March 09, 2018 at 08:28PM

Today I learned: 1) According to Harvard professor Johan Paulsson, if you fuse most fluorescent proteins to a protein that naturally multimerizes (that is, a protein that forms a complex of two or more copies of itself), the fluorescent protein attachment will cause the whole protein to clump dramatically. I'd read this before, but misread it slightly and thought that this applied to *any* fluorescent protein fusion. The thinking is that fluorescent proteins normally bind to each other, but only very weakly; however, when two or three or ten of them are all fused to one complex, it acts as a nucleation site for larger-scale aggregation. Citation: http://ift.tt/2HisT4D 2) You know the weird thing in quantum mechanics where particles kind of appear and disappear at random in a kind of quantom froth? Well, there's a way of viewing that phenomena as a consequence of simple formulations of quantum mechanics married to special relativity -- essentially, quantum systems get random spikes in energy, and special relativity says that you can interconvert between matter an energy, so there must be occasional production of particles from random QM fluctuations. According to Anthony Zee, the "marriage of QM with special relativity" is also one of the primary motivations for developing quantum field theory. I don't yet understand this claim, nor why it should be true. 3) Say you're a cell, and you want to make some specific amount of a protein. There are, roughly, two variables you can (dependently) vary to get the right amount of output protein -- transcription speed and translation speed*. For a fixed amount of output, you could have TONS of transcription and a little bit of translation on each of the many mRNAs you make, or extremely little transcription and TONS of translation on every mRNA you make, or anywhere in between. Today I learned that, across a wide variety of organisms, cells overwhelmingly choose to have low transcription and high translation over high transcription and low translation. Citation: http://ift.tt/2oIM3K9. This flies in the face of experimental data I've seen before that tells us that translation is much, much more energetically expensive for a cell than transcription and, in particular, that high-strength RBSs are *even more* energetically expensive than you'd expect. So... I don't know why cells would do this. The Alon paper has some arguments that don't make sense to me. One possibility, though, is that expressing low transcriptional rates makes gene expression *noisier*, which could be better for some processes. Still, I'd be surprised if the *vast majority* of genes are better expressed noisily than consistently. * Okay, you can also modify degradation speed and a couple other things, but I'm going to neglect those, because they turn out not to be too interesting in this story.

March 04, 2018 at 04:58AM

Today I learned: 1) Can you guess the most-played race in D&D? Today I learned that it's humans, by a pretty wide margin, according to Wizards of the Coast's polling. 2) Here's a potentially useful narrative trick -- the main character of a story doesn't have to be as interesting as the other characters, especially if it's a first-person story. In general, you can get a reader to go along with a main character by sheer dint of them being a main character. Learned this from a fellow student and part-time writer who had a problematic character that needed to exist for plot/connective reasons, but wasn't very interesting. So they flipped the story to first-person around that character. Instant fix. 3) Romans... ancient Romans were a special people. Incredible, but also so, so terrible. Case in point on the "Romans are the worst people ever" side of the ledger -- fatal charades. This was a Roman practice of performing plays using condemned criminals as actors. The only catch was that the plays involved the deaths of main characters, which were performed for real, live, on stage. Like... imagine Hamlet, but all the actors are on death row, and they actually die on stage. The Romans did that. I'm a bit curious how they convinced the prisoners to go along with it. Also, they must have had awful rehersals.

