Today I Learned:
1) Transposable elements* are preferentially found in areas with open chromatin structure. Makes perfect sense — open-chromatin regions are more accessible to most things, so it stands to reason that a transposable element would be more likely to land in one — and it turns out to be true. Beautiful.
Thanks to Andrew Halleran for pointing this out to me.
* These are “genes” that, as far as we know, do nothing but move themselves around the genome, sometimes duplicating themselves.
2) With very few exceptions (as in, awardees of very prestigious scholarships), you have to pay money to get a PhD at Cambridge University (the british one). Thank goodness for the American model. To be fair, British PhDs aren’t really the same as American PhDs — they’re much faster and in some ways closer to a Master’s degree. Still, that’s three years of no income, which sucks.
3) It’s a bad idea to let the last little bits of soap bars go down the shower drain — they’ll nucleate hairballs and clog it up.
Sunday, August 30, 2015
Saturday, August 29, 2015
A Small Piece of a Big World, Lines of Code, and Basil
Today I Learned:
1) …a small piece of the intricacies of high-level Super Smash Bros. I learned about wave-dashing, and about a few of the one- or two- or three- frame tricks with various characters. I performed my first-ever short jump, and learned how to double-shine with Fox. Just a heads-up — Erik Jue is very, very good at that game. It’s beautiful to watch, if a bit bewildering to a plebe like I.
2) A modern fighter jet has about as many lines of code as an old-ish operating system, like one of the Linux kernels from a couple of versions back… but a modern smart car has some of the most code of any single system, far more than, say, Windows 7. Also, something I knew the pieces of but never put together… pretty much all modern operating systems, with the possible exceptions of some mobile OSes, have more information content than most bacteria. That makes bacteria all the more impressive to me.
3) A handful of fresh basil does wondrous things to jarred pasta sauces, even to sauces that already nominally have basil. Just chop it into fine strips and throw into the sauce in a saucepan, you won’t regret it. Trader Joe’s sells really convenient packs of basil for a couple bucks that are each good for something like two to four jars of sauce.
1) …a small piece of the intricacies of high-level Super Smash Bros. I learned about wave-dashing, and about a few of the one- or two- or three- frame tricks with various characters. I performed my first-ever short jump, and learned how to double-shine with Fox. Just a heads-up — Erik Jue is very, very good at that game. It’s beautiful to watch, if a bit bewildering to a plebe like I.
2) A modern fighter jet has about as many lines of code as an old-ish operating system, like one of the Linux kernels from a couple of versions back… but a modern smart car has some of the most code of any single system, far more than, say, Windows 7. Also, something I knew the pieces of but never put together… pretty much all modern operating systems, with the possible exceptions of some mobile OSes, have more information content than most bacteria. That makes bacteria all the more impressive to me.
3) A handful of fresh basil does wondrous things to jarred pasta sauces, even to sauces that already nominally have basil. Just chop it into fine strips and throw into the sauce in a saucepan, you won’t regret it. Trader Joe’s sells really convenient packs of basil for a couple bucks that are each good for something like two to four jars of sauce.
Thursday, August 27, 2015
Idaho Power, Auto, and Hot Cores... and a Bonus!
Today I Learned:
1) Idaho is a geologically active state, and has some of the best geothermal power in the States, with an estimated 800 MW of untapped geothermal potential*. Idaho also has the oldest geothermal power system in the country, and its state capitol building is the only US state capitol building powered geothermal.
*which isn’t really *that* much, in the grand scheme of things, but hey, maybe it’s enough for Idaho
2) The “auto” keyword in C++ — it replaces any type declaration and automatically infers the correct type at compile-time.
3) Why the Earth’s core is hot! I knew that radioactive decay was involved (which was what threw off Lord Kelvin’s famous and abysmally wrong calculation of the age of the Earth). Quite a bit of the heat is still residual from the formation of the Earth. When the planet formed, it formed from tons of little chunks of matter falling into its gravity well… the potential energy of all that stuff was largely converted into heat via the usual means, and a lot of that has been locked away under the crust, where it can’t escape very quickly, to the present day.
