Today I Learned:
1) Hair cells (the kinds that grow hair, not the kind that let you hear) live much longer than the rest of the body after death, and Human corpses grow lots of hair very quickly for a few days after… becoming corpses. Especially on their toes.
Thanks to Bear Bear Bear for this tidbit.
2) A “nucleomorph” is a small, nucleus-like organelle found inside the chloroplasts of a few clades of algae* (for the curious, the cryptophyta and the chlorarachniophyta, and maybe the euglena? I couldn’t confirm this). They typically contain about three linear chromosomes of a few hundred kilobases total size, and invariably contain ribosomal genes (among others).
Why would a chloroplast have a nucleus-like structure, you might ask? Well, chloroplasts are thought to be descendants of photosynthesizing bacteria (probably cyanobacteria) that were endocytosed and symbiontized by an early eukaryote, the same way as mitochondria**. Plants and several other major eukaryotic lineages have chloroplasts directly derived from that line. Somewhere along the way, though, a eukaryote ingested and endosymbiontized *another* chloroplast-bearing eukaryote, an event called secondary endosymbiosis. This probably happened multiple times, but not *many* times — possibly as few as three. Since the endosymbionts in these cases were eukaryotes, they had nuclei.
In most of those lineages, those nuclei have been lost, but in a few, a presumably-vestigial nucleus remains — and this is the nucleomorph.
Thanks to Mengsha Gong for leading me down this rabbit hole of fascinating literature. Speaking of which, chloroplast evolution is really cool — I recommend “Recycled plastids: a ‘green movement’ in eukaryotic evolution” by Archibald and Keeling
*incidentally, I want to go on record saying that “algae” is terrible classification. It just means “green or red planty or slimy thing that photosynthesizes and doesn’t look like a traditional plant. Oh, and that isn’t a bacteria. Or archaea.”. The algaes are not particularly related to each other, and lots of things that are closely related to algaes are not considered algaes, so it’s useless for understanding relationships between species. Urgh.
**to head off one question I’m sure at least one of you is thinking (you know who you are), we have strong reason to believe that all chloroplasts are descendants of a single endosymbiont event about a billion and a half years ago (of course, there’s one lone exception — the amoeba Paulinella chromatophora, which relatively recently acquired a photosynthetic symbiont of its own). Most of the evidence for this is from comparative genetics — see the second section of “The Origin and Establishment of the Plastid in Algae and Plants” by Reyes-Prieto, Weber, and Bhattacharya for a short summary of the evidence, or the first half of “THE SYMBIOTIC BIRTH AND SPREAD OF PLASTIDS: HOW MANY TIMES AND WHODUNIT?” by Jeffrey Palmer for more details.
3) To get the most value out of Mongolian barbecue, stuff your bowl with vegetables before noodles — the noodles are more coherent and can be piled quite high. For even greater cost-efficiency, fan the edges of your bowl with carrots or other large, rigid vegetables to increase the effective height of the bowl. Thanks to Erik Jue for those tips.
Wednesday, September 30, 2015
Foxconn, Restriction Enzyme Buffers, and The Developmental Hourglass
Today I Learned:
1) A bit more about the Foxconn suicides. I had known that Foxconn had a lower suicide rate than the rest of China, but today I dug a bit more into the numbers.
There are a few complications with my blithe statement above about Foxconn. Firstly, Foxconn is a *huge* company, and many of its employees don’t work in the Chinese plants that were such a focus during the suicide spates. Also, China itself has a pretty high suicide rate, so it might not be the best country to compare against.
Turns out accounting for those two complications doesn’t really change the picture much. There are varying estimates for how many employees work in Chinese Foxconn factories (anywhere from 200,000 to 450,000), but even if we take the lowest number of estimated employees, at the height of the Foxconn suicides, Foxconn’s Chinese factories had a suicide rate of about 7 in 100,000 people. If Foxconn’s Chinese factories were a country, it would have about the 100th highest (or 70th lowest) suicide rate of countries with suicide rates according to the WHO 2012 report on Wiki, or right around Costa Rica, Cameroon, and Singapore.
Now, I’m not saying Foxconn is a nice company — I can’t speak to the working conditions at their factories, but from what I hear it’s pretty miserable — but I do think this is an important lesson in number-checking. 14 suicides at a company may sound like a lot, but if that’s the *highest ever* reported suicide rate for Foxconn (talk about a selection bias), then they’re doing a better job of keeping their people suicide-free than, oh, the Netherlands, Swizerland, Germany, the US, Canada, or New Zealand. Just saying.
2) The restriction enzyme BsaI works just fine in T4 ligase buffer. Whatdyaknow.
3) There’s this idea in developmental biology of a developmental hourglass — super early embryonic development, when the enbryo is just a few cells, is really, really different even in closely-related animals; late embryonic development is also really different between different species; but among relatively closely-related species (say, among insects or among mammals) the embryos in the middle stages are very, very similar, to the point where they can be quite difficult to tell apart. Today I learned that the developmental hourglass seems to hold true for gene expression as well as morphology and developmental patterns.
1) A bit more about the Foxconn suicides. I had known that Foxconn had a lower suicide rate than the rest of China, but today I dug a bit more into the numbers.
There are a few complications with my blithe statement above about Foxconn. Firstly, Foxconn is a *huge* company, and many of its employees don’t work in the Chinese plants that were such a focus during the suicide spates. Also, China itself has a pretty high suicide rate, so it might not be the best country to compare against.
Turns out accounting for those two complications doesn’t really change the picture much. There are varying estimates for how many employees work in Chinese Foxconn factories (anywhere from 200,000 to 450,000), but even if we take the lowest number of estimated employees, at the height of the Foxconn suicides, Foxconn’s Chinese factories had a suicide rate of about 7 in 100,000 people. If Foxconn’s Chinese factories were a country, it would have about the 100th highest (or 70th lowest) suicide rate of countries with suicide rates according to the WHO 2012 report on Wiki, or right around Costa Rica, Cameroon, and Singapore.
Now, I’m not saying Foxconn is a nice company — I can’t speak to the working conditions at their factories, but from what I hear it’s pretty miserable — but I do think this is an important lesson in number-checking. 14 suicides at a company may sound like a lot, but if that’s the *highest ever* reported suicide rate for Foxconn (talk about a selection bias), then they’re doing a better job of keeping their people suicide-free than, oh, the Netherlands, Swizerland, Germany, the US, Canada, or New Zealand. Just saying.
2) The restriction enzyme BsaI works just fine in T4 ligase buffer. Whatdyaknow.
3) There’s this idea in developmental biology of a developmental hourglass — super early embryonic development, when the enbryo is just a few cells, is really, really different even in closely-related animals; late embryonic development is also really different between different species; but among relatively closely-related species (say, among insects or among mammals) the embryos in the middle stages are very, very similar, to the point where they can be quite difficult to tell apart. Today I learned that the developmental hourglass seems to hold true for gene expression as well as morphology and developmental patterns.
Monday, September 28, 2015
Frog Blinks, Data Munging, and Pandas (no, not that kind)
Today I Learned:
1) Frogs (at least, South American horned frogs) close their eyes when they strike their prey. http://ift.tt/1YLpRtZ for evidence.
2) There's a term for all the stuff I've done writing little annoying scripts to move data around and mesh together data from different souces with different slightly quirky annoying formats -- "data munging".
3) Speaking of data munging, today I learned a few tricks for using Pandas (the dataframe package I mentioned a few TILs ago) to analyze database/CSV-style datasets surprisingly rapidly. Pandas has some really nice graphing support with matplotlib or seaborn (two Python packages for graphing).
1) Frogs (at least, South American horned frogs) close their eyes when they strike their prey. http://ift.tt/1YLpRtZ for evidence.
2) There's a term for all the stuff I've done writing little annoying scripts to move data around and mesh together data from different souces with different slightly quirky annoying formats -- "data munging".
