Molecular Visualizations of DNA
September 23, 2009 2:48 PM Subscribe
I would love to see that in higher definition. Amazing.
posted by HumanComplex at 2:58 PM on September 23, 2009
posted by HumanComplex at 2:58 PM on September 23, 2009
Life is pretty amazing, isn't it?
posted by Blazecock Pileon at 2:59 PM on September 23, 2009
posted by Blazecock Pileon at 2:59 PM on September 23, 2009
Not all RNAs are converted into Proteins. Some can fold up themselves and be used by the cell directly. I think that it's been shown that an RNA molecule can do anything that a protein can, but not as quickly. In fact, The core of the Ribosome, which you see in the video converting RNA into protein is actually made out of mostly RNA with some protein.
Some scientists actually think that cells evolved with all RNA first, and then created proteins later, that theory is called RNA World Hypothesis
posted by delmoi at 3:07 PM on September 23, 2009
Some scientists actually think that cells evolved with all RNA first, and then created proteins later, that theory is called RNA World Hypothesis
posted by delmoi at 3:07 PM on September 23, 2009
Whirrs, blubs and clicks in the background are irritating and unnecessary, otherwise basis of life is amazingly like a Turing machine. Cool.
posted by Free word order! at 3:08 PM on September 23, 2009
posted by Free word order! at 3:08 PM on September 23, 2009
Nice to see they avoided the "flying down the center of a DNA helix" visual cliché.
posted by benzenedream at 3:16 PM on September 23, 2009
posted by benzenedream at 3:16 PM on September 23, 2009
Whirrs, blubs and clicks in the background are irritating and unnecessary, otherwise basis of life is amazingly like a Turing machine. Cool.
This better?
posted by peppito at 3:18 PM on September 23, 2009
Whirrs, blubs and clicks in the background are irritating and unnecessary, otherwise basis of life is amazingly like a Turing machine. Cool.
Not that much like a Turing machine. The Polymerase doesn't go back and forth along the DNA and and make changes like a Turing machine does with it's tape. A cell can do computation, though (and lots of other stuff) A cell will have chemical feedback systems so that when one chemical level gets too high, certain DNA will start getting transcribed to deal with it. You can have entire networks of these chemical triggers that can do simple computations like an electrical circuit. Genetic engineers have created flashing clocks based on these networks.
But anyway it's not very much like a (theoretical) Turing machine.
posted by delmoi at 3:18 PM on September 23, 2009
Not that much like a Turing machine. The Polymerase doesn't go back and forth along the DNA and and make changes like a Turing machine does with it's tape. A cell can do computation, though (and lots of other stuff) A cell will have chemical feedback systems so that when one chemical level gets too high, certain DNA will start getting transcribed to deal with it. You can have entire networks of these chemical triggers that can do simple computations like an electrical circuit. Genetic engineers have created flashing clocks based on these networks.
But anyway it's not very much like a (theoretical) Turing machine.
posted by delmoi at 3:18 PM on September 23, 2009
Yep. Fuck steampunk, the more you learn about molecular biology, the more you understand that our bodies contain systems more baroque, elegant, complex and just goddamn beautiful than anything we've managed to even think about building ourselves.
If you want to see another cool video, check out this TED talk, in which a medical illustrator called Dave Bolinsky shows an awesome video showing various molecular mechanisms within the cell. The whole talk is worth watching, but feel free to skip to about 6:55 for some awe-inspiring eye candy.
I'm sure I speak for a load of other biologists here when I say that molecular biology is awesome, in the truest sense of the word.
posted by metaBugs at 3:20 PM on September 23, 2009 [6 favorites]
If you want to see another cool video, check out this TED talk, in which a medical illustrator called Dave Bolinsky shows an awesome video showing various molecular mechanisms within the cell. The whole talk is worth watching, but feel free to skip to about 6:55 for some awe-inspiring eye candy.
I'm sure I speak for a load of other biologists here when I say that molecular biology is awesome, in the truest sense of the word.
posted by metaBugs at 3:20 PM on September 23, 2009 [6 favorites]
Better than a SLYT, watch these clips and particularly this one, awesome whatever your level of understanding
posted by Blasdelb at 3:22 PM on September 23, 2009 [5 favorites]
posted by Blasdelb at 3:22 PM on September 23, 2009 [5 favorites]
The video didn't explain to me why one side of the DNA molecule has to be transcribed in reverse. Can anyone fill me in? It sure makes the helicase doohicky more complicated (and cooler).
posted by Popular Ethics at 3:32 PM on September 23, 2009
posted by Popular Ethics at 3:32 PM on September 23, 2009
I believe that you meant to link here, Blasdelb ?
posted by It's Raining Florence Henderson at 3:32 PM on September 23, 2009 [1 favorite]
posted by It's Raining Florence Henderson at 3:32 PM on September 23, 2009 [1 favorite]
Cool site. Thanks!
posted by It's Raining Florence Henderson at 3:40 PM on September 23, 2009
posted by It's Raining Florence Henderson at 3:40 PM on September 23, 2009
When the narration says, "You're seeing this in real time," what does that mean, exactly? Is that actually how long it takes a single strand of DNA to copy, and for ribosomes to generate a protein chain? I understand we're seeing a single iteration out of trillions-- but does she mean it when she says "real time"?
