
Molecular Visualisations of DNA [video] - sethbannon
http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/
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bradchoate
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)

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fakenBisEsRult
Here's the link to the actual video:

[http://www.wehi.edu.au/education/wehitv/molecular_visualisat...](http://www.wehi.edu.au/education/wehitv/molecular_visualisations_of_dna/)

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tokipin
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)

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grannyg00se
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
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.

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jostmey
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.

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agumonkey
Maybe that is 'simple' when solving the problem nature had, it's just that
we're not used to this kind of problems.

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cristianpascu
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.

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agumonkey
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.

~~~
cristianpascu
Living organisms are not structures. Not sure if that's what you say, but I
have heard this many times, in the context of origin of life. Where life is
seen as self-replicating structures.

The complexity of a geometrical structure (like a cube, or a protein) is one
thing. The complexity of a process that fulfills a function (engine of a car)
is another thing. One is static, the other is dynamic. One just sits there.
Like a pile of rocks. The other one takes an input and process it into an
output, in a specified, repeatable manner.

A pile of rocks, in a particular context, solves the problem of surviving the
surrounding conditions. Is it the simplest solution? Who cares!

DNA replication on the other hand? What did Mother Nature drink to come up
with this problem and try to solve it?

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agumonkey
That's why I added 'abstract' it's not fixed, things move underneath but the
abstract properties remain.

Funny about the rock thing, I never know what to make about them, I would need
to add an 'adaptability' rule to my core ones.

DNA replication did not emerge from the early organisms. Before replication,
we could investigate about DNA or prototypical forms of DNA as forms of
variable input transformation. This kind of meta-encoding (sorry programmer
POV leaking) of input tranformation is probably not the first minimum but
pressure + time pushed the versatility needs up (again programmer POV).

~~~
cristianpascu
I'm a programmer too, but also a physicist, and it's also hard for me to read
through explanations/narratives that use a lot of metaphorical language. And
there's a lot of that in evolutionary narratives.

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thelogos
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.

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dnautics
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)

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pointernil
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 ;)

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dnautics
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.

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pointernil
I agree.

>>You have to isolate the components that you're showing otherwise it's just a
big mess that's hard to understand.

That's for sure. No way to depict all of it at once...

>>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.

I disagree partly here. I imagine (hope! ;) "professionals" do know about the
missing and false color "stuff" BUT every picture flushed towards __broad
public __(vs professional publication f.e.) consumption should contain as much
context as possible, context "disturbing" the mechanical picture presented of
bio-molecular actually all natural reactions today. "knowing where to go" is
wrong as you say and it would not "fit" / "work" / "be accepted" / "look
believable" the moment the surrounding soup gets visible.

Leaving this kind of context out, i think, propels many misunderstandings
about the way science is actually understanding nature.

>> which I suppose could be 'beauty' in its own way, but very different from
the way it's presented.

Very true.

cheers

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gourneau
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.

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Ygg2
Second part (DNA replication) reminds me of a really complex machine. Like a
sewing machine, that cuts and folds and splits threads.

~~~
pixl97
Like a sewing machine, that cuts and folds and splits threads.

And in doing so makes another sewing machine.

Life is awesomely complex stuff.

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danielsiders
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)

~~~
rotskoff
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.

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icegreentea
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
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.

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

~~~
atmosx
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
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.

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AlexanderDhoore
Nature is awe-some!

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kylek
(2003) - but still cool :)

