Since gaining actual friends at college (I know, I know), I've been repeatedly surprised by how often people skip lecture. I must have noticed this earlier -- after all, I did observe that lecture halls tended to get less full as the semester went on -- but somehow I thought that all good students always went to lecture or some such. Apparently this is not the case.
Also, it seems like people are supposed to know by this time whether they're "visual learners" or "audio learners" or some such. I have never been able to figure this out. But apparently I learn pretty well by going to lectures (as opposed to doing the reading), although this is probably a motivation problem rather than anything else.
For 2.5 years this strategy served me well, but now that I run into courses with mediocre-to-poor lecturers who are always unclear and often omit large quantities of important material, it's becoming problematic.
Thursday, February 25, 2010
Thursday, February 18, 2010
Learning to read all over again: Addendum
The project of learning to critically read the primary literature is going pretty well so far. I'd like to add another stage to the four stages I mentioned:
5. Selectivity. At this point you become able to read "the literature" as a whole, not just individual papers. You can make a good guess about what's important without having to read everything in excruciating detail.
I'll also note that the stages overlap quite a bit. I'm still mostly in Credulity, but there are some papers I can actually criticize, and some I still fail to understand.
5. Selectivity. At this point you become able to read "the literature" as a whole, not just individual papers. You can make a good guess about what's important without having to read everything in excruciating detail.
I'll also note that the stages overlap quite a bit. I'm still mostly in Credulity, but there are some papers I can actually criticize, and some I still fail to understand.
Wednesday, February 17, 2010
Impressions
The water dispenser outside my lab has a cold spigot and a hot spigot. The hot spigot dispenses water which is actually quite hot. However, I couldn't figure out how to use it at first... until I realized that you have to put the handle in a certain position, which is not its natural low-energy gravity-ordained position, and then press it. It's a safety interlock! Good thinking! *makes tea*
I drove in snow for the first time recently. Well, not snow, but there was some kind of sleet-like substance on the roads and falling (slowly) from the sky. It was also the first time I ever skidded (a small amount). I've been on a skid mat, but it was a while ago and I remember it very poorly. I think the problem with the skit mat was either that I was unable to actually skid, or that it made no sense out of the context of a street and the slight hazard of hitting parked cars. There's no spatial reference on an infinite frictionless plane, after all.
Plates of fermenting bacteria on a phenol-red containing medium have this wonderful tendency to grow into miniature sunrises (although they do develop a rather off-putting smell).
Figure 1: Like viewing the sunrise from a mountaintop outhouse.
I just reread Terry Pratchett's Going Postal, and I really liked it. He gives the sort of lovely far-off impressions of the world of the clacks towers that I want to go there but that might destroy the mystique -- you know, the same thing people always say about why the Silmarillion is written in such a dreamy mythic tone. And if Thief of Time is the Discworld's The Matrix, then Going Postal is its Jargon File.
I drove in snow for the first time recently. Well, not snow, but there was some kind of sleet-like substance on the roads and falling (slowly) from the sky. It was also the first time I ever skidded (a small amount). I've been on a skid mat, but it was a while ago and I remember it very poorly. I think the problem with the skit mat was either that I was unable to actually skid, or that it made no sense out of the context of a street and the slight hazard of hitting parked cars. There's no spatial reference on an infinite frictionless plane, after all.
Plates of fermenting bacteria on a phenol-red containing medium have this wonderful tendency to grow into miniature sunrises (although they do develop a rather off-putting smell).
Figure 1: Like viewing the sunrise from a mountaintop outhouse.I just reread Terry Pratchett's Going Postal, and I really liked it. He gives the sort of lovely far-off impressions of the world of the clacks towers that I want to go there but that might destroy the mystique -- you know, the same thing people always say about why the Silmarillion is written in such a dreamy mythic tone. And if Thief of Time is the Discworld's The Matrix, then Going Postal is its Jargon File.
Tuesday, February 16, 2010
Ruuuuuuuuuuuuuun!
I was reading my perfectly innocent-looking homework assignment, when all of a sudden I saw this:
Figure 1: Augh!
You know, I figured a biomechanics class (which is, after all, all about the realistic physicality of biology as opposed to magic cartoon enzymes that always work) would feature more realistic estimates of a bacterium's size.