March 03, 2018 at 04:26AM

Today I learned: 1) Cave bacteria! There are bacteria that live exclusively on the inside surfaces of cave rock. They form visible sheets, and sometimes excrete really pretty minerals. I don't know much about them, but they can somehow live off of the rock face -- I'm not sure whether they're filter-feeding stuff that comes by, or if they're actually reacting the rock for energy. Whatever they're eating, it's not a particularly *accessible* source of food -- they are VERY SLOW GROWING, taking decades to fill small gaps in their mats. Some kind scientists at University of New Mexico compared the community compositions of cave bacteria and soil bacteria (http://ift.tt/2F8VxVa). Their conclusion was that the broad distribution of taxa was quite similar in the caves and in the soil above, but that there was quite a bit of divergence between *species* in the two climes. In other words, it looks like all of the usual inhabitants of soil got into the caves and colonized with roughly the same success, but then they evolved to look pretty different from their above-ground ancestors. Thanks to Patricia Prewitt for tipping me off to the existence of these critters! 2) RAND corporation has a new meta-study on the effects of gun policy. I've only read their summaries, but it looks pretty comprehensive. The big take-away is that there isn't enough data to make strong conclusions about most questions around the effets of gun control. There isn't a ton of data on gun violence, and what data there is isn't sufficient to reliably detect small effect sizes (which could still add to thousands of deaths per year). None of this is surprising, since the US government is BARRED BY LAW FROM FUNDING RESEARCH ON GUN CONTROL. It's usually not a good sign if someone feels they have to ban research on a topic, especially a poitically-charged one. Frankly, I don't take much of a hard stand on gun control one way or another, but IMHO the current research climate on gun control reeks of Lysenkoism. ANYWAY, the second-biggest take-away from the RAND meta-study is that there are *some* policies that appear to be effective at reducing violent crime, accidental deaths, and suicides (especially suicides). The first figure at this link is a good summary (http://ift.tt/2HYu9uF). For those who prefer a written digest, here it is: background checks and child access prevention laws help reduce suicides pretty dramatically; child-access prevention laws also almost certainly reduce accidental gun deaths; background checks and mental health screening probably decrease violent crime, and (perhaps surprisingly) stand-your-ground laws probably *increase* violent crime; concealed-carry laws might increase both accidental and homicidal deaths from guns, but the evidence is weak; most surprisingly to me, there is not evidence that bans on assault weapons and high-capacity magazines have much effect at all on anything. You can read the rest of the report here, if you're super-interested in gun control research and you have a lot of time on your hands: http://ift.tt/2t87FE9 3) Cells in a developing embryo can detect their position within the embryo within about 1% error, we think only using the concentrations of four transcription factors that are distributed in specific ways around the embryo. We don't know exactly how they do it, and that's quite close to the inforamtion-theretical limit of precision for the amount of information available in those transcription factor signals (unless, of course, there are channels they're exploiting that we don't know about). Thanks to Andy Halleran for this one!

February 08, 2018 at 03:38AM

Today I Learned: 1) A couple of data facts for you, brought you to in part by Andy Halleran. Current total data of the human race is estimated at around 10^24 bytes. That's a trillion terabytes, or a yottabyte. I know some pretty big metric prefixes, but I had to look that one up. The estimated total data size of all (unique) genomes on the planet is 10^36 bytes. That's... a truly ludicrus amount of data. But we're catching up. For a (three-year-old) overview of some of our biggest data generators, see this (open-access!) review article: http://ift.tt/1HcOjIi. A few highlights: a) The Australian Square Kilometre Array Pathfinder project acquires 7.5 terabytes *every second*. b) Twitter's data storage needs are estimated at around 500 terabytes per year. Not massive by big data standards, but it does put into perspective why Twitter doesn't, in general, make their Tweets algorithmically searchable*, and makes it all the more impressive that they can serve up selected data as quickly as they do. c) We're predicting to store somewhere on the order of 2 to 40 *exabytes* (~8.5 billion terabytes) of human genome sequences alone. * You can collect random tweets from a couple of Twitter APIs, known as the twitter firehoses, and you're welcome to make your own mini-database. 2) A couple of rocket facts for you today, courtesy of Andrey Shur. Liquid-fuel rocket engines use (effectively) a turbojet to pressurize their fuel just before it's burned. To rocket good, you have to make really, really high-pressure air. One way to pressurize air really efficiently is to burn it; that's why explosions are useful in rockets. Another way to pressurize air is to use a pump; that's why turbojets are useful in rockets. The "turbojet" in a rocket is actually called a "turbopump", and its job is to pressurize incoming liquid fuel (as it's aerosolized coming out of the fuel tanks, I gather) so it can be exploded really efficiently. Now, pumping fuel requires a lot of energy. You *can* run turbopumps electrically, if you want, but a much more common strategy is to *pre*burn a bit of your fuel and use *that* explosion to spin up the turbopump. It is not intuitive to me that this should be efficient, but apparently it is. I guess pressurizing fuel before burning it must give you a disproportionate boost in thrust post-burn. There are (at least) two main kinds of turbopumps. An "axial flow" turbopump looks pretty much like a turbojet, which is the big spinning engine on the wing of a commercial plane. Basically, it's a bunch of high-density propellors that force air through a narrowing chamber, compressing them. The "centrifugal" turbopump is more common in rockets, and it's the one that makes me giggle -- it works by spinning really fast and *flinging fluid to the outside* where it's collected at high speed. So now you know -- these things (https://www.youtube.com/watch?v=PfHu-UJaK0Q) are, when you get right down to it, centrifugal squirrel pumps. Not quite a fact, but here's a gem from the Wikipedia page on rocket engines, on the topic of the dangers of liquid propellants: "With liquid propellants (but not gaseous), failure to ignite within milliseconds usually causes too much liquid propellant to be inside the chamber, and if/when ignition occurs the amount of hot gas created can exceed the maximum design pressure of the chamber, causing a catastrophic failure of the pressure vessel. This is sometimes called a hard start or a rapid unscheduled disassembly (RUD)." 3) You know how you're not supposed to daisy-chain together power strips? If you don't already know this, you're not supposed to plug power strips into other power strips. Ever wonder why? Like, why would that be dangerous? I've been told these terrible stories of daisy-chained power strips sparking and causing fires, but nobody ever gave me a reason that they would do that. Well, today I got fed up and googled the answer. It turns out that daisy-chained power strips are dangerous mostly because they make it much, much easier to accidentally draw too much total power at once. Power strips (and, for that matter, house circuits) are only rated for so much current draw, and if you exceed it, you risk overheating or shorting the strip. Practically speaking, most power strips have fuses and will commit suicide before they do any real damage, but it's still a hazard. The upshot -- you should be safe daisy-chaining power strips *if* you are quite sure you're not going to exceed the max draw for your power strips (say, if you fill every plug with cell phone chargers).

