Yob, Spatial Transcriptomics, and Boston Dynamics

Today I Learned:

1) New in Science this week: English scientists have isolated the gene responsible for maleness in an important malaria species, which they dub Yob. Mosquitos (and, apparently, many other insects) use an XY sex determining system much like humans, but we don't know what gene actually causes maleness in most of those species. In the mosquito Anopheles gambiae (which, if I recall correctly, is one of the major vectors of malaria), maleness is determined by Yob, which turns on when the male egg is fertilized and never turns off. Yob changes the way another gene, called doublesex, is spliced as an mRNA. Through a mechanism that isn't yet know, this causes the mosquito to turn male.

The authors of the paper tried silencing Yob in male mosquitos, and also tried adding Yob transcripts to female eggs. Silencing Yob killed males during development. Adding Yob to female eggs caused them to develop as males. This could be really useful in a gene drive* as a way to force maleness through a population, which could be a pretty efficient way to wipe out a population.

*A gene drive is a genetic construct introduced into a population that forcibly inserts itself into the sister chromosome of whatever chromosome it's expressed on, ensuring that every descendent of an organism with the gene drive gets a copy of the gene drive, and that *its* children also have the gene drive, and so on. This can be used to "drive" a desired gene into a population, even if it doesn't particularly raise fitness. They have also been proposed as a mechanism for wiping out the select mosquito species that carry malaria, either by forcing maleness, forcing succeptibility to some normally-harmless insecticide, or other means.

2) Also from Science: There's a new kind of RNA-Seq out of the Karolinska Institute in Sweden that can produce a full transcriptome (more or less) with pretty good *spatial* resolution (order of magnitude tens of micrometers). Here's the gist of the protocol -- you slice up the sample you want to sequence using the usual histological methods (usually a really sharp, cold knife). You lay each layer out on a grid of sequencing primers, barcoded by location. You somehow reverse-transcribe all the RNAs and amplify in-situ, then extract all the amplified DNA and sequence it. Then you can reconstruct where each read came from based on its positioning barcode.

3) Google (actually, Alphabet, now) has indicated that they want to sell Boston Dynamics! For those not in the know, Boston Dynamics is an extremely well-known robotics lab, in the field of robotics, which is probably most famous for building BigDog (check it out on youtube if you haven't already. If you have, check it out anyway and note the videos of its more advanced descendants.) Why?

Apparently Alphabet didn't think Boston Dynamics aligned particularly well with the way they run things. In particular, Boston Dynamics' manager, Andy Rubin, apparently has a management style that doesn't mesh well with the rest of Alphabet. I guess Alphabet figures it's better to sell off Boston Dynamics, make some profit, and let another company do something cool with them than to fire the management and try to rebuild it.

June 30, 2016 at 01:48AM

Today I Learned: 1) If you happen to be drying down proteins under vacuum and at warm temperatures (as in, room temperature), beware of salts! As you dry down the protein, you go through a super-high-salt-density phase that can seriously damage proteins if they're warm enough to react. This fact brought to you be Erik Jue. 2) Watermelon gazpacho soup is really tasty. I had a cold version with watermelon (obviously), lots of cilantro, and... tomato, I think. Definitely something a bit sour/acidic, and something that gave it a red color. I suspect the right vinegar, applied carefully, could give a similar effect. Highly recommend, if you can find a good recipe. 3) We have a baby bird from the middle Cretaceous, trapped in an amber fossil. Well, not a whole baby bird, but a good part of a wing, complete with bones and feathers. It's a beautiful specimen, and really highlights just how birdlike Cretaceous dinosaurs could be. More details here: http://ift.tt/29ctyqH This fact brought to you by Mengsha Gong. Thanks Mengsha!

June 29, 2016 at 02:52AM

Today I Learned: 1) ...how to mop. There was a bit of a flood in the lab, which needed cleaning up.... I learned that it really helps to have one of those squeezy thingies or rolly thingys for squeegying the water out of mops, but that you can do it by hand if you really have to. It's fascinating watching the mop fibers as you squeeze them out -- you squeeze them, and they start leaking water everywhere, but as soon as you release it you can see it instantly dry out as it sucks water back into the interior. Also, our lab floor is disgustingly dirty. That or our old mops are disgustingly dirty.... 2) The Occupational Safety and Health Administration is, in fact, responsible for many lab safety standards. Not all of them, though. There are a lot of agencies responsible for various bits of laboratory safety in the US. Educational institutions mostly follow OSHA guidelines, but it's voluntary and decided on a state-by-state basis. 3) So, Hegel is a pretty weird philospher as far as I'm concerned. Most of his theories involve things like historical dialectics and movements of change and other things that seem too ontologically unreal to me to take particularly seriously. In particular, Hegel talks a lot about the master-slave relationship. Today I learned that the master-slave relationship, at least in large part, does not refer to a master person and a slave person. It refers, in metaphor (at least according to some interpretations!), to two parts within one person, which embody a kind of complicated self-relationship that Hegel found important... honestly, it's pretty complex, and I find it hard to follow. Still, at least I'm now ever-so-slightly less ignorant of Hegel's philosophy now.

June 28, 2016 at 02:10AM

Today I Learned: 1) Anybody remember VDJ recombination from a TIL about a month ago? Today I learned some evidence, from a lab class, strongly suggesting that VDJ recombinase does, in fact, cut pretty strongly at VDJ recognition sites with one base pair mismatches from the canonical recognition sequence (jury's still out on whether it cuts less at all). That implies that the VDJ recombination system, which is critical for generating new antibody variants in young immune cells, should also be cutting in a few hundred of the wrong places in the genome. Which really ought to be bad. 2) The word "hermaphrodite" comes from the Greek story of Hermaphroditus, a minor god of great beauty. A naiad by the name of Salmacis fell in love with Hermaphroditus (and possibly raped him? I'm not clear on this point yet). She prayed to the gods to be "united with him forever", so the gods literally merged their two bodies into one for all of eternity. I'm glad to see that particular pun works in both ancient Greek and modern English. Also of note: the name Hermaphroditus comes from the names of the god's parents, Hermes and Aphrodite. Yeah. Thanks to Mengsha Gong for this delightful little tidbit. Not sure how she found it.... 3) ...that a teacher I've been working with for the last term studied alongside Robin Hanson as a physics student. She moved on to engineer devices for laser labs; he went on to study economics and speculate about the economics of futurist scenarios. Who knew! (well, she did, obviously.)