If so... dope.
posted by grillcover at 3:44 PM on September 23, 2009
If so... dope.
posted by grillcover at 3:44 PM on September 23, 2009
Holy Shit Blasdelb. That video was incredible. Even the smallest process (getting white blood cells out of the blood vessel) involves hundreds of nanomachines. I had no idea we knew this much. It looks like I'm using this evening to learn molecular biology!
posted by Popular Ethics at 3:46 PM on September 23, 2009
posted by Popular Ethics at 3:46 PM on September 23, 2009
The video didn't explain to me why one side of the DNA molecule has to be transcribed in reverse.
Yeah, it not only has a machine that replicates that stuff, it has another one that does the same thing, only backwards and in high heels.
posted by Faze at 3:55 PM on September 23, 2009 [2 favorites]
Yeah, it not only has a machine that replicates that stuff, it has another one that does the same thing, only backwards and in high heels.
posted by Faze at 3:55 PM on September 23, 2009 [2 favorites]
The video didn't explain to me why one side of the DNA molecule has to be transcribed in reverse. Can anyone fill me in? It sure makes the helicase doohicky more complicated (and cooler).
posted by Popular Ethics
DNA is made of two one-way strands. There is a 5' (five prime) end and a 3' end. So one side of the DNA runs 5' -> 3' and the corresponding side runs 3' -> 5'. The molecular machine that copies the DNA can only add molecules one direction, from 5' to 3'. So one side copies as it unwinds, the other lags. Here's another animation (not as impressive as the linked video) that makes it clear.
posted by Grundlebug at 3:56 PM on September 23, 2009 [1 favorite]
posted by Popular Ethics
DNA is made of two one-way strands. There is a 5' (five prime) end and a 3' end. So one side of the DNA runs 5' -> 3' and the corresponding side runs 3' -> 5'. The molecular machine that copies the DNA can only add molecules one direction, from 5' to 3'. So one side copies as it unwinds, the other lags. Here's another animation (not as impressive as the linked video) that makes it clear.
posted by Grundlebug at 3:56 PM on September 23, 2009 [1 favorite]
Popular Ethics
DNA has a polarity, in that the way the subunits (the "letters") link together is not symmetrical. The DNA replication machinery is set up to only work in one direction: 5' to 3' or "5 prime to 3 prime", referring to the positions of the bonds on the carbon rind. See this wiki page for diagrams and a more detailed explanation.
A double stranded DNA molecule is arrange like this:
5' --------------------------- 3'
3' --------------------------- 5'
...so the polymerase can run straight along the top strand (5' to 3') but has to keep jumping ahead of the replication fork and working backwards (again 5' to 3') on the bottom strand.
Hopefully that makes sense; I'm a little drunk.
As a side note, RNA synthesis works the same way, in only one direction. Although uncommon in cells, some viruses are set up in such a way that reading the top strand 5'-3' produces one useful gene and reading the bottom strand of the bottom stretch 5'-3' (i.e. backwards relative to the top strand) produces a different but still useful gene. One of the things that eukaryotic cells (those making up all plants and animals) constantly look for is double stranded RNA; if a cell finds dsRNA within itself, it's interpreted as a sign of viral infection and all sorts of fancy countermeasures swing into place to stop viral replication and, ultimately, make the cell commit suicide to stop the viral progeny from escaping to infect neighbouring cells.
When you consider than this is akin to a recipe or instruction set that produces a different but useful output when read in either direction, that's pretty amazing. Viruses have evolved this because having as little DNA as possible is a strong selective advantage, both in terms of speed (you can make more copies of a shorter genome and therefore more copies of the virus in the limited time before the host cell dies) and antigenicity (physically smaller viruses tend to be less visible to the immune system).
posted by metaBugs at 3:56 PM on September 23, 2009 [1 favorite]
DNA has a polarity, in that the way the subunits (the "letters") link together is not symmetrical. The DNA replication machinery is set up to only work in one direction: 5' to 3' or "5 prime to 3 prime", referring to the positions of the bonds on the carbon rind. See this wiki page for diagrams and a more detailed explanation.
A double stranded DNA molecule is arrange like this:
5' --------------------------- 3'
3' --------------------------- 5'
...so the polymerase can run straight along the top strand (5' to 3') but has to keep jumping ahead of the replication fork and working backwards (again 5' to 3') on the bottom strand.
Hopefully that makes sense; I'm a little drunk.
As a side note, RNA synthesis works the same way, in only one direction. Although uncommon in cells, some viruses are set up in such a way that reading the top strand 5'-3' produces one useful gene and reading the bottom strand of the bottom stretch 5'-3' (i.e. backwards relative to the top strand) produces a different but still useful gene. One of the things that eukaryotic cells (those making up all plants and animals) constantly look for is double stranded RNA; if a cell finds dsRNA within itself, it's interpreted as a sign of viral infection and all sorts of fancy countermeasures swing into place to stop viral replication and, ultimately, make the cell commit suicide to stop the viral progeny from escaping to infect neighbouring cells.
When you consider than this is akin to a recipe or instruction set that produces a different but useful output when read in either direction, that's pretty amazing. Viruses have evolved this because having as little DNA as possible is a strong selective advantage, both in terms of speed (you can make more copies of a shorter genome and therefore more copies of the virus in the limited time before the host cell dies) and antigenicity (physically smaller viruses tend to be less visible to the immune system).
posted by metaBugs at 3:56 PM on September 23, 2009 [1 favorite]
Go Mefites! Thanks guys. I had just assumed that the DNA structure is symmetrical (it looks it). Now you've got me wondering why. Perhaps the directionality makes certain operations exothermic...? I'm off to learn more!
posted by Popular Ethics at 4:08 PM on September 23, 2009
posted by Popular Ethics at 4:08 PM on September 23, 2009
Hopefully that makes sense; I'm a little drunk.
