
OpenWorm: A Digital Organism In Your Browser - turing
https://www.kickstarter.com/projects/openworm/openworm-a-digital-organism-in-your-browser
======
Micand
I remember reading about OpenWorm a few years ago and thinking it was
ridiculously cool. I'm glad to see the project has persisted. They do a bad
job, however, of selling themselves.

1\. What have they accomplished to date? I see little more than an animated
worm. Tell me about how you're trying to model the worm, and how these
approaches may accurately capture its behavior.

2\. Why should I care about having an animated worm in my browser? Why is this
an appropriate medium to deliver the simulation? If I want to do any kind of
science, how will this help me? What I've seen to date looks scarcely more
useful than Bonzi Buddy. The most interesting part seems the Academy, but I
must donate at least $250 to gain access. This seems counter to the "open"
part of "OpenWorm."

3\. What academic affiliations does the project have? If the project is useful
and has experienced success to date, surely they can recruit
students/postdocs/whatever to work on it full-time, with well-established labs
making major contributions. Are they computational people? Biology people?

4\. What are the bona fides of the people involved? If they can't typeset or
capitalize the species' name properly ("C. Elegans") in their video, that
doesn't lend much faith to their expertise. The gentleman in the video marvels
over the mere "1000 cells" in the worm, but does nothing to put this number in
context (with, say, the 10 trillion cells of humans).

I'd love to see this project succeed, and I admire its attempt to recruit
funding through a novel means, but the pricing seems too steep, and the
overall quality of the pitch is regrettably poor.

~~~
g_idili
FYI the capitalization of C. elegans is correct with a lowercase 'e' \-->
[http://en.wikipedia.org/wiki/Caenorhabditis_elegans](http://en.wikipedia.org/wiki/Caenorhabditis_elegans)

------
Lambdanaut
This project is huge. I'm glad to see it has come this far. It's the first
ever simulation of a multi-cellular organism at a really useful detail,
presented and made available to the masses.

It's work like this that is going to help explode the use of citizen scientist
work. Imagine being able to run your own experiments on a simulation first
without having to buy and breed your own worms. So many more experiments can
be carried out, and in parallel too.

It's not an exact model yet, but it's getting closer. The end goal is to get
the model to the point where if you run an experiment on the virtual worm, you
can be certain you'll get the same results on the real worm.

~~~
scottfr
I'm sorry, but this sounds like a fantasy land. I am extremely skeptical that
you could get a detailed and accurate enough simulation to reveal any useful
novel results.

The list of "unknown unknowns" that we don't even know about, yet alone are
able to attempt to simulate, is impossibly large.

This reminds me of the old Star Trek episodes where they would simulate the
effect of the new-fangled quantum-slipstream-tachion-whatever-warp-drives in
their Holodeck and then obtain meaningful results.

Of course, that was nonsensical fiction. I don't see how this could be
different.

Simulations and models need to be incredibly focused. The art of modeling is
figuring out what to exclude from the model, not what to include. Any attempt
to make a really general purpose model/simulation is almost bound to overreach
and fail.

~~~
hyperion2010
This is the mindset that has prevented people from even attempting such
projects, it is poisonous and anti-intellectual.

One thing that we almost NEVER do is with models is force them to interact
with each other. This means that we are completely blind to an entire aspect
of isolated models: namely that inputs may not have the structure we expect,
or that their outputs don't actually have the anticipated affect on downstream
models. Most current model validation is purely speculative or based only on a
finite dataset. If you take two models that you think effectively represent
how the world works and put them together and suddenly they no longer work,
then you reveal a huge gap in our knowledge. In a sense this is the ultimate
form of model validation and until you do it any interpretation you make about
how models might or might not work together is complete bullshit.

~~~
scottfr
I spend a lot of time working on models. This is not a "poisonous and anti-
intellectual" statement, it is simple a statement grounded in experience.

There are dozens of failed projects to make different models work together. It
would be such a beautiful concept if we could "snap" different models people
built together like legos and watch how they interact and develop together. It
is also a concept very inline with the hacker mindset where we all observe the
phenomenal success of the UNIX building block approach to getting things done.

It is a great idea in theory, but in practice making models work together is
incredibly difficulty. You have massive issues of scale (specifically in
regards to temporal scale with process going on at very different rates) and
context. This has been tried again and again. There are many software packages
designed to make this easy. As a general rule, they simply do not work outside
of narrowly focused domains.