Bonus) How to say “electrophoresis” in Spanish. It’s “electroforesis”.
1) Idaho is a geologically active state, and has some of the best geothermal power in the States, with an estimated 800 MW of untapped geothermal potential*. Idaho also has the oldest geothermal power system in the country, and its state capitol building is the only US state capitol building powered geothermal.
*which isn’t really *that* much, in the grand scheme of things, but hey, maybe it’s enough for Idaho
2) The “auto” keyword in C++ — it replaces any type declaration and automatically infers the correct type at compile-time.
3) Why the Earth’s core is hot! I knew that radioactive decay was involved (which was what threw off Lord Kelvin’s famous and abysmally wrong calculation of the age of the Earth). Quite a bit of the heat is still residual from the formation of the Earth. When the planet formed, it formed from tons of little chunks of matter falling into its gravity well… the potential energy of all that stuff was largely converted into heat via the usual means, and a lot of that has been locked away under the crust, where it can’t escape very quickly, to the present day.
Bonus) How to say “electrophoresis” in Spanish. It’s “electroforesis”.
Wednesday, August 26, 2015
Make Tricks, Microfluidic Timings, and One Big Haplotype
Today I Learned:
1) I actually learned this on Monday, but it’s useful enough to cheat with — you can run “make” using more than one core with the -j flag! So if you have a 4-core machine, you can run “make -j 4” to build your program four times as quickly!
2) It takes between 4 and 8 hours to etch microfluidic channels into a set (2-4(?)) of typical glass slides.
3) I knew that Genghis Khan had a lot of descendants. Thanks to Chris Lennox, I now know that he had a lot of *direct* descendants — specifically, about 10% of the population of Asia, which is *way* more than can be accounted for even by his stunningly large collection of wives. Evolutionary biologists studying the Genghis Khan haplotype hypothesize that simply being a descendent of the Khan has been culturally selected for over the last 800 years.
1) I actually learned this on Monday, but it’s useful enough to cheat with — you can run “make” using more than one core with the -j flag! So if you have a 4-core machine, you can run “make -j 4” to build your program four times as quickly!
2) It takes between 4 and 8 hours to etch microfluidic channels into a set (2-4(?)) of typical glass slides.
3) I knew that Genghis Khan had a lot of descendants. Thanks to Chris Lennox, I now know that he had a lot of *direct* descendants — specifically, about 10% of the population of Asia, which is *way* more than can be accounted for even by his stunningly large collection of wives. Evolutionary biologists studying the Genghis Khan haplotype hypothesize that simply being a descendent of the Khan has been culturally selected for over the last 800 years.
Tuesday, August 25, 2015
Khanian Meritocracy, Lukewarm Superconductivity, and Cas9 Strikes Again
Today I Learned:
1) Although Genghis Khan was well known as a ruthless leader who would execute basically anyone who messed up or showed the slightest hint of disloyalty, and for massacring any enemies who did not immediately surrender, he was also known for taking in enemies who has particular talents, particularly particular leadership ability, and giving them rank and power according to their abilities. He may have been a cruel dictator, but he was at least a meritocratic one.
2) Scientists have just achieved superconductivity at -70 C! That’s pretty cold… but it’s a temperature that *exists on Earth in the wild*. You could occasionally make that work in Antarctica. With no cooling. Or you could do it in a standard -80 C freezer in any molecular biology lab. That’s a lot better than other superconductivity experiments!
Thanks to Alex Alexander for linking me to this one.
3) Scientists in Ireland and Scotland have successfully used cas9 to treat a mouse model of Meesmann’s epithelial corneal dystrophy. I have no idea what Meesmann’s epithelial corneal dystrophy is, except that it’s caused by a well-known single-nucleotide polymorphism, and it’s apparently dominant. The researchers used a more-or-less standard cutting variant to introduce a frameshift specifically into the mutant allele, knocking it out, while leaving the wild-type, healthy allele intact.
Thanks to the AddGene Facebook page for linking me to this one.