Ugh, then perhaps this is a good time to read this: Alcohol and Cancer.
posted by peppito at 4:08 PM on September 23, 2009
Ugh, then perhaps this is a good time to read this: Alcohol and Cancer.
posted by peppito at 4:08 PM on September 23, 2009
Popular Ethics, a DNA strand can only be replicated in one direction and each strand is oriented anti-parallel to the other ie:
<>
So when a cell decides to get its groove on and replication starts, proteins will bind to specific points called origins of replication in your DNA tearing it apart. Thus you get two machines like the one in the video going at the same time in opposite directions, each handling one strand pointed in one direction and one pointed in the other. They both work identically, just upside-down from each other
<>)---------------
-------------(<>)------------->
.. Machine 1^....^Machine 2
so, as explained in the movie, the one strand that is being pulled apart in the same direction that that strand is replicated is easy and amazingly fast. While the other strand must be replicated toward the origin of replication or where there should already be DNA. Our cells accomplish this by doing it in chunks called Okazaki fragments. A process displayed more cartoonishly here.
posted by Blasdelb at 4:10 PM on September 23, 2009
<>
So when a cell decides to get its groove on and replication starts, proteins will bind to specific points called origins of replication in your DNA tearing it apart. Thus you get two machines like the one in the video going at the same time in opposite directions, each handling one strand pointed in one direction and one pointed in the other. They both work identically, just upside-down from each other
<>)---------------
-------------(<>)------------->
.. Machine 1^....^Machine 2
so, as explained in the movie, the one strand that is being pulled apart in the same direction that that strand is replicated is easy and amazingly fast. While the other strand must be replicated toward the origin of replication or where there should already be DNA. Our cells accomplish this by doing it in chunks called Okazaki fragments. A process displayed more cartoonishly here.
posted by Blasdelb at 4:10 PM on September 23, 2009
My diagrams looked much better in the preview I swear
posted by Blasdelb at 4:13 PM on September 23, 2009
posted by Blasdelb at 4:13 PM on September 23, 2009
delmoi is entirely correct to write
Not all RNAs are converted into Proteins. Some can fold up themselves and be used by the cell directly.
As well as most of the Ribosome, the transfer molecules you can see that provide the ribosome with amino acids (building blocks of proteins) are entirely built from RNA. The sequences of these transfer RNAs (tRNA) and the ribosome are strongly conserved between species, meaning that they change very slowly over evolutionary time, because their structure -- and therefore their sequence -- is so crucial to the efficiency of one of the most basic processes in the cell. So when you see news reports that scientists have found an evolutionary link between two species, it generally means that they've sequenced the ribosomal RNAs (rRNA) and/or tRNAs and compared it to hundreds (thousands?) of sequences from other species and worked out when the accumulation of changes to that sequence split from the accumulation of changes in its nearest neighbours.
Also, I've just been awarded my PhD for studying a viral RNA that folds into a complex shape and does a task directly instead of being translated into protein. Yay for RNA!
...and that last sentence is why I shouldn't be allowed to talk about science when drunk.
peppito - Believe me, I know. In excruciating detail. On the upside, I was drinking red wine which contains a phytochemical called resveratrol, which recent research (unpublished, by a friend in my lab) shows is beneficial in treating some cancers. And a glass of wine a day is about the right balance between preventing cancer (never drink alcohol!) and preventing heart disease (drink 1-2 glasses a day). Finally, I was with labmates from a cancer research department, and building our morale like this will make us work faster toward a cure.
My justifications for excessive drinking are no more rational than anyone else's, but I like to think they sound more impressive.
posted by metaBugs at 4:24 PM on September 23, 2009 [1 favorite]
Not all RNAs are converted into Proteins. Some can fold up themselves and be used by the cell directly.
As well as most of the Ribosome, the transfer molecules you can see that provide the ribosome with amino acids (building blocks of proteins) are entirely built from RNA. The sequences of these transfer RNAs (tRNA) and the ribosome are strongly conserved between species, meaning that they change very slowly over evolutionary time, because their structure -- and therefore their sequence -- is so crucial to the efficiency of one of the most basic processes in the cell. So when you see news reports that scientists have found an evolutionary link between two species, it generally means that they've sequenced the ribosomal RNAs (rRNA) and/or tRNAs and compared it to hundreds (thousands?) of sequences from other species and worked out when the accumulation of changes to that sequence split from the accumulation of changes in its nearest neighbours.
Also, I've just been awarded my PhD for studying a viral RNA that folds into a complex shape and does a task directly instead of being translated into protein. Yay for RNA!
...and that last sentence is why I shouldn't be allowed to talk about science when drunk.
peppito - Believe me, I know. In excruciating detail. On the upside, I was drinking red wine which contains a phytochemical called resveratrol, which recent research (unpublished, by a friend in my lab) shows is beneficial in treating some cancers. And a glass of wine a day is about the right balance between preventing cancer (never drink alcohol!) and preventing heart disease (drink 1-2 glasses a day). Finally, I was with labmates from a cancer research department, and building our morale like this will make us work faster toward a cure.