3) Speaking of data munging, today I learned a few tricks for using Pandas (the dataframe package I mentioned a few TILs ago) to analyze database/CSV-style datasets surprisingly rapidly. Pandas has some really nice graphing support with matplotlib or seaborn (two Python packages for graphing).
Sunday, September 27, 2015
Supermoons, Balsamic Penne, and the Project for Awesome
Today I Learned:
1) A “Supermoon” is what happens when the moon is at its closest to Earth in its orbit during a full moon. It’s significantly brighter and bigger than the same moon at its farthest away (and, obviously, than when new).
2) Penne pasta works with balsamic toppings. This is a game-changer.
3) …about the Project for Awesome, and its parent corporation, the Foundation to Reduce World Suck. Project for Awesome hosts yearly fund- and publicity-raising campaigns where they invite Youtube users to upload videos advertising their favorite charities. Videos that garner the most publicity (measured, I presume, by likes) get a bunch of money from the Project. There’s also some sort of mechanism for soliciting donations for the advertised charities, but I don’t know the details about those.
1) A “Supermoon” is what happens when the moon is at its closest to Earth in its orbit during a full moon. It’s significantly brighter and bigger than the same moon at its farthest away (and, obviously, than when new).
2) Penne pasta works with balsamic toppings. This is a game-changer.
3) …about the Project for Awesome, and its parent corporation, the Foundation to Reduce World Suck. Project for Awesome hosts yearly fund- and publicity-raising campaigns where they invite Youtube users to upload videos advertising their favorite charities. Videos that garner the most publicity (measured, I presume, by likes) get a bunch of money from the Project. There’s also some sort of mechanism for soliciting donations for the advertised charities, but I don’t know the details about those.
Jellyfish Sleep, The Most Abundant Natural Molecule On The Planet, and BONCAT (with a bonus on Mitochondria)
Today I Learned:
1) Jellyfish (at least one species, Cassiopea, the upside-down jellyfish) sleep.
2) Think for a second on the following question: what is the most abundant natural product (molecule) on the planet? The answer, I learned today, is probably “hopanoids”. Hopanoids are a class of steroid(!) used in plasma membranes by a number of bacterial species, and are important in not-entirely-clear ways for bacteria/plant interactions. They’re found in *vast* quantities in any kind of sedimented, biologically-produced material.
3) …the scientific technique “BONCAT”, for “BioOrthogonal Non-Canonical Amino acid Tagging. It’s a rather sophisticated way to accurately measure the quantities of specific proteins in a biological sample (say, a bacterial culture or cell culture or mouse embryo). For those interested, it works by… well, this isn’t going to fit in one sentence.
You basically replace the methionines in a cell’s proteome with a non-natural amino acid called azidohomoalanine (Aha), which seems to be functionally nearly identical to methionines BUT has the side-chains necessary for click-chemistry. Ridiculously enough, you can do this by simply replacing methionine in the cells’ media with azidohomoalanine. Then you can lyse the cells, click the proteins onto click-compatible biotin, purify it out with streptavidin, and do whatever you want to it (usually mass-spec, using a spiked heavy-isotope version as a control to give absolute quantitation).
4) This was a heavy-learning day, so y’all get a fourth fact. Actually a constellation of related facts… about mitochondria!
Most mitochondria in most eukaryotes have thirteen protein-coding genes (with rare variation of one or two genes) on a single circular chromosome (with tens to hundreds of copies per mitochondria). Some protists, however, have mitochondria with *linear* DNA, which has its own distinct form of telomere at the ends. Bizarrely but not surprisingly, plant mitochondrial genomes are often very large (there’s a 2.5 Mb plant mitochondrial genome), even though they contain the same genes as all the other eukaryotes. Oh, and cucumbers have three distinct mitochondrial genomes in every mitochondria. Cucumber genetics is weird.
Last but not least, there are eukaryotes with no mitochondria at all! They’re basically all obligate parasites, including Giardia, which explains how they’re able to get away with not having mitochondria.
1) Jellyfish (at least one species, Cassiopea, the upside-down jellyfish) sleep.
2) Think for a second on the following question: what is the most abundant natural product (molecule) on the planet? The answer, I learned today, is probably “hopanoids”. Hopanoids are a class of steroid(!) used in plasma membranes by a number of bacterial species, and are important in not-entirely-clear ways for bacteria/plant interactions. They’re found in *vast* quantities in any kind of sedimented, biologically-produced material.
3) …the scientific technique “BONCAT”, for “BioOrthogonal Non-Canonical Amino acid Tagging. It’s a rather sophisticated way to accurately measure the quantities of specific proteins in a biological sample (say, a bacterial culture or cell culture or mouse embryo). For those interested, it works by… well, this isn’t going to fit in one sentence.
You basically replace the methionines in a cell’s proteome with a non-natural amino acid called azidohomoalanine (Aha), which seems to be functionally nearly identical to methionines BUT has the side-chains necessary for click-chemistry. Ridiculously enough, you can do this by simply replacing methionine in the cells’ media with azidohomoalanine. Then you can lyse the cells, click the proteins onto click-compatible biotin, purify it out with streptavidin, and do whatever you want to it (usually mass-spec, using a spiked heavy-isotope version as a control to give absolute quantitation).
4) This was a heavy-learning day, so y’all get a fourth fact. Actually a constellation of related facts… about mitochondria!
Most mitochondria in most eukaryotes have thirteen protein-coding genes (with rare variation of one or two genes) on a single circular chromosome (with tens to hundreds of copies per mitochondria). Some protists, however, have mitochondria with *linear* DNA, which has its own distinct form of telomere at the ends. Bizarrely but not surprisingly, plant mitochondrial genomes are often very large (there’s a 2.5 Mb plant mitochondrial genome), even though they contain the same genes as all the other eukaryotes. Oh, and cucumbers have three distinct mitochondrial genomes in every mitochondria. Cucumber genetics is weird.
Last but not least, there are eukaryotes with no mitochondria at all! They’re basically all obligate parasites, including Giardia, which explains how they’re able to get away with not having mitochondria.
Tuesday, September 22, 2015
E. O. Wilson, Winston Churchill, and Sewall Wright('s shifting balance theory)
Today I Learned:
1) The famous scientist E. O. Wilson has recently been publically championing group selection as an explanation for the evolution of eusocial animals (bees, ants, naked mole rats, etc). This has been pretty massively unpopular among evolutionary biologists, and is particularly odd because in the 70s, Wilson argued strongly that kin selection was a much better theory than group selection. He has also argued that group selection is responsible at least in part for humanity's success, and that we may be in a transitionary stage on the way to eusociality.
For my part, I think this is romantic nonsense that seems to stem from a conflation of group selection and altruistic, moralistic thinking. Then again, I'm arguing against one of the greatest minds in mondern biology here, so do not take my word for it. Here's an interview with Wilson that involves the topic: http://ift.tt/1KwSnoD
2) Winston Churchill was born ten years after the end of the US civil war, and died in the same year as Malcom X. That's a heck of a lot of change to live through.
Among other things, he was the head of the British admiralty at the time when the British admiralty was a) most of British military power and b) the overwhelmingly most powerful navy in the world; he was kicked out of that post, joined the front lines in WWI, and helped spearhead the invention and deployment of the first tanks; and went on to be the Prime Minister of Brittain during WWII, after warning the world about the dangers of Nazi Germany for a decade.
3) "Shifting balance theory" is an evolutionary theory proposed in the 1930s by Sewall Wright. It proposes that evolution can happen more readily when subpopulations are mostly isolated from each other. Basically the theory says that small, isolated populations can more easily drift between locally optimum evolutionary fitness peaks, and if they find one that's higher than their neighbors, that trait will eventually filter to the other populations and quickly take over.
So far, there is little empirical evidence to support shifting balance theory.
