As requested, I put a car-related analogy here. Since you technically asked a slightly different question, though, I'll give you a computer analogy to round things out.
Imagine you had an incredibly weird job scheduler that evaluated a huge probabilistic boolean expression, and then ran a given program afterwards if the expression evaluated to true. Then imagine that it ran this check several million times per second, and that all of the programs currently running had access to all of the variables used by all of the conditions, and could change them at any time. This is, essentially, how the cell decides what genes to express normally. No gene is ever expressed with 0% probability or 100% efficiency.
Methylation is like commenting out individual lines of code. An effect similar to block comments—with the same hilarious consequences if you make a typo in the end tag—is produced by another mechanism called an intron. We don't have to worry about this for the time being. Typically methylation applies to the header of a gene to prevent it from ever getting expressed (and to save on methyl groups) and the whole gene isn't methylated out.
The other thing you need to know about biology is that 'running' a program actually consists of copying a sequence of 6-bit numbers and then sending that copy to a synthesizer, which maps those 6-bit numbers onto a list of 20 small nanobot parts, and produces a string of these parts glued together. (3 of the 64 numbers are reserved for a special fake robot part adapter that causes the synthesizer to break apart, effectively stopping the synthesis.) The copy of the sequence used by the synthesizer also has a special header tag and a magic number, and most of the time the synthesizer is so lousy that it skips over it and just ejects the transcript completely. Some really strong header tags use sticky numbers to try and counteract this by slowing it down. Finally, the string of parts assembles itself by exploiting quantum electric effects that we still don't fully understand.
This, for fairly obscure reasons, is called the Central Dogma. The only actual part of the above that's metaphorical is the claim that there are variables—in fact, it's actually nanobots that physically attach themselves to the DNA. They're not very good at sticking, though, so it's a fair gamble as to whether or not they'll apply at a given moment. (Also, the nanobots are really called proteins, the synthesizer is called a ribosome, the 6-bit numbers are called codons, the robot parts are called amino acids, synthesis is called translation, the 'sticky numbers' are called Kozak sequences, and the magic number is "AUG".)
In this case, the body is uncommenting a handful of specialized genes that it only wants turned on when lots of resources are available. We believe that the caffeine tells the body to speed up usage of one particular common resource, called ATP. You don't want every gene in the body to be unmethylated, though: most of them only work properly in one type of cell in one part of the body, and many of them don't even work properly because they've fallen into severe disrepair, or even been corrupted. Even these genes could be harmful under the wrong conditions—giving caffeine to someone who's starving to death will only make him or her starve faster.
I hope that helps!
(One question I used to get a lot from students doing work in single-celled organisms was how the body can tell which tissue is which. The answer is very elegant to a computer scientist, but baffling to a biologist who hasn't done specialized research: different arguments passed in recursive calls. When the parent stem cell splits in two, it's programmed to turn variables on and off depending on which half the chromosomes are in.)
Unfortunately this one calls for a computer analogy—most things work better that way—but I'm... hey wait, I can give you a road analogy. It's not as good, but I'm pretty short on road analogies, so I'll take it.
Methylation is like a 'DO NOT ENTER' sign placed in front of a road. There are lots of roads that are blocked off: roads that lead to Centralia, roads that the city started repairing but never finished, highway bypasses that are too steep to use safely in the winter, and so on.
The genes in question are that last kind of road: steep but fast. They take too much energy to go up normally, but when the body has evidence that it's got lots of fuel available (caffeine is believed to fake out normal metabolic pathways that produce ATP, a major energy carrier: in essence it tells your body that your gas tank's impossibly full) then the cell has no reason not to go up the hill. In contrast, if you're famished, then the body will keep those steep roads blocked off, and take the gentle (but less efficient) long way around.
This is a bad metaphor because the destination of all this driving is increased energy usage.
Pfft. Summer job. I spend most of my day waiting for lecture to start and avoiding horrible Databases classes. Still in fourth year. Thanks for the vaguely stalkerish awareness, though.:)
Clearly, there is a moral lesson here: if you don't know enough about your computers to keep child porn off them, you will probably not be an effective parent. East Riding social services should be complimented for bringing to light this previously unknown connection. Perhaps other similar relationships exist, such as improperly weeded gardens leading to revocation of driver's licences, or lawyers disbarred for insufficient knowledge of breakfast cereal jingles.
In any major heart or lung transplant the patient's own organs must be bypassed for the duration of the surgery. Usually this is as short as possible because the non-rhythmic pumping in a heart and lung machine can cause plaques to break loose and block vessels. The surgery typically lasts anywhere from 4 to 12 hours depending on how many lungs are involved.
An engineer, a physicist, and a statistician go out hunting together. They spot a deer, and take turns shooting. The physicist does a quick bit of mental math to anticipate the trajectory of the bullet and fires, but his shot falls five metres short because he failed to account for wind resistance. The engineer tries next, adding in a fudge factor to compensate, but her bullet lands five metres too long. The statistician declares: "We got it!"
(You're right, but the high infant mortality rate still essentially supports the argument that things are significantly better.)