June 27, 2016 at 03:13AM

Today I Learned: 1) Here's an interesting new form of accidental racism -- racist machine learning algorithms are more common than you'd think. Example: about a year ago, Google's automatic image-tagging algorithms would identify pictures of black people as gorillas. There have been at least two instances where camera software didn't work on non-whites (Nikon's software thought Asians were blinking, and HP's had trouble with dark skin). Why? Almost certainly it's an issue of not having enough non-whites in the training data, but it's hard to know with complete certainty. But wait! It gets worse! It turns out that a lot of police departments in big cities use predictive algorithms for forecasting crime hotspots. Since those algorithms use past data, and minority neighborhoods are almost universally patrolled and criminalized more heavily than white neighborhoods, that software is much more likely to assign *yet more* policing to places already discriminated against. Similar problems exist for software used in predicting individual risk of criminal activity. Then there's an example from Amazon, which isn't actually a racist machine learning algorithm so much as racist policy, where Amazon denied same-day deliveries to majority-black neighborhoods for some time. And, of course, there are sexist AIs too. For example, here's a (non-paywalled) article on google ad tracking in which the authors accidentally discovered that women are much less likely (about 1/6 as likely) to receive adds for high-paying (>$200k/year) jobs than men. It's not clear whether this is due to some subtle effect of google's ad-matching software or some explicit policy on behalf of any of the many agents at play in the online ad marketplace. This TIL is essentially a distilled version of this article from the NY Times: http://ift.tt/29eRoQb. The only real problem I have with the article is the author's relative dismissal of existential risks of AI. I realize that racist algorithms are a problem *right now* and should be addressed, but comparing racism to the possible extinction of the human race is a bit appauling. 2) Stomachs are much higher in the body than I thought. They're actually held *within* the ribcage, held right up against the lungs. This fact brought to you by Kevin Cherry. 3) ...some of the differences between extruded and cast acrylic plastic. Cast acrylic is made by mixing the right chemicals inside a mold, which harden into a hard plastic. Extruded acrylic is made with a similar mixing, but instead of being made inside a mold, the plastic is forced through a pair of rollers or another thin channel, which makes it come out as a sheet. Cast acrylic is generally considered "better", largely because a) it is harder to deform and b) because it has the same physical properties in every direction. Extruded plastic is a bit more warpy, and has different properties on the axis on which it was rolled than in the other direction. Cast acrylic also comes out with smoother edges when laser-cut, and the two plastics turn different colors when engraved.

June 26, 2016 at 02:28AM

Today I Learned: 1) Took apart an old Xbox 360 controller today. It's not difficult, except that it requires a special type of star-shaped screwdriver with a hole in the middle, and it has a secret screw under a barcode in the battery enclosure. The inside is pretty comparable to an Xbox One controller, the biggest difference being that the Xbox One controller comes apart in two stages -- the case comes off to reveal circuitry, thumbsticks, and vibrators, with the buttons and triggers requiring more disassembly to get at. The one-stage disassembly of the Xbox 360 controller is both nice, in that disassembly is easier, and annoying, in that you have to put everything back together at once to reassemble it, which requires a bit more coordination. The two-stage disassembly of the Xbox One is *particularly* annoying because it uses a smaller screw on the interior components, which I don't have a screwcriver for. I suspect the extra hard points on the Xbox One controller helps give it its slightly more solid, smooth feel. Another interesting tidbit -- the right vibrator on the 360 controller has considerably more mass than the left one. Any ideas why? 2) Complex numbers (any number of the form a + bi, where i is the square root of -1 and b is not 0) were discovered in their algebraic form by an Italian mathematician in the mid 1500s named Rafael Bombelli, who ran aground on them while considering the intersections of cubic curves with straight lines (which sometimes has a solution which can really only be found analytically using complex numbers). Complex numbers were then known, but mistrusted, neglected, and/or misused for hundreds of years. Leibniz and Newton both apparently dismissed complex numbers as useless nonsense and probably not real (in the metaphysical sense). What changed? I'm not certain, but according to Tristan Needham, it was the discovery (By Gauss and several other mathematicians independently) that complex numbers have a sensible geometric interpretation on the complex plane. Basically all of the important parts of complex analysis were developed in the 50 years following that discovery, after 250 years of essentially no use of complex numbers since their initial discovery. 3) How to get fingerprinted. You make an appointment with any fingerprint-providing service (there are apparently offices that do nothing but manage official kinds of paperwork, which is where I got mine done). You need to bring some forms, which as far as I could tell only exist so that the information on them can be copied to fingerprinting request software (and for official records, I suppose). There's a little box with a glass panel on the top, illuminated in green. You roll each of your fingerpads across the glass panel, which it scans apparently quite nicely, you pay some money, and the scanner software sends a request to... someone. I don't know who.

June 25, 2016 at 02:53AM

Today I Learned: 1) Somebody has been reading my TIL blog (positivederivative.blogspot.com) from France. I don't know why, but I suspect web crawlers. 2) If you have a vacuum pump in a critical operation on an expensive piece of equipment, it's a good idea to buffer the pump with a large vacuum reservoir. That way, if the pump goes out for a short time, or loses pressure for some reason, or has to draw really strongly for a short time, the downstream vacuum-sink will draw from the reservoire instead of breaking the pump or just plain breaking. 3) There is such a thing as a reusable zip-tie! Sort of. It's a C-shaped piece of fairly tough plastic that's almost closed off, with opposing teeth that click together when you shove the C-arms past each other. If you slide the arms sideways, the teeth disengage and the thing pops off, ready to use again!

June 24, 2016 at 02:39AM

Today I Learned: 1) The vampire is a curious creature, in that it is neither vampire nor squid. It's an ancient relative of both squid and octopuses that swims around languidly in a band of heavily oxygen-depleted ocean waters where there aren't a lot of predators. There also isn't a lot to *eat* there, so the vampire squid feeds off of marine snow (i.e., bits of dead things that float down from more shallow waters). Since its food doesn't really move, unlike that of octopodes and squid, the vampire squid doesn't chase down its food. Instead, it has a long, thin, sticky tendrel that it lets float around. When the tendrel is nice and saturated with snow, it scrapes off food into a pouch formed by the skin between its tentacles. It also looks like an evil demon fish, which is just not fair for such a chill creature. These facts on the vampire squid brought to you by Mengsha Gong, via a post on Science Friday. 2) Lead is way softer than I thought. I mean yes, I know lead is supposed to be soft, but I didn't expect it to be *that* soft. In this case, I was handling a chip off of a lead pipe, which was pretty flaky. The texture (and impurities) may have largely contributed to its pliability, as it was much tougher after being melted over flame and re-cooled. 3) The word "butterfly" has a couple of possible etymologies. It may come from an amalgam of Old English for "beater" and "fly", as in, an insect that beats around to fly. It may have once referred only to yellow, buttery-colored butterflies, or possibly been related to a belief that butterflies ate milk and butter. Or, as is speculated in the good old OED, "Wedgwood points out a Dutch synonym boterschijte in Kilian, which suggests that the insect was so called from the appearance of its excrement." Also, the word "butterfly" is *old* -- the OED has (Anglo-Saxon) references as far back as ~1000 AD. It looks like "butterfly" used to be used more liberally and more poetically than we use it now, with the OED listing definitions including "a vain, gaudily attired person", "applied to persons whose periods of work or occupation of a place are transitory or seasonal", and, perhaps my favorite, the phrase "to break a butterfly on a wheel", meaning "to use unnecessary force in destroying something fragile".