What is "poisonous" to science (and science funding) is to overpromise and
underdeliver. What is also "poisonous" is to ignore a long history of modeling
and simulation work and the hard-earned lessons and failures gained from that
work.

~~~
hyperion2010
The only reason I say that mindset is problematic is because the way you frame
your statement is "this can't be done" when what is actually the case is that
we have never really tried because there are many other easier problems to
solve. I don't think anyone who has spent even a limited amount of time
modelling expects to be able to stick a few equations together and have it all
work. It is still an open question as to whether we can capture say 95% of the
variance in a system using a collection of simplified models or whether we
have to go full monte carlo and study models that have the full complexity of
the system they represent because you really do need every last single part
and can't simplify anything.

There will be novel results no matter what happens, maybe not about c elegans,
but certainly about the models themselves.

------
hyperion2010
I will definitely be donating. I met Stephen about a year and a half ago when
this was just getting off the ground and he was (and still is) incredibly
enthusiastic about going after such a challenging problem. When I mentioned
that we had had relatively little success building such complex models he
pointed me to the work modelling Mycoplasma genitalium [1]. The problem is not
that we don't have the mathematical or computational tools or even the data to
do it, it is that the social and practical aspects of organizing and
integrating such a major engineering project are usually only available at
companies with massive amounts of capital. Serious attempts to completely
model complex systems are also usually beyond the scope of the least
publishable unit. Hopefully open science will be able to bridge the gap. Good
luck to the whole OW team!

[1]
[http://www.sciencedirect.com/science/article/pii/S0092867412...](http://www.sciencedirect.com/science/article/pii/S0092867412007763)

~~~
QuadDamaged
I met John who worked on their (paid) iPhone app for the earlier prototype.
There's one thing you can say it's that they are passionate about their
project. The old prototype is here: (paid, is it OK to link this on HN?)
[https://itunes.apple.com/us/app/openworm-
browser/id595581306...](https://itunes.apple.com/us/app/openworm-
browser/id595581306?mt=8)

~~~
rstoner
The iOS source code is on github:
[https://github.com/openworm/openwormbrowser-
ios](https://github.com/openworm/openwormbrowser-ios)

Plenty of bugs to fix.

(disclaimer: I wrote a good chunk of it.)

~~~
adinb
As an honest question, any particular reason you guys haven't updated the
AppStore version in a year?

------
Theodores
On a lighter note there is always 'Triop World':

[http://www.amazon.co.uk/Interplay-UK-5026175001302-Triop-
Wor...](http://www.amazon.co.uk/Interplay-UK-5026175001302-Triop-
World/dp/B00008OS3U)

The aim is you grow worms and see what happens. Here is the 'must read'
review:

 _Is it possible to become emotionally attached to a kill-crazy cannibalistic
worm that looks like a facehugger from the Alien movies and spends most of its
time attempting to eat its siblings?_

 _Having recently shed a tear while burying my last one - Chompy - in the back
garden, I 'd say yes. These little beasties inspired fear and disgust in my
girlfriend, but to me they were true friends._

 _How could I forget the way Chompy used to play with his smaller brothers,
chasing them around their tank for hours on end? Every couple of days, one of
the brothers would vanish completely, and Chompy would do an extra-long poo to
show how much he missed them._

 _After about 30 days, Chompy disposed of the final, equally large brother -
Ripley - by eating him from the tail up. I caught the two of them playing on
the bottom of the tank - Chompy had Ripley 's face in his mouth, and was
munching away without a care in the world. The rest of Ripley was nowhere to
be seen._

 _Heartbroken, Chompy only lasted another week after that. For a while, he ate
his fish pellets and bits of carrot as normal, but a triops is only half a
triops without his playmates. Eventually Chompy turned green, and the end was
nigh._

 _Would I repeat the experience? Maybe, but next time I would have to steel
myself for the inevitable tragic end. Triops might not live long, but they 've
got personality. And they eat Sea Monkeys for breakfast._

So, if this open source 'digital organism' can evolve to be as cool as Chompy
then there could be quite some appeal.

