9 ms·

Molecular Visualisations of DNA [video]

83 points by sethbannon 13y ago

fakenBisEsRult 13y ago
Here's the link to the actual video: http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/ http://www.wehi.edu.au/education/wehitv/molecular_visualisat...
icegreentea 13y ago
I remember watching these animations in high school biology class. They've definitely had this big long-term impact on how I visualize and reason about cellular and subcellular components. Just always see little components bobbling around and randomly flipflopping.
- 3rd3 13y ago
  Growing up in an environment that was in certain regards ignorant, even hostile against science and technology I remember hearing about DNA for the first time I had this uneasy feeling that DNA is pretty much like computer code.
tokipin 13y ago
be sure to check out Bjork's music video: http://www.youtube.com/watch?v=Wa1A0pPc-ik http://www.youtube.com/watch?v=Wa1A0pPc-ik
- grannyg00se 13y ago
  Thanks for that. I found it to be quite fascinating but at the same time somewhat unsettling. The depth of complexity seemed limitless. As though there would be no end to the layers of abstraction one could reason about - and must reason about, if we are to truly understand ourselves.
  - tokipin 13y ago
    I think finding it unsettling is actually a good reaction. I think people get too encultured into simplistic views of the world. It's good to recognize how fundamentally deep and strange the universe is with respect to our everyday experience of it, if for nothing more than the sake of perspective.
- enb 13y ago
  Both this and the visualisations in the article are created by Drew Berry
AlexanderDhoore 13y ago
Nature is awe-some!
kylek 13y ago
(2003) - but still cool :)
cellover 13y ago
I'm wondering if the replication process has some sort of unit tests stored somewhere. Thank you for posting this!
- JunkDNA 13y ago
  Not unit tests, but a fair bit of in-line verification that the correct base has been added. There are numerous DNA proofreading mechanisms to prevent errors. If they didn't exist, we would be riddled with mutations.
- atmosx 13y ago
  More specifically, it's DNA-Polymerase who proofreads. You should also check out the T-Cells (innate and acquired immunity) work. It blew my mind the level of complexity, diversification, etc: There are cells that perform profiling, cells the memorize information about viruses (that's how vaccines work) already encountered, etc. Molecular biology is like entering the rabbit whole.
  - pixl97 13y ago
    Imagine a wormhole opening up in front of you and a computer from the unimaginably distant future drops out in front of you. You very likely wouldn't know it's even a computer. Countless billions of hours a futures mankinds time has been poured into it shrinking each component to the atomic scale. Generation after generation of hardening against future hackers attacks, and even self aware viruses have increased the machines complexity beyond human understanding. The code the computer interprets would be a lost language from a civilization that doesn't exist yet. And that is pretty much where we are in understanding the interworkings of DNA today. Nature has a 3 billion year jump on us, and it's going to take us a long time to unravel it all.
  - cellover 13y ago
    Thank you for adding some context! I will be sure to read about these mechanics, and probably not understand a word... pixl97 > nice analogy!
Ygg2 13y ago
Second part (DNA replication) reminds me of a really complex machine. Like a sewing machine, that cuts and folds and splits threads.
- pixl97 13y ago
  Like a sewing machine, that cuts and folds and splits threads. And in doing so makes another sewing machine. Life is awesomely complex stuff.
jostmey 13y ago
I've spent a great deal of time wondering why biological systems are so complex. Seeing this videos leads me to ponder this question yet again. I keep coming back to the same answer. Evolution as a process proceeds forward without regard for complexity. In other words, the outcome of an Evolutionary does not have to be simple - it just has to work. I fear that most biological systems are in many ways unnecessarily complicated, which makes research in Biology and Medicine even more difficult.
- agumonkey 13y ago
  Maybe that is 'simple' when solving the problem nature had, it's just that we're not used to this kind of problems.
  - yeison 13y ago
    That's a really great way to look at it. Thanks for sharing your perspective.
  - pointernil 13y ago
    That's really a very profound way to see it! Thanks. I'd add to that: there is even a chance (quite high btw) we are not yet seeing all the problems nature solves AND maybe we never will even though we are constantly and exponentially growing our understanding... always, forever, now.
  - cristianpascu 13y ago
    Nature does not solve problems. Molecules bump into each others. There's no purpose in their doing so. There is not simple for nature and complex for us. If you want a scientific approach to complexity, you would not insert a term in the definition that reads as 'us', or 'nature', or frogs.
    - agumonkey 13y ago