January 28, 2018 at 11:16PM

Two days ago I learned: (I wrote up most of this on Friday and forgot to finish it out; instead of letting it die, I'm cheating and pushing it out today.) 1) ...a bit about the Impossible Burger, widely hailed as the most meat-like non-meat burger in the marketplace. My impression is that the Impossible Burger is a very, very heavily engineered food. A lot of effort went into making the texture, taste, and sound (yes, sound) of the Impossible Burger similar to that of a beef patty. However, if I were to collapse the Impossible Burger's design into one trick, that trick would be leghemoglobin. Leghemoglobin is a protein normally produced in the root nodules of soy plants, where it has something to do with oxygen buffering. The protein is structurally similar to animal hemoglobin and myoglobin, and acts similarly -- it complexes with a heme molecule, which allows it to efficiently bind dissolved oxygen. Heme, it turns out, is why bloody meats are red, and gives meat a lot of its rich, metallic flavor. Impossible Foods (the makers of the Impossible Burger) decided to make a burger with plant-based heme using leghemoglobin as a heme source. Unfortunately, soybeans don't make a lot of leghemoglobin, and it's a *pain* to extract, so Impossible Foods moved the gene for leghemoglobin (and, presumably, the enzymes required to make heme) into yeast, which is *very* easy to grow and relatively easy to extract proteins out of. That lets Impossible Foods make a rich, hemefull burger patty that's 0% animal. There's only one small catch, legally speaking -- leghemoglobin isn't FDA approved. It seems it doesn't *need* to be -- it's being sold anyway -- but just to be on the up-and-up, Impossible Foods sought FDA GRAS approval of leghemoglobin. They have some data feeding mass amounts of leghemoglobin to rats (no effects) and, perhaps more importantly, argued that leghemoglobin is an ancestral protein that we have no particular reason to think is toxic that's structurally very similar to tons of proteins we already eat all the time. The FDA rejected the approval request, I think on the basis that a) leghemoglobin might just be an allergen and b) there could be small amounts of other yeast proteins that make it through purification along with leghemoglobin that aren't necessarily human-safe (they're not using bakers' yeast, and I don't think the kind of yeast they are using is typically eaten in any appreciable quantity). 2) On a related note, Impossible Foods claims that 90% of the rennet used to make cheese is now yeast-produced. Whatdyaknow. This explains the multiple times I've run into "vegan cheese" that used rennet. I guess they were (probably) vegan after all. Those cheeses, when I've tried them, were significantly better than non-rennet vegan cheese, so I'm kind of excited to get back into the cheese substitute game. 3) If you want to burn little tea-light candles in water, don't take them out of their metal shells -- the wick of one of those candles is attached to a little metal pad, and when it heats sufficiently it will drill through the bottom of the candle and fall into the water, taking the rest of the wick with it. Bonus candle fact -- it's pretty easy to modify candles with tin foil by heating the tin foil over a lit flame and quickly pushing it into the candle somewhere.