June 23, 2016 at 02:57AM

Today I Learned: 1) http://ift.tt/1Ssn3OR 2) Mid-evening, when the sun is still up but it has cooled down a bit, seems to be a good time for finding bees, butterflies, flies, and other flying insects (at least on a Summer day in California). 3) Dry ice manufacture is a fascinating process. You start with liquid CO2 under very high pressure. You release the liquid CO2 into a relatively closed (but not airtight) space. The drop in pressure causes the liquid CO2 to instantly boil off. The boiling process absorbs a ton of energy, so the whole assembly flash-cools down to below -80 C, which is about the freezing point of CO2. This causes the CO2, which was just sublimed off of a liquid, to solidify. About 50% of the liquid CO2 will go into solid form, with the rest escaping into the air. You can, technically (BUT PROBABLY YOU DON'T WANT TO DO THIS UNLESS YOU REALLY KNOW WHAT YOU'RE DOING) do this yourself with a CO2 fire extinguisher. Basically you just release the CO2 into a pillowcase, and you get a bunch of CO2 snow. This is pretty dangerous, as you're dealing with very high pressures and very cold temperatures in close proximity to your body. I don't recommend it. But I *do* recommend you check out youtube videos of it and marvel at how well it works.

June 22, 2016 at 02:17AM

Today I Learned: 1) You can totally use a PCR clean-up kit on salty plasmids. 2) Beavers have a scent gland called a castor sac, which is used to mark territory. Very rarely, castor sac excretions are used as "natural flavoring" in place of vanilla. 3) ...so there are supposedly these things called "stationary promoters", which are DNA motifs that turn on gene expression when bacteria are in stationary phase, which is when they're really densely grown and heavily nutrient-limited. Today I learned that those promoters may not be so "stationary phase" after all... I got to see some data that sure looks like the standard stationary phase promoters (consensus and variant binding sites for sigma-38, for those interested) actually turn on in late log phase, when a culture is just about to go into stationary phase. Once the cells are stationary, they no longer seem to continue producing protein... though whether that's because the promoter is off or because they run out of resources or they're degrading stuff really fast and hit steady state, I still don't know.

June 21, 2016 at 04:02AM

Today I Learned: 1) Our university gets a roughly 50% discount on DNA oligos from IDT. That adds up really damned quick! 2) There are squid that take care of their eggs! A female of the deep-sea squid Gonatus onyx will lay a gigantic sack of eggs, which she will carry around in front of her for quite a while (not sure how long) until they hatch, protecting and aerating them. This comes at quite a cost to the mother -- it's thought that she gnaws off her feeding tentacles when she lays the eggs so that they won't get in the way, and she definitely can't hunt or eat during the brooding. 3) On a related note, today I also learned that the longest-lived known eggs are those of the deep-sea octopus Graneledone boreopacifica. Eggs of this species can take as long as 53 months, and possibly longer, to develop and hatch. How do we know this? As described inn one of the more peculiar articles I've read in a while (free: http://ift.tt/28LlIpw, it's an oddly... personal article), a mother G. boreopacifica was observed on five separate occasions brooding the same nest over a period of 4 years, 4 months. She very likely did not eat during that time. For reference, that's more than twice as long as the entire lifespan of most shallow-water octopus species. How could gestation possibly take so long? That's almost certainly due to the frigid temperatures at the depths in which G. boreopacifica thrives -- the temperature of the nest site varied between 2 and 4 degrees celcius. That cold temperature leads to very slow metabolisms, which explains 1) why the baby octopodes take so long to grow and 2) how the mother can survive such a long wait. For a list of some other species with extremely long gestation times, check out the linked article above, third paragraph of the Discussion. The stand-outs are frilled sharks, which carry live embryos for 42 months, and alpine salamanders, which gestate for up to four years before giving birth! This fact, and the previous one, brought to you by Mengsha Gong. Thanks Mengsha!

June 20, 2016 at 02:15AM

Today I Learned: 1) ...some delightful tidbits about parakeets, via Ching-Ching Shiue. I'm actually not sure which species we were talking about, so... keep that in mind. Your milage may vary for other parakeets. Firstly, those birds grow up quickly! It's a couple of weeks from egg-laying to hatching, and by a month of growth they look more or less like grown parakeets, though smaller. Apparently it's really important to let mother parakeets keep their eggs, or to give them a replacement. Taking them away is quite stressful. What does a stressed parakeet look like? Well, one way to tell the comfort of a bird is to check for fluffing. A bird with fluffed feathers is more likely to be happy (or cold -- fluffed feathers are a great way to stay insulated), while a smooth-feathered bird is more likely to be on edge (or hot). Making noise may also be a sign of comfort in a bird -- scared parakeets aren't likely to make a lot of sound, which makes some sense. 2) There are a *lot* of mantis species. About 2400, to be (sort of) precise. I haven't been able to find solid figures on how many of those live in the US, but there seem to be somewhere around a dozen common species. 3) So, I've been wondering for a while what happened to Moore's Law when it comes to processing speed. I remember seeing 4.0 GHz one-core processors (and 2.5-ish GHz two-core processors) on the market about 7 years ago. By Moore's law, that means we should be seeing processors operating at something like 50 GHz by now. We don't. Most commercial processors are now in the 2.5-3.5 GHz range. What gives? Well, it turns out that Moore's law for processors has been doing just fine, at least in the supercomputer world. Both highest-end processor speed and cost-per-FLOP have been improving roughly exponentially at least until a couple years ago, which is where the data on Wiki stops. Part of this is increasing paralleliztion -- more cores per processor die -- but that can't be most of the improvement. I'm actually still not certain how processors are getting faster without their clock speeds getting faster, but I think it has to do with improved efficiency and bigger caches. Fun fact: In 1961, a gigaFLOP of processing power would have cost roughly $8.3 trillion. Actually, I'm sure it would have actually cost much more than that to do -- by the time you built half of the computers required to get to a gigaflop, I suspect you'd have unbalanced the world market for things like heavy metals enough to make it even more expensive. As of January 2015, that cost is more like $0.08 (someone built an 11.5 teraFLOP supercomputer for $902.57).

June 19, 2016 at 04:13AM

Today I Learned: 1) The octopus genome is a somewhat unusual thing. Specifically, the California two-spot octopus (Octopus bimaculoides) has just over 33,000 protein coding genes, which is a good 50% more genes than in humans. It has a large number of rearrangements relative to other molluscs, possibly because of an abundance of transposons, which are (probably parasitic) DNA sequences that can splice themselves in and out of the genome. In particular, O. bimaculoides (and probably other cephalapods) has a large expanded set of cadherins and zinc-finger transcription factors. More details behind a paywall here: http://ift.tt/1ZZL2aO 2) A multi-level marketing (MLM) company is one that pays employees based on both the sales they are responsible for and for the sales of anyone they recruit. This is generally considered a pyramid scheme, and is illegal a lot of the time, based on the fact that virtually everyone involved ends up not coming out of them well, except for the few people who start the process. Nevertheless, MLMs persist in America. 3) A praying mantis will definitely eat a spider, if it's small enough. I think it will attack a ladybug, but I don't think it can eat it very well.