My justifications for excessive drinking are no more rational than anyone else's, but I like to think they sound more impressive.
posted by metaBugs at 4:24 PM on September 23, 2009 [1 favorite]
What's even more impressive is that no rational thought is needed. We are replicants.
posted by effluvia at 4:28 PM on September 23, 2009
posted by effluvia at 4:28 PM on September 23, 2009
peppito - Believe me, I know. In excruciating detail. On the upside, I was drinking red wine which contains a phytochemical called resveratrol, which recent research (unpublished, by a friend in my lab) shows is beneficial in treating some cancers. And a glass of wine a day is about the right balance between preventing cancer (never drink alcohol!) and preventing heart disease (drink 1-2 glasses a day). Finally, I was with labmates from a cancer research department, and building our morale like this will make us work faster toward a cure.
I understand, this definitely isn't uncommon behavior for molecular biologists, physiologists, cancer researchers, or other bio/science researchers I've known either.
It's ironic and very sad when it sometimes leads to the ultimate irony. But people are people.
posted by peppito at 4:43 PM on September 23, 2009
I understand, this definitely isn't uncommon behavior for molecular biologists, physiologists, cancer researchers, or other bio/science researchers I've known either.
It's ironic and very sad when it sometimes leads to the ultimate irony. But people are people.
posted by peppito at 4:43 PM on September 23, 2009
It's ironic and very sad when it sometimes leads to the ultimate irony. But people are people.
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
posted by metaBugs at 4:54 PM on September 23, 2009
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
posted by metaBugs at 4:54 PM on September 23, 2009
It's ironic and very sad when it sometimes leads to the ultimate irony. But people are people.
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
I know what you mean, I think it's the stress - the unending, spine twisting stress. I don't recommend this career path to anyone I know. Not that other jobs aren't as stressful, but academia and the bio-science industry seem to be terribly harsh on people's nerves - even the pharmacologists.
posted by peppito at 5:18 PM on September 23, 2009
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
I know what you mean, I think it's the stress - the unending, spine twisting stress. I don't recommend this career path to anyone I know. Not that other jobs aren't as stressful, but academia and the bio-science industry seem to be terribly harsh on people's nerves - even the pharmacologists.
posted by peppito at 5:18 PM on September 23, 2009
Am good friend of mine, who happens to be both a PHD in Path and a fundy of sorts says the more you know about molecular biology the harder it is to accept it created itself.
I obviously don't know enough about molecular biology then.
posted by Samuel Farrow at 5:23 PM on September 23, 2009
I obviously don't know enough about molecular biology then.
posted by Samuel Farrow at 5:23 PM on September 23, 2009
Sam Farrow, the proper answer to that is that it didn't "create itself." A sharpening influence created it through long, long aeons of trial and error, with most changes resulting in errors that go unremembered.
posted by localroger at 6:22 PM on September 23, 2009
posted by localroger at 6:22 PM on September 23, 2009
as a layperson, this was truly awe-inspiring to watch. thanks so much for bringing it to our attention!
posted by ericbop at 7:11 PM on September 23, 2009
posted by ericbop at 7:11 PM on September 23, 2009
MetaFilter: hopefully that makes sense; I'm a little drunk.
posted by intermod at 7:49 PM on September 23, 2009 [1 favorite]
posted by intermod at 7:49 PM on September 23, 2009 [1 favorite]
Surely your God, who is awe-ing up your shit with his ability to Design a complex biological machine, will further be able to kick you in the balls with the way He designed the wholly deterministic system that produces that machine? You think RNA is impressive, wait'll you see the system that created it!
People tend to reach the limits of their knowledge and plant down a flag. "Aha! God starts here!" And later, someone else comes along and disproves it.
Thinking that you've turned your microscopes up high enough to finally find God is an irreligious act, and is far too common among the faithful. Evolution is a mechanistic process, just like cell biology, just like boiling water. If you don't believe that God can be the secret master of a mechanistic process whose proof of existence you will never find, I posit that your faith is damaged, that the God you believe in is crippled, outmoded, dead.
Be humble before God—stop looking for his fucking fingerprints.
posted by fleacircus at 7:50 PM on September 23, 2009 [2 favorites]
People tend to reach the limits of their knowledge and plant down a flag. "Aha! God starts here!" And later, someone else comes along and disproves it.
Thinking that you've turned your microscopes up high enough to finally find God is an irreligious act, and is far too common among the faithful. Evolution is a mechanistic process, just like cell biology, just like boiling water. If you don't believe that God can be the secret master of a mechanistic process whose proof of existence you will never find, I posit that your faith is damaged, that the God you believe in is crippled, outmoded, dead.
Be humble before God—stop looking for his fucking fingerprints.
posted by fleacircus at 7:50 PM on September 23, 2009 [2 favorites]
The first time I saw a video of how the transcription machinery works in concert, I was blown away. It's one thing to know how it works, what the parts do, the chemistry behind it, etc., it's another to see it happening.
Damn, I love science.
The Polymerase doesn't go back and forth along the DNA and and make changes like a Turing machine does with its tape.
Incidentally, your genome does code for various proteins that will go back and alter not just your RNA but also your DNA. Some of these are temporary, or at least reversible - acetylation and methylation of histones can influence whether or not a given gene gets copied and made into protein. (It turns out that under certain circumstances, gene-production modifiers like these can be passed on from parent through child; much of the same machinery allows the cells in your body- which all have the same genetic code - to behave differently. Epigenetics is wild stuff.) There are also, of course, the protein networks you talk about - proteins directly modifying each other, or interacting with each other - but a fair amount of what happens in your cell involves the cell self-regulating to change what DNA is actually available to its machinery.
Some DNA modifications are permanent, though. These modifications are generally part of how a cell tries to deal with DNA damage. The fact that you have two strands of DNA means that your cell's machinery can see when there's a mismatch in DNA. As long as the strand was copied relatively recently, the proteins can tell which strand was the new one and which strand was the template, and they can take out the incorrect bit of DNA and send the transcription machinery back in again to do it right.