January 22, 2018 at 03:29AM

Today I learned: 1) I kind of knew this from experience, but Andrey Shur confirmed for me today that it's rare to find a 2 amp USB phone charger, largely because USB isn't quite rated to carry 2 amps. This is curious, as Raspberry Pis recommend you use a 2 amp charger. As I am learning, Raspberry Pis were made with some really odd design decisions. 2) ...a bit about Hilbert curves. Or, technically, *the* Hilbert curve, which is the limit of pseudo-Hilbert curves of N iterations as N approaches infinity. If you google image search for "Hilbert curve", you'll find a bunch of example pictures, which is going to be much easier than reading me awkwardly try to explain the shape... but in short, a pseudo-Hilbert curve of N iterations is a fractal line that neatly visits every grid point in a square (with side length log2(N)). As you take larger and larger iterations of the pseudo-Hilbert curve, it becomes a denser and denser nest of curves. The cool thing about the Hilbert curve is that, in the infinite limit, it is "space-filling", which means that it eventually visits every single point in the square it's defined over. Essentially, that makes the Hilbert curve a mapping from a line to a plane... which sounds obviously wrong, but is mathematically provable. It turns out that a (the?) key property of the Hilbert curve for analyzing its space-filling-ness is that it's "stable", in the sense that if you follow a point on the pseudo-Hilbert curves as you add more iterations to it, that point will converge to a fixed position, and it's possible to calculate what that position is. That's important, because without this property, the concept of "the curve that this curve approaches as you iterate to infinity" doesn't make sense -- if the mapping of every point doesn't converge, then the curve doesn't really "converge" either. If you'd like to learn more about Hilbert curves, I highly recommend this video, "Hilbert Curve: Is infinite math useful?": https://www.youtube.com/watch?v=3s7h2MHQtxc 3) ...a little bit about screenplay script formatting. Industry screenplays are... weird, coming from someone who has never written one before. For one thing, everything's centered. Scenes open with a description of the scene, usually one sentence, using the whole page width and ALL IN CAPS. Those scene-setup sentences also usually start with "INT." or "EXT." for interior and exterior scenes, respectively. Most of a screenplay is dialogue, of course, and all dialog is written with insanely large margins, so it reads like a little column of text smack in the middle of the page. The name of the speaking character gets its own line. Description of *how* a line is delivered come in the form of parentheticals, which also get their own line, are contained within parentheses, and have about an extra half inch on each margin relative to the actual dialogue. (I didn't say I learned anything about writing a *good* screenplay, just that I learned how to *format* one.)

January 20, 2018 at 09:05PM

Today I learned: 1) https://www.youtube.com/watch?v=ciStnd9Y2ak If you care about the environemnt, and you haven't written to your congressperson about nuclear power, I highly recommend the above TED talk. Basically, we're killing about 7 million people a year around the globe by using fossil fuels instead of nuclear. For comparison, total deaths from all the nuclear disasters in the world are in the four-digit range, and something like 90% of that was deaths during unnecessary evacuations that had nothing to do with radiation exposure (i.e., traumatically moving people from nursing homes and emergency care facilities). Oh, and nuclear is also cheaper than renewables *and* generates less emissions and other waste. Honestly, I'm having a hard time thinking of a bigger failure of humanity than that of our not using nuclear power as our primary energy source. Maybe world war II? Any other suggestions? 2) ...how to test the power supply on a Raspberry Pi! There are a couple of test points you can stick a multimeter to that will tell you what kind of voltage the Pi actually gets. Sadly, my Pi is getting plenty of power and still won't boot. =( 3) So, according to George Church, the off-target mutation rate of Cas9 in humans is now below background mutation rate, using off-the-shelf tools and good, proper computational design. Gonna be honest, I thought it was a lot higher than that.