I just discovered Bitesize Bio, an awesome site full of discussions of common molecular-bio lab questions and problems. It has an RSS feed but is also set up with categories and menus for non-blog-style browsing. The ~5 posts I've read have all been informative, well-written, and interesting. I got a couple about interesting new techniques, a couple about theoretical questions and their practical consequences, and a couple about being a good grad student or a good mentor. It's really shiny, especially for a new lab member like me who wants to know the reasoning behind the magical incantations we sometimes do. "Wash with 0.75mL Buffer PE"? What does Buffer PE even do? ...OK, that's a cheating example -- Buffer PE is a proprietary mix from a commercial kit (but I'm told that after you add ethanol to it, as you must, it's just an improvement on straight ethanol).
For example, I just read an article about touchdown PCR, a neat hack on traditional PCR.
Sometimes in a PCR reaction you'll have trouble with the primers binding in incorrect places, because there happens to be some random sequence in your sample that's sorta-kinda complementary to your primers. Then you get nonspecific amplification of random crap, which can drown the gene fragment you actually wanted to amplify. What do you do?
You can calculate the optimal annealing/melting temperature (Tm) of your primers, and make sure to do your annealing step at that temperature. But random salts and stuff in your reaction can affect the Tm, so the calculated Tm is only an approximation. And at any temperature reasonably close to the Tm, even if it's not optimum, some annealing will happen. Maybe not much, but some. That's thermodynamics for you.
The idea of touchdown PCR is that there's a sweet-spot temperature where, statistically, it's too hot for nonspecific annealing, but just cool enough that the correct annealing can happen. You can't know exactly where this temperature is -- and you wouldn't want to run your whole reaction at that temperature anyway, because you'd only get a small amount of primer annealing and your yield would be low. So instead, for your first cycles you use an annealing temperature significantly higher than the calculated Tm for your primers (about 10 C higher). Then, in subsequent cycles, you gradually lower the annealing temperature. So in early cycles, only a few primers will anneal, and they'll almost all anneal to your actual sequence of interest, and not to random other sequences that are close-but-a-little-off. By the end of the cycle, you've amplified your correct sequence by a little bit relative to incorrect sequences. Run through several more cycles, and by the time you get to a "standard" annealing temperature where nonspecific annealing can happen, you've hopefully amplified the correct sequence quite a bit already, so nonspecific annealing becomes less of a problem because there are just more copies of the correct sequence available for the primers to bind to.
When I read about that, I was blown over. It's such a clever thermodynamics hack! -- it takes advantage of the fact that chemical reactions (DNA base-pairing or anything else) have fuzzy, stochastic behavior. For a given reaction, there isn't a sharp cutoff temperature where it goes from "too hot to react" suddenly to "OK now reaction proceeds fully". It's fuzzy. If it's too hot, a few molecules will react. Get a bit closer to the optimal temperature, and more molecules go. If you have two competing reactions with slightly different optimal temperatures (like specific and nonspecific annealing!), it's like having two bell curves overlapping, centered at slightly different values. You can find a value where one bell curve is acceptably high and the other is very low -- and then once you've amplified your chosen sequence N-fold, the game changes and you don't have to worry about the incorrect sequences nearly as much. It's like magic!
References (from original post):
1. Roux KH. Genome Research. 1995. 4: S185-194.
2. Mattick JS et al. Nature Protocols. 2008. 3(9). 1452 - 1456
Friday, July 31, 2009
Thursday, July 30, 2009
I return
Hello all,
Yes, I've been away from this blog for a very long time. But I find myself having more science content that I want to talk about, so I figure it's time to revive the Dendritic Arbor.
(Originally, I tied this blog not to my main Gmail account, but a different one. This turned out to be really annoying because every time I signed in to Blogger, I got signed out of my email. This was a major disincentive to post, and since I didn't realize you could transfer blog ownership between accounts, I just posted less and less. But now everything is fixed. Hooray.)