June 18, 2016 at 04:33AM

Today I Learned: 1) Termite mounds can be extremely old. One abandoned mound in the Democratic Republic of the Congo was radio-carbon-dated at about 2200 years old. Several other, smaller mounds nearby measured in the hundreds of years old. This is way, way longer than a single colony lives -- termite queens only live a few decades. It's suspected that mounds are built up over successive generations, through multiple rounds of abandonment and recolonization. This fact brought to you by Kevin Cherry. 2) The Lac repressor protein in E. coli is notable for only being expressed at a level of about 10 copies per cell. Today I found a chart (this one, to be precise: http://ift.tt/1Yyqyr7) of per-cell copy numbers and numbers of binding sites for various DNA-binding proteins known as of 1998. If that chart is to be believed, LacI is a rather unusual repressor. For one thing, it's the only repressor with typical copy number of less than about 100. For another thing, it has extremely few binding sites -- LacI has between 1 and 5 predicted binding sites, depending on how threshold binding sites, while most binding proteins have hundreds to thousands of binding sites. 3) A couple of interesting details of ballroom competitions. The way most competitions work is that somewhere between several and a bunch of dance pairs all dance at once on a single dance floor, and several judges watch the whole thing and give marks to the various pairs. One of the more important goals of ballroom, then, is to get the attention of the judges, since you're literally competing with the other dance pairs for physical and visual space. There is, for example, a careful balance to be struck when walking out onto the dance floor and claiming space -- you and your partner want to collectively take up as much space as possible, so you will stand out and have room to maneuver, but if you stand too far apart you won't look like a cohesive pair. Another interesting thing that can happen -- sometimes a ballroom dance pair will move into a corner for one reason or another. If they time it badly (or other teams time themselves well), they can end up pinned in the corner by other teams, making it awfully difficult to continue dancing.... Ballroom dance details courtesy of Mengsha Gong.

June 17, 2016 at 01:09AM

Today I Learned: 1) If you (presumably accidentally...) try to boil water in a rice cooker with dried out leftover rice still in it, it will froth and fill the rice cooker with bubbles. This doesn't appear to affect its steaming properties, however, and it will cook steamed buns just fine. 2) A monk's spade is a curious and fascinating polearm weapon with a concave crescent-shaped blade at one and and a convex crescent-shaped blade at the other. According to wikipedia, the monk's spade is descended from a practical variation on a walking stick carried by travelling Buddhist monks in China. A shovel on one end was used to properly bury any corpses the monk came across; a crescent-shaped, unsharpened implement at the other was used as a non-lethal weapon against animals, designed to be pushed up against the animal's throat to keep it at bay. So says wiki. 3) Big metal heating elements, like the ones found in pressure cookers or on old electric stovetops, aren't generally just big pieces of metal that conduct electricity. That, as one might guess, would be dangerous, and easy to short to boot. The actual conducting material is a relatively small coil of wire wrapped around solonoid-style inside the heating element. This is packed in a heat-conducting, electrically-insulating paste-like substance, which is covered by a metal sheath to hold the whole thing together and protect it from damage. This metal sheath is what you see when you look at a heating element. Thanks to Andrey Shur for teaching me about how heating elements are built!

June 15, 2016 at 10:56PM

Today I Learned: 1) Slime molds are... not a real thing. Specifically, they're not a real taxonomic group. More to the point, they are no longer considered fungi! Instead, the different species of slime mold are classified as different clades of non-fungus, non-animal, non-plant eukaryote (the "group" commonly known as "protists"). This is huge news, as far as I'm concerned. 2) Photons in sunlight carry 2 or 3 electron volts of energy. 3) ...a new way of thinking about aging, as a biological process. A reasonable way (though not the only reasonable way) to define "aging" is as an increase in rate of death and/or decrease in rate of fertility over time in an organism under ideal conditions (plenty of food, good environment, no predators or diseases, etc). Under this operational definition, many species actually stop aging after they've lived long enough. Many insects, for example, become more prone to death over time for most of their lives, but after a certain point, they stop becoming more death-prone. They still die, and at a high rate, but the *rate* of death doesn't increase. They effectively stop aging. Humans may do this too, by the way. I'm not sure exactly what the aging cutoff is, but mortality in the very elderly stops increasing at a certain age. Unfortunately, it's really hard to tell if that's "real" or just because of some cohort effect or selection process or other, secondary cause. It was curiosity about this point that prompted the aging experiments with insects that showed that they stop aging. There are also species that don't age at all, as far as we can tell. Many, but not all, species of hydra maintain a mostly-constant rate of death their whole lives, as determined by some relatively famous and quite lengthy hydra-rearing experiments. A key point is that every hydra that reproduces asexually, by budding or splitting, doesn't age. All of the ones that reproduce sexually age. Why would this be? One plausible explanation is that in sexually-reproducing species, there is inherently less selection pressure against traits that only pop up in older organisms. Consider, for example, a gene variant that is 100% lethal. If it is expressed at birth, then it will be 100% selected against, because every organism that gets that gene will die before reproducing. If it is only expressed well after the organism reaches sexual maturity, then there will be less pressure against it, because the organism may have already reproduced several times before the effects of the gene took hold. By contrast, in a species that splits symmetrically (or, to a lesser degree, in a species that buds), there is less difference in selection pressures for traits that pop up at different ages because there aren't really "children", just copies of the parent. In any case, it seems that aging is, in general, not inevitable. It is not even normal, in the grand scheme of things. It is a temporary period of declining health and fertility experienced by sexually-reproducing organisms.

June 15, 2016 at 01:26AM

Today I Learned: 1) I thought I knew everythin there was to know about woodpeckers' adaptations to avoid braining themselves when they smash their faces into trees, but today Chris Lennox proved me wrong. So the most dramatic woodpecker anti-braining mechanism is their indreculously long tongues, which are wrapped up the back of their skulls and *above their heads* to act as a shock-absorbing cushion. Today I learned that woodpecker tongues are also AWESOME. They are very, very long, in general (it depends on the species, as usual), and most are topped either with harpoon-like spiny bits that are great for spearing insects, or fuzzy brushlike fronds that are good for extracting sap, or some combination of the two. Still not quite as awesome as hummingbird tongues, but pretty cool. I am continually reminded that birds' experiences of mouths and tongues are very, very different from our own. I also learned a couple of other woodpecker brain protection mechanisms, via this article (http://ift.tt/1rp43Hx), via Chris Lennox. 1) Woodpecker brains fit very tightly into their skulls so they don't slosh around. 2) Woodpeckers have ridiculously strong neck muscles. 3) Woodpecker brains are oriented to best spread out the impact over a large surface. 4) Woodpecker skulls have parts that can slide around a bit, acting like a spring and damping the effect of the impact. Here's something to consider -- somewhere in the woodpecker's evolutionary past is a bird that was *not* as well-protected from brain damage as its modern descendents, yet it impacted its face against things frequently enough that evolution favored those adaptations. That's an interesting position for a bird to be in. 2) Ok, so maybe foreverspin.com doesn't have the best tops in the world. I would still argue that they may have the most *beautiful* tops in the world, but darksucks.com (which actually primarily manufacturs extremely high-end flashlights) has a (possibly discontinued) line of seriously awesome tops called Lambda Spin tops (http://ift.tt/1tvrfpt). Aside from the tops' high-texture grips and general overall quality, the major feature of the Lambda Top is its tip, which is spherical instead of pointy. This makes the top much, much more stable and precesses less, and maintains its tip much better than a normal top. To get the tip machined to the highest possible tolerances, the guy who makes (made?) Lambda Spin tops builds (built?) them with a ruby tip, as ruby is apparently highly machinable and keeps its surface better than metal. So yeah, it's a top with a ruby in it. There are some seriously impressive videos on the site I linked above, including a ten minute spin and an example of a spinning top so perfectly balanced that it looks like it's still. Thanks to Dean Clamons for finding this, somehow! 3) Today I got to try a portable induction stove. It's really, really fast. Once we figured out how to use it, we were able to bring 200 mL of water in a glass beaker to near-boiling in... one minute? Two? I'm impressed, anyway.