1) The famous scientist E. O. Wilson has recently been publically championing group selection as an explanation for the evolution of eusocial animals (bees, ants, naked mole rats, etc). This has been pretty massively unpopular among evolutionary biologists, and is particularly odd because in the 70s, Wilson argued strongly that kin selection was a much better theory than group selection. He has also argued that group selection is responsible at least in part for humanity's success, and that we may be in a transitionary stage on the way to eusociality.
For my part, I think this is romantic nonsense that seems to stem from a conflation of group selection and altruistic, moralistic thinking. Then again, I'm arguing against one of the greatest minds in mondern biology here, so do not take my word for it. Here's an interview with Wilson that involves the topic: http://ift.tt/1KwSnoD
2) Winston Churchill was born ten years after the end of the US civil war, and died in the same year as Malcom X. That's a heck of a lot of change to live through.
Among other things, he was the head of the British admiralty at the time when the British admiralty was a) most of British military power and b) the overwhelmingly most powerful navy in the world; he was kicked out of that post, joined the front lines in WWI, and helped spearhead the invention and deployment of the first tanks; and went on to be the Prime Minister of Brittain during WWII, after warning the world about the dangers of Nazi Germany for a decade.
3) "Shifting balance theory" is an evolutionary theory proposed in the 1930s by Sewall Wright. It proposes that evolution can happen more readily when subpopulations are mostly isolated from each other. Basically the theory says that small, isolated populations can more easily drift between locally optimum evolutionary fitness peaks, and if they find one that's higher than their neighbors, that trait will eventually filter to the other populations and quickly take over.
So far, there is little empirical evidence to support shifting balance theory.
Monday, September 21, 2015
Owl Ears, Evolutionary Escape, and Evolutionary Not-Escape
Today I Learned:
1) Many owls have asymmetric ears! One ear is higher than the other, so that they can use use binocular (binaural?) hearing to locate prey in the up-down axis as well as the left-right axis.
2) I’ve been wondering for a while how much of a deal evolutionary escape of genetic circuits is. The idea is that when you put a genetic circuit to, say, detect the presence of a small molecule or metabolize a drug, into a bacteria (or other creature), it’s often not particularly healthy for the organism. It might not be *terrible*, but the bacteria that’s spending energy making insulin isn’t going to grow as effectively as the wild-type bacteria — in other words, there’s a fitness penalty associated with the genetic circuit. Which means there’s evolutionary pressure against having that circuit. Evolutionary escape is what happens when one bacteria happens to evolve a trait that somehow shuts down your circuit, a trait which then rapidly spreads and takes over your population.
So… how often does this happen? How big a problem is it? It turns out the answer is, “a lot”, and “potentially big”. For instance, it turns out that it’s really hard to clone and miniprep (i.e., isolate DNA from) some plasmids with constitutively active genes on them because the activity is *so deleterious* that you end up cloning almost exclusively broken plasmids that don’t do anything anymore.
It’s also a problem in industrial contexts — apparently most industrial bioreactors run in “batches”, where a reactor gets filled with bacteria, runs for a few days or a couple of weeks, then gets cleaned out and replaced with a new batch. One of the reasons is that the bacteria start escaping their circuits quite rapidly, and after a few days there’s no point in keeping the reactor going.
3) More on evolutionary escape — turns out circuits in yeast cells escape much more slowly, and can be run continuously on the order of months or years. Why would this be? (For those who wonder, lots of places still use bacteria because it’s much easier to develop genetic circuits that work in bacteria.)
1) Many owls have asymmetric ears! One ear is higher than the other, so that they can use use binocular (binaural?) hearing to locate prey in the up-down axis as well as the left-right axis.
2) I’ve been wondering for a while how much of a deal evolutionary escape of genetic circuits is. The idea is that when you put a genetic circuit to, say, detect the presence of a small molecule or metabolize a drug, into a bacteria (or other creature), it’s often not particularly healthy for the organism. It might not be *terrible*, but the bacteria that’s spending energy making insulin isn’t going to grow as effectively as the wild-type bacteria — in other words, there’s a fitness penalty associated with the genetic circuit. Which means there’s evolutionary pressure against having that circuit. Evolutionary escape is what happens when one bacteria happens to evolve a trait that somehow shuts down your circuit, a trait which then rapidly spreads and takes over your population.
So… how often does this happen? How big a problem is it? It turns out the answer is, “a lot”, and “potentially big”. For instance, it turns out that it’s really hard to clone and miniprep (i.e., isolate DNA from) some plasmids with constitutively active genes on them because the activity is *so deleterious* that you end up cloning almost exclusively broken plasmids that don’t do anything anymore.
It’s also a problem in industrial contexts — apparently most industrial bioreactors run in “batches”, where a reactor gets filled with bacteria, runs for a few days or a couple of weeks, then gets cleaned out and replaced with a new batch. One of the reasons is that the bacteria start escaping their circuits quite rapidly, and after a few days there’s no point in keeping the reactor going.
3) More on evolutionary escape — turns out circuits in yeast cells escape much more slowly, and can be run continuously on the order of months or years. Why would this be? (For those who wonder, lots of places still use bacteria because it’s much easier to develop genetic circuits that work in bacteria.)
Sunday, September 20, 2015
Chicken Dinosaurs, More on Fairy Wasps, and Pandas
Today I Learned:
1) So, there’s an experiment that I’ve wanted to do for a while that’s basically impossible, so I haven’t done it yet. The experiment is about how much animals are born knowing how to use their bodies versus how much they *learn* to use their bodies. For example, birds under a certain size almost universally move on the ground by hopping, while larger birds move on the ground by running or walking. Is that because each species has evolved innate movement behaviors that are ideal for its size? Or is it because each bird learns what’s efficient and does that?
The experiment is simple, conceptually. Take a small bird (say, a finch) and a large bird (say, a roadrunner) and switch their brains at birth. If the innate theory is correct, you should see the roadrunner body hopping around stupidly and the finch body running around very cutely. If the birds learn their movements based on their bodies, then you should see more or less the same movement patterns as though you hadn’t swapped them. Unfortunately, this experiment is beyond my technical abilities.
Well, Bruno Grossi et al have gone and done it. Sort of. They actually showed that by attaching an artificial weighted tail to the back end of a chicken for its whole life, they could get the chickens to walk with dinosaur postures. It’s not a knock-down experiment against innate movement by any means, but it’s strongly suggesting to me.
Bruno Grossi won this year’s Ignobel Prize in biology for his work on artificially-induced dinosaur gaits.
This one’s open-access, thanks to PLOS One: http://tinyurl.com/no6mnzl
2) More facts about the fairy wasp, mentioned in yesterday’s TIL:
* Fairy wasps are actually a family of wasps, with about a hundred genera and over a thousand species. The most popular one on blogs and posts like mine is Dicopomorpha echmepterygis because of its tiny size (specifically, because of the males’ tiny size) — most are more reasonably-sized, like half a millimeter.
* Fairy wasps are the most abundant form of wasp on the planet. They’re just really hard to spot.
* Fairy wasps are also the oldest known extant group of wasps, with an abundant fossil record going back to the Cretaceous. How they fossilize well without disintegrating I really can’t say, though I would guess amber has something to do with it.
* There are aquatic fairy wasps! They live underwater for many days at a time, which has got to be most of their lives (most fairy wasps only live a couple of days). They’re so small that they can’t break the surface tension of water, so they have to climb up the stalks of plants to get out.
* Fairy wasps are egg-parasites. Some have very specific hosts, but many seem to lay in just about whatever insect eggs they can find. Several are specific to agricultural pests, and have been successfully used as pest control in a couple of cases.
* There’s quite a diversity of fairy wasp wing structure. Many have more-or-less wasp-like wings, typically longer than they are wide, often with feathery bits at the ends. Many have truncated micro-wings, or no wings at all. Some have club-like wings, and a few have very strange wings indeed.