Figure 2: I also figured it would feature less fleeing and primal terror. [Source]
Of course, the answer is that E. coli are measured in μm (micrometers), not meters, and that the micro sign simply failed to render due to some strange failure of MS Word. The lesson is clear: Mistakes in character encodings will kill us all. Go forth boldly, my friends, and godspeed.
Figure 1: Augh!You know, I figured a biomechanics class (which is, after all, all about the realistic physicality of biology as opposed to magic cartoon enzymes that always work) would feature more realistic estimates of a bacterium's size.
Figure 2: I also figured it would feature less fleeing and primal terror. [Source]Of course, the answer is that E. coli are measured in μm (micrometers), not meters, and that the micro sign simply failed to render due to some strange failure of MS Word. The lesson is clear: Mistakes in character encodings will kill us all. Go forth boldly, my friends, and godspeed.
Monday, February 15, 2010
Journal Club: The enzyme bucket brigade
JE Dueber, GC Wu, GR Malmirchegini, TS Moon, CJ Petzold, AV Ullal, KLJ Prather, & JD Keasling. Synthetic protein scaffolds provide modular control over metabolic flux. Nature Biotechnology 27, 753–759 (1 August 2009) | doi:10.1038/nbt.1557
I read and presented this paper in my lab class this past fall -- and I thought it was just one of the coolest papers I'd ever read. Cool concept, rational design, elegant solution to a Hard Problem, multiple benefits, modularity/composability, real-world results... this paper has it all.
You can look at cells as little factories, taking in raw materials and churning out interesting molecules. A cell's naturally occurring assembly lines are optimized by evolution in various ways, to increase efficiency and decrease interference ("cross-talk") with other processes in the cell. In particular, natural metabolic pathways are regulated so that they don't go wildly out of control and start overproducing whatever chemical, because that would be wasteful and expensive (not to mention potentially harmful).
But when you're putting an artificial assembly line into a cell, you have to undo some of these constraints and not others. You have to maximize efficiency, minimize cross-talk, and avoid making toxic products in the middle of the pathway as much as possible. These goals all line up with the goals of the cell. However, your main goal is different from the cell's goal of "produce just enough": you want to produce as much product as possible. More medicine. More biofuel. More super-protein-material-thing. More whatever. So this should be easy, right? The metabolic pathway is made up of enzymes that convert Chemical A to Chemical B to Chemical C, and you're inserting the genes for those enzymes into a bacterium. Why can't you just put very strong promoters in front of those genes, so you get massive quantities of each enzyme, and massive output?
This simple maxing-out approach causes several problems. First of all, it does nothing about the intermediate chemicals along the pathway -- they could still be toxic, or even just float away and go to waste. Second of all, this approach doesn't bother to optimize the ratio of the two enzymes. (If Enzyme 1 is half as efficient as Enzyme 2, then you ought to have twice as much of Enzyme 1.) Third of all, this doesn't do anything to stop the pathway cross-talking with other pathways. Fourth, and possibly most important, there's no guarantee that forcing each individual cell to make as much product as it possibly, possibly can is the most efficient way to convert cell food into useful chemicals. It's probably more efficient to let the cell divert plenty of energy into maintaining its own health and into spawning more cells, so you end up with more product overall.
To solve this dilemma, Dueber et al borrowed a trick that cells often use to regulate their own pathways. A scaffold is a structural protein that grabs on to all the enzymes in a given pathway, and holds them together into something like an assembly line or a bucket brigade.
I read and presented this paper in my lab class this past fall -- and I thought it was just one of the coolest papers I'd ever read. Cool concept, rational design, elegant solution to a Hard Problem, multiple benefits, modularity/composability, real-world results... this paper has it all.
You can look at cells as little factories, taking in raw materials and churning out interesting molecules. A cell's naturally occurring assembly lines are optimized by evolution in various ways, to increase efficiency and decrease interference ("cross-talk") with other processes in the cell. In particular, natural metabolic pathways are regulated so that they don't go wildly out of control and start overproducing whatever chemical, because that would be wasteful and expensive (not to mention potentially harmful).