June 14, 2016 at 12:59AM

Today I Learned: 1) I think I found the most sublime spinning tops on the planet. No joke. Check out foreverspin.com -- this is way more dedication to tops than I ever imagined possible. (For some reason, I got an add for these on a sidebar while accessing a journal article. Go figure) 2) Apparently a good deal of German pop music is sung in English. I knew this was a thing in France, but singing in English is apparently more widespread than I thought. Thanks Mengsha Gong! 3) Shining UV in one's eye is, generally speaking, an awful idea. Today I learned of one case where it is a good idea -- corneal collagen cross-linking surgery. It's a technique used to stop thinning of the cornea by zapping the cornea with UV light, forming cross-links between the collagen molecules in the cornea and essentially fixing it in place. This is though to be what happens naturally, albeit too slowly -- corneal thinning is one of the rare diseases that is worst during youth and progressively flattens out with age, because the kinds of crosslinks induced by UV are the same as ones that form naturally with age.

June 13, 2016 at 04:00AM

Today I Learned: 1) I'm one very small step closer to understanding statistical mechanics. Today I read through most of a 1957 paper on Information Theory and Statistical Mechanics by E. T. Jaynes (see here: http://ift.tt/1UuZbs8). The general thrust of the paper is that you can derive pretty much all the important equations from statistical mechanics by just assuming the least informative probability distribution on whatever quantity you're interested. Jaynes' point is that statistical mechanics (and much of thermodynamics) really boils down to a question of this form: If you know the mean of some value of a bunch of variables, what's the mean of the value of some other function of those variables? A classic example is calculating the temperature of a bunch of molecules given their average energy -- you know the average energy of the system, but you don't know all of the energies of the individual particles, yet you *need* to somehow figure out how fast the molecules are, on average, moving. That's an impossible thing to calculate explicitly, because it's a massively underdetermined system. You can, however, put a probability distribution on the spread of energies across particles, which lets you put a probability distribution on the possible speeds of those particles, which gives you a probability distribution on the temperature of the system. It turns out that if you use the least-informative prior probability distribution on the spread of energies across particles (where here "least-informative" can be formally defined as "highest Shannon entropy"), there's only one such prior, and it gives you the Boltzmann distribution on energies of the particles, and an extremely tightly-peaked posterior distribution on temperatures around the one we actually measure. According to the article, just abuot all of the important equations in statistical mechanics can be derived this way... put a least informative prior on whatever variables you don't know, crunch through Bayes' theorem, and you almost always get a tight posterior around the value scientists think you should get. To be honest, I'm trusting Jaynes on the math, but I'd love to go through it in more detail with someone well-qualified (Bear Bear Bear?). A bonus from this article: I also learned another set of rules that can be used to derive the formula for Shannon entropy. Shannon entropy, which was supposed to quantify the information content or "average surprise" in a probability distribution, was invented using the following assumptions: 1) Entropy is a continuous function of the probabilities of each possible event; 2) If all possible outcomes are equally likely, then more possible outcomes results in higher entropy; and 3) the sum of the entropies of two events is the entropy of the sum of the two events. There is only one functional form that satisfies those three conditions, and that's the one Shannon entropy uses (it can be stated using any base logarithm). 2) The contents of soylent! Actually, of two different formulations of soylent. The one my roommate and I tried yesterday was soylent 1.5, which is mostly brown rice protein, oat flour, and sunflower oil, mixed with all the additional vitamins and minerals known to be important for human health. There's also now a soylent 2.0, which is a bottled meal-drink made from isolated soy protein, algal oil, isomaltulose (a beet dissacharide that supposedly releases energy more smoothly than glucose), and the aforementioned vitamins and minerals. The marketing on soylent 2.0 is a little different from 1.5 -- they're no longer selling it as a total food replacement, rather claiming it's a meal replacement for when you just need some cheap food without having to cook. They also claim it's tastier (we'll see) and much more environmentally friendly due to the large fraction of algae oil, which is produced in high density in bioreactors. 3) My pogonomyrmex ants aren't particularly into soylent. I gave them a crumb of soylent cookie, and a couple of workers sat on it for a while, but they didn't stay for long.

June 12, 2016 at 02:15AM

Today I Learned: 1) ColorBrewer. This is now my go-to method for picking color schemes for figures. 2) LA smells funny when it rains... a little bit like sewage.... It makes me miss Williamsburg. 3) A good optical density for running whole-cell industrial chemical reactions is 30-40, which is roughly 10-fold higher than most bacteria will grow on their own. To get densities that high, you have to pellet down a thick culture and resuspend it in less media. Thanks Anders Knight!

June 11, 2016 at 02:05AM

Today I Learned: 1) The number of possible pairs of objects from a pool of N objects, with replacement, is the sum of whole numbers up through N-1. Exercise for the reader: Why? 2) Tel Aviv students have demonstrated a method of extracting RSA encryption keys from a computer by monitoring it with a microphone, at a distance of a few meters. I don't know most of the details, but they track very high-frequency sounds given off by the computer's solid-state electronics, mostly capacitors and solonoids and other things that have to work hard to keep voltage levels steady. There's a delightful FAQ here: http://ift.tt/1UrENrO 3) Swiss PhD students make about as much money as American postdocs. Just saying. This fact brought to you by: Mengsha Gong