Check out their wiki page for more.
3) Pandas — not just a mammal! It’s also a scientific computing package for Python that provides data frames, which are data structures that essentially act like excel tables. If you’ve used R, it’s basically the data frames from R.
1) So, there’s an experiment that I’ve wanted to do for a while that’s basically impossible, so I haven’t done it yet. The experiment is about how much animals are born knowing how to use their bodies versus how much they *learn* to use their bodies. For example, birds under a certain size almost universally move on the ground by hopping, while larger birds move on the ground by running or walking. Is that because each species has evolved innate movement behaviors that are ideal for its size? Or is it because each bird learns what’s efficient and does that?
The experiment is simple, conceptually. Take a small bird (say, a finch) and a large bird (say, a roadrunner) and switch their brains at birth. If the innate theory is correct, you should see the roadrunner body hopping around stupidly and the finch body running around very cutely. If the birds learn their movements based on their bodies, then you should see more or less the same movement patterns as though you hadn’t swapped them. Unfortunately, this experiment is beyond my technical abilities.
Well, Bruno Grossi et al have gone and done it. Sort of. They actually showed that by attaching an artificial weighted tail to the back end of a chicken for its whole life, they could get the chickens to walk with dinosaur postures. It’s not a knock-down experiment against innate movement by any means, but it’s strongly suggesting to me.
Bruno Grossi won this year’s Ignobel Prize in biology for his work on artificially-induced dinosaur gaits.
This one’s open-access, thanks to PLOS One: http://tinyurl.com/no6mnzl
2) More facts about the fairy wasp, mentioned in yesterday’s TIL:
* Fairy wasps are actually a family of wasps, with about a hundred genera and over a thousand species. The most popular one on blogs and posts like mine is Dicopomorpha echmepterygis because of its tiny size (specifically, because of the males’ tiny size) — most are more reasonably-sized, like half a millimeter.
* Fairy wasps are the most abundant form of wasp on the planet. They’re just really hard to spot.
* Fairy wasps are also the oldest known extant group of wasps, with an abundant fossil record going back to the Cretaceous. How they fossilize well without disintegrating I really can’t say, though I would guess amber has something to do with it.
* There are aquatic fairy wasps! They live underwater for many days at a time, which has got to be most of their lives (most fairy wasps only live a couple of days). They’re so small that they can’t break the surface tension of water, so they have to climb up the stalks of plants to get out.
* Fairy wasps are egg-parasites. Some have very specific hosts, but many seem to lay in just about whatever insect eggs they can find. Several are specific to agricultural pests, and have been successfully used as pest control in a couple of cases.
* There’s quite a diversity of fairy wasp wing structure. Many have more-or-less wasp-like wings, typically longer than they are wide, often with feathery bits at the ends. Many have truncated micro-wings, or no wings at all. Some have club-like wings, and a few have very strange wings indeed.
Check out their wiki page for more.
3) Pandas — not just a mammal! It’s also a scientific computing package for Python that provides data frames, which are data structures that essentially act like excel tables. If you’ve used R, it’s basically the data frames from R.
Bronze Age Collapse, Harvard Admissions, and Owl Affection
Today I Learned:
1) What’s the biggest civilizational collapse you know about? Until today I would have said “the fall of the Roman Empire”. Today I can say “the end of the bronze age”. The end of the bronze age happened somewhere between 1300 and 1100 BC, and it involved the destruction of almost all of the great civilizations of the fertile crescent. Unfortunately, we don’t really know why it happened — it was followed by a dark age rather like The Dark Age in terms of recorded history.
2) The modern academic requirements of college admissions were essentially institutionalized by a couple of guys, namely James Conant and Kingman Brewster, presidents of Harvard and Yale, respectively, during the 1930s. Before them, admissions were decided by means apparently devised to select for high-society future aristocrats — preference for those with wealthy parents and athletic prowess, personal interviews to ensure personability, quotas on Jewish entrants, proficiency with classical languages, and other stuff like that. In the 30s, the ivy leagues started adding academic requirements to their admissions process, removing Jewish quotas and adding SAT and grade requirements, among other things.
3) Owls actually seem to like physical affection. This comes with some caveats — most owls *emphatically do not* like to be touched by humans. That’s because most owls have very little experience being touched by humans, and being touched by a human is really scary and stressful if you’re not used to it. Owls raised in captivity, however, and trained to accept human touch, can be surprisingly affectionate, and apparently many wild owls are very physically affectionate with each other.
(note: this does not mean you should keep an owl as a pet. Don’t do this unless you are incredibly passionate about owls, are willing to devote a lot of time and money to them, don’t mind the risk of bodily injury, and have proper legal permits to do so.)
1) What’s the biggest civilizational collapse you know about? Until today I would have said “the fall of the Roman Empire”. Today I can say “the end of the bronze age”. The end of the bronze age happened somewhere between 1300 and 1100 BC, and it involved the destruction of almost all of the great civilizations of the fertile crescent. Unfortunately, we don’t really know why it happened — it was followed by a dark age rather like The Dark Age in terms of recorded history.
2) The modern academic requirements of college admissions were essentially institutionalized by a couple of guys, namely James Conant and Kingman Brewster, presidents of Harvard and Yale, respectively, during the 1930s. Before them, admissions were decided by means apparently devised to select for high-society future aristocrats — preference for those with wealthy parents and athletic prowess, personal interviews to ensure personability, quotas on Jewish entrants, proficiency with classical languages, and other stuff like that. In the 30s, the ivy leagues started adding academic requirements to their admissions process, removing Jewish quotas and adding SAT and grade requirements, among other things.
3) Owls actually seem to like physical affection. This comes with some caveats — most owls *emphatically do not* like to be touched by humans. That’s because most owls have very little experience being touched by humans, and being touched by a human is really scary and stressful if you’re not used to it. Owls raised in captivity, however, and trained to accept human touch, can be surprisingly affectionate, and apparently many wild owls are very physically affectionate with each other.
(note: this does not mean you should keep an owl as a pet. Don’t do this unless you are incredibly passionate about owls, are willing to devote a lot of time and money to them, don’t mind the risk of bodily injury, and have proper legal permits to do so.)
Friday, September 18, 2015
Fairy wasps, SLURM, and "Iran"
Today I Learned:
1) I’ve written before about the the fairy wasp, which as far as I know is the smallest insect known to mankind (for reference, it’s a couple hundred micrometers long — about the size of an amoeba). It’s so small that its neurons (yes, it has a brain) are renucleated to save space. Today I learned that the lack of nuclei isn’t the only strange thing about fairy wasp neurons — they also shouldn’t work according to our understanding of physics and biology. I don’t actually know the physics involved, but basically at the scale of those neurons, conductance of electrical signals shouldn’t… work. Some scientists think that they may use mechanical linkages and physical movement in lieu of chemical linkages and electrical movement — which would mean they essentially have clockwork brains.
As a side note, I also learned that we have a much clearer picture of a fairy wasp than the standard photo I always find. The following link has three plates; the second one is the one I always find, the third is the one I learned about today.
http://ift.tt/1im7k6c
2) Possibly my favorite acronym ever: the Simple Linux Utility for Resource Manager, or SLURM (it’s a program that handles job allocations on Linux closers). Interestingly, I believe the use of the word “slurm” in Futurama predates SLURM by about four years… was the acronym a happy coincidence? Perhaps, perhaps.
3) The correct pronunciation of “Iran” is like “ear-ahn”, not like “eye-ran”.
1) I’ve written before about the the fairy wasp, which as far as I know is the smallest insect known to mankind (for reference, it’s a couple hundred micrometers long — about the size of an amoeba). It’s so small that its neurons (yes, it has a brain) are renucleated to save space. Today I learned that the lack of nuclei isn’t the only strange thing about fairy wasp neurons — they also shouldn’t work according to our understanding of physics and biology. I don’t actually know the physics involved, but basically at the scale of those neurons, conductance of electrical signals shouldn’t… work. Some scientists think that they may use mechanical linkages and physical movement in lieu of chemical linkages and electrical movement — which would mean they essentially have clockwork brains.