Where am I now? Well, I'm between my sophomore and junior years at MIT, I've radically changed my social circle, and I've pledged a (coed) fraternity, Epsilon Theta. More relevantly, I've finally entered a lab where I'm doing productive work on an interesting project in an environment I like, after a couple of short and ill-fated other lab positions. I'm working in one of the wellsprings of synthetic biology, Tom Knight's lab, studying a very intriguing and not very well-known bacterium.
At the same time, I'm also trying to get more into DIY Bio -- cheap open source lab equipment, electrophoresis gels in drinking straws, that sort of thing. We'll see how this goes. I may or may not be too busy to ever get started on this, what with classes (those random annoying peripheral activities that colleges insist you participate in).
It's good to be back.
Yes, I've been away from this blog for a very long time. But I find myself having more science content that I want to talk about, so I figure it's time to revive the Dendritic Arbor.
(Originally, I tied this blog not to my main Gmail account, but a different one. This turned out to be really annoying because every time I signed in to Blogger, I got signed out of my email. This was a major disincentive to post, and since I didn't realize you could transfer blog ownership between accounts, I just posted less and less. But now everything is fixed. Hooray.)
Where am I now? Well, I'm between my sophomore and junior years at MIT, I've radically changed my social circle, and I've pledged a (coed) fraternity, Epsilon Theta. More relevantly, I've finally entered a lab where I'm doing productive work on an interesting project in an environment I like, after a couple of short and ill-fated other lab positions. I'm working in one of the wellsprings of synthetic biology, Tom Knight's lab, studying a very intriguing and not very well-known bacterium.
At the same time, I'm also trying to get more into DIY Bio -- cheap open source lab equipment, electrophoresis gels in drinking straws, that sort of thing. We'll see how this goes. I may or may not be too busy to ever get started on this, what with classes (those random annoying peripheral activities that colleges insist you participate in).
It's good to be back.
Monday, September 29, 2008
Open Courseware is not the be-all and end-all
MIT's Open Courseware gets a lot of press. And a lot of it is well deserved -- it's fairly comprehensive, and does a good job managing the technical side of throwing vast amounts of material up on the internets (hooray for PDF). But it's not everything.
The past few days I've been stressing over various topics from my genetics class, mostly yeast tetrad analysis. Going to lecture hardly helps; for this class, it's been generally true that the more confusing topics are very poorly explained. Usually the textbook does a good job of explaining things, but it doesn't cover yeast tetrads hardly at all. And I have a test in two days.
(Yeast tetrad analysis is pretty interesting, by the way. I might write a post about it if I ever actually understand it.)
Turning to OCW didn't help, because more or less the same professors have been teaching the class for N years, so the lecture notes are exactly the same. I can get practice problems (old homeworks and exams), which are very useful once I actually understand something, but not in this case.
So I turned to Google. And lo and behold, googling {yeast tetrad analysis} brings up several universities' intro-genetics webpages about yeast tetrad analysis! With clear, coherent explanations and well-drawn diagrams! UC Berkeley (pdf), Indiana U (pdf), U of Saskatchewan, and U of Rochester, just to name a few.
(Even better, some of those are straight-up webpages. Better than everything being PDF, although not better than everything being .doc, which sometimes happens.)
I often hear, second or third hand, how people from other schools use MIT OCW all the time. And I'm not denying that OCW is awesome. But it's not perfect, and there are other places to go if the OCW explanation of a topic happens to be consistently lousy.
The past few days I've been stressing over various topics from my genetics class, mostly yeast tetrad analysis. Going to lecture hardly helps; for this class, it's been generally true that the more confusing topics are very poorly explained. Usually the textbook does a good job of explaining things, but it doesn't cover yeast tetrads hardly at all. And I have a test in two days.
(Yeast tetrad analysis is pretty interesting, by the way. I might write a post about it if I ever actually understand it.)