But when you're putting an artificial assembly line into a cell, you have to undo some of these constraints and not others. You have to maximize efficiency, minimize cross-talk, and avoid making toxic products in the middle of the pathway as much as possible. These goals all line up with the goals of the cell. However, your main goal is different from the cell's goal of "produce just enough": you want to produce as much product as possible. More medicine. More biofuel. More super-protein-material-thing. More whatever. So this should be easy, right? The metabolic pathway is made up of enzymes that convert Chemical A to Chemical B to Chemical C, and you're inserting the genes for those enzymes into a bacterium. Why can't you just put very strong promoters in front of those genes, so you get massive quantities of each enzyme, and massive output?
This simple maxing-out approach causes several problems. First of all, it does nothing about the intermediate chemicals along the pathway -- they could still be toxic, or even just float away and go to waste. Second of all, this approach doesn't bother to optimize the ratio of the two enzymes. (If Enzyme 1 is half as efficient as Enzyme 2, then you ought to have twice as much of Enzyme 1.) Third of all, this doesn't do anything to stop the pathway cross-talking with other pathways. Fourth, and possibly most important, there's no guarantee that forcing each individual cell to make as much product as it possibly, possibly can is the most efficient way to convert cell food into useful chemicals. It's probably more efficient to let the cell divert plenty of energy into maintaining its own health and into spawning more cells, so you end up with more product overall.
To solve this dilemma, Dueber et al borrowed a trick that cells often use to regulate their own pathways. A scaffold is a structural protein that grabs on to all the enzymes in a given pathway, and holds them together into something like an assembly line or a bucket brigade.
A question about scaffolds
There are two bits of signal transduction dogma that have started to bother me. I don't know why I didn't spot this before.
Kinases are proteins that activate other proteins by attaching phosphate groups to them. Kinase cascades (several kinases in a row) are fairly common in all kinds of signaling pathways. Their main benefits are amplifying and diversifying the signal. Since a kinase is after all an enzyme, it can catalyze the same reaction over and over; it can activate many copies of the next kinase in the cascade, each of which can activate many copies of... and so on into exponential growth. That's how you get amplification, turning a tiny-but-important input into a massive cell-wide response. Diversification comes in when a kinase has more than one target. This comes in handy when the cell needs to respond to one signal by doing several different things all at once.
Scaffolds are large structural proteins that grab several other proteins from a signaling (or metabolic) pathway and hold them together. This helps them get their job done more efficiently. They help make pathways specific. If Enzyme 2 is stuck on a scaffold between Enzyme 1 and Enzyme 3, it can't very well run off to some other part of the cell and mess something up.
So, I perceive a slight conflict here. On one hand, it's helpful to diversify a signal; on the other hand, signals ought to be specific. On one hand, enzyme cascades amplify signals by working catalytically instead of stoichiometrically; on the other hand, when kinases are bound to a scaffold, their stoichiometric ratio is locked at one-to-one. What's going on here?
The obvious answer is that each type of signal processing is used where it's appropriate, and all types are appropriate in different contexts. If this is the explanation, then you would never expect to find a kinase cascade associated with a scaffold. But that's exactly what the MAP kinase cascade does! What gives? I thought the whole point of having a kinase cascade was to amplify and diversify the signal, which is exactly what the scaffold seems to be preventing.
Figure 1: MAP kinase cascade shamelessly associating with scaffold protein. Have they no shame? What has the yeast mating pathway courting ritual come to these days? [Source]
Kinases are proteins that activate other proteins by attaching phosphate groups to them. Kinase cascades (several kinases in a row) are fairly common in all kinds of signaling pathways. Their main benefits are amplifying and diversifying the signal. Since a kinase is after all an enzyme, it can catalyze the same reaction over and over; it can activate many copies of the next kinase in the cascade, each of which can activate many copies of... and so on into exponential growth. That's how you get amplification, turning a tiny-but-important input into a massive cell-wide response. Diversification comes in when a kinase has more than one target. This comes in handy when the cell needs to respond to one signal by doing several different things all at once.
Scaffolds are large structural proteins that grab several other proteins from a signaling (or metabolic) pathway and hold them together. This helps them get their job done more efficiently. They help make pathways specific. If Enzyme 2 is stuck on a scaffold between Enzyme 1 and Enzyme 3, it can't very well run off to some other part of the cell and mess something up.