But that's exactly what I figured would happen. They'll abandon all attempts at serious digital distribution after it becomes obvious that the service they're offering can't even begin to compete with other DVD ripping and digital distribution solutions, both legitimate and not so. The blame will land on piracy, because they can't admit that things like the Mythbox (mentioned by an AC in another response to my post) and other DVRs totally wreck their scheme. Any guesses as to what they'll pull after that? Maybe use it as whiny evidence in another SOPA bill? Start issuing people smart ID cards that charge based on consumption?
Don't be silly; obviously this is the most exciting revolution the film industry has ever seen! Can't you see how cutting-edge and novel this technology is? Why, I'm sure absolutely everyone will line up to use this revolutionary and convenient service before you can blink! The future is today!
...now wait for them to kill it, and whine about how it's obviously impossible to capitalize on digital distribution.
Actually, the summary is slightly in error—it wasn't the porn company, it was on behalf of the porn company, an IP troll called Degban. Like Righthaven, only way, way more stupid and aimless. Degban claims to have been hacked, on top of that. Pretty sketchy, I gotta say.
Nope. Not this story. Come back in five years, maybe. This is just an incrementally better method of doing a test we've had computers doing since the early nineties... and that we've been doing by hand for (close to) twice that period of time.
Of course it only uses RefSeq! Don't you remember what your third-year professors taught you about the uncurated GenBank pool? Wikipedia users and terrorists post in there!
...actually, I'm pretty sure the only usage of RefSeq data is to establish the correct profile of what a splice site should look like. You can still feed it any FASTA sequence.
It's not really a simulation; it just tells you if a given sequence appears to resemble a splice site, and the probability that the single-nucleotide mutation specified by the user will alter that site's tendency to splice. Not a new accomplishment in biology by any means; the headline is sadly and totally overblown.
Humans aren't very good at the problem of RNA splice site finding, unfortunately. Like Reversi/Othello, it involves detecting a large number of subtle changes in closely-related states that have dramatic downstream effects. The game would consist primarily of looking at a bunch of roughly hill-shaped graphs and trying to determine which ones cross certain thresholds or most closely resemble certain other curves. Computationally those are pretty manageable tasks.
Slashdot Mirror
You'd think the Beeb would get that right. o_O
I am honoured, and I realise you have a psychotic ex, but studies suggest forever is at least 20% longer than most people expect. (p < 0.005)
(Caught your Twitter note. Thanks!)
As requested, I put a car-related analogy here. Since you technically asked a slightly different question, though, I'll give you a computer analogy to round things out.
Imagine you had an incredibly weird job scheduler that evaluated a huge probabilistic boolean expression, and then ran a given program afterwards if the expression evaluated to true. Then imagine that it ran this check several million times per second, and that all of the programs currently running had access to all of the variables used by all of the conditions, and could change them at any time. This is, essentially, how the cell decides what genes to express normally. No gene is ever expressed with 0% probability or 100% efficiency.
Methylation is like commenting out individual lines of code. An effect similar to block comments—with the same hilarious consequences if you make a typo in the end tag—is produced by another mechanism called an intron. We don't have to worry about this for the time being. Typically methylation applies to the header of a gene to prevent it from ever getting expressed (and to save on methyl groups) and the whole gene isn't methylated out.
The other thing you need to know about biology is that 'running' a program actually consists of copying a sequence of 6-bit numbers and then sending that copy to a synthesizer, which maps those 6-bit numbers onto a list of 20 small nanobot parts, and produces a string of these parts glued together. (3 of the 64 numbers are reserved for a special fake robot part adapter that causes the synthesizer to break apart, effectively stopping the synthesis.) The copy of the sequence used by the synthesizer also has a special header tag and a magic number, and most of the time the synthesizer is so lousy that it skips over it and just ejects the transcript completely. Some really strong header tags use sticky numbers to try and counteract this by slowing it down. Finally, the string of parts assembles itself by exploiting quantum electric effects that we still don't fully understand.
This, for fairly obscure reasons, is called the Central Dogma. The only actual part of the above that's metaphorical is the claim that there are variables—in fact, it's actually nanobots that physically attach themselves to the DNA. They're not very good at sticking, though, so it's a fair gamble as to whether or not they'll apply at a given moment. (Also, the nanobots are really called proteins, the synthesizer is called a ribosome, the 6-bit numbers are called codons, the robot parts are called amino acids, synthesis is called translation, the 'sticky numbers' are called Kozak sequences, and the magic number is "AUG".)
In this case, the body is uncommenting a handful of specialized genes that it only wants turned on when lots of resources are available. We believe that the caffeine tells the body to speed up usage of one particular common resource, called ATP. You don't want every gene in the body to be unmethylated, though: most of them only work properly in one type of cell in one part of the body, and many of them don't even work properly because they've fallen into severe disrepair, or even been corrupted. Even these genes could be harmful under the wrong conditions—giving caffeine to someone who's starving to death will only make him or her starve faster.
I hope that helps!
(One question I used to get a lot from students doing work in single-celled organisms was how the body can tell which tissue is which. The answer is very elegant to a computer scientist, but baffling to a biologist who hasn't done specialized research: different arguments passed in recursive calls. When the parent stem cell splits in two, it's programmed to turn variables on and off depending on which half the chromosomes are in.)