Turning to OCW didn't help, because more or less the same professors have been teaching the class for N years, so the lecture notes are exactly the same. I can get practice problems (old homeworks and exams), which are very useful once I actually understand something, but not in this case.
So I turned to Google. And lo and behold, googling {yeast tetrad analysis} brings up several universities' intro-genetics webpages about yeast tetrad analysis! With clear, coherent explanations and well-drawn diagrams! UC Berkeley (pdf), Indiana U (pdf), U of Saskatchewan, and U of Rochester, just to name a few.
(Even better, some of those are straight-up webpages. Better than everything being PDF, although not better than everything being .doc, which sometimes happens.)
I often hear, second or third hand, how people from other schools use MIT OCW all the time. And I'm not denying that OCW is awesome. But it's not perfect, and there are other places to go if the OCW explanation of a topic happens to be consistently lousy.
Thursday, August 21, 2008
To be intellectually uncomfortable
From one of Uncertain Principles' link dumps comes this piece from Inside Higher Ed: Tolerant Faculty, Intolerant Students. Apparently, despite the myth of the politically stubborn professor forcing his views on poor openminded students, the truth is more like students haranguing each other and professors doing fairly well at not inappropriately expressing political views. (Well, at least in Georgia. The study might have turned out differently if done on CRAZY CALIFORNIAN COLLEGES!!!!1!11!one.)
(I should note that I have only been in actual political discourse once all year, and it was with a student on my hall who fervently supported Ron Paul. Perfectly friendly, civil discussion; I didn't enjoy it because I don't enjoy political discourse, period. I haven't seen any politics in classes, probably because I haven't taken any classes where it's even marginally relevant. Coulomb's Law? Politicize that, bitches.)
The thing that really struck me about this article, though, was one particular quote: universities are a place to go to feel uncomfortable intellectually. Obviously, the article means this with regard to one's political beliefs -- but it's applicable in a much larger sense.
When I encounter something I can't understand, something really confusing, I get anxious and upset. This happens a lot because I'm at a difficult school, and it's to be expected that I will encounter confusing things. But why should I get upset? This is an artifact of tying understanding to Success and Achievement (TM), rather than understanding for its own sake. Even though I went to one of those hippie elementary schools where there are no grades, I suppose I still have kind of a hang-up about 'succeeding' versus being way outside of my comfort zone.
I really admire people who respond to confusing things by first feeling humble, and then feeling happy that they have another puzzle to solve. People who get suspicious if it looks like they understand everything. It's not that I think such people never get frustrated, but that seems like a highly useful mindset for a scientist or intellectual, much more so than getting upset and frustrated. (Certainly, given the complexity of the real world, if you think you understand everything about X, you're almost certainly wrong.) This mindset should also make for a happier person overall. Apart from that, it feels like the right thing to do -- it appeals to the idealist in me.
Universities are a place to go to feel uncomfortable intellectually.
The world is a place to go to feel uncomfortable intellectually!
I'm going to try and embrace this mindset, embrace this mantra. A form of "intellectual asceticism, perhaps?" Hopefully I can change my knee-jerk reaction to the difficult and the confusing.
(I should note that I have only been in actual political discourse once all year, and it was with a student on my hall who fervently supported Ron Paul. Perfectly friendly, civil discussion; I didn't enjoy it because I don't enjoy political discourse, period. I haven't seen any politics in classes, probably because I haven't taken any classes where it's even marginally relevant. Coulomb's Law? Politicize that, bitches.)
The thing that really struck me about this article, though, was one particular quote: universities are a place to go to feel uncomfortable intellectually. Obviously, the article means this with regard to one's political beliefs -- but it's applicable in a much larger sense.
When I encounter something I can't understand, something really confusing, I get anxious and upset. This happens a lot because I'm at a difficult school, and it's to be expected that I will encounter confusing things. But why should I get upset? This is an artifact of tying understanding to Success and Achievement (TM), rather than understanding for its own sake. Even though I went to one of those hippie elementary schools where there are no grades, I suppose I still have kind of a hang-up about 'succeeding' versus being way outside of my comfort zone.