------
dm2
Here is the current browser based version:

[http://browser.openworm.org/](http://browser.openworm.org/)

[http://caltech.wormbase.org/virtualworm/](http://caltech.wormbase.org/virtualworm/)

Human version (much cooler):
[http://www.zygotebody.com/](http://www.zygotebody.com/)

Cow version:
[http://open-3d-viewer.googlecode.com/svn/trunk/web/index.htm...](http://open-3d-viewer.googlecode.com/svn/trunk/web/index.html)

Source code for the viewer for all of these:
[https://code.google.com/p/open-3d-viewer/](https://code.google.com/p/open-3d-viewer/)

Note: you're going to want to use hardware acceleration for these, otherwise
they'll be very slow.

~~~
rstoner
They released an iOS port (GLKit-based) of their worm browser on the app
store.

Source code is here: [https://github.com/openworm/openwormbrowser-
ios](https://github.com/openworm/openwormbrowser-ios)

------
dfc
Worm Tangent: If you have children and enjoy gardening you should look into
setting up a worm compost bin in your basement. I do not have kids but a lot
of the kids in the neighborhood enjoy looking at the worms in the compost bin
and seeing how they move up a new layer once they have eaten all of the food
in the bottom layer. The biggest hit with the kids is the moving pink brillo
pad that is pile of baby worms. When I got the worm farm setup my only goal
was cheaper food for my roses. The worm casing/compost is great for my roses
and the neighborhood diplomacy is a great side benefit.

------
abritishguy
Strange use of the word "open" and whilst this project is very interesting, I
don't think people want to pay to play with a worm in their browser.

~~~
userbinator
The word "worm" has also not-so-positive connotations when talking about
computers, thanks to this:

[http://en.wikipedia.org/wiki/Morris_worm](http://en.wikipedia.org/wiki/Morris_worm)

------
LazerBear
It would be much more exciting if they could get a SINGLE cell (of whichever
organism) simulated with virtual subatomic particles. Has anything like that
been attempted? Do we even have the data?

~~~
jjoonathan
Agreed, this would be much more exciting, but we decidedly do NOT have the
data and do NOT have the processing power to do this in general. Nor will we
for the forseeable future, even if Moore's law holds and we figure out quantum
computers.

Still, thanks for asking: it's an important question that deserves a thorough
answer. There are four separate "simulation domains" lying between simulations
of subatomic particles and simulations of whole cells. In each domain, one
might expect to answer a single targeted question through years of painstaking
accumulation and application of expert knowledge.

(0) Let's start by ignoring the fifth domain (that I didn't count): simulating
the behavior of the atomic nucleus. Nature has granted us a reprieve here in
that biological activity is independent of what goes on at this scale.

(1) The first domain happens when you try to simulate an atom (not a molecule,
a single dinky little atom) starting from a point-nucleus and an electron
cloud. Time-stepping a Newtonian Mechanics simulation is typically between
O(N) and O(N^2) in space and time. Unfortunately, newtonian mechanics and
classical E&M can't tell you anything remotely connected to reality about an
atom. The wheels come completely off: they predict that electrons radiate away
their potential energy and crash into the nucleus, saying nothing about the
"orbitals" we observe them stacking into. Quantum Mechanics is necessary, and
the full equations are O(M^N) in both time and space, where M is the
resolution along each axis of your simulation (every possible "universe" (set
of particle locations) has a complex probability associated with it). There
are decent approximations, but none of them suffice to answer all the relevant
questions at once. Expert knowledge and experimental verification must be used
to select the appropriate approximations.

(2) The second domain happens when you try to simulate a molecule from atoms.
Nature grants us a huge reprieve in that we can safely ignore most atomic
behavior: only the valence orbitals have interesting interactions, and nuclei
are much heavier than electrons, so we can model the electrons' behavior
independently. Still, the full problem is O(M^N) in time and space, and no
single approximation works in all cases. A grad student with several years of
training in quantum mechanics might spend months finding the appropriate set
of assumptions to simplify and simulate a single chemical reaction.

(3) The third domain happens when you try to go from the scale of small
molecules (dozens of atoms at most) to the scale of biological macromolecules
(proteins, with tens of thousands to millions of atoms -- completely
impractical even for heavily simplified QM models). Nature grants us a huge
reprieve in that Netwonian mechanics becomes relevant at this scale. We can
ignore most of the quantum mechanics most of the time and model it using
struts, springs, and repulsive forces (at the price of ignoring chemical
reactions, which we must separately account for if necessary). The difficulty
here is the timescale: individual "wiggles" and collisions happen every
femtosecond or so, while meaningful reactions often happen on the scale of
milliseconds. If you let the width of a large pencil lead (1mm) stand for the
time of a typical "wiggle," a single second of simulated time stretches from
the Earth to the Sun. Cutting edge custom-ASIC supercomputers can simulate
single small proteins for 1.5 milliseconds:
[http://en.wikipedia.org/wiki/Anton_(computer)](http://en.wikipedia.org/wiki/Anton_\(computer\))
. Last year's Noble Prize in chemistry went to people who spent their lives
whittling away at the problem of integrating (2) with (3).

(4) The fourth domain happens when you try to go from the scale of a single
molecule or macromolecule to the scale of a cell. Nature grants us a huge
reprieve in that typical macromolecules usually only have a small number of
functions and often only act in a statistical sense (they can be well
characterized by their concentration and the concentration of their substrates
in different compartments). Unfortunately, this data is very difficult to
collect with certainty. How do you know that a given protein interacts with a
given substrate in a given way? There are many ways to guess and many ways to
measure, but for the most part we have to tackle proteins one-at-a-time. This
is what biologists do, and after hundreds of years, billions of dollars per
year, and countless underpaid PhDs plunking away at the task of characterizing
individual pathways, there is enough of a picture to perform a very rough
simulation of the whole thing by specifying a chemical kinetic ODE between
various species in various compartments.

Note the pattern at each scale: A full simulation within the domain is
impossible, but nature grants us a reprieve which lets experts answer specific
questions with tremendous expenditure of effort and a quantity of data that
grows dramatically in the number of the layer.

In a theoretical sense, we do have all the data we need: the only thing
stopping us from going from 1-4 is computational power, however the gulf is so
large it will almost certainly never be spanned by a single simulation. In a
practical sense, where we want to ask high-level questions on the scale of (4)
or higher, there is a great deal of data missing, since data plays the role of
simplifying the lower layers of the simulation, or of allowing us to skip (4)
altogether and ask a question on the scale of (3) or (2).

