
The life cycle of HIV in 3D [video] - duncanmeech
https://blogs.scientificamerican.com/observations/watch-the-life-cycle-of-hiv-in-colorful-new-detail/
======
cornholio
As a technologist, I have mixed feelings when I see the fascinating details of
life. On one hand, mastering this molecular machine would give us literally
God-like powers: we could fabricate, grow or heal anything. We could solve all
current problems, we could terraform planets using a few milligrams of DNA and
literally redefine what it means to be human.

On the other, I see the human body as a completely unsecured cybernetic
system, that can be so easily tricked to pick up any random bit of programming
and insert it into it's own code. There is no forethought or design, no
rational defense, just good enough systems that have evolved randomly against
non-rational adversaries that happened to emerge out of the protein soup
surrounding us.

The troubling fact is that mastering the wondrous biomolecular machine
necessarily comes with the power to kill every human on the planet. Truly God-
like powers.

~~~
ekianjo
> power to kill every human on the planet. Truly God-like powers.

You can't really design a perfect virus that will wipe out the human race,
because anything you do to affect its properties will also affect its ability
to spread. I'd be way more concerned about the destructive power of nuclear
weapons, still numerous enough to destroy a very large part of humanity and
our vital infrastructures.

~~~
cornholio
Are you sure you aren't still thinking in the conventional, evolutionary
paradigm?

A highly engineered bioweapon could circumvent such problems by separating the
infection phase (which could be completely silent and airborne) from the
eradication phase. The payload could be triggered deliberately at a later date
when a certain secret artificial protein is released in the environment - and
then produced in industrial quantities by infected hosts. Or maybe airdropped
over areas that should be cleansed.

And that's just scratching the surface of what's conceptually possible. It
could trigger specific ethnic characteristics or individuals, it could set up
exotic cyber-hybrids like public key decryption in DNA for commands from its
command and control. It could create side channels among infected hosts, for
example by triggering minute anatomical modifications in the inner ear and the
vocal centers, making them able to send and receive ultra- or infrasounds
controlled by the mallware.

As a more subtle cyberattack, an infected individual could grow a whole
parasitic subsystem that extracts select visual and auditory data and stores
them in DNA memory for later broadcast.

~~~
sizzle
Wow these are novel concepts, do you read a lot of sci fi? How did you come up
with these interesting scenarios?

~~~
cornholio
I'm not really inspired by scifi - but I'm sure some authors have had similar
and probably much wilder ideas.

Been thinking for years about the human body as a cybernetic attack surface
with no engineered cyberdefense. Most people seem not able to make that mental
leap; no, the human body can't behave like a vulnerable Windows 95 machine
giving kernel privileges to any ActiveX control it can download, because
reasons.

But once you see the biological world like a hacker and DNA like a programming
medium, as opposed to a representation of what evolution produced, an endless
array of nefarious possibilities become obvious. The rational power of our
minds far exceeds what evolution could ever concoct - or defend against.

------
baobrien
I think articles like Ken Shirriff's "Cells are very fast and crowded
places"[1] are good companions for visualizations like this. It helps to keep
in mind that the things moving around in cells are flying around at break-neck
speeds if you scale them up linearly.

1 - [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)

~~~
TeMPOraL
Where "flying around" means "constantly bumping into everything else". This
means small stuff doesn't just fly around the cell, it has to _diffuse_
through it. A nice side effect is that eventually, everything gets into
contact with everything else. That, as I understand, is how small molecules
get to their right place.

Also, this means that it's too tight for large stuff to move around at all.
Hence the specialized machinery within the cell that transports large
molecules.

Source for both: I'm 1/3d of th way through The Machinery of Life[0].
Incidentally, I learned about this book from HN. It's absolutely amazing. The
biggest selling point are the drawings - David S. Goodsell created a lot of
illustrations (like these[1]) that give you a good perspective on how stuff is
packed within cells.

EDIT: that blog post you linked covers the diffusion aspect well, I second the
recommendation to read it.

\--

[0] - [https://www.goodreads.com/book/show/6601267-the-machinery-
of...](https://www.goodreads.com/book/show/6601267-the-machinery-of-life)

[1] -
[http://mgl.scripps.edu/people/goodsell/illustration/public](http://mgl.scripps.edu/people/goodsell/illustration/public)

------
imranq
Absolutely insane how this is actual reality. That millions of people have
died from such a small object that seems to have more creativity and
complexity than I’ve ever seen.