I really admire people who respond to confusing things by first feeling humble, and then feeling happy that they have another puzzle to solve. People who get suspicious if it looks like they understand everything. It's not that I think such people never get frustrated, but that seems like a highly useful mindset for a scientist or intellectual, much more so than getting upset and frustrated. (Certainly, given the complexity of the real world, if you think you understand everything about X, you're almost certainly wrong.) This mindset should also make for a happier person overall. Apart from that, it feels like the right thing to do -- it appeals to the idealist in me.
Universities are a place to go to feel uncomfortable intellectually.
The world is a place to go to feel uncomfortable intellectually!
I'm going to try and embrace this mindset, embrace this mantra. A form of "intellectual asceticism, perhaps?" Hopefully I can change my knee-jerk reaction to the difficult and the confusing.
Friday, August 15, 2008
New Look & Feel!
So I changed the blog template.
The main thing that bothered me about the old template was that the main text column, the most important part, was of fixed width. Which is annoying if you have a wide monitor. With this new template, go ahead and change the width of your browser window, and the Dendritic Arbor will change right along with you. We strive to provide a customizable reader experience. We strive to be adaptable, plastic, and dynamic, like actual dendritic arbors.
(It also bothered me that approximately 80,000,000,000 other people are using the old template. Then again, this is Blogger, what was I expecting, hmm?)
I chose this particular theme via the complex and deliberate heuristic of seeing which one looked the most like the one Larry Moran picked for Sandwalk. I've been reading his series on protein structure and admiring Sandwalk's look-and-feel. I guess this is the exact same theme as Sandwalk has, just with different colors.
By the way, the protein structure series is excellent and here are links to all its items. There isn't really a 'best' order to read them in, but I've put them in an order that sort of makes sense.
Evolution and Variation in Folded Proteins
Levels of Protein Structure
The Alpha Helix
Beta Strands and Beta Sheets
Loops and Turns
Examples of Protein Structure
The main thing that bothered me about the old template was that the main text column, the most important part, was of fixed width. Which is annoying if you have a wide monitor. With this new template, go ahead and change the width of your browser window, and the Dendritic Arbor will change right along with you. We strive to provide a customizable reader experience. We strive to be adaptable, plastic, and dynamic, like actual dendritic arbors.
(It also bothered me that approximately 80,000,000,000 other people are using the old template. Then again, this is Blogger, what was I expecting, hmm?)
I chose this particular theme via the complex and deliberate heuristic of seeing which one looked the most like the one Larry Moran picked for Sandwalk. I've been reading his series on protein structure and admiring Sandwalk's look-and-feel. I guess this is the exact same theme as Sandwalk has, just with different colors.
By the way, the protein structure series is excellent and here are links to all its items. There isn't really a 'best' order to read them in, but I've put them in an order that sort of makes sense.
Evolution and Variation in Folded Proteins
Levels of Protein Structure
The Alpha Helix
Beta Strands and Beta Sheets
Loops and Turns
Examples of Protein Structure
Tuesday, August 12, 2008
Why I am a hard agnostic
I believe that the nature of deity is both unknown and unknowable (by humans).
As I understand it, "the nature of deity is unknown (and may or may not be knowable)" equals 'soft' or 'weak' agnosticism, and my position is 'hard' or 'strong' agnosticism. I was a soft agnostic up until relatively recently.
(Quick aside: that terminology bothers me because it's possible to be a strong weak agnostic -- i.e. you believe very strongly in the soft-agnostic position -- or a hard soft agnostic, or also a soft hard agnostic ("I'm pretty sure the nature of deity is unknowable as well as unknown"). Not sure what would be good alternative terms, though. Also, hard agnosticsim != militant atheism.)
I've been fairly sure for many years that the nature of deity is unknown, what with implausible theologies and the power of science, etc etc, blah blah woof woof -- this argument has been made, and people have responded to it, a million times.