There's also the less-good kind of modification of the DNA code: ultimately, there is some DNA damage that a cell cannot really deal with. The damaged base of DNA may have nasty polycyclic aromatic crap bound to it, for example, meaning it doesn't even fit into most proteins correctly, and the cell's normal DNA-damage machinery can't effectively cut it out or otherwise repair it. At this point, your cell is sitting there saying "fuck, if I cannot continue copying this DNA, I will not have two copies of my genome, I will not be able to divide, and oh God, this is not good." So it calls in specialized transcription machinery - the Y-family polymerases, which specialize in getting past damaged DNA, no matter what. They're pretty mutation prone, because while they'd prefer to choose the right DNA base to insert across from the damaged one, it is mostly important that there is a base there. There's at least a chance that a mutation will not hurt, while not being able to copy DNA is guaranteed to be bad.
So it's not entirely true that the cell can't act somewhat like a Turing machine, inasmuch as it can effectively edit its own code. The big difference is this: at all costs, the cell wants to keep a nice, complete, undamaged copy of its genome. Information loss is not acceptable. So, some of its efforts are devoted to making sure that all that very necessary modification of its DNA is reversible; other sets of proteins are there to ensure that the cell can deal with involuntary edits.
posted by ubersturm at 8:20 PM on September 23, 2009 [3 favorites]
Damn, I love science.
The Polymerase doesn't go back and forth along the DNA and and make changes like a Turing machine does with its tape.
Incidentally, your genome does code for various proteins that will go back and alter not just your RNA but also your DNA. Some of these are temporary, or at least reversible - acetylation and methylation of histones can influence whether or not a given gene gets copied and made into protein. (It turns out that under certain circumstances, gene-production modifiers like these can be passed on from parent through child; much of the same machinery allows the cells in your body- which all have the same genetic code - to behave differently. Epigenetics is wild stuff.) There are also, of course, the protein networks you talk about - proteins directly modifying each other, or interacting with each other - but a fair amount of what happens in your cell involves the cell self-regulating to change what DNA is actually available to its machinery.
Some DNA modifications are permanent, though. These modifications are generally part of how a cell tries to deal with DNA damage. The fact that you have two strands of DNA means that your cell's machinery can see when there's a mismatch in DNA. As long as the strand was copied relatively recently, the proteins can tell which strand was the new one and which strand was the template, and they can take out the incorrect bit of DNA and send the transcription machinery back in again to do it right.
There's also the less-good kind of modification of the DNA code: ultimately, there is some DNA damage that a cell cannot really deal with. The damaged base of DNA may have nasty polycyclic aromatic crap bound to it, for example, meaning it doesn't even fit into most proteins correctly, and the cell's normal DNA-damage machinery can't effectively cut it out or otherwise repair it. At this point, your cell is sitting there saying "fuck, if I cannot continue copying this DNA, I will not have two copies of my genome, I will not be able to divide, and oh God, this is not good." So it calls in specialized transcription machinery - the Y-family polymerases, which specialize in getting past damaged DNA, no matter what. They're pretty mutation prone, because while they'd prefer to choose the right DNA base to insert across from the damaged one, it is mostly important that there is a base there. There's at least a chance that a mutation will not hurt, while not being able to copy DNA is guaranteed to be bad.
So it's not entirely true that the cell can't act somewhat like a Turing machine, inasmuch as it can effectively edit its own code. The big difference is this: at all costs, the cell wants to keep a nice, complete, undamaged copy of its genome. Information loss is not acceptable. So, some of its efforts are devoted to making sure that all that very necessary modification of its DNA is reversible; other sets of proteins are there to ensure that the cell can deal with involuntary edits.
posted by ubersturm at 8:20 PM on September 23, 2009 [3 favorites]
how did that speck of super-concentrated matter come to be there before the Big Bang?
well...there was no 'there' there before the big bang...the space came out of it, too. also the time...talking about 'before' the big bang is roughly equivalant to asking someone who went to the north pole why they didn't go any further north.
/derail
Some DNA modifications are permanent, though. These modifications are generally part of how a cell tries to deal with DNA damage.
jeez...wish i could find the article (probably on futurepundit, a great blog on genetics/health/solar power/and etc)...theres been some research lately on just this subject...apparently there's signs that starvation can affect your genetics...they're apparently studying the decendants of folks from (i forget) norway or sweden that suffered food shortages during the nazi blockade in ww2...
posted by sexyrobot at 2:13 AM on September 24, 2009
well...there was no 'there' there before the big bang...the space came out of it, too. also the time...talking about 'before' the big bang is roughly equivalant to asking someone who went to the north pole why they didn't go any further north.
/derail
Some DNA modifications are permanent, though. These modifications are generally part of how a cell tries to deal with DNA damage.
jeez...wish i could find the article (probably on futurepundit, a great blog on genetics/health/solar power/and etc)...theres been some research lately on just this subject...apparently there's signs that starvation can affect your genetics...they're apparently studying the decendants of folks from (i forget) norway or sweden that suffered food shortages during the nazi blockade in ww2...
posted by sexyrobot at 2:13 AM on September 24, 2009
Drew Berry who is the guy that created these animations in 2003. More of his (recent) work under the wehi.tv name can be found here. In the past I worked on a bunch of the sound design for some of his animations for Franc Tetaz who is responsible for all the sound design you hear here. For those of you that may have seen the movie Wolf Creek - Franc also composed the music for that film as well. I may have worked on the DNA replication one, but it was a while ago and I don't remember... Anyhow, I thought I'd chime in with some stuff about how Drew makes these animations.