Unfortunately this one calls for a computer analogy—most things work better that way—but I'm ... hey wait, I can give you a road analogy. It's not as good, but I'm pretty short on road analogies, so I'll take it.
Methylation is like a 'DO NOT ENTER' sign placed in front of a road. There are lots of roads that are blocked off: roads that lead to Centralia, roads that the city started repairing but never finished, highway bypasses that are too steep to use safely in the winter, and so on.
The genes in question are that last kind of road: steep but fast. They take too much energy to go up normally, but when the body has evidence that it's got lots of fuel available (caffeine is believed to fake out normal metabolic pathways that produce ATP, a major energy carrier: in essence it tells your body that your gas tank's impossibly full) then the cell has no reason not to go up the hill. In contrast, if you're famished, then the body will keep those steep roads blocked off, and take the gentle (but less efficient) long way around.
This is a bad metaphor because the destination of all this driving is increased energy usage.
Pfft. Summer job. I spend most of my day waiting for lecture to start and avoiding horrible Databases classes. Still in fourth year. Thanks for the vaguely stalkerish awareness, though. :)
I don't know! Who are you quoting?! What website is this?!
You noticed?
Greetings from scenic Clueville! Woosh you were here.
Clearly, there is a moral lesson here: if you don't know enough about your computers to keep child porn off them, you will probably not be an effective parent. East Riding social services should be complimented for bringing to light this previously unknown connection. Perhaps other similar relationships exist, such as improperly weeded gardens leading to revocation of driver's licences, or lawyers disbarred for insufficient knowledge of breakfast cereal jingles.
No, the private market has already put forth a more cost-effective bid. ($39.95)
In any major heart or lung transplant the patient's own organs must be bypassed for the duration of the surgery. Usually this is as short as possible because the non-rhythmic pumping in a heart and lung machine can cause plaques to break loose and block vessels. The surgery typically lasts anywhere from 4 to 12 hours depending on how many lungs are involved.
An engineer, a physicist, and a statistician go out hunting together. They spot a deer, and take turns shooting. The physicist does a quick bit of mental math to anticipate the trajectory of the bullet and fires, but his shot falls five metres short because he failed to account for wind resistance. The engineer tries next, adding in a fudge factor to compensate, but her bullet lands five metres too long. The statistician declares: "We got it!"
(You're right, but the high infant mortality rate still essentially supports the argument that things are significantly better.)
Well, pirates are better than Ninja, so... :)
But that's exactly what I figured would happen. They'll abandon all attempts at serious digital distribution after it becomes obvious that the service they're offering can't even begin to compete with other DVD ripping and digital distribution solutions, both legitimate and not so. The blame will land on piracy, because they can't admit that things like the Mythbox (mentioned by an AC in another response to my post) and other DVRs totally wreck their scheme. Any guesses as to what they'll pull after that? Maybe use it as whiny evidence in another SOPA bill? Start issuing people smart ID cards that charge based on consumption?
Don't be silly; obviously this is the most exciting revolution the film industry has ever seen! Can't you see how cutting-edge and novel this technology is? Why, I'm sure absolutely everyone will line up to use this revolutionary and convenient service before you can blink! The future is today!
...now wait for them to kill it, and whine about how it's obviously impossible to capitalize on digital distribution.
They sure did! All the way up to the ripe old age of forty or so. What has medicine ever done for us, anyway?
I hope this post finds its way into a history textbook some day. I can't think of a better summary—or damnation—with which to stir.
Interestingly, Oracle also has a set of rules of acquisition. You can read about them here.
Actually, the summary is slightly in error—it wasn't the porn company, it was on behalf of the porn company, an IP troll called Degban. Like Righthaven, only way, way more stupid and aimless. Degban claims to have been hacked, on top of that. Pretty sketchy, I gotta say.
Nope. Not this story. Come back in five years, maybe. This is just an incrementally better method of doing a test we've had computers doing since the early nineties... and that we've been doing by hand for (close to) twice that period of time.
Of course it only uses RefSeq! Don't you remember what your third-year professors taught you about the uncurated GenBank pool? Wikipedia users and terrorists post in there!
...actually, I'm pretty sure the only usage of RefSeq data is to establish the correct profile of what a splice site should look like. You can still feed it any FASTA sequence.
Still got it in Canada. I'll find another one for future reference, though. :)
It's not really a simulation; it just tells you if a given sequence appears to resemble a splice site, and the probability that the single-nucleotide mutation specified by the user will alter that site's tendency to splice. Not a new accomplishment in biology by any means; the headline is sadly and totally overblown.
Humans aren't very good at the problem of RNA splice site finding, unfortunately. Like Reversi/Othello, it involves detecting a large number of subtle changes in closely-related states that have dramatic downstream effects. The game would consist primarily of looking at a bunch of roughly hill-shaped graphs and trying to determine which ones cross certain thresholds or most closely resemble certain other curves. Computationally those are pretty manageable tasks.
What sex education class in Arkansas?