There are two possible arguments, I think, for why we cannot know the nature of deity (as opposed to merely "we don't know it, but we might figure it out"). One is the "perverse liar god" argument, and it's sort of tongue-in-cheek. If there's an omnipotent deity, then it could make itself unknowable, never mind why it would want to. It could even put on an understandable mask while leaving its true nature hidden.
The other possible argument is "fundamental limits of human understanding". The human brain may be the most amazingly complex awesome thing in the universe, capable of conceiving arbitrarily complex and abstract ideas... but is it capable of understanding something omnipotent, omnipresent, omni-everything, possibly vaster than the universe? I highly doubt it, given how hard it is to truly grasp (say) the sheer size of a galaxy. (And I do mean truly grasp. Saying "oh, it's so many frillion light years across" does not count.) A galaxy has got to be a lot smaller than an omni-deity.
You'll note I said "fundamental limits of human understanding", not "fundamental limits of any understanding". I don't doubt that an omnipotent deity could understand itself perfectly well. It's perfectly possible that there are forms of understanding out there that are orders of magnitude more powerful than our piddling little thoughts, or maybe even have a completely different basis -- call them "super-understanding". But given that humans are limited to human understanding, can we understand super-understanding? I doubt it.
(For a very readable, math-flavored analogy to the topic of super-understanding, see Scott Aaronson's fabulous essay Who Can Name the Bigger Number?, which you should read anyway. He discusses Turing machines and Super-(Super-Super-...)Turing machines, among many other fascinating topics.)
And by the way, I have high standards for what I'm willing to call understanding deity. I'm not willing to settle for a grammatical string of English words, or a bunch of math, or whatever, that describes deity perfectly. I am perfectly capable of 'understanding' (sneer quotes!) a sentence like "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, and truth", in that I know what all its words mean and I can parse the sentence, because that is perfectly fine English. But can I fully appreciate the impact of a spirit, infinite, eternal and unchangeable, in its being, wisdom, power, etc? Can my body generate a sufficiently large visceral/emotional reaction to the import of that idea, or will it run out of neurotransmitters first? Can my humble heart and mind contain the infinite? I think not.
Now, since I'm feeling a bit Hofstadterian, try this one on for size: "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, truth, abstraction, recursion, subtlety, and inscrutability." Can this new, improved sentence give us a true, visceral understanding of an omni-deity? It's certainly an improvement.
(God-sentence is from Chapter 7 of Anne of Green Gables. I love that book.)
As I understand it, "the nature of deity is unknown (and may or may not be knowable)" equals 'soft' or 'weak' agnosticism, and my position is 'hard' or 'strong' agnosticism. I was a soft agnostic up until relatively recently.
(Quick aside: that terminology bothers me because it's possible to be a strong weak agnostic -- i.e. you believe very strongly in the soft-agnostic position -- or a hard soft agnostic, or also a soft hard agnostic ("I'm pretty sure the nature of deity is unknowable as well as unknown"). Not sure what would be good alternative terms, though. Also, hard agnosticsim != militant atheism.)
I've been fairly sure for many years that the nature of deity is unknown, what with implausible theologies and the power of science, etc etc, blah blah woof woof -- this argument has been made, and people have responded to it, a million times.
There are two possible arguments, I think, for why we cannot know the nature of deity (as opposed to merely "we don't know it, but we might figure it out"). One is the "perverse liar god" argument, and it's sort of tongue-in-cheek. If there's an omnipotent deity, then it could make itself unknowable, never mind why it would want to. It could even put on an understandable mask while leaving its true nature hidden.
The other possible argument is "fundamental limits of human understanding". The human brain may be the most amazingly complex awesome thing in the universe, capable of conceiving arbitrarily complex and abstract ideas... but is it capable of understanding something omnipotent, omnipresent, omni-everything, possibly vaster than the universe? I highly doubt it, given how hard it is to truly grasp (say) the sheer size of a galaxy. (And I do mean truly grasp. Saying "oh, it's so many frillion light years across" does not count.) A galaxy has got to be a lot smaller than an omni-deity.