Drew works very closely with all of the people at WEHI to ensure that these animations are as scientifically correct as possible. Clearly things like the colour scheme are altered so that it's easier describe what is happening. Drew holds both a science and design degree (I think?) and he prides himself on making sure these animations are as close to accurate as possible. I'm not sure what tools Drew is using now, but when these animations were made I'm sure he was using Maya pretty heavily for the bulk of the work. Drew is also one of the Maya Masters.
I let Drew know about this, so who knows he may join in on the convo? Drew has also done animations like these in a similar style for planetariums. I saw some working footage of this stuff and it looked awesome! I didn't get to see it in a planetarium, but having just finished some music for a planetarium show myself, I can imagine this would look and sound incredible in a dome!
posted by bozmond at 4:27 AM on September 24, 2009 [3 favorites]
Drew works very closely with all of the people at WEHI to ensure that these animations are as scientifically correct as possible. Clearly things like the colour scheme are altered so that it's easier describe what is happening. Drew holds both a science and design degree (I think?) and he prides himself on making sure these animations are as close to accurate as possible. I'm not sure what tools Drew is using now, but when these animations were made I'm sure he was using Maya pretty heavily for the bulk of the work. Drew is also one of the Maya Masters.
I let Drew know about this, so who knows he may join in on the convo? Drew has also done animations like these in a similar style for planetariums. I saw some working footage of this stuff and it looked awesome! I didn't get to see it in a planetarium, but having just finished some music for a planetarium show myself, I can imagine this would look and sound incredible in a dome!
posted by bozmond at 4:27 AM on September 24, 2009 [3 favorites]
Wow, bozmond, thanks so much for chiming in here!
posted by It's Raining Florence Henderson at 6:53 AM on September 24, 2009
posted by It's Raining Florence Henderson at 6:53 AM on September 24, 2009
Am good friend of mine, who happens to be both a PHD in Path and a fundy of sorts says the more you know about molecular biology the harder it is to accept it created itself.
I happen to have a PhD in molecular evolutionary biology, and the more that I learn, the more impossible it seems that this astounding machinery came about in any other way than the action of evolution and natural selection.
Your good friend needs to hit the books a bit more, I think.
posted by grouse at 8:13 AM on September 24, 2009 [2 favorites]
I happen to have a PhD in molecular evolutionary biology, and the more that I learn, the more impossible it seems that this astounding machinery came about in any other way than the action of evolution and natural selection.
Your good friend needs to hit the books a bit more, I think.
posted by grouse at 8:13 AM on September 24, 2009 [2 favorites]
When I first started learning physiology and molecular biology, I thought that biological systems were elegant and cleverly arranged.
Over time as I did more genomics work, the "fingerprints" of random evolutionary processes became more obvious throughout the genome. The genome and many molecular biological processes are horrendous Rube Goldberg devices that work well at a macro level because evolution works at the macro level. Just take a look at some physiology flowcharts. This is one reason why making safe drugs is so hard - many enzymes and structures in biology are reused because it's a lot more likely that an existing gene is randomly duplicated, or mutated so that it expresses in a different organ, than it is for a whole new independent system to arise all at once. Thus you get ugly cases where the same gene plays roles in (a) embryonic development (b) digestion in the adult small intestine and (c) a completely unrelated function in a brain subregion.
We are all coded in millions of molecular GOTO statements that have been ruthlessly pruned and trimmed by evolution until we get amazingly complex emergent phenomena like anthrax, hummingbirds, or hot vent bacteria.
posted by benzenedream at 12:16 PM on September 24, 2009 [3 favorites]
Over time as I did more genomics work, the "fingerprints" of random evolutionary processes became more obvious throughout the genome. The genome and many molecular biological processes are horrendous Rube Goldberg devices that work well at a macro level because evolution works at the macro level. Just take a look at some physiology flowcharts. This is one reason why making safe drugs is so hard - many enzymes and structures in biology are reused because it's a lot more likely that an existing gene is randomly duplicated, or mutated so that it expresses in a different organ, than it is for a whole new independent system to arise all at once. Thus you get ugly cases where the same gene plays roles in (a) embryonic development (b) digestion in the adult small intestine and (c) a completely unrelated function in a brain subregion.
We are all coded in millions of molecular GOTO statements that have been ruthlessly pruned and trimmed by evolution until we get amazingly complex emergent phenomena like anthrax, hummingbirds, or hot vent bacteria.
posted by benzenedream at 12:16 PM on September 24, 2009 [3 favorites]
It's ironic and very sad when it sometimes leads to the ultimate irony. But people are people.
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
I know what you mean, I think it's the stress - the unending, spine twisting stress. I don't recommend this career path to anyone I know. Not that other jobs aren't as stressful, but academia and the bio-science industry seem to be terribly harsh on people's nerves - even the pharmacologists.
Whoops, less I get misinterpreted or misunderstood here, let me clarify what I said: the stress I mentioned is due to working long, long hours for what is usually not much money and under stressful conditions to hopefully do something that is new, useful and not a waste of time and money. That's what is truly difficult about that work.
posted by peppito at 2:45 PM on September 24, 2009
Yeah, you should see the number of cancer scientists and medical doctors I know who smoke. At some point you just have to look at the numbers and decide what's an acceptable risk in return for the fun you get from it. I'm pretty sure that I'm at a greater risk of dying while cycling to work (or diving or fire juggling or other daft things that I do with my time) than I am of getting cancer from an occasional night at the pub.