~~~
LazerBear
Great reply, thank you for clarifying!

I sometimes like to think about the ethical consequences of having that type
of data and computation power. For example it's very likely for it to be used
to perform experiments in biology.

But who's to say that an organism simulated in that low level is any different
from the real thing? If there even such a thing as "the real thing".

And it gets even weirder when simulating human beings. Is a simulated person
any different from us? Is he really conscious or does he merely "behave"
conscious? Is it ethical to use it for experiments? What about entertainment?
And also, it raises the possibility that we ourselves might be simulated in
one level or another.

I think that in some point humanity will have to face these questions. Though
from what I understand from you, we still have a few centuries to get there...
Man, that's something I'd love to see.

~~~
dsego
[http://en.wikipedia.org/wiki/The_Emperor's_New_Mind](http://en.wikipedia.org/wiki/The_Emperor's_New_Mind)

The Emperor's New Mind: Concerning Computers, Minds and The Laws of Physics is
a 1989 book by mathematical physicist Sir Roger Penrose.

Penrose presents the argument that human consciousness is non-algorithmic, and
thus is not capable of being modeled by a conventional Turing machine-type of
digital computer. Penrose hypothesizes that quantum mechanics plays an
essential role in the understanding of human consciousness. The collapse of
the quantum wavefunction is seen as playing an important role in brain
function.

------
sarreph
When those worms start asexually reproducing, mutating, and subsequently
evolving at a rapid simulation speed, we'll all be sorry...

~~~
paulojreis
"When those worms start asexually reproducing" \- I think they already do.

~~~
Lambdanaut
No. The simulation hasn't modeled the reproductive system as of yet. I'm not
sure it ever will. A lot of the power of the reproductive system is in the
DNA, and this simulation does not model DNA.

~~~
Snail_Commando
> ...I'm not sure it ever will. A lot of the power of the reproductive system
> is in the DNA, and this simulation does not model DNA.

I'm not sure what you mean by the last sentence. Not incorporating a full
simulation of genetic expression does not preclude the authors from
incorporating a simulation of C. Elegans reproduction or the reproductive
system in some capacity.