So, I perceive a slight conflict here. On one hand, it's helpful to diversify a signal; on the other hand, signals ought to be specific. On one hand, enzyme cascades amplify signals by working catalytically instead of stoichiometrically; on the other hand, when kinases are bound to a scaffold, their stoichiometric ratio is locked at one-to-one. What's going on here?
The obvious answer is that each type of signal processing is used where it's appropriate, and all types are appropriate in different contexts. If this is the explanation, then you would never expect to find a kinase cascade associated with a scaffold. But that's exactly what the MAP kinase cascade does! What gives? I thought the whole point of having a kinase cascade was to amplify and diversify the signal, which is exactly what the scaffold seems to be preventing.
Figure 1: MAP kinase cascade shamelessly associating with scaffold protein. Have they no shame? What has the yeast Journal Club: The amber-suppressing AND gate
Anderson JC, Voigt CA, Arkin AP. Environmental signal integration by a modular AND gate. Molecular Systems Biology 3:133 (2007) | doi:10.1038/msb4100173
Logic gates (AND, OR, NOT, etc.) are the basis of electronic computation. If we'd like to implement biological computation, one of our first steps has to be implementing similar logic gates using proteins and DNA. That is, we need to make devices that accept a few inputs, perform a logical operation on them, and then spit out the result. In the case of an AND gate, we want the output to be ON whenever both of the inputs are ON, and OFF when either input is OFF. It seems easy, but of course, this turns out to be a lot harder in biology (hence, people writing papers about it).
Figure 1: The result of this paper, if you abstract away all the interesting stuff. [Source]
What makes it hard to make an AND gate out of biochemical parts?
Lack of standard connectors. In electronics, every signal is carried by a current, and every connector is a wire. That isn't the case in biology. Biological signals are typically carried by the presence or absence of some protein that carries out some particular chemical reaction that affects other proteins. This is wildly nonstandardized, and it means if Protein A interacts with Receptor A, you can't just plug in Receptor B and expect things to work.
Fuzzy, non-discrete behavior. It's nearly impossible for a biological system to have a perfect ON or OFF state. Even if a signal is mostly off, there'll be a few molecules of it floating around somewhere. And when you go to turn it on, it'll take time. Basically, biological things tend to vary continuously and not discretely (in large jumps).
Crosstalk. If a biological device relies on some particular molecule, then that molecule is going to be everywhere in the cell. So, you can't put two copies of the same device into a cell and expect them to operate independently. They'll interfere or "crosstalk" with each other in ways you don't expect. In contrast, you can throw down dozens of electronic circuit elements onto a breadboard and they won't interfere with each other because they're separated by physical space. In biology, everything's in the same soup.
Logic gates (AND, OR, NOT, etc.) are the basis of electronic computation. If we'd like to implement biological computation, one of our first steps has to be implementing similar logic gates using proteins and DNA. That is, we need to make devices that accept a few inputs, perform a logical operation on them, and then spit out the result. In the case of an AND gate, we want the output to be ON whenever both of the inputs are ON, and OFF when either input is OFF. It seems easy, but of course, this turns out to be a lot harder in biology (hence, people writing papers about it).
Figure 1: The result of this paper, if you abstract away all the interesting stuff. [Source]What makes it hard to make an AND gate out of biochemical parts?
Lack of standard connectors. In electronics, every signal is carried by a current, and every connector is a wire. That isn't the case in biology. Biological signals are typically carried by the presence or absence of some protein that carries out some particular chemical reaction that affects other proteins. This is wildly nonstandardized, and it means if Protein A interacts with Receptor A, you can't just plug in Receptor B and expect things to work.
Fuzzy, non-discrete behavior. It's nearly impossible for a biological system to have a perfect ON or OFF state. Even if a signal is mostly off, there'll be a few molecules of it floating around somewhere. And when you go to turn it on, it'll take time. Basically, biological things tend to vary continuously and not discretely (in large jumps).
Crosstalk. If a biological device relies on some particular molecule, then that molecule is going to be everywhere in the cell. So, you can't put two copies of the same device into a cell and expect them to operate independently. They'll interfere or "crosstalk" with each other in ways you don't expect. In contrast, you can throw down dozens of electronic circuit elements onto a breadboard and they won't interfere with each other because they're separated by physical space. In biology, everything's in the same soup.
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