I know what you mean, I think it's the stress - the unending, spine twisting stress. I don't recommend this career path to anyone I know. Not that other jobs aren't as stressful, but academia and the bio-science industry seem to be terribly harsh on people's nerves - even the pharmacologists.
Whoops, less I get misinterpreted or misunderstood here, let me clarify what I said: the stress I mentioned is due to working long, long hours for what is usually not much money and under stressful conditions to hopefully do something that is new, useful and not a waste of time and money. That's what is truly difficult about that work.
posted by peppito at 2:45 PM on September 24, 2009
Hello World,
I created the DNA animations you guys are talking about. I find it completely awesome they made it on MetaFilter!
If you'd like to see more of my work, check out wehi.tv – Although I haven't posted those particular "Molecular Visualizations of DNA" animations on my website yet...but plan on getting around to it in the next month or so.
Be gentle with me - I don't usually post comments on the web...
drew
PS The evidence for evolution is everywhere in biology. It gives the whole system a deeper, comprehensible and more fascinating edge.
posted by drewb at 6:23 PM on September 24, 2009 [3 favorites]
I created the DNA animations you guys are talking about. I find it completely awesome they made it on MetaFilter!
If you'd like to see more of my work, check out wehi.tv – Although I haven't posted those particular "Molecular Visualizations of DNA" animations on my website yet...but plan on getting around to it in the next month or so.
Be gentle with me - I don't usually post comments on the web...
drew
PS The evidence for evolution is everywhere in biology. It gives the whole system a deeper, comprehensible and more fascinating edge.
posted by drewb at 6:23 PM on September 24, 2009 [3 favorites]
drewb, you're amazing! How on earth are you able to accurately render the 3d shapes of these molecules? Have you considered producing a video series for grade schools? Seriously, do it. You'll inspire a lot of future biologists to enter the field.
posted by Popular Ethics at 6:55 PM on September 24, 2009
posted by Popular Ethics at 6:55 PM on September 24, 2009
Hi Popular Ethics
Actually, student and public education is the key purpose for my animations. There are numerous DVDs, textbooks and websites that the animations appear on, such as the BAFTA winning "DNA Interactive" DVD, designed for classroom teaching, available in the US from dnai.org - Tens of thousands of these DVDs have been distributed.
They are free if you are in Australia if you send an email wehi-tv at wehi.edu.au
Unfortunately there is a fee in other parts of the world, depending on the local distributor.
drew
posted by drewb at 7:11 PM on September 24, 2009 [1 favorite]
Actually, student and public education is the key purpose for my animations. There are numerous DVDs, textbooks and websites that the animations appear on, such as the BAFTA winning "DNA Interactive" DVD, designed for classroom teaching, available in the US from dnai.org - Tens of thousands of these DVDs have been distributed.
They are free if you are in Australia if you send an email wehi-tv at wehi.edu.au
Unfortunately there is a fee in other parts of the world, depending on the local distributor.
drew
posted by drewb at 7:11 PM on September 24, 2009 [1 favorite]
Well done, DrewB. I did a PhD in a lab that 'solved'/made some of the structures you used in the transcription segment. As someone rather familiar with the 'real chemistry' happening here, I commend you for staying really consistent with the actual science. So much of what is accessable to the layperson almost offends the specialist; This is nice stuff.
Now go back and add Mediator to the transcription picture! (This maybe wasn't accepted dogma in 2003 when you made the animation and the ideas of how transcription starts may have been somewhat murkier. It's crystal clear now, though, the role that Mediator plays.)
posted by u2604ab at 11:10 PM on September 24, 2009
Now go back and add Mediator to the transcription picture! (This maybe wasn't accepted dogma in 2003 when you made the animation and the ideas of how transcription starts may have been somewhat murkier. It's crystal clear now, though, the role that Mediator plays.)
posted by u2604ab at 11:10 PM on September 24, 2009
Hello u2604ab,
Here is an animation with the mediator protein at the initiation complex:
http://www.hhmi.org/biointeractive/media/DNAi_transcription_vo2-lg.mov
Note, that these models are extremely crude representations of the overall shape of the molecules, let alone their atomic arrangement. This was because of the limitation of the hardware I was using at the time and working to a tough deadline.
After the DNA project in 2002-3, I explored more efficient ways of incorporating protein crystallography models directly in the animation. The result of this technique development was the 'Apoptosis' signal transduction animation – an exploration of what a protein signal cascade would look like.
Apoptosis:
*WARNING* the movie is 35MB if that matters anymore
http://www.molecularmovies.com/movies/berry_apoptosis.html
The apoptosis movie takes a while to get going and show the molecular stuff. This was because it was designed to have an introduction-narration that never happened.
posted by drewb at 11:50 PM on September 24, 2009 [1 favorite]
Here is an animation with the mediator protein at the initiation complex:
http://www.hhmi.org/biointeractive/media/DNAi_transcription_vo2-lg.mov
Note, that these models are extremely crude representations of the overall shape of the molecules, let alone their atomic arrangement. This was because of the limitation of the hardware I was using at the time and working to a tough deadline.
After the DNA project in 2002-3, I explored more efficient ways of incorporating protein crystallography models directly in the animation. The result of this technique development was the 'Apoptosis' signal transduction animation – an exploration of what a protein signal cascade would look like.