You'll note I said "fundamental limits of human understanding", not "fundamental limits of any understanding". I don't doubt that an omnipotent deity could understand itself perfectly well. It's perfectly possible that there are forms of understanding out there that are orders of magnitude more powerful than our piddling little thoughts, or maybe even have a completely different basis -- call them "super-understanding". But given that humans are limited to human understanding, can we understand super-understanding? I doubt it.
(For a very readable, math-flavored analogy to the topic of super-understanding, see Scott Aaronson's fabulous essay Who Can Name the Bigger Number?, which you should read anyway. He discusses Turing machines and Super-(Super-Super-...)Turing machines, among many other fascinating topics.)
And by the way, I have high standards for what I'm willing to call understanding deity. I'm not willing to settle for a grammatical string of English words, or a bunch of math, or whatever, that describes deity perfectly. I am perfectly capable of 'understanding' (sneer quotes!) a sentence like "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, and truth", in that I know what all its words mean and I can parse the sentence, because that is perfectly fine English. But can I fully appreciate the impact of a spirit, infinite, eternal and unchangeable, in its being, wisdom, power, etc? Can my body generate a sufficiently large visceral/emotional reaction to the import of that idea, or will it run out of neurotransmitters first? Can my humble heart and mind contain the infinite? I think not.
Now, since I'm feeling a bit Hofstadterian, try this one on for size: "God is a spirit, infinite, eternal and unchangeable, in His being, wisdom, power, holiness, justice, goodness, truth, abstraction, recursion, subtlety, and inscrutability." Can this new, improved sentence give us a true, visceral understanding of an omni-deity? It's certainly an improvement.
(God-sentence is from Chapter 7 of Anne of Green Gables. I love that book.)
Monday, August 11, 2008
The Right Way to Respond to Getting Hacked / Cracked
Wired: Boston Subway Officials Sue to Stop DefCon Talk on Fare Card Hacks
Three MIT students have figured out how to hack the fare card system used on the Boston-area public transit ("the T"), to ride for free, add money to a stored-value card, and other such things. They cracked both the RFID card and the magnetic-stripe card. Here is a PDF of their presentation.
They were planning to give a talk on their discoveries at DefCon, the big annual hacker/cracker convention. The Massachusetts Bay Transit Authority (MBTA), which runs the T, sued them to prevent them from giving the talk. The talk will not be given. The students' faculty advisor, Dr. Ron Rivest, is being given a hard time.
The MBTA are going about this exactly the wrong way! (Although their response is understandable.)
Security systems are only trustable if they are thoroughly tested in actual use -- including normal users, hackers, and crackers. No matter how hard the MBTA try to hush up their security flaw, it will not make their security flaw magically go away. They should fix the flaw. Yes, it will cost money, but my sympathy is limited.
It is basically a given that many people will hear about this security flaw, whether or not there is a DefCon talk about it. Hello, Internet. But if people hear about this flaw only through underground/unofficial channels, what impression does that give them of the MBTA? It gives the impression that they either don't know about the flaw, or know about it and aren't doing anything about it. It gives the impression that the people who run all of Boston's public transit are a bunch of incompetents.
Moreover, by stage-whispering "Shh! Don't tell anyone about this!", they're also saying "Hey, this is significant! And leaves us very vulnerable!"
(By the way, if their goal is to decrease the number of people who hear about their security flaw, they have failed dramatically, because it's getting all over the news now. For example, I don't know anything about the presentations at DefCon, but now I know there's a security flaw in the subway system I use all the time, precisely because they're suing my classmates over it.)
What should the MBTA be doing? Shouting this as loudly as possible: "Yes, we have a security flaw! Thank you guys so much for pointing it out! We're working around the clock to fix it!" This would give the impression that the MBTA is run by intelligent people who can face reality instead of frantically trying to make it magically disappear. People would realize that the MBTA is serious about fare security.