      Alright, there is no inherent purpose (something I always say to others and here I am giving the opposite impression :) but if we agree that things 'are' because they sustain some abstract structure in some context then can't we allow saying 'to sustain' is a problem to solve ? and if the context is very diverse thus high in complexity. And as we lack information, the observed structure will elude our understanding, 'complex for us'. From my very limited point of view, I'd believe nature follow some sort of simplest path possible (~lagrangian) law, hence my 'simple for nature' expression. Feel free to correct me further.
danielsiders 13y ago
There are some other great biomolecular visualizations out there, particularly around kinesin https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=7sRZy9PgPvg https://www.youtube.com/watch?v=7sRZy9PgPvg
- yeison 13y ago
  And the award for goofiest looking motor protein goes to: Kinesin.
- rotskoff 13y ago
  This is actually a heavily criticized animation within the computational biophysics community. Our intuition for physical determinism breaks down at the nanoscale. One major fault of this video is that, at low Reynolds number, there's essentially no inertia. So the representation of kinesin taking deterministic, 100% processive steps is an absurd idealization. The motion is dominated by thermal fluctuations (which, by the way, are occurring on a nanosecond timescale). At the same, even as a biophysicist, I think these animations are superb learning tools. Those beautifully rendered animations actually describe the mechanism in far greater detail than, say, textbook diagrams. One should just be aware that fluctuations dominate at these scales.
gourneau 13y ago
If any one is looking to get into BioTech Ion Torrent is always hiring good engineers. We are looking for folks that know Python, C++, CUDA.
thelogos 13y ago
A fully functioning life-form depends on so many things going right. With such precision needing to be met, I'm just surprised that there aren't more debilitating genetic diseases out there and that so many people are seemingly healthy. Of course, it also has plan B and C in case plan A fail and is remarkable at adapting. Just for example, look at all the people with genetic diseases still hopping along day after day.
bradchoate 13y ago
That video was from 2003. Here's a more recent visualization (2011) by the same person: https://www.youtube.com/watch?v=dMPXu6GF18M https://www.youtube.com/watch?v=dMPXu6GF18M
dnautics 13y ago
The WEHI videos are really fantastic, because they do a good job of 'random-walking' components into place. Compare and contrast the WEHI videos to the Harvard molecular visualization videos, where pieces come together with unrealistic symmetry: https://www.youtube.com/watch?v=B_zD3NxSsD8&t=2m50s https://www.youtube.com/watch?v=B_zD3NxSsD8&t=2m50s
- pointernil 13y ago
  This unrealistic symmetry and lego like snappiness, plus: in almost every visualization of these tiny tiny structures and processes involving them most of the "environment" is missing! Think about all the school, high-school and even college visualizations showing the organelles f.e. just hanging there pinned into place. Between them wast areas of ... what? Now look around you. What do you see? Maybe the furniture of you room resp. office... now wave your hand in front of your eyes (nooo, they are not laughing AT you ;) ... did you feel the interaction of the molecules "in the air" with those of your skin? They are filling the gap between us and the things we are capable to perceive with our eyes... The "invisible" content of these gaps is interacting with the visible parts. At molecular levels those invisible elements contribute hugely to the non-deterministic, non-lego like snappiness, to the "random walk" way of things working out. This kind of insight I think should be replacing the "deterministic machinery" view when describing and picturing molecular and micro-biological processes. Visualizations by Dr. David S. Goodsell present this kind of ideas in a fascinating way. (you can stop waving your hand now ;)
  - dnautics 13y ago
    I don't think the 'missing environment' is as much a big deal. Without getting too reductionist: You have to isolate the components that you're showing otherwise it's just a big mess that's hard to understand. I think the implicit "there's actually a lot of stuff in between there" is not a big deal, much as the implicit "these molecules aren't really colored" is not a big deal in the service of explanatory power. The reductionist view is not complete, but it's not wrong. Hypersymmetric assembly and molecules that 'know where to go' is wrong, and in a very subtle way that biases perception. The guy who makes the harvard video, in his TED talk, goes on and on about beauty in science. Well yeah, he created that beauty himself. The real system is sloppy and kludgey.... which I suppose could be 'beauty' in its own way, but very different from the way it's presented.
deleted 13y ago
[deleted]

83 points by sethbannon 13y ago

Here's the link to the actual video: http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/ http://www.wehi.edu.au/education/wehitv/molecular_visualisat...

icegreentea 13y ago

I remember watching these animations in high school biology class. They've definitely had this big long-term impact on how I visualize and reason about cellular and subcellular components. Just always see little components bobbling around and randomly flipflopping.