~~~
DINKDINK
You might enjoy: Influenza A (H1N1) – How many bits does it take to kill a
human?
[https://www.bunniestudios.com/blog/?p=353](https://www.bunniestudios.com/blog/?p=353)

~~~
rqs
Also, video: [https://www.youtube.com/watch?v=NPr-i-
IbA7s](https://www.youtube.com/watch?v=NPr-i-IbA7s)

This one is about Influenza:
[https://www.youtube.com/watch?v=7Omi0IPkNpY](https://www.youtube.com/watch?v=7Omi0IPkNpY)
(not H1N1, but quality is better)

I learned a lot today (At least that's what I felt) LOL

------
sytelus
The amazing part for me was that virus "code" automatically finds the
unrelated host "code" in what is effectively an equivalent of space travel
inside a host body, does copy and paste to insert itself somewhere in host
code and everything just works! I can't think of any of our computing models
that is capable of doing this and so robust at errors.

~~~
JackFr
Lisp

------
colordrops
I know it's just my own biased anthropomorphizing but the virus almost looks
sinister and intentional in its actions.

~~~
baobrien
The music really helps with that. The video gave me a spooky feeling.

~~~
colordrops
Ha, I didn't even watch it with sound. Will have to do that when I get home.

------
juancampa
I would love to know how this animation was made. Is there any sort of
simulation happening?

~~~
fizixer
It's two separate things, both mentioned in your question: simulation then
animation. Both steps are computationally expensive enough that they can't be
done in one run.

For simulation, typically a molecular dynamics code is used along with
features specific to biological analysis (since MD by itself is a physics
simulator). NAMD is one of the well-known MD tools used for bio work.
Depending on the complexity and features/accuracy sought, a whole host of
other tools might be involved. The timeframe of simulation is of the order of
weeks to months given massive computational power (e.g., a large allocation on
one of the national supercomputing grids).

Once tons of simulation data is generated (as the output of simulation), then
3D visualization tools can be used. NAMD has a sister vis tool called VMD.
Blender is another option. Incidentally, Janet Iwasa (the narrator and
researcher behind this work) is a visualization expert, so it's likely she
only worked on the second step (animation) by using existing simulation data,
or collaborating with a simulation group. (Again the computation required for
rendering is very high, on the order of days to weeks using a large allocation
on a supercomputer).

------
titzer
Makes one really wonder just what, exactly, is out there mindlessly gobbling
and reproducing itself in an endless quest to just keep going. Puts human life
in perspective too. We're all just mindless gobblers when zoomed out enough.

------
czardoz
Hard to believe that no one has programmed this. Evolution is insane.

~~~
danielmain
Seems that you are not a programmer. Even with Intelligence people can write
code (much much simpler and buggy) how can chaos build such a complex thing?
Can you answer what was first? information (RNA/DNA) or the first cell?

~~~
czardoz
What makes you think I'm not a programmer? I was marveling at how evolution
can lead so something so systematic.

> Can you answer what was first? information (RNA/DNA) or the first cell?

No I can't. What are you getting at?

------
kevin2r
Question. How is that even knowing the lifecycle of HIV at this level of
detail, there is not a cure for it?

~~~
rqs
I Googled it for you:

[https://www.ted.com/talks/janet_iwasa_why_it_s_so_hard_to_cu...](https://www.ted.com/talks/janet_iwasa_why_it_s_so_hard_to_cure_hiv_aids)

[https://www.seeker.com/will-we-ever-cure-
hiv-1792546668.html](https://www.seeker.com/will-we-ever-cure-
hiv-1792546668.html)

[https://en.wikipedia.org/wiki/Management_of_HIV/AIDS](https://en.wikipedia.org/wiki/Management_of_HIV/AIDS)

Also you may interested:

[https://en.wikipedia.org/wiki/The_Berlin_Patient](https://en.wikipedia.org/wiki/The_Berlin_Patient)

~~~
jacobwilliamroy
>in the U.S. HIV kills 10,000 people per year

I remember an early passage from Buckminster Fuller's Grunch of Giants where
he tells the reader to visualize fully packed stadium and explains that's what
10,000 people looks like.