As a side note, I also learned that we have a much clearer picture of a fairy wasp than the standard photo I always find. The following link has three plates; the second one is the one I always find, the third is the one I learned about today.
http://ift.tt/1im7k6c
2) Possibly my favorite acronym ever: the Simple Linux Utility for Resource Manager, or SLURM (it’s a program that handles job allocations on Linux closers). Interestingly, I believe the use of the word “slurm” in Futurama predates SLURM by about four years… was the acronym a happy coincidence? Perhaps, perhaps.
3) The correct pronunciation of “Iran” is like “ear-ahn”, not like “eye-ran”.
Thursday, September 17, 2015
Gros Michels, Poisons, and Mushrooms
Today I Learned:
1) Banana-scented things don't smell like banana because they smell like the Gros Michel banana, a now-extinct cultivar that was the overwhelmingly dominant banana cultivar until the 1950s, when it was wiped out by pestilence.
2) The mechanisms of action of strychnine (overstimulation of muscular neurons, causing spastic, uncontrollable muscular contractions and death usually by asphyxiation), ricin (ribosome inhibitor, which shuts down all protein production -- it could be interesting to compare the symptoms of ricin vs the symptoms of radiation poisoning, which mostly destroys DNA), and whatever the toxin is in destroying angels (also ribosome inhibition, but specifically targeted to liver and kidney cells, so death is from kidney failure several days after ingestion. Ugh.).
3) Speaking of deadly things, there apparently aren't really deadly mushrooms (like the aforementioned destroying angel) in the far East, which may be why eastern cuisine uses mushrooms more and of a greater variety than Western cuisine. Another consequence is that most mushroom poisoning cases are, if my sources are correct, Eastern immigrants who were used to eating similar-looking mushrooms back home.
1) Banana-scented things don't smell like banana because they smell like the Gros Michel banana, a now-extinct cultivar that was the overwhelmingly dominant banana cultivar until the 1950s, when it was wiped out by pestilence.
2) The mechanisms of action of strychnine (overstimulation of muscular neurons, causing spastic, uncontrollable muscular contractions and death usually by asphyxiation), ricin (ribosome inhibitor, which shuts down all protein production -- it could be interesting to compare the symptoms of ricin vs the symptoms of radiation poisoning, which mostly destroys DNA), and whatever the toxin is in destroying angels (also ribosome inhibition, but specifically targeted to liver and kidney cells, so death is from kidney failure several days after ingestion. Ugh.).
3) Speaking of deadly things, there apparently aren't really deadly mushrooms (like the aforementioned destroying angel) in the far East, which may be why eastern cuisine uses mushrooms more and of a greater variety than Western cuisine. Another consequence is that most mushroom poisoning cases are, if my sources are correct, Eastern immigrants who were used to eating similar-looking mushrooms back home.
Monday, September 14, 2015
Ribosome Exit Tunnels, Cas9 Tricks, and Theories of Others of Ducks
Today I Learned:
1) I quote: “…the exit tunnel of the ribosome admits ~28 amino acids of the extended polypeptide”. So while a protein is being translated into existence, *28* of its amino acids are ensconced inside the ribosome at any given time. That’s way more than I thought — I usually think of the ribosome as a little unit about the size of an amino acid, but that’s clearly very wrong — it’s made up of RNA, after all, and RNA is made of nucleic acids, and nucleic acids are bigger than amino acids. This seems like a fun number to know.
Quote quoted from http://ift.tt/1FbxJhA (free access).
2) A couple of new tricks with cas9. In particular, there’s a way to functionalize dCas9 (that’s the version of cas9 lacking DNA-cutting capability) without fusing stuff to your dCas9. It’s a bit technical and a drawing might help, so here’s a rough diagram of Cas9 and its associated RNAs: http://ift.tt/1LvoXYH
The trick is to use the sgRNA loop shown at the top of the diagram in the REC domain to recruit other proteins. You extend the loop out of the protein (it normally sticks out at least somewhat) and add a single-stranded loop with a known DNA binding site for some DNA binding protein. Then you can make a fusion of that DNA binding protein with whatever you want to functionalize your cas9 with, and it will bind to the sgRNA. This gives you an extra level of indirection between your target sequence and your cas9-mediated function, which as any computer scientist can tell you will can solve a lot of problems before they crop up.
3) Ducks, apparently, do not have much of a theory of others when it comes to turtles. That or they’re just jerks. Today I observed several incidents of ducks swimming, walking, and flapping on and around turtles with no apparent regard for said turtles’ existence. Poor things.
Not really related, but I also watched a turtle crawl around on land for a while before grabbing a rather large twig (several times longer than its body) and dragging it straight back to the water. It then dropped the twig, hung around for a minute, and left with no further ceremony. Did it think the twig was food, only to discover otherwise when it got to the water? I have a theory that turtles (unlike tortoises) can’t really eat or taste effectively unless they’re in water, which would support this interpretation. What do you think?
1) I quote: “…the exit tunnel of the ribosome admits ~28 amino acids of the extended polypeptide”. So while a protein is being translated into existence, *28* of its amino acids are ensconced inside the ribosome at any given time. That’s way more than I thought — I usually think of the ribosome as a little unit about the size of an amino acid, but that’s clearly very wrong — it’s made up of RNA, after all, and RNA is made of nucleic acids, and nucleic acids are bigger than amino acids. This seems like a fun number to know.
Quote quoted from http://ift.tt/1FbxJhA (free access).
2) A couple of new tricks with cas9. In particular, there’s a way to functionalize dCas9 (that’s the version of cas9 lacking DNA-cutting capability) without fusing stuff to your dCas9. It’s a bit technical and a drawing might help, so here’s a rough diagram of Cas9 and its associated RNAs: http://ift.tt/1LvoXYH
The trick is to use the sgRNA loop shown at the top of the diagram in the REC domain to recruit other proteins. You extend the loop out of the protein (it normally sticks out at least somewhat) and add a single-stranded loop with a known DNA binding site for some DNA binding protein. Then you can make a fusion of that DNA binding protein with whatever you want to functionalize your cas9 with, and it will bind to the sgRNA. This gives you an extra level of indirection between your target sequence and your cas9-mediated function, which as any computer scientist can tell you will can solve a lot of problems before they crop up.
3) Ducks, apparently, do not have much of a theory of others when it comes to turtles. That or they’re just jerks. Today I observed several incidents of ducks swimming, walking, and flapping on and around turtles with no apparent regard for said turtles’ existence. Poor things.
Not really related, but I also watched a turtle crawl around on land for a while before grabbing a rather large twig (several times longer than its body) and dragging it straight back to the water. It then dropped the twig, hung around for a minute, and left with no further ceremony. Did it think the twig was food, only to discover otherwise when it got to the water? I have a theory that turtles (unlike tortoises) can’t really eat or taste effectively unless they’re in water, which would support this interpretation. What do you think?
Humus, Glue, and Tahini.
Today I Learned:
1) How to make humus! Thanks to Bear Bear Bear! I kind of already knew what all was in humus, but the trick is in the proportions, which Bear Bear Bear nicely demonstrated for myself and Erik.
2) Apparently glue-stick glue sticks better to room-temperature materials than to hot materials. At least, it sticks better to 3D printer beds when room temperature… not sure if this generalizes to all materials.
3) Tahini needs to be refrigerated. This is a good thing to know when using tahini! Also thanks to Bear Bear Bear.
1) How to make humus! Thanks to Bear Bear Bear! I kind of already knew what all was in humus, but the trick is in the proportions, which Bear Bear Bear nicely demonstrated for myself and Erik.