3rd3 13y ago
Growing up in an environment that was in certain regards ignorant, even hostile against science and technology I remember hearing about DNA for the first time I had this uneasy feeling that DNA is pretty much like computer code.

tokipin 13y ago

be sure to check out Bjork's music video: http://www.youtube.com/watch?v=Wa1A0pPc-ik http://www.youtube.com/watch?v=Wa1A0pPc-ik

grannyg00se 13y ago
Thanks for that. I found it to be quite fascinating but at the same time somewhat unsettling. The depth of complexity seemed limitless. As though there would be no end to the layers of abstraction one could reason about - and must reason about, if we are to truly understand ourselves.
- tokipin 13y ago
  I think finding it unsettling is actually a good reaction. I think people get too encultured into simplistic views of the world. It's good to recognize how fundamentally deep and strange the universe is with respect to our everyday experience of it, if for nothing more than the sake of perspective.
enb 13y ago
Both this and the visualisations in the article are created by Drew Berry

AlexanderDhoore 13y ago

Nature is awe-some!

kylek 13y ago

(2003) - but still cool :)

cellover 13y ago

I'm wondering if the replication process has some sort of unit tests stored somewhere. Thank you for posting this!

JunkDNA 13y ago
Not unit tests, but a fair bit of in-line verification that the correct base has been added. There are numerous DNA proofreading mechanisms to prevent errors. If they didn't exist, we would be riddled with mutations.
atmosx 13y ago
More specifically, it's DNA-Polymerase who proofreads. You should also check out the T-Cells (innate and acquired immunity) work. It blew my mind the level of complexity, diversification, etc: There are cells that perform profiling, cells the memorize information about viruses (that's how vaccines work) already encountered, etc. Molecular biology is like entering the rabbit whole.
- pixl97 13y ago
  Imagine a wormhole opening up in front of you and a computer from the unimaginably distant future drops out in front of you. You very likely wouldn't know it's even a computer. Countless billions of hours a futures mankinds time has been poured into it shrinking each component to the atomic scale. Generation after generation of hardening against future hackers attacks, and even self aware viruses have increased the machines complexity beyond human understanding. The code the computer interprets would be a lost language from a civilization that doesn't exist yet. And that is pretty much where we are in understanding the interworkings of DNA today. Nature has a 3 billion year jump on us, and it's going to take us a long time to unravel it all.
- cellover 13y ago
  Thank you for adding some context! I will be sure to read about these mechanics, and probably not understand a word... pixl97 > nice analogy!

Ygg2 13y ago

Second part (DNA replication) reminds me of a really complex machine. Like a sewing machine, that cuts and folds and splits threads.

pixl97 13y ago
Like a sewing machine, that cuts and folds and splits threads. And in doing so makes another sewing machine. Life is awesomely complex stuff.

jostmey 13y ago

I've spent a great deal of time wondering why biological systems are so complex. Seeing this videos leads me to ponder this question yet again. I keep coming back to the same answer. Evolution as a process proceeds forward without regard for complexity. In other words, the outcome of an Evolutionary does not have to be simple - it just has to work. I fear that most biological systems are in many ways unnecessarily complicated, which makes research in Biology and Medicine even more difficult.

agumonkey 13y ago
Maybe that is 'simple' when solving the problem nature had, it's just that we're not used to this kind of problems.
- yeison 13y ago
  That's a really great way to look at it. Thanks for sharing your perspective.
- pointernil 13y ago
  That's really a very profound way to see it! Thanks. I'd add to that: there is even a chance (quite high btw) we are not yet seeing all the problems nature solves AND maybe we never will even though we are constantly and exponentially growing our understanding... always, forever, now.
- cristianpascu 13y ago
  Nature does not solve problems. Molecules bump into each others. There's no purpose in their doing so. There is not simple for nature and complex for us. If you want a scientific approach to complexity, you would not insert a term in the definition that reads as 'us', or 'nature', or frogs.
  - agumonkey 13y ago
    Alright, there is no inherent purpose (something I always say to others and here I am giving the opposite impression :) but if we agree that things 'are' because they sustain some abstract structure in some context then can't we allow saying 'to sustain' is a problem to solve ? and if the context is very diverse thus high in complexity. And as we lack information, the observed structure will elude our understanding, 'complex for us'. From my very limited point of view, I'd believe nature follow some sort of simplest path possible (~lagrangian) law, hence my 'simple for nature' expression. Feel free to correct me further.