June 10, 2016 at 12:52AM

Today I Learned: 1) There's a new player in the genome editing game called NgAgo (short for Natronobacterium gregoryi Argonaute). Argonaute proteins important components of the RNA interference system in eukaryotes, which destroys RNAs that match any double-stranded RNA found in the cell, probably evolved first to combat RNA viruses*. Argonautes are the nucleases that do the RNA cleaving when RNA interference is invoked. They can also be used to cut DNA under specific circumstances, and they've been used in CRISPR/Cas-like ways in bacteria, but until now argonautes haven't been used in eukaryotes because they only function at high temperatures. Enter NgAgo. The argonaute found in the bacteria Natronobacterium gregoryi was discovered by searching for proteins with homology to other bacterial argonautes, and happens to work at body temperature. That makes it an attractive alternative to Cas9 as a programmable DNA cutter. There are a few differences between the two enzymes, which make NgAgo more attractive at least for some applications. One inarguable advantage of NgAgo is its lack of PAM sequence -- it can be targeted to any DNA sequence, not just DNA sequences next to a PAM. One arguable disadvantage is NgAgo's mechanism of cutting -- instead of making a clean cut, NgAgo tends to cut each strand *back* a few nucleotides, causing deletions. That could be good, if all you want to do is knock out a gene, or totally irrelevant if you're going for some kind of template-mediated recombination, but for certain kinds of precision edits, it's pretty annoying. One feature that's just plain different is that NgAgo uses a *DNA* guide instead of an RNA one. That means that it's really simple to induce cutting in a petri dish, because you can just drop in a DNA oligo (like, literally drop in, with a pipette) instead of having to transcribe out delicate RNA or put together some sort of guide expression construct. It also means you can't easily turn on NgAgo with some sort of genetic circuitry, because it's hard to make a cell produce DNA oligos. The authors who just published about NgAgo also claim that NgAgo is less prone to off-target cutting than Cas9... I'm inclined to chalk that up to NgAgo being new and relatively unvetted, and I give it about 25% odds that NgAgo is actually significantly more accurate than Cas9. *or, stated somewhat less teleologically, evolved because pre-RNA interference eukaryotes were more vulnerable to RNA viruses. 2) ...how to ship scientific materials internationally! There is, as you might imagine, some paperwork. There was more such paperwork than I expected, but not as much as I probably should have. I also learned a bit about European address formats. I didn't know that most European countries use a postal code equivalent to a US ZIP code. Also, a number of countries, including Switzerland and Denmark, use a state-equivalent code in addition to the ZIP. Others have an optional *country* code. Perhaps unsurprisingly, postal codes from Great Brittain are the longest and have the most complex address format of any European country I've seen... or, indeed, of any country I've seen at all.... 3) There's a short film with a screenplay written by an AI. It's called Sunspring, and it's... pretty typical neural net output. Check it out here, it's probably worth the 10 minutes: http://ift.tt/1UFIfij

June 09, 2016 at 01:32AM

Today I Learned: 1) Gromia sphaerica is a curious protist. It's a single-celled, shell-walled amoeba that grazes the sea floor. I don't think it's the largest single-celled organism, nor the largest protist, but I'm pretty sure it's the largest *something*, as it can range from a few millimeters in diameter to a few *centimeters* in diameter. Remember, this is an amoeba. It's particularly noted for leaving trails on ocean floors that look an awful lot like the kind of tracks commonly found from the precambrian. Until the discovery of these trails, those tracks were considered strong evidence of soft-bodied multicellular life in the precambrian, as there aren't other unicellular organisms that can leave those tracks. G. sphaerica's tracks open up the possiblity that the precambrian was actually dominated by unicellular organisms, pushing back the theorized onset of multicellularity significantly. Gromia sphaerica looks exactly like a floured lump of dough. 2) When performing a Gillespie simulation, it can sometimes make sense to cache the prpensity arrays of states your system visits. If your system spends a lot of time in a relatively small neighborhood of state space, this can save a lot of propensity calculation time. 3) Rumor has it that you can make small but consistent profits by buying natural gas options in the summer, when prices are low, and selling in the winter, when natural gas demand is high and prices are high. Can anybody confirm or disconfirm?

June 08, 2016 at 05:22AM

Today I Learned: 1) Ligase Cycling Reaction (LCR) is a cloning method that's sort of like Gibson cloning but without the whole recombinase part -- it's all done with DNA and ligase. It works by "stapling" two strands of DNA together, blunt end, using a short oligo bridging the two. I think the best way to grok LCR is probably to look at the abstract figure here (http://ift.tt/1t8c5Wv), but I'm not sure if that's behind a paywall or not, and I'd like to take a crack at explaining it in words. So. Here's how it works. Start with two pieces of (double stranded) DNA that you want to glue together, call them A and B. Add a short single stranded DNA oligo that matches A on the 5' end and B on the 3' end (or vice versa). Mix these with some DNA ligase. Cycle pretty much just like normal PCR -- heat to denature A and B into single-stranded DNA, cool down to re-anneal the DNA, then raise the temperature a little bit for efficient ligation (with a thermostable ligase). When you anneal, some of the A and B strands are going to hybridize to the bridging oligo instead of to their full-size reverse complements. If a strand of A and a strand of B hybridize to the same bridge, then the ligase can glue them together, giving you the full-size DNA strand you want. Keep cycling -- now the one full-size fragment can bridge the reverse complement strand, giving you a nice blunt-end ligation. I'm pretty sure ligase is more expensive than Gibson mix, so you might not want to use this if you're already doing Gibson cloning. Then again, you don't need giant oligos for LCR, so maybe it's cheaper sometimes...? According to the authors of the paper linked above, LCR and Gibson have virtually identical accuracy and efficiency when ligating a small number of pieces, but LCR is good for much larger assemblies (12+ pieces). Note: not to be confused with Ligation Chain Reaction (also LCR), which is a variant of PCR where the "primers" are just the front and back havles of the target, and you just ligate together instead of actually doing any replication. 2) Important news for molecular biologists out there using Phusion polymerase -- don't! According to every source I can find, Q5 polymerase is strictly better. It runs faster, it's twice as accurate, it handles high GC content better, and it's oh-so-slightly cheaper. Just do Q5. 3) ...a little more about V(D)J recombination, a key (and awesome) part of the adaptive immune system. This one's a long one. A little background -- the adaptive immune system works by producing lots (millions? I'm guessing tens of millions to hundreds of millions) of B cells which each produce a different, randomly antibody. By expressing bajillions of different antibodies, the body is likely to have at least one antibody for any foreign invader. When a B cell happens to produce an antibody that binds to an intruder, it undergoes crazy-fast replication and starts producing a ton of the antibody, which either directly kills the foreign thing, targets it for clearance by more active cells, or both. Here's the problem -- the immune system needs to produce millions and millions of different antibody variants, but it doesn't have millions and millions of genes. Furthermore, every B cell has to produce a random antibody, distinct from its sisters, but consistent over time. How? The answer, as you might be able to guess from the pedagological format of this particular TIL, is V(D)J recombination. Here's the one sentence version of V(D)J recombination: Antibody protein genes have a bunch of copies of slightly different variants of a few different domains, and each B cell randomly splices together a few of these at the DNA level to make a unique combination of domains with unique binding properties. This is really unusual because it's a *DNA-level* modification -- for the most part, Eukaryotes don't like editing their DNA except during reproduction. It tends to lead to cancer, for one thing (more on that at the end). But it's important to have a functioning adaptive immune system, too, so it's worth it in this particular instance. Today I learned a bit more about *how* V(D)J recombination works. Perhaps unsurprisingly for a recombination process, it involves lots of recombination enzymes. Specifically, V(D)J recombination is performed by a complex complex (as in, a hard-to-understand collection, not a typo) of enzymes called VDJ recombinase. These are enzyme names I can get behind. Anyway. VJD includes, among other things, one of the enzymes involved in non-homologous end joining repair, some nucleases, at least one DNA ligase, and two genes called RAG 1 and RAG 2 which target V(D)J recombination. The RAGs recognize a pair of DNA motifs 7 and 9 nucleotides long, separated by a constant-length sequence, which tells VDJ recombinase where to clip. When it does, it clips in a really weird way that produces a blunt end on the side of the cut with the coding antibody subunit while ligating *together* the two strands on the other side of the cut, converting that piece of DNA into a hairpin. Recognition domains are found at the end of each coding subdomain; by randomly binding to and cutting at two domains, VDJ recombinase can splice together two random domains. The coding regions are ligated together (presumably with that non-homologous-end-joining enzyme), and the bit in the middle is spliced together in a *single-stranded circle* of loose DNA, which is pretty unusual. There's some evidence that these circles can sometimes re-integrate into the genome, which is a good way to get cancer... way to go, immune system.... Speaking of getting cancer, here's something to consider. As far as we know, VDJ recombinase recognizes its targets using a 7-nucleotide recognition site and a 9-nucleotide recognition site. That's effectively a 16 bp recognition site, which means it should occur, on average, once every 4^16 ~ 4 billion base pairs. Now that's not particularly common (once or twice in a human genome, assuming a perfectly random human genome), but the recognition site isn't perfect. It's a bit fuzzy. We would expect sequences that are *close enough* to the recognition sequence to initiate V(D)J recombination to occur much more frequently. In fact, a quick (read: not that quick) check shows that there are about 250 occurrences of sequences within one base pair mismatch of the VDJ recognition sequence. So how does VDJ recombinase avoid snipping the chromosome where it really shouldn't? The answer may be "it doesn't". Today I also learned that cancers tend to be heavily enriched for active immune system genes. That's thought to largely be due to the fact that the immune system does try to kill the cancer, so cancers tend to have a lot of healthy immune cells mixed in with them. Ready for a bit of pure speculation? Perhaps cancers are more likely to arise when immune system lineage genes are active, because VDJ recombination can screw up genomes in addition to its usual function. I'll bet Virginia Rutten can give a more complete explanation of V(D)J recombination, and/or correct any misunderstandings I've unintentionally propagated, so hopefully she's watching if you have any questions!