DNA is just a container of letters that ultimately form the words that are
amino acids. These amino acids are formed into sentences and phrases that are
proteins. Should these proteins be arranged in a functional grammar, their
structure and actions collectively express the language of life.

DNA is just the machine code for the emergent system that is life.

A biological system, such as the reproductive system, is comprised of some
components that are several layers of abstraction above the DNA; as each
system is an emergent property of the symphony of molecular machinery and
interaction that constitutes a living organism.

Since many authors were already able to simulate abstractions over other
structures and systems, there is no reason why the C. Elegans simulation could
not extend their model further. As far as I know, they were not simulating
gene expression at all.

Saying that a particular biological abstraction cannot be simulated because it
does not contain a lower level simulation of genetic expression is a bit like
saying you cannot simulate a ball bouncing because you do not include an
atomic resolution molecular force simulation of rubber molecules. Or, that you
cannot program a football simulation, like FIFA, because you do not include
lower level simulations of aerobic and anaerobic respiration.

Obviously, molecular force dynamics and respiration are integral phenomena
that enable bouncing balls and football matches, respectively. (I'm unaware of
existing respiring balls.) But those phenomena can be closed over by
abstraction, in order to create sufficiently educational simulations for
particular scopes of understanding.

Of course, it _would_ be computationally difficult to simulate each level of
abstraction, all at once, at atomic "resolution" (or molecular or
macromolecular etc. "resolution"). It would be impractical to simulate
molecular dynamics, or transcription and translation, or protein folding; when
all you care about is the general concept of reproduction and the more
abstract structures involved.

You could certainly produce a sufficiently useful naive simulation that is
faithful to the spirit of an organism's reproductive system.

There is always a hard boundary on the "resolution" of a biological system
simulation, limited by computational power, but there is no logical limitation
preventing _some_ simulation of the reproductive system at _some_
educationally valuable level.

------
tsenkov
As much as I understood, this project isn't so much about AI, as it is about a
better understanding of biology.

I don't know if the project still lives, or are there other many such works,
but Polyworld seemed like an interesting idea (developing AI through
evolution):
[https://www.youtube.com/watch?v=_m97_kL4ox0](https://www.youtube.com/watch?v=_m97_kL4ox0)

~~~
maaaats
I may have misunderstood you, but anyways: Developing AI through evolution is
pretty common in AI nowadays. Using genetic algorithms (GA) to evolve
parameters for other AI solutions, for instance the weights in an artificial
neural network (ANN).

Just finished a project where we did exactly that. A simple ANN with feedback
(memory) where the different weights between nodes, gain, bias etc. were
trained through GA. After a few generations intelligent behavior started to
emerge.

------
based2
[http://www.openworm.org/getting_started.html](http://www.openworm.org/getting_started.html)

------
Ortsac
They call it "open", then turn around and charge ~$50 to access the web-
browser version of the sim for a year? Doesn't feel very open to me.

I recognize just how important C. elegans is to neural/bio research, and how
ambitious the project probably is. I just think this would be so much cooler
if they were offering it to all curious minds free of charge.

~~~
maaaats
They need to spend money on infrastructure/raw power for the interactive worm
sims simulation.

The code is open, so I guess that means you can host your own version if you'd
like?

~~~
Ortsac
It does look like they're providing their results for free.[1]

That makes a lot more sense. You're paying to host the virtual "organism", not
paying for the sim itself.

[1]
[http://www.openworm.org/downloads.html](http://www.openworm.org/downloads.html)

------
auvi
Do the simulation happens in the browser? Is it some sort of BOINC in the
browser? Watching the videos to check.

------
dkarapetyan
The icky factor is a little too high. Marketing wise they could have done much
better.

~~~
goldenkey
I actually felt that the video was frank as can be, without the usual
kickstarteresque shameless jazzy sales and marketing schmutz.

Openworm is genuine out to improve biology. Not the money, they just need it
to continue working on the project. Many kick starter campaigns, can easily be
deduced as shameless money grubbing through fake passion pleas. Not this one.
And yes, you may call it poor marketing. But hell, that's at being genuine
appears to be. We're not used to genuine kick starters.

------
bmaeser
tamagotchi 2.0? (a very sophisticated one)

------
x1024
wat?