danielsiders 13y ago

There are some other great biomolecular visualizations out there, particularly around kinesin https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=7sRZy9PgPvg https://www.youtube.com/watch?v=7sRZy9PgPvg

yeison 13y ago
And the award for goofiest looking motor protein goes to: Kinesin.
rotskoff 13y ago
This is actually a heavily criticized animation within the computational biophysics community. Our intuition for physical determinism breaks down at the nanoscale. One major fault of this video is that, at low Reynolds number, there's essentially no inertia. So the representation of kinesin taking deterministic, 100% processive steps is an absurd idealization. The motion is dominated by thermal fluctuations (which, by the way, are occurring on a nanosecond timescale). At the same, even as a biophysicist, I think these animations are superb learning tools. Those beautifully rendered animations actually describe the mechanism in far greater detail than, say, textbook diagrams. One should just be aware that fluctuations dominate at these scales.

gourneau 13y ago

If any one is looking to get into BioTech Ion Torrent is always hiring good engineers. We are looking for folks that know Python, C++, CUDA.

thelogos 13y ago

A fully functioning life-form depends on so many things going right. With such precision needing to be met, I'm just surprised that there aren't more debilitating genetic diseases out there and that so many people are seemingly healthy. Of course, it also has plan B and C in case plan A fail and is remarkable at adapting. Just for example, look at all the people with genetic diseases still hopping along day after day.

bradchoate 13y ago

That video was from 2003. Here's a more recent visualization (2011) by the same person: https://www.youtube.com/watch?v=dMPXu6GF18M https://www.youtube.com/watch?v=dMPXu6GF18M

dnautics 13y ago

The WEHI videos are really fantastic, because they do a good job of 'random-walking' components into place. Compare and contrast the WEHI videos to the Harvard molecular visualization videos, where pieces come together with unrealistic symmetry: https://www.youtube.com/watch?v=B_zD3NxSsD8&t=2m50s https://www.youtube.com/watch?v=B_zD3NxSsD8&t=2m50s

pointernil 13y ago
This unrealistic symmetry and lego like snappiness, plus: in almost every visualization of these tiny tiny structures and processes involving them most of the "environment" is missing! Think about all the school, high-school and even college visualizations showing the organelles f.e. just hanging there pinned into place. Between them wast areas of ... what? Now look around you. What do you see? Maybe the furniture of you room resp. office... now wave your hand in front of your eyes (nooo, they are not laughing AT you ;) ... did you feel the interaction of the molecules "in the air" with those of your skin? They are filling the gap between us and the things we are capable to perceive with our eyes... The "invisible" content of these gaps is interacting with the visible parts. At molecular levels those invisible elements contribute hugely to the non-deterministic, non-lego like snappiness, to the "random walk" way of things working out. This kind of insight I think should be replacing the "deterministic machinery" view when describing and picturing molecular and micro-biological processes. Visualizations by Dr. David S. Goodsell present this kind of ideas in a fascinating way. (you can stop waving your hand now ;)
- dnautics 13y ago
  I don't think the 'missing environment' is as much a big deal. Without getting too reductionist: You have to isolate the components that you're showing otherwise it's just a big mess that's hard to understand. I think the implicit "there's actually a lot of stuff in between there" is not a big deal, much as the implicit "these molecules aren't really colored" is not a big deal in the service of explanatory power. The reductionist view is not complete, but it's not wrong. Hypersymmetric assembly and molecules that 'know where to go' is wrong, and in a very subtle way that biases perception. The guy who makes the harvard video, in his TED talk, goes on and on about beauty in science. Well yeah, he created that beauty himself. The real system is sloppy and kludgey.... which I suppose could be 'beauty' in its own way, but very different from the way it's presented.

deleted 13y ago

[deleted]