2) Apparently glue-stick glue sticks better to room-temperature materials than to hot materials. At least, it sticks better to 3D printer beds when room temperature… not sure if this generalizes to all materials.
3) Tahini needs to be refrigerated. This is a good thing to know when using tahini! Also thanks to Bear Bear Bear.
Thursday, September 10, 2015
Insure/Ensure, Spectral Lines, and Ants
Today I Learned:
1) The word “insure” is, according to the OED, properly a variant of the word “ensure”, and was originally interchangeable with it. I found a published scholarly work from 1996 that uses “insure” in the modern sense of “ensure”… I’m not sure if that means it was acceptable practice as recently as twenty years ago or if it means that there were grammatical mistakes in the text.
2) It’s rather difficult to tell if a very young, hot star is getting nearer or farther away. Why? Well, the way you can typically tell whether a star is getting nearer or farther is by looking for red-shift or blue-shift in the spectral lines of the star. Spectral lines are specific wavelengths of light that are emitted or *not* emitted by hot matter, and they’re extremely specific — so if you see the spectral lines for, say, hydrogen, but they’re a little more blue than they should be, then that has to be from doppler shift.
The thing is, spectral lines are caused by absorption and emission of photons by the electrons in an atom. In a super-young, super-hot star, the outer layers of the star are so hot that their molecules are *stripped of electrons* — i.e., they’re plasma — so they have nothing to produce spectral lines. Ergo, no visible red- or blue-shift.
3) Ant trails are not so straightforward as I expected. Twice today, I tried tracing a line of ants back to the colony. I figured in one direction, it would fan out and dissipate, or converge on some sort of food, and in the other direction it would thicken and lead me to the next. Instead, in *both* directions, it thinned for a time, then would thicken in places and thin in other and branch in yet others… in neither case did I find a colony before I gave up (admittedly only a few minutes of searching).
1) The word “insure” is, according to the OED, properly a variant of the word “ensure”, and was originally interchangeable with it. I found a published scholarly work from 1996 that uses “insure” in the modern sense of “ensure”… I’m not sure if that means it was acceptable practice as recently as twenty years ago or if it means that there were grammatical mistakes in the text.
2) It’s rather difficult to tell if a very young, hot star is getting nearer or farther away. Why? Well, the way you can typically tell whether a star is getting nearer or farther is by looking for red-shift or blue-shift in the spectral lines of the star. Spectral lines are specific wavelengths of light that are emitted or *not* emitted by hot matter, and they’re extremely specific — so if you see the spectral lines for, say, hydrogen, but they’re a little more blue than they should be, then that has to be from doppler shift.
The thing is, spectral lines are caused by absorption and emission of photons by the electrons in an atom. In a super-young, super-hot star, the outer layers of the star are so hot that their molecules are *stripped of electrons* — i.e., they’re plasma — so they have nothing to produce spectral lines. Ergo, no visible red- or blue-shift.
3) Ant trails are not so straightforward as I expected. Twice today, I tried tracing a line of ants back to the colony. I figured in one direction, it would fan out and dissipate, or converge on some sort of food, and in the other direction it would thicken and lead me to the next. Instead, in *both* directions, it thinned for a time, then would thicken in places and thin in other and branch in yet others… in neither case did I find a colony before I gave up (admittedly only a few minutes of searching).
Not-Diatoms, Membrane Proteins, and Yellow Fever
Today I Learned:
1) Not all toothpaste contains diatoms! Erik Jue and I were curious about what the solvent in toothpaste is (water, glycerine, SLS), and I noticed that the toothpaste had no calcium carbonate in it. I thought all toothpaste was calcium carbonate, but apparently lots of it is made from silica or other abrasives instead.
2) Membrane proteins, for some reason, tend to be toxic to cells when expressed in high quantities. Perhaps it’s because having lots of one membrane protein disrupts membrane fluidity? In any case, this little tidbit makes me suspect that cell membranes are more carefully balanced machines than I thought.
3) Yellow fever is a truly terrible disease. Most of the time, it’s not *so* bad — it’s basically like a bad flu. About 15% of the time, though, it’s basically slightly less deadly (but no less gruesome) ebola, right down to the disintegrating soft tissues everywhere. I’ve heard of yellow fever plenty, mostly in the context of explorers coming down with it… now I know what kind of symptoms that disease implies.
1) Not all toothpaste contains diatoms! Erik Jue and I were curious about what the solvent in toothpaste is (water, glycerine, SLS), and I noticed that the toothpaste had no calcium carbonate in it. I thought all toothpaste was calcium carbonate, but apparently lots of it is made from silica or other abrasives instead.
2) Membrane proteins, for some reason, tend to be toxic to cells when expressed in high quantities. Perhaps it’s because having lots of one membrane protein disrupts membrane fluidity? In any case, this little tidbit makes me suspect that cell membranes are more carefully balanced machines than I thought.
3) Yellow fever is a truly terrible disease. Most of the time, it’s not *so* bad — it’s basically like a bad flu. About 15% of the time, though, it’s basically slightly less deadly (but no less gruesome) ebola, right down to the disintegrating soft tissues everywhere. I’ve heard of yellow fever plenty, mostly in the context of explorers coming down with it… now I know what kind of symptoms that disease implies.
Wednesday, September 9, 2015
Regulars and Homeopathics, Chris Voigt, and Stack Smash Protection
Today I Learned:
1) There was a time, during the mid 19th century, when three* major factions of doctors in the United States vied for legitimacy and control of the medical establishment, as it were… those three (very loose) factions were the homeopathics, who used homeopathy; esoterics, who used almost exclusively herbal medicine; and regulars, who practiced scientific inquiry, impeccable manners, and exploration of hypotheses… and were best known for their use of purging, bleeding, and mercury. *sigh*.
*this, I suspect, is a vast oversimplification — I think there were many, many schools of medicine at the time, but the most popular ones clustered into these three.
2) Chris Voigt, of synthetic biology fame, went to Caltech, where he worked on computational optimization of directed evolution under Francis Arnold. Who knew!
3) GCC has built-in protection against “stack smashing”, which is a method of computer attack* based on writing outside the bounds of an array to cause a function to return to the wrong (arbitrary) address. Futhermore, the output you get from GCC when you *try* a stack smash is surprisingly verbose! None of this “abort trap 6” business — it actually gives you a stack trace and tells you a fair bit about what variables are in scope, if you can decipher it. …and in case you’re wondering, I found this out because it turns out to not be terribly difficult to accidentally stack smash if an array is smaller than you think.
*though why this isn’t just called an “illegal operation” is a bit beyond me.
1) There was a time, during the mid 19th century, when three* major factions of doctors in the United States vied for legitimacy and control of the medical establishment, as it were… those three (very loose) factions were the homeopathics, who used homeopathy; esoterics, who used almost exclusively herbal medicine; and regulars, who practiced scientific inquiry, impeccable manners, and exploration of hypotheses… and were best known for their use of purging, bleeding, and mercury. *sigh*.
*this, I suspect, is a vast oversimplification — I think there were many, many schools of medicine at the time, but the most popular ones clustered into these three.
2) Chris Voigt, of synthetic biology fame, went to Caltech, where he worked on computational optimization of directed evolution under Francis Arnold. Who knew!
3) GCC has built-in protection against “stack smashing”, which is a method of computer attack* based on writing outside the bounds of an array to cause a function to return to the wrong (arbitrary) address. Futhermore, the output you get from GCC when you *try* a stack smash is surprisingly verbose! None of this “abort trap 6” business — it actually gives you a stack trace and tells you a fair bit about what variables are in scope, if you can decipher it. …and in case you’re wondering, I found this out because it turns out to not be terribly difficult to accidentally stack smash if an array is smaller than you think.
*though why this isn’t just called an “illegal operation” is a bit beyond me.