The "Fare Security: SERIOUS BUSINESS" attitude would help decrease all kinds of subway sleaziness, including people who break fare security by the super-advanced hack of jumping over the fare gates. Not to mention things like littering, graffiti, and panhandling (none of which are huge problems on the T, I'm glad to say!). If I see someone fare-jumping, it makes me think the subway system is for shit anyway, so what does it matter if I stick gum to my seat?
And besides, the MBTA's anti-hacker attitude will just annoy crackers and make them more inclined to crack the T fares. Being realistic, and trumpeting increased security, will make crackers less inclined to attack the T.
Come on, MBTA. Have the grace to admit you've been hacked, instead of going into denial. Fix the vulnerability. Show us all you're serious about fare security. In fact, why don't you talk civilly to the people who hacked you? I'm sure they could help you build a better system.
...And, because I need some levity, here's a related episode in the adventures of Domo-kun. Hooray, cute pictures.
Three MIT students have figured out how to hack the fare card system used on the Boston-area public transit ("the T"), to ride for free, add money to a stored-value card, and other such things. They cracked both the RFID card and the magnetic-stripe card. Here is a PDF of their presentation.
They were planning to give a talk on their discoveries at DefCon, the big annual hacker/cracker convention. The Massachusetts Bay Transit Authority (MBTA), which runs the T, sued them to prevent them from giving the talk. The talk will not be given. The students' faculty advisor, Dr. Ron Rivest, is being given a hard time.
The MBTA are going about this exactly the wrong way! (Although their response is understandable.)
Security systems are only trustable if they are thoroughly tested in actual use -- including normal users, hackers, and crackers. No matter how hard the MBTA try to hush up their security flaw, it will not make their security flaw magically go away. They should fix the flaw. Yes, it will cost money, but my sympathy is limited.
It is basically a given that many people will hear about this security flaw, whether or not there is a DefCon talk about it. Hello, Internet. But if people hear about this flaw only through underground/unofficial channels, what impression does that give them of the MBTA? It gives the impression that they either don't know about the flaw, or know about it and aren't doing anything about it. It gives the impression that the people who run all of Boston's public transit are a bunch of incompetents.
Moreover, by stage-whispering "Shh! Don't tell anyone about this!", they're also saying "Hey, this is significant! And leaves us very vulnerable!"
(By the way, if their goal is to decrease the number of people who hear about their security flaw, they have failed dramatically, because it's getting all over the news now. For example, I don't know anything about the presentations at DefCon, but now I know there's a security flaw in the subway system I use all the time, precisely because they're suing my classmates over it.)
What should the MBTA be doing? Shouting this as loudly as possible: "Yes, we have a security flaw! Thank you guys so much for pointing it out! We're working around the clock to fix it!" This would give the impression that the MBTA is run by intelligent people who can face reality instead of frantically trying to make it magically disappear. People would realize that the MBTA is serious about fare security.
The "Fare Security: SERIOUS BUSINESS" attitude would help decrease all kinds of subway sleaziness, including people who break fare security by the super-advanced hack of jumping over the fare gates. Not to mention things like littering, graffiti, and panhandling (none of which are huge problems on the T, I'm glad to say!). If I see someone fare-jumping, it makes me think the subway system is for shit anyway, so what does it matter if I stick gum to my seat?
And besides, the MBTA's anti-hacker attitude will just annoy crackers and make them more inclined to crack the T fares. Being realistic, and trumpeting increased security, will make crackers less inclined to attack the T.
Come on, MBTA. Have the grace to admit you've been hacked, instead of going into denial. Fix the vulnerability. Show us all you're serious about fare security. In fact, why don't you talk civilly to the people who hacked you? I'm sure they could help you build a better system.
...And, because I need some levity, here's a related episode in the adventures of Domo-kun. Hooray, cute pictures.
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