1) Although Genghis Khan was well known as a ruthless leader who would execute basically anyone who messed up or showed the slightest hint of disloyalty, and for massacring any enemies who did not immediately surrender, he was also known for taking in enemies who has particular talents, particularly particular leadership ability, and giving them rank and power according to their abilities. He may have been a cruel dictator, but he was at least a meritocratic one.
2) Scientists have just achieved superconductivity at -70 C! That’s pretty cold… but it’s a temperature that *exists on Earth in the wild*. You could occasionally make that work in Antarctica. With no cooling. Or you could do it in a standard -80 C freezer in any molecular biology lab. That’s a lot better than other superconductivity experiments!
Thanks to Alex Alexander for linking me to this one.
3) Scientists in Ireland and Scotland have successfully used cas9 to treat a mouse model of Meesmann’s epithelial corneal dystrophy. I have no idea what Meesmann’s epithelial corneal dystrophy is, except that it’s caused by a well-known single-nucleotide polymorphism, and it’s apparently dominant. The researchers used a more-or-less standard cutting variant to introduce a frameshift specifically into the mutant allele, knocking it out, while leaving the wild-type, healthy allele intact.
Thanks to the AddGene Facebook page for linking me to this one.
Monday, August 24, 2015
Externs, Acrylamides, and Chaos Game Representations
Today I Learned:
1) In C, if you’re using an external variable and you malloc it (which, I suppose, you have to do sometime), be careful how you do it. If you declare its type when you malloc it, it will be allocated as a local variable unconnected to the external variable. If you want to actually use it as an extern, you have to declare it *without* its type. So
extern int* x;
x = malloc(2048);
will give you the *actual external variable x*, while
extern int* x;
int* x = malloc(2048);
will give you a *local* variable named x that isn’t related. Intuitive, right? …
2) …why acrylamide is toxic. Acrylamide is a small molecule used a lot in molecular biology to make gels, which you can run proteins or DNA (usually proteins) through to separate them out by size or charge or other things. Acrylamide gels are perfectly harmless, and can, for instance, be thrown out safely in regular garbage. Unpolymerized acrylamide powder, on the other hand, is a neurotoxin and has to be handled pretty carefully.
Today I learned *why* acrylamide powder is toxic. It turns out it’s because acrylamide in the bloodstream can very easily enter the brain… and polymerize there. Well how about that.
3) The Chaos Game Representation (CGR) I talked about a few TILs ago can be used to draw Sierpinski triangles and other fractals. Here’s the algorithm for a Sierpinski triangle:
* Start with a triangle
* Draw a point at the center
* Randomly pick a corner and draw a point halfway between that corner and the last point you drew. Repeat this step a bunch.
From a little experimentation of mine (and ideas from Robert Johnson), I’ve found that you can probably get a Sierpinski-looking fractal from any similar algorithm with more “dimensions” than degrees of freedom — for instance, you can do the same thing by drawing inside a pentagon but only picking from four points.
EDIT: Whoops, looks like it might not have to have more dimensions than degrees of freedom — it still makes a fractal if you use all of the points of a pentagon.
1) In C, if you’re using an external variable and you malloc it (which, I suppose, you have to do sometime), be careful how you do it. If you declare its type when you malloc it, it will be allocated as a local variable unconnected to the external variable. If you want to actually use it as an extern, you have to declare it *without* its type. So
extern int* x;
x = malloc(2048);
will give you the *actual external variable x*, while
extern int* x;
int* x = malloc(2048);
will give you a *local* variable named x that isn’t related. Intuitive, right? …
2) …why acrylamide is toxic. Acrylamide is a small molecule used a lot in molecular biology to make gels, which you can run proteins or DNA (usually proteins) through to separate them out by size or charge or other things. Acrylamide gels are perfectly harmless, and can, for instance, be thrown out safely in regular garbage. Unpolymerized acrylamide powder, on the other hand, is a neurotoxin and has to be handled pretty carefully.
Today I learned *why* acrylamide powder is toxic. It turns out it’s because acrylamide in the bloodstream can very easily enter the brain… and polymerize there. Well how about that.