~~~
piker
I'm not sure 10,000 packs a stadium in the US. Maybe the bleachers of a high
school football stadium.

------
kartan
When I see the animations I can't stop thinking about a Turing machine. How it
works in a similar fashion, copying symbols to keep track of the program while
generating the result in the process.

It will be nice to know if you can build a Turing complete machine using DNA
and the cellular mechanisms. [https://www.quora.com/Is-DNA-a-Turing-
machine](https://www.quora.com/Is-DNA-a-Turing-machine)

------
ubershmekel
Here's the video on vimeo
[https://vimeo.com/260291607](https://vimeo.com/260291607)

------
betolink
Related to this type of animation, there is a great book called "The Machinery
of Life" that talks abut molecular level biology with amazing illustrations.
[https://www.amazon.com/Machinery-Life-David-S-
Goodsell/dp/03...](https://www.amazon.com/Machinery-Life-David-S-
Goodsell/dp/0387849246)

------
8iterations
A better animation is the winner of the AutoPACK challenge few years back:
[https://vimeo.com/62635232](https://vimeo.com/62635232)

Those guys did an awesome job because: a) use of brownian motion b) sick af
music.

~~~
Retric
That's a poor visual of Brownian motion. Things don't giggle they randomly fly
around at ~250 miles an hour.

It's still a great video just IMO misleading in its own way.

------
iandanforth
Mindblowing. To think that chance+time produced something like that is
staggering.

~~~
Liron
+reproduction +selection

~~~
Cogito
I haven't yet seen a good explanation as to why this focus on randomness is so
prevalent, but chance really is almost irrelevant when it comes to evolution.

The main mechanisms of reproduction and selection that you point out have
almost no randomness at a population level.

Selection of individuals has some randomness associated with it, as death can
come unexpectedly to anyone, but at population levels it is the genes that
make it more likely for an individual to survive/pass on their genes that are
the ones that get passed on. It's possible that an entire population gets
wiped out, or a particular gene gets wiped out due to chance, but as long as
the population is reproducing then on average the genes that are passed on are
the ones that help the population survive.

Similarly reproduction isn't random at population levels either. Sexually
reproducing populations mix their surviving genes evenly within geographical
locations over evolutionary timescales (such as trees), or selectively if
individuals choose their mates (like humans!). Neither of those things are
random. Mutations that happen during reproduction are somewhat random but, as
for asexual populations, the amount of mutation at the population level is not
random. It's reasonable to expect the reproductive mechanisms to be selected
for in such a way to maintain coding errors and the like (at an appropriate
level) so that mutations continue to develop and strengthen the gene pool.

While there are lots of single events where randomness and chance come into
play, as soon as you have a collection of things that reproduce those things
must either get better at reproducing or cease to exist. Chance has nothing to
do with it.

~~~
lawrenceyan
ENTROPY BABY.

------
Liron
Living in 2018 is quite a privilege. Most microbiologists who spent their
lives trying to puzzle this out won't get to sit back and watch the answer.

------
sizzle
This is why I'll never go on tinder or screw around, frightened about getting
stds. My friends act like STDs are no big deal and joke around about the times
they've contracted chlamydia and gonorrhea etc like it's a cost of doing
business (getting laid).

I'll stick to long term relationship.

------
yread
Amazing! So there is self-replicating, self-modifying code (HIV quickly
mutates to avoid detection) code, that sometimes jumps into middle of an
instruction (GAG proteins being cut into the enveloping proteins).

------
callesgg
Wow that gives me shivers, creepy.

------
stanislavb
That looks scary. VERY scary!

