
Close-Up View of DNA Replication - mgalka
https://www.ucdavis.edu/news/close-view-dna-replication-yields-surprises
======
ekianjo
For anyone interested in the molecular process of DNA replication, here's a
pretty cool video that explains what happens at the protein level. It's always
amazing to watch what is in practice a molecular-sized machine:

[https://www.youtube.com/watch?v=OjPcT1uUZiE](https://www.youtube.com/watch?v=OjPcT1uUZiE)

~~~
mk7
I'm looking at this video and can't stop thinking: "Who created this process?"
With all advances in technology and know-how we are not able to put such
sophisticated process together... And it is present in EVERY living creature
and happens millions of times in every body... So how this process came into
existance?

~~~
0xfeba
And thus, the argument from incredulity was born, with a dash of
personification.

~~~
mrybczyn
Here's the argument from Phys.org: [https://phys.org/news/2013-04-law-life-
began-earth.html](https://phys.org/news/2013-04-law-life-began-earth.html)

~~~
0xfeba
Huh? That's one self-described "thought experiment" by two scientists that
attempts to fit Moore's law (you know, governing CPU speeds) to evolution. It
doesn't fit, surprise. This is after they arbitrarily define "genetic
complexity".

That's not _the_ argument from Phys.org which is just a online news
organization, anyway.

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ValleyOfTheMtns
Something I've never understood is how the nucleotides arrive to be included
in the DNA strand. These animations always just show them appearing in perfect
sequential order when they're needed, which is of course not what happens.

How are they delivered to the polymerase in the first place? How do they
"know" where to be?

Are there just so many of them in the cytosol that through sheer numbers,
there's enough random chance they'll just shuttle into place when the
polymerase needs them?

~~~
kens
I wrote a blog post a few years ago explaining how molecules get to the right
place at the right time. The short answer is that cells are nothing like the
nice, peaceful animations. Cells are extremely crowded and things move
extremely fast. Glucose molecules, for instance, move around cells at 250
miles per hour and collides with something billions of times a second. An
enzyme might collide with a reactant 500,000 times a second. And proteins can
spin a million times per second. So as you suspect, by random chance molecules
are in the right spot very frequently.

[http://www.righto.com/2011/07/cells-are-very-fast-and-
crowde...](http://www.righto.com/2011/07/cells-are-very-fast-and-crowded-
places.html)

~~~
undershirt
Thank you for writing this. I used to wonder how flies have such terrific
reaction times and whip around the air with insane agility. And then I
wondered if we are just seeing them in fast forward, due to the relatively
slow clock in our heads. I imagined it was why they had such a short lifespan
of just several days. And I imagined them seeing us as glacially moving
statues—"man this guy hasn't moved in years!"

Reading your description of cells as moving imperceptibly fast only fills me
more with this sense—that we are very slow moving giants, waiting on the
billions of "years" of inner machinery time to tick us forward ever so slowly.

~~~
op00to
Time for you to read "Dragon's Egg", a hard sci-fi book about a civilization
that evolves on a time scale far shorter than humans ultimately leading up to
interaction with humans and this civilization. Awesome book which explores
different time scales.

[https://en.m.wikipedia.org/wiki/Dragon%27s_Egg](https://en.m.wikipedia.org/wiki/Dragon%27s_Egg)

~~~
iUsedToCode
Dude, that was awesome. Thanks a lot!

I haven't had a book this good in some weeks. Cheers!

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bwang29
I can feel there is something really interesting here but the writing, title
and explanation here seems to be poor. The surprise here is the random starts
and stops as well as 10X speed difference in the DNA replication process.
Wouldn't it be more surprising that these processes run at the same speed?

"...started watching individual DNA strands..." I'm wondering how important
the visualization and nature of "filming" helped to form the idea or prove the
hypothesis that replication is a async process. I didn't quite gather which is
more impressive, the filming or the discovery.

“Sometimes the traffic in the next lane is moving faster and passing you, and
then you pass it. But if you travel far enough you get to the same place at
the same time.” also doesn't quite make sense to me as the video clearly shows
no queuing structure as seen in real life traffic, and there is no real
hypothesis to explain the sudden stops and starts.

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darkkindness
> “It’s a real paradigm shift, and undermines a great deal of what’s in the
> textbooks,” he said.

Sorry, but is this really that new? I've never been taught that the DNA
strands coordinate with each other while replicating, so it seems quite
possible that synthesis of each strand can be independent of each other.

~~~
nerdponx
The "paradigm shift" is referring to the "stochastic" nature of replication,
which apparently was not known before.

~~~
dekhn
i was taught all the things they're saying in this press release ~20 years ago
in biochem class.

------
ekianjo
> “We’ve shown that there is no coordination between synthesis of the two
> strands. They are completely autonomous,” Kowalczykowski said.

Couldn't that be the unintended effect of doing things in a flow chamber?

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sidcool
This is amazing. I can't wrap my head around the fact that some brilliant
people discovered this long back. Scientists and Physicists are so talented!
And I can't center a <div> without googling. Sigh...

~~~
flamedoge
text-align: center

align: center

~~~
cyphunk
only works horizontally :/

~~~
amelius
This says more about the talent of the designers of the CSS spec.

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saagarjha
Hmm…possibly there's some other process going on during those "slowdowns" that
we haven't observed yet?

~~~
KasianFranks
I agree, that's part of the import here.

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jcims
My mind always boggles at the sophistication of this little machinery, and
what forces drove random chemicals into the first primitive forms of encoding
and reproducing heritable traits subject to selective pressure. The
bootstrapping of evolution.

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Companion
Not sure if the apparent stop start observation, and also one strand sometimes
getting synthesized while the other isn't would actually occur in-vivo. This
is a pretty cool technology but a heavily artificial in-vitro system at the
end of the day.

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cortic
\- "Almost all life on earth is based on DNA being copied, or replicated" \-
Can anyone tell me what they are referring to here? (life on earth that isn't
based on DNA)

~~~
kittiepryde
RNA I believe. ( Which I only existed at one time, in theory? Or some people
think viruses count as life )

~~~
cortic
i did spend an embarrassing amount of time trying to find an example of RNA
life after reading your initial reply lol.

I suppose viruses do count as 'life' in some sense, so fair enough, thanks for
clearing that up.

~~~
dekhn
viruses don't count as life. they have no metabolism (but satisfy the other
requirements).

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Angostura
I really appreciate science journalists who can explain accurately and clearly
in this manner. Good job.

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inetknght
As someone who works in the DNA analysis software industry...

#neat

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hirundo
Most explicit porn ever!

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YCode
I have no idea what I'm seeing here.

I don't doubt what they are saying, but that looks nothing like the models of
DNA that are used as eye candy in movies and such.

~~~
comatosesperrow
It doesn't look like DNA models you are used to because a microscope that
would give you that level of resolution does not exist.

Even in the best images that exist, all you are going to see are little bits
that look like string.

~~~
YCode
I guess I'm just struggling to see how the animation maps to the DNA or how
the scattering of dots becomes a double helix.

