://ift.tt/1V8eEmN). That's ridiculous. What about Teflon cookware? Well, PTFE itself is pertty damned stable at cooking temperatures, but there are chemicals in old teflon cookware involved in sticking the teflon to the actual pan that could volatilize and potentially cause some respiratory damage. Bonus: A dialectic, in the classical, Socratic sense (as opposed to the Hegelian sense) is a discussion in which two people with different opinions argue in order to figure out the truth. I really, really should have already known this, and now I do thanks to Eliza Dickinson Urban!

April 05, 2016 at 01:54AM

Today I Learned: 1) ...a trick for bounding the possible number of real roots of a polynomial with relatively few terms (but possibly very high-order). In short (I'll give a specific example in a second) you want to look for the number inflection points in the function, which you do by taking the second derivative... and finding roots. If taking the second derivative gives you something that's easy to determine the root number for, then you're done. If not, then you recursively apply the same trick to figure out the number of roots of *that* polynomial.... Example: How many real roots does the equation ax^100 + bx + c = 0have? In general, figuring out how many real roots a high-order polynomial has is difficult. Here, though, you can put a bound on it pretty quickly. The key is that for the equation to have lots of roots, it has to squiggle up and down a lot so it crosses the y-axis a bunch. Each squiggle potentially gives you a new root, but it also requires an additional inflection point in the function, which is a location where the second derivative is zero. So, how many inflection points does ax^100 + bx + c have? To figure that out, take the second derivative and find its roots -- that gives you something like ax^98 = 0 (the constant becomes a new constant, but who cares what that constant is?). Now *that* equation is easy to solve -- x = 0. That means that the function ax^100 + bx + c has exactly one inflection point, which means it has at most three roots (try drawing out a polynomial with only one inflection point and it will pretty quickly become apparent why). What about ax^100 + bx^37 + cx^2 + dx + e = 0? When you take the second derivative, you get ax^98 + bx^35 + c = 0 -- not so easy to figure out how many inflection points this function has. But! You can use the same procedure on the new function, taking the second derivative and ending up with ax^96 + bx^33 = 0, or x^33(ax^63 + b) = 0. 0 is a root, as are the two 63rd roots of ax^63 + b = 0, so the original function can't have more than three inflection points, therefore the polynomial ax^100 + bx^37 + cx^2 + dx + e = 0 can't have more than 5 roots. This only puts an upper limit on the number of roots -- depending on the constants involved, you might or might not actually get y-axis crossings for those extra inflection points. But it's a nice way of bounding high-order polynomials with very few terms. Even better, you can use this technique to bound polynomials with known form but unknown order. As an example exercise for the reader, can you put an upper bound on the number of real roots in the polynomial ax^N + bx^(N-1) + cx + d = 0, for unknown whole number N>3? Also, for those real math majors out there, is this something I should have learned back in college or high school as a matter of course? It feels like the kind of thing that I might have just missed somewhere.... 2) PCR plates for qPCR don't have to be clear. Probably. Which makes sense, really -- both sample excitation and scanning is done from the top, so who cares what the sides are made out of? 3) It looks like Tesla Motors is now profitable! Sort of. Over the last couple of years*, Tesla has operated on revenues in the single-digit billions of dollars and still managed to lose between a few and a bunch of hundreds of millions each year. But! As of a few days ago, Tesla as about 276,000 reservations (!!!) for their Tesla 3, most of which were placed within the last week. That's almost $10 billion in sales on its own, which represents a couple years' worth of operation *on its own* at their current rate of spending. Of course, they don't actually *have that money* yet -- it's just promises to buy -- but it's still a lot of value that Tesla can pretty well count on seeing. Thanks to Andy Halleran for alerting me to this. Also, apologies for misinterpreting some of their financial numbers in an earlier conversation today -- it's not quite so ridiculously rosy as I thought for Tesla. * Tesla's a young enough and fast-growing enough company that looking back farther than "a few years" doesn't make sense to me.

April 04, 2016 at 02:07AM

Tody I Learned: 1) Ant boquets (the blend of pheromonal hydrocarbons unique to an ant colony) are, at least in some cases, dependent on the food source of the ants. For instance, ants that live in twiggish soil have different hydrocarbon ratios depending on the species of tree whose twigs they live in. 2) Today I watched my first (partial) game of Warhammer 40k, and learned some of the rules (there are a lot). It's a game that requires way, WAY more time and money and effort than I want to put into anything new right now, but boy it's cool to watch a couple of experienced players with big armies duke it out. 3) Sweden has one of the highest tax rates in the world (swapping regularly with Denmark for first and second place) clocking in between 45% and 50% of GFP collected as taxes! Sweden also has a nice tax return system where you receive a tax form filled out by the government, which you can modify if anything's incorrect or you want to add anything. This makes a lot of sense to me -- the IRS in the US already has most of the information required to tell you how much you owe in taxes. Making you figure it out yourself just adds a step where you can get it wrong (or lie).