June 07, 2016 at 04:30AM

Today I Learned: 1) The Windsor Beauties are a set of 10 portraits from the 1660s of the the most beautiful women in the court of King Charles II. It seems Charles took after Zeus's style of rule, except he somehow didn't get into serious trouble with his wife...? In any case, wooing King Charles and bearing his children was an efficient way for a beautiful woman of the era to gain power, prestige, and a title, and many, many women pursued that path. 2) Teachers know way more about classroom politics than I thought. Also, high school is way more political than I remember. 3) ...what the inside of a PTC-100 Thermal Cycler (with heated bonnet) looks like! I had some fun repairing one of these today... by which I mean I reset a screw on one and failed to fix the lid.... The PTC-100 is, in my humble opinion, a quite well-put-together little thermal cycler. First off, it *is* quite little -- about the same overall size as a toaster oven, though taller and narrower. The lid detaches with two screws, which is probably necessary because it comes with two different lid types (one heated and one unheated). The heated lid has a heat plate that can be adjusted by a screw controlled by a plastic wheel accessible from the outside. The innards of the lid can be accessed by simply screwing down the heat plate until it falls out. Unfortunately, one of the PTCs I wanted to repair has a broken plastic-wheel-screwy-thingy on the lid... which means I can't really get into the lid to fix it... this is, I admit, something of a design flaw. The frame of the main body comes off with just four screws, exposing a board of electronics, a second board that seems to control I/O, and the thermal cycling block itself. The I/O board detaches from the frame with a single wire and from the other electronics with two more, but it's tethered to the thermal cycling block (and through it, the power supply) by a hot-glued power connector. Again, something of an annoyance. Everything else comes out quite nicely, though -- the power cycling block can be detached by taking out six screws accessible from the outside, and then it slides right out in one big piece. Very convenient. PTC-100s are all over Ebay, and they're pretty cheap for a thermal cycler ($150-$800). The interface is pretty clunky and outdated, but it works just fine, and if the two I got are any indication, it's a good line. I *have* heard that they have a tendancy to burn out... but they do have a pair of fuses that presumably can be replaced in just that event. Aaaand that's probably way more than you wanted to know about the PTC-100 thermal cycler. But you didn't come here for ordinary facts, did you?

June 06, 2016 at 01:25AM

Today I Learned: 1) ...about a proposed system of interstellar travel involving laser propulsion. This isn't a new idea at all, but I did learn some new tidbits, as well as a proposed *implementation* that's gotten some early-stage funding. The basic idea of laser propulsion comes roughly from the solar sail idea. The spacecraft would have (or be) a large solar sail, but instead of being powered by solar ejecta, it would be pushed by a laser, beaming power from Earth, Earth orbit, or some other, more convenient location. The nice thing about laser propulsion is that the spacecraft would require virtually no fuel -- all the actual power generation would occur at the launch site. The only problem is that you can't really decelerate at the other end... but it's the only vaguely-plausible mechanism we currently have for getting things to the speeds required for interstellar travel. One thing I didn't know about is that there's a recently-proposed project at NASA to actually build these things, along with a proof-of-concept grant to show that it could plausibly work. The *really* cool thing... well, there's a couple of cool things, but the *most* cool thing about this particular project is that it's designed to be *scalable* in the sense that NASA can start by building a small, kilowatt-scale laser for short-distance, low-mass flights, then scale it up by either building progressively larger lasers or building *more* of the small ones. That means there's a smooth path from proof-of-concept prototypes through dozen-gigawatt-scale interstellar probe launchers. The *other* really cool thing about the laser propulsion system is the sheer ridiculousness of what it can do once scaled up. The ultimate goal is to build a 50-100 gigawatt orbital laser (with a total mass of about 100 times that of the ISS) that would be capable of accellerating a wafer-thin, several-kg probe to about a quarter of the speed of light. In 10 minutes. At that speed, we could get a probe to Alpha Centauri in about 17 years after launch, which means we'd have telemetry from that probe about 21 years after launch. The younger among us could be hearing back from another star system *in our lifetimes*. 2) I've noticed while interacting with high schoolers on the subject of biology that I'm often surprised about what the students know... and also by what they don't know. That makes it really hard to teach effectively. Today I learned that this is one of the big known problems in teaching, and that there are a ton of tricks and tips out in the literature for getting around it. For example, I also learned today about the idea of an "exit ticket". In a class with an exit ticket, a student can't leave the class until they've filled out some kind of "ticket" with a problem solution, an answer to a question, or simply a self-evaluation of how well that student understood everything from the class. It's a simple way of getting some valuable feedback about what everyone knows, doesn't know, or thinks they know but don't. Thanks to Kamila Laliv Goldin for sending me down this educational path! 3) ...how to play Netrunner! It's a cyberpunk asymmetric strategy card game where one player takes on the role of a corporation, trying to advance corporate agendas, while the other player takes on the role of a hacker who tries to reveal, steal, or otherwise disrupt those agendas. There's a lot of hacking and a level of tech-speak I find quite pleasing. Thanks to Andrey Shur for teaching me!