Monday, September 7, 2015
Ginkgo Seeds, Sweetgum Balls, and Copywrite Protection
1) You can eat Ginkgo seeds! The fruit are what give male ginkgo trees their distinctive fermented cheese scent, and you don't want to eat those. In fact, you'll want to handle those carefully -- they can cause a similar rash to poison ivy or poison oak, if you're sensitive to them. However, if you peel off the fruit (using gloves or similar protection), there's a nut inside that's similar in structure to a pistachio without the split down one side. You can bake those and crack open the shells, yielding a soft, rich nut inside, almost a bean more than a nut. They're pretty tasty.
2) You know the spiky balls on sweetgums? Well, if you don't, sweetgums have very distinctive round spiky balls. You've probably seen them. Anyway, today I learned that the trees those come from are called sweetgums, *BUT* that's not the cool thing I learned -- the cool thing I learned is that when they're ripe (green, not shriveled and brown like you'll often find them), they're full of tiny little seedy things, and if you shake them they sprinkle those tiny little seedy things all over the place.
3) That woman I mentioned a couple of days ago, Jane Marset, who wrote one of the most popular chemistry books of the 19th century? Turns out she received neither attribution nor pay for most of the American editions of that book -- she was British, and America didn't offer copyright protection for foreign authors at the time (that came in 1891).
2) You know the spiky balls on sweetgums? Well, if you don't, sweetgums have very distinctive round spiky balls. You've probably seen them. Anyway, today I learned that the trees those come from are called sweetgums, *BUT* that's not the cool thing I learned -- the cool thing I learned is that when they're ripe (green, not shriveled and brown like you'll often find them), they're full of tiny little seedy things, and if you shake them they sprinkle those tiny little seedy things all over the place.
3) That woman I mentioned a couple of days ago, Jane Marset, who wrote one of the most popular chemistry books of the 19th century? Turns out she received neither attribution nor pay for most of the American editions of that book -- she was British, and America didn't offer copyright protection for foreign authors at the time (that came in 1891).
Wolves, Rings, and a Certain Scientific Textbook
Today I Learned:
1) The reintroduction of wolves to Yellowstone had a surprising number and variety of effects on the Yellowstone ecosystem. Most of the effect seems to have come from scaring elk and caribou and other ungulates away from overgrazed riverbanks and some forested areas, which gave those areas a chance to grow much more thickly and densely. This had a number of impacts, including attracting songbirds that like the forest; attracting bears and other animals that eat the berries off of mature plant life; attracting beavers that like to eat the full-grown trees and which themselves created ponds which attracted more kinds of wildlife; and stabilizing riverbanks and changing the flows and geography of rivers in the park.
More here: https://www.youtube.com/watch?v=ysa5OBhXz-Q. I’m not sure exactly how credible this video is, but if only half of it is true it’s still pretty cool.
2) Saturn’s rings have seasons! Just like Earth, Saturn has tilt, which causes some parts of the rings to be exposed to more sunlight than others at different times. Moreover, scientists are now using anomalies in the heating and cooling rates of the different bands to study the makeup of the rings.
3) Michael Faraday was apparently inspired to study science by a chemistry textbook by one Jane Marset. It’s kind of unusual to see an early 19th century chemistry textbook *written by a woman*, but it turns out that that book was wildly successful in several countries (though it failed miserably in Germany?), was printed 23 times, and imitated by most of the chemistry textbooks of the period.
Apparently there was some debate at the time of whether young women should learn chemistry. An argument was put forth that chemistry taught useful skills and knowledge for domestic work, and that knowledge of chemistry would lead to “spiritual insight”, though I’m not sure how that was supposed to work. These, at least, were the justifications given by instructors and administrators of schools for women. I’m no historian, and I certainly don’t know the historical consensus on this particular topic, but there’s some reason to believe that those teachers, and Jane Marset in particular, were really more interested in teaching the science behind chemistry for the sake of the science, and used the “domestic” and “spiritual” arguments as a cover for a (for the time) more radical move to educate women in the theory and practice of chemistry.
1) The reintroduction of wolves to Yellowstone had a surprising number and variety of effects on the Yellowstone ecosystem. Most of the effect seems to have come from scaring elk and caribou and other ungulates away from overgrazed riverbanks and some forested areas, which gave those areas a chance to grow much more thickly and densely. This had a number of impacts, including attracting songbirds that like the forest; attracting bears and other animals that eat the berries off of mature plant life; attracting beavers that like to eat the full-grown trees and which themselves created ponds which attracted more kinds of wildlife; and stabilizing riverbanks and changing the flows and geography of rivers in the park.
More here: https://www.youtube.com/watch?v=ysa5OBhXz-Q. I’m not sure exactly how credible this video is, but if only half of it is true it’s still pretty cool.
2) Saturn’s rings have seasons! Just like Earth, Saturn has tilt, which causes some parts of the rings to be exposed to more sunlight than others at different times. Moreover, scientists are now using anomalies in the heating and cooling rates of the different bands to study the makeup of the rings.
3) Michael Faraday was apparently inspired to study science by a chemistry textbook by one Jane Marset. It’s kind of unusual to see an early 19th century chemistry textbook *written by a woman*, but it turns out that that book was wildly successful in several countries (though it failed miserably in Germany?), was printed 23 times, and imitated by most of the chemistry textbooks of the period.
Apparently there was some debate at the time of whether young women should learn chemistry. An argument was put forth that chemistry taught useful skills and knowledge for domestic work, and that knowledge of chemistry would lead to “spiritual insight”, though I’m not sure how that was supposed to work. These, at least, were the justifications given by instructors and administrators of schools for women. I’m no historian, and I certainly don’t know the historical consensus on this particular topic, but there’s some reason to believe that those teachers, and Jane Marset in particular, were really more interested in teaching the science behind chemistry for the sake of the science, and used the “domestic” and “spiritual” arguments as a cover for a (for the time) more radical move to educate women in the theory and practice of chemistry.
Saturday, September 5, 2015
iPython Notebooks, Git and Dropbox, and Squirrel Teeth
Today I Learned:
1) …how an iPython notebook works. It’s essentially literate programming — you write what you’re doing, in English, then insert blocks of code. The code runs, and the results are stored and displayed with the code. That way, your code, its output, and some English commentary on what it all does are all intimately connected.
2) It is highly recommended to NOT mix dropbox and mercurial/git. Highly.
3) Squirrels (the usual kind) have red teeth! How have I lived among them for so long and not noticed?!
1) …how an iPython notebook works. It’s essentially literate programming — you write what you’re doing, in English, then insert blocks of code. The code runs, and the results are stored and displayed with the code. That way, your code, its output, and some English commentary on what it all does are all intimately connected.
2) It is highly recommended to NOT mix dropbox and mercurial/git. Highly.
3) Squirrels (the usual kind) have red teeth! How have I lived among them for so long and not noticed?!
Thursday, September 3, 2015
TMS, mitoSENS, and ginkgo fruit
Today I Learned:
1) Transcranial magnetic stimulation has been approved for medical use! ...for treating drug-resistant depression. Really? I mean, if it helps, that's awesome, but of all the amazing things that technology could do, we're using it solely to treat depression? I'm a bit disappointed. At least this means it checks out as safe by the FDA.
(For those not in the know yet, transcranial magnetic stimulation, or TMS, is the use of a giant multi-Tesla magnet to temporarily shut down parts of the brain. It's been played with fairly extensively, and is surprisingly less dangerous than it sounds -- rare side effects include fainting, dizziness, and VERY rarely, seizures. Oh, and some forms make a really loud clicking noise that can be hard on the ears. And there's a version that uses magnets on the scalp that can get hot enough to irritate. And that's about it.)
2) SENS has come up, supposedly, with a way to target mRNAs to the mitochondria. That's kind of a game-changer for their mitoSENS program (moving copies of the mitochondrial genes into the nucleus). Before, they'd had a lot of trouble getting nuclearly-expressed proteins shuttled to the mitochondria -- there are lots of proteins that already do that, but the remaining ones are much more polar and therefore hard to get through the membrane. By targeting mRNAs instead of proteins, SENS gets around that entirely. Brilliant!