Apoptosis:
*WARNING* the movie is 35MB if that matters anymore
http://www.molecularmovies.com/movies/berry_apoptosis.html
The apoptosis movie takes a while to get going and show the molecular stuff. This was because it was designed to have an introduction-narration that never happened.
posted by drewb at 11:50 PM on September 24, 2009 [1 favorite]
hi drewb,
how much of what you've recreated here is visible to someone with the proper instruments? i'm a complete layperson, here, so I know virtually nothing about DNA and the science surrounding it. where does the information for what we can't see directly yet become the visualization you've created?
posted by shmegegge at 1:02 PM on September 25, 2009
how much of what you've recreated here is visible to someone with the proper instruments? i'm a complete layperson, here, so I know virtually nothing about DNA and the science surrounding it. where does the information for what we can't see directly yet become the visualization you've created?
posted by shmegegge at 1:02 PM on September 25, 2009
drewb: One question -- how accurate is the wiggling of the DNA strands? Did you use a thermodynamic approach to animating the random motions?
posted by benzenedream at 2:02 PM on September 25, 2009
posted by benzenedream at 2:02 PM on September 25, 2009
The technologies for direct-observation of molecules and atoms is improving rapidly and revealing amazing new discoveries. However we are still a long way from being able to 'watch' the molecular systems that these animations are depicting. Browsing current research, you will find thousands of observations from a diverse range of devices and clever experimental apparatus that provide insights into what is going on down at the molecular scale.
These animations present a 'if we could view it, it would look something like this...' story, gathering data from the scientific literature I described above. It is designed to make the processes and molecules watchable to a human audience, so very heavy-handed design choices have to be made. For example, the use of colour, when these objects are smaller than the wavelength of visible light. The speed and dynamics have been slowed down enormously (The real rates of molecular activity are unimaginably fast, occurring at micro-timescales that cause fuses in my brain to pop if I try to envision them in my mind)
There are free molecular simulation apps (VMD is a good one) out there that can create much more accurate visualizations of molecular dynamics (eg http://www.ks.uiuc.edu/Gallery/Movies/) but they typically require a scientific eye to interpret what you are viewing.
The wiggling of the DNA strands that I added is not scientifically accurate, but is a reasonable representation. The wiggling is there to help convey to an audience the sorts of motions and behavior that is going on down at the molecular scale. I created it with a fractal-generated rig in maya. It's not bad for a visualization for education though.
posted by drewb at 3:35 PM on September 25, 2009 [4 favorites]
These animations present a 'if we could view it, it would look something like this...' story, gathering data from the scientific literature I described above. It is designed to make the processes and molecules watchable to a human audience, so very heavy-handed design choices have to be made. For example, the use of colour, when these objects are smaller than the wavelength of visible light. The speed and dynamics have been slowed down enormously (The real rates of molecular activity are unimaginably fast, occurring at micro-timescales that cause fuses in my brain to pop if I try to envision them in my mind)
There are free molecular simulation apps (VMD is a good one) out there that can create much more accurate visualizations of molecular dynamics (eg http://www.ks.uiuc.edu/Gallery/Movies/) but they typically require a scientific eye to interpret what you are viewing.
The wiggling of the DNA strands that I added is not scientifically accurate, but is a reasonable representation. The wiggling is there to help convey to an audience the sorts of motions and behavior that is going on down at the molecular scale. I created it with a fractal-generated rig in maya. It's not bad for a visualization for education though.
posted by drewb at 3:35 PM on September 25, 2009 [4 favorites]
Drew, those are fantastically cool, and thanks for dropping by to answer questions!
posted by LobsterMitten at 6:28 PM on September 25, 2009
posted by LobsterMitten at 6:28 PM on September 25, 2009
One of the hardest things to appreciate about biochemistry is the speed and chaos with which molecules react on that scale. It's hard to appreciate, because it's almost impossible to comprehend. What's even more mind-boggling is how well our proteins have adapted to work in that environment.
There's something called a kinetically perfect enzyme. The speed at which it functions is limited only by how fast its substrate can get to it (the diffusion rate). In other words, the enzyme reacts faster than its substrate can move in solution. How fast is that? Well, carbonic anhydrase can complete somewhere between 104 and 106 reactions per second. Just try and imagine that.
I think these sorts of videos do a lot to help convey the speed at which these processes occur, though of course there's always a tradeoff. The more accurately you portray it, the less sense it makes visually. But I think you did a good job at balancing, drewb, especially compared to The Inner Life of the Cell—which, as cool as it is, doesn't get that aspect across.
posted by dephlogisticated at 4:03 PM on September 26, 2009
There's something called a kinetically perfect enzyme. The speed at which it functions is limited only by how fast its substrate can get to it (the diffusion rate). In other words, the enzyme reacts faster than its substrate can move in solution. How fast is that? Well, carbonic anhydrase can complete somewhere between 104 and 106 reactions per second. Just try and imagine that.
I think these sorts of videos do a lot to help convey the speed at which these processes occur, though of course there's always a tradeoff. The more accurately you portray it, the less sense it makes visually. But I think you did a good job at balancing, drewb, especially compared to The Inner Life of the Cell—which, as cool as it is, doesn't get that aspect across.
posted by dephlogisticated at 4:03 PM on September 26, 2009
Thanks for all the great feedback. I really appreciate it.
Looking over the comments in this thread, I have to say that I am surprised and impressed with the informed and thoughtful discussion that you guys have created. From what I have seen on the web, this does not happen often, particularly between people with different expertise and interests.
drew
posted by drewb at 4:42 AM on September 27, 2009
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posted by peppito at 2:53 PM on September 23, 2009 [1 favorite]