April 03, 2016 at 02:43AM

Tody I Learned: 1) So I knew that ants carry their dead to special graveyard recepticles, but today I learned a bit more about that behavior, called necrophoria. When an ant comes upon a dead nestmate, she will scan it briefly with her antennae (solid rule of thumb when it comes to ants -- the first thing an ants does to *anything* is to scan it with her antennae), pick it up, and carry it directly to a graveyard location, usually quite far from the nest. If you house ants in a container smaller than the ideal graveyard radius (as is common in captivity), then the ant will carry her fallen sister to the edge of the container, then wander around the perimeter for several (many?) minutes before dropping it at random. Furthermore, if a dead body is dropped this way, and another ant comes across it, *she* will then pick up the dead ant again and random-walk it around the perimeter some more. Here's the fun part. It turns out that necrophoria is triggered by one very specific class of molecules, specifically olefins produced by the decaying body. If you clean the corpse of olefins and re-introduce it to the nest, workers will eat it or treat it as any other refuse instead of disposing of it properly. Furthermore, if you paint or spray pretty much any other object with the olefins, you can get workers to treat that object as an ant corpse. You can even paint other nestmates as dead ants. If you do, nestmates will carry the painted sister (without resistance) to the graveyard and set her down. The painted sister will vigorously clean herself and wander right back to the nest, where she will usually be picked up and carried right back. 2) My showerhead has multiple action modes! 3) Watched some showcased ballroom dancing today. I learned a few little things (like what a cha-cha looks like), but the thing that really stood out to me was the rhythm of ballroom waltzes. Fair warning, I'm talking from a sample size of about N=3, so it may be too early to generalize, but it looked to me like ballroom waltzes are quite... loose with their rhythm. About half the time, I saw moderately strong "one-two-three" rhythm. The other half of the time was mixed rhythms that kind of sort of fit into the beat. In particular, one of the waltzes looked like it spent a fair amount of time in a one-two-threepausefour rhythm, where the third beat was split into a triplet with steps on the first and third sub-beat, presumably to make the balance or footwork (foot-fingering? footing? what's the word for this?) work out. Ironically, one of the waltzes with the strongest one-two-three rhythm wasn't actually performed to a waltz -- the piece they danced to was 4/4 or 2/4 rhythm, and they just danced three-against-four. Thanks to Mengsha Gong for suggesting I come out to see some dancing, and for a beautiful performance. Also, Sean Chen was awesome, and it was a pleasure to see him perform. Bonus: Bonus ant fact! Today I learned a bit more about how ant identification works. All ants produce a hydrocarbon mix that's unique to the species (or to a few related species), usually with some sub-blend that's unique to the colony and further specifying blends that sometimes identify individuals. The ants produce these hyrdocarbons in specialized internal organs (ants have a LOT of organs for producing chemicals). The hydrocarbons are then distributed internally, and go into cuticle production. Ants also are thought to spit out hydrocarbons and "wash" themselves with them -- in fact, the fastideous self-cleaning demonstrated by ants may be as much to distribute hydrocarbons as it is for hygenic purposes. Also, ants will clean nestmates who have been away from the nest for a long time with extra vigorousness. Second Bonus: Second bonus ant fact! Apparently if an ant finds an offending object in the nest and can't carry it away, it will instead bury it with some dirt. So maybe my pogonomyrmex keep burying their water cap because they find it an offending object?

April 02, 2016 at 02:05AM

Today I Learned: 1) ...a bit more about the evolution of trophallaxis, or sharing of food by regurgitation, in ants. The most evolutionarily-basal ant clades (ponerine and one I forget) don't regurgitate food -- they can only carry droplets back to the nest and offer them to other nestmates. They can't perform trophallaxis, in fact, because they lack a specialized trophallaxic gut (not the real name) that holds food without digesting it. Fun trophallaxis fact -- some species of ants will regurgitate and offer food during combat with ants from other colonies, particularly when they take submissive stances. This is thought to be a kind of surrender gesture, though it may just be accidental firing of the trophallaxis behavior reflex, which is triggered by a friendly ant tapping the offerer's antannae. 2) There is no solid evidence that ants communicate with each other through any kind of visual means, and not for lack of trying. Ants just don't communicate by visual signals. 3) Ok, so I still don't understand why temperature does what it does in the Boltzmann equation, but I've at least found a more concrete nugget of not-understanding to try to hack apart. In statistical mechanics, where Boltzmann's equation reigns supreme, it seems that temperature has a really funny definition. Specifically, the temperature T of a system is defined as 1/T = dS/dE, where S is the entropy of the system (the log of the number of microstates possible in that system) and E is the energy of the system. That is, temperature is a measure of the change in the number of states accessible by the system as the energy of the system is raised. Actually, it's 1 over that rate of change. I find this really frustrating, because this is where every text I can find on statistical mechanics starts, when it comes to temperature, but this gives me no intuition of how temperature is related to either the thermodynamic definition (average kinetic energy of the molecules) or the everyday experience of temeperature. Chris Lennox, I know you've worked with definition before -- why the hell is that what temperature is?!