3) The Chaos Game Representation (CGR) I talked about a few TILs ago can be used to draw Sierpinski triangles and other fractals. Here’s the algorithm for a Sierpinski triangle:
* Start with a triangle
* Draw a point at the center
* Randomly pick a corner and draw a point halfway between that corner and the last point you drew. Repeat this step a bunch.
From a little experimentation of mine (and ideas from Robert Johnson), I’ve found that you can probably get a Sierpinski-looking fractal from any similar algorithm with more “dimensions” than degrees of freedom — for instance, you can do the same thing by drawing inside a pentagon but only picking from four points.
EDIT: Whoops, looks like it might not have to have more dimensions than degrees of freedom — it still makes a fractal if you use all of the points of a pentagon.
Friday, August 21, 2015
Biological Composition, Leaklessness, and Otter Deaths
Today I Learned:
1) A couple of tricks for composing biological parts (genetically encoded logic gates, switches, sensors, and the like). First, use really strong terminators! Transcriptional leakage is common, and using better terminators can help quite a bit. Second, put a ribozyme motif between your promoter and your ribosomal binding sites (RBSs). It will cleave off the promoter after transcription, which prevents different promoters from interacting differently with the RBS.
Also, Chris Voigt’s lab is working on a piece of software called Cello, which should be available on the web soon, which can design complex genetic circuits based on a logical specification. It uses the tricks mentioned above, and has pretty detailed empirical characterization of performance and error for its parts, which it propagates through the circuits it designs to determine their expected performance. Also Voigt lab’s web page has a nice compendium of (mostly external) tools for synthetic biologists (and other biologists!): http://web.mit.edu/voigtlab/webtools.html
2) A motif for leafless strand displacement reactions! See http://solo.ucsf.edu/papers/dsd-leakless.pdf for details. Basically, there’s a whole bunch of nano tech things you can build from DNA that use a technique called DNA strand displacement, or DSD — it’s a really simple and elegant way of making DNA strands in a test tube dynamically interact with each other. The trouble is, DSD almost always features “leak”, which is unwanted reactions between certain kinds of strands that end up killing the whole thing over the long term. Today I heard a proposal for essentially eliminating leak reactions, which is a big deal in the field.
3) Most sea otters die from infectious diseases. Most of the infectious diseases are protists. Remember all the nasty little choanoflagellates and flagellate parasites from AP/Intro Bio? Yeah, sea otters get those a lot. There’s also a fair amount of death to injuries and predation (about 2.5% of otter deaths are from gunshot wounds).
1) A couple of tricks for composing biological parts (genetically encoded logic gates, switches, sensors, and the like). First, use really strong terminators! Transcriptional leakage is common, and using better terminators can help quite a bit. Second, put a ribozyme motif between your promoter and your ribosomal binding sites (RBSs). It will cleave off the promoter after transcription, which prevents different promoters from interacting differently with the RBS.
Also, Chris Voigt’s lab is working on a piece of software called Cello, which should be available on the web soon, which can design complex genetic circuits based on a logical specification. It uses the tricks mentioned above, and has pretty detailed empirical characterization of performance and error for its parts, which it propagates through the circuits it designs to determine their expected performance. Also Voigt lab’s web page has a nice compendium of (mostly external) tools for synthetic biologists (and other biologists!): http://web.mit.edu/voigtlab/webtools.html
2) A motif for leafless strand displacement reactions! See http://solo.ucsf.edu/papers/dsd-leakless.pdf for details. Basically, there’s a whole bunch of nano tech things you can build from DNA that use a technique called DNA strand displacement, or DSD — it’s a really simple and elegant way of making DNA strands in a test tube dynamically interact with each other. The trouble is, DSD almost always features “leak”, which is unwanted reactions between certain kinds of strands that end up killing the whole thing over the long term. Today I heard a proposal for essentially eliminating leak reactions, which is a big deal in the field.
3) Most sea otters die from infectious diseases. Most of the infectious diseases are protists. Remember all the nasty little choanoflagellates and flagellate parasites from AP/Intro Bio? Yeah, sea otters get those a lot. There’s also a fair amount of death to injuries and predation (about 2.5% of otter deaths are from gunshot wounds).
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