Also, if you donate $30,000 to the project, you get to travel to SENS headquarters in San Francisco and have dinner with James Edward Olmos. Seriously.
3) ...the smell of ginkgo tree fruit. It's somewhere beween blue cheese and the back of an unwashed ear. It's not an entirely unpleasant smell... but I can see why they have a reputation for being smelly.
1) Transcranial magnetic stimulation has been approved for medical use! ...for treating drug-resistant depression. Really? I mean, if it helps, that's awesome, but of all the amazing things that technology could do, we're using it solely to treat depression? I'm a bit disappointed. At least this means it checks out as safe by the FDA.
(For those not in the know yet, transcranial magnetic stimulation, or TMS, is the use of a giant multi-Tesla magnet to temporarily shut down parts of the brain. It's been played with fairly extensively, and is surprisingly less dangerous than it sounds -- rare side effects include fainting, dizziness, and VERY rarely, seizures. Oh, and some forms make a really loud clicking noise that can be hard on the ears. And there's a version that uses magnets on the scalp that can get hot enough to irritate. And that's about it.)
2) SENS has come up, supposedly, with a way to target mRNAs to the mitochondria. That's kind of a game-changer for their mitoSENS program (moving copies of the mitochondrial genes into the nucleus). Before, they'd had a lot of trouble getting nuclearly-expressed proteins shuttled to the mitochondria -- there are lots of proteins that already do that, but the remaining ones are much more polar and therefore hard to get through the membrane. By targeting mRNAs instead of proteins, SENS gets around that entirely. Brilliant!
Also, if you donate $30,000 to the project, you get to travel to SENS headquarters in San Francisco and have dinner with James Edward Olmos. Seriously.
3) ...the smell of ginkgo tree fruit. It's somewhere beween blue cheese and the back of an unwashed ear. It's not an entirely unpleasant smell... but I can see why they have a reputation for being smelly.
Reddit, Extern, and Java
Today I Learned:
1) A physicist named Travis Hoppe recently wrote a program to suggest content for posts to the TIL subreddit. 8% of its suggestions made the top story of TIL. He was banned from the redit after revealing what he had done (after something like a year of posting).
Thanks to Jeanne Morin-Leisk, who happens to know the guy.
2) Your C fact for the day -- a variable declared with the 'extern' keyword doesn't actually get declared at all. 'Extern' simply notifies the compiler that the variable has been declared *elsewhere* and can be accessed without the program having to make it again. This is important because if you're using an extern variable, you have to *actually* declare it somewhere. Or the compiler gets mad. Or worse.
3) Java (the programming langauge) was originally developed to be used in an interactive television. It turned out that virtual machines were a bit too advanced for the cable companies of the time, so Sun Microsystems moved it onto desktop computers and servers instead.
1) A physicist named Travis Hoppe recently wrote a program to suggest content for posts to the TIL subreddit. 8% of its suggestions made the top story of TIL. He was banned from the redit after revealing what he had done (after something like a year of posting).
Thanks to Jeanne Morin-Leisk, who happens to know the guy.
2) Your C fact for the day -- a variable declared with the 'extern' keyword doesn't actually get declared at all. 'Extern' simply notifies the compiler that the variable has been declared *elsewhere* and can be accessed without the program having to make it again. This is important because if you're using an extern variable, you have to *actually* declare it somewhere. Or the compiler gets mad. Or worse.
3) Java (the programming langauge) was originally developed to be used in an interactive television. It turned out that virtual machines were a bit too advanced for the cable companies of the time, so Sun Microsystems moved it onto desktop computers and servers instead.
Wednesday, September 2, 2015
Mongols, Japanese, and Unix
Today I Learned:
1) Probably the only reason the Mongols didn't completely conquer Europe in the 13th century under Ogadai Khan's rule was because Ogadai died. The Empire had a rather massive army in Hungary at the time, which had just finished easily wiping out the largest army in all of Europe, when news of Ogadai's death reached them. They promptly marched back home to participate in the selection of the next Khan, probably saving the lives of millions of Europeans.
2) Japanese has *at least* two forms of "I" -- 'watashi' and 'atashi'. I will not attempt to write those properly here. 'Watashi' is the general form of "I", useable more or less anytime (again, as far as I know). "Atashi" is an interesting one -- it's an optional feminine form of "I", whose use emphasizes femininity. I think there's a lot of subtlety to it, but basically using "watashi" draws attention to one's female-ness, or makes it explicitly clear.
...and just now I learned that Python's quotation convention (interchangeable "'"s and '"'s) is creeping into my everyday writing. What do you know.
3) Unix (or just Linux?) has a system for leaving mail for users -- by convention, mail goes into files somewhere like /etc/var/spool/<username>. There is much to learn about this breed of OS....
1) Probably the only reason the Mongols didn't completely conquer Europe in the 13th century under Ogadai Khan's rule was because Ogadai died. The Empire had a rather massive army in Hungary at the time, which had just finished easily wiping out the largest army in all of Europe, when news of Ogadai's death reached them. They promptly marched back home to participate in the selection of the next Khan, probably saving the lives of millions of Europeans.
2) Japanese has *at least* two forms of "I" -- 'watashi' and 'atashi'. I will not attempt to write those properly here. 'Watashi' is the general form of "I", useable more or less anytime (again, as far as I know). "Atashi" is an interesting one -- it's an optional feminine form of "I", whose use emphasizes femininity. I think there's a lot of subtlety to it, but basically using "watashi" draws attention to one's female-ness, or makes it explicitly clear.
...and just now I learned that Python's quotation convention (interchangeable "'"s and '"'s) is creeping into my everyday writing. What do you know.
3) Unix (or just Linux?) has a system for leaving mail for users -- by convention, mail goes into files somewhere like /etc/var/spool/<username>. There is much to learn about this breed of OS....
Tuesday, September 1, 2015
RIP Oliver Sacks
Today I Learned:
1) Oliver Sacks is dead. This is the kind of thing that pushed me into Bioengineering in the first place.
Thanks to Menghsa Gong for bringing this to my attention.
2) Phobos is a really weird little moon. It’s incredibly close to its parent planet (9,000 km, compared to more than 30,000 km for our moon). It’s tiny — only about 14 miles across. It’s also getting closer to Mars, and in about 50 megayears it will cross the Roche Limit, which is the point where tidal forces of its parent will rip it apart into rubble.
Deimos, for the record, is even smaller (about half the radius), but has an orbit closer to that of the moon. I’m not sure if it’s getting closer or father away.
Thanks to Bungie’s Ride Along: Mars video.
3) One more Mars fact from that video — at least some of Mars’s dunes have visible rivulets on them that are probably from water. Through a process I don’t entirely understand, water trapped in the dunes sometimes melts and lightly erupts from the dunes, leaving little channels that we can see.
1) Oliver Sacks is dead. This is the kind of thing that pushed me into Bioengineering in the first place.
Thanks to Menghsa Gong for bringing this to my attention.
2) Phobos is a really weird little moon. It’s incredibly close to its parent planet (9,000 km, compared to more than 30,000 km for our moon). It’s tiny — only about 14 miles across. It’s also getting closer to Mars, and in about 50 megayears it will cross the Roche Limit, which is the point where tidal forces of its parent will rip it apart into rubble.
Deimos, for the record, is even smaller (about half the radius), but has an orbit closer to that of the moon. I’m not sure if it’s getting closer or father away.
Thanks to Bungie’s Ride Along: Mars video.
3) One more Mars fact from that video — at least some of Mars’s dunes have visible rivulets on them that are probably from water. Through a process I don’t entirely understand, water trapped in the dunes sometimes melts and lightly erupts from the dunes, leaving little channels that we can see.
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