June 05, 2016 at 02:46AM

Today I Learned: 1) Antifreeze proteins (proteins that protect the cell against freezing, intuitively enough) are remarkably diverse and have evolved many times in plants, animals, and bacteria (and probably other things I don't know about). They have a number of different mechanisms, but the most common function* appears to be to bind small ice crystals and block their growth. They also look kind of like space docks from Star Trek. Thanks Anders Knight! *NOT TO IMPLY TELEOLOGICAL PURPOSE 2) Credit reports can be obtained for free, a limited number of times per... year...? Credit *scores*, however, it seems require a fee to acquire. 3) Three ring carbon groups function very similarly to double carbon bonds, and, in particular, can often substitute for double carbon bonds for the purpose of shape, BUT they are much less reactive. This makes them a good alternative to double bond functional groups in, for example, drugs that work by docking to some target, where you don't want any side-chemistry that might disrupt the drug, but you also don't want to change the drug's shape. This bit of chemistry brought to you by... also Anders Knight!

June 04, 2016 at 01:55AM

Tody I Learned: 1) You can't pickle lambda functions in Python. Also, to use multiprocessing on a function, all of the arguments must be picklable. 2) Some (many?) refrigerators use a two-stage cooling system -- freon or another similar substance is cooled by expansion, then run alongside a secondary coolant (antifreeze is a good choice), which cools off and carries that coldness through the rest of the refrigerator. This fact brought to you via Andrey Shur and his recent explorations into the inner workings of a thermal cycler. 3) Many stepper motors (motors that have a large number of pre-defined positions they can snap to) have their own built-in microcontroller. These are operated by sending the microcontroller digital instructions, must like a number of plug-and-play devices. This fact also courtesy of Andrey Shur

June 03, 2016 at 12:19AM

Tody I Learned: 1) "Neural lace", also known as "Syringe-injectable electronics". It's a mesh-like metal device so thin and diaphanous that it can be injected with, you guessed it, a syringe. Right now they don't do a ton, but last year a Harvard team of scientists built a neural lace device for reading neural activity, injected it into mouse brains, and read out cell activity. The mice were completely unharmed as far as the researchers could tell, and continued to be unharmed by the presence of the lace for five weeks after injection (after which they were sacrificed for autopsy and histology). More interestingly, the mouse's brain cells incorporated the mesh, growing around it and forming tight junctions with it. 2) ...another terrifying way the Earth can kill you called a limnic eruption, or lake overturn. Limnic eruptions are very rare (fortunately), only occurring in large bodies of water that develop massive pockets of CO2 from geologic activity. A sufficiently large geologic disturbance can cause all the CO2 to erupt from the lake, displacing air in a huge radius and killing most everything in its path. Example: In 1986, Lake Nyos, in Camaroon, erupted. Scientists believe it probably created a 100-meter-tall fountain of water and foam, creating a tidal wave 25 meters high. Nobody's sure, though, because the massive cloud of CO2 killed pretty much everyone within 25 km of the lake, and knocked out everyone else. !!!!!! 3) On a *highly* related note, CO2 is about 50% denser than air, so large amounts of CO2 released at once will roll like fog.

June 01, 2016 at 11:25PM

Today I Learned: 1) In California, early-stage school building construction is exempt from environmental regulation if it is on existing school grounds and won't increase the school's population by more than 25% or 10 classrooms, whichever is smaller. 2) So there's this weird bit of notation in calculus where derivatives of functions of single variables are notated like df/dt, but partial derivatives of functions with more than one variable are written like ∂f/∂t. Why the different notation? The operator is the same, isn't it? I've now asked two people I trust to know basically everything important in math, and they have both told me they have little to no idea. The best answer I've gotten is that the ∂ is a signifier that there are other variables at play that are being held constant. To my programmer's mind, this is absolute nonsense. If you apply the "∂" operation to a function of one variable, it does *exactly the same thing* as applying the "d" operation, so why not call it the same thing? This is a weirdly non-informative TIL, but I thought it worth noting. 3) Dealing with cybercrime is a Hard Problem. Cybercriminals do the superhero thing where their real identities are secret, making them incredibly difficult to find and punish them. Moreover, cybercrime almost invariably crosses lots of national borders, which makes it really hard for any single nation's police force to track down a criminal. Crack down on drug dealers hacking passwords from a base in Russia, and they'll just up and move to China. Today I learned that the weakest link in many illegal criminal networks is the banks that process the criminals' activities. In 2010, researchers at UCSD put together a honeypot net of computers that harvested spam and followed every link they could find to try to figure out the economic topology of the organizations behind the spam. It turned out that something like 95% of all the illegal internet activity they found was running out of three banks. The next year, Microsoft went to Visa and asked them to "encourage" those banks to stop servicing the vendors that were responsible for pirated Microsoft products. This worked amazingly well, at least temporarily. Pirates have since moved on to other banks, but it still looks like banks are the weak point for cyber crime.

June 01, 2016 at 04:04AM

Today I Learned: 1) There are now a number of companies offering "robots as a service". In particular, there's something of a booming industry in renting robots to small farms. For example, one company (whose name I've lost track of) rents out drones that monitor growth and look for problems, like rust or irrigation problems. Another company rents out tiny drones about the size of a cat or dog that dart between rows of plants, depositing small amounts of fertilizer where it's needed. This model makes a lot of sense to me. We desperately need more efficient agriculture if we're going to keep using this planet (right now, we're using 40% of the arable land on the planet for farms. That leaves 60% for cities, residencies, industrial areas, and the wild). Robots are a good way to do that, but robots usually require a heavy initial investment and plenty of specialty to maintain. Companies offering robots as a service can absorb that upfront cost and specialize in maintenance, making the robots affordable to small farmers... and they make money while they're at it! 2) The human ear is a funny thing. Have you looked at an ear lately? Pretty weird-looking. It turns out that the shape of the ear distorts incoming sounds in a manner that depends on the direction from which the sound comes. The brain can identify the underlying sound, and based on the kind of distortion it detects, can figure out to some degree which direction the sound came from. Experimental evidence for this was published in a 1998 Nature Neuroscience paper by the title "Relearning sound localization with new ears". Scientists added a mold to subjects' ears to change their shape. The subjects immediately got worse at localizing sound, though they re-calibrated their hearing over the course of several weeks. 3) All references to the Great Barrier Reef, which has been doing quite poorly according to recent oceanographic surveys (as in, about a third of it is severaly bleached and/or dead), were removed from a recent Unesco report on tourism and climate change. Why? Because the Australian government asked them to, claiming that it might cause "confusion" and might hurt tourism. You know what else is bad for tourism? Losing your country's greatest natural treasure. Will politicians ever listen to the scientific community? I don't have high hopes.