Re: [FRIAM] Any non-biological complex systems?

[Eric Smith]

Thanks for this Marcus, 

> One could imagine coupling a physical simulation to a search procedure for 
> functional behaviors like memories and doorways.   The detection 
> combinatorics would be challenging, assuming the physical simulation were 
> possible at sufficient fidelity, but perhaps could be constrained by virtue 
> of spatial locality.   

Yes.  I can’t bring to mind anybody who seems to be doing important work in 
this entirely within simulation, but Leroy Cronin in Glasgow is trying to 
combine highly parallel robot-maintained reaction vessels with pattern-matching 
computation and feedback, so see if he can search for properties and then 
extract chemical mixtures that will instantiate them.
http://www.chem.gla.ac.uk/cronin/
Lee is a handful, and his group is the size of a small town (larger than some 
small towns in NM, I suspect), so one gets the sense of massive seiving for 
most-anything, with the hope that some fraction of that will remain of interest 
for longer than the time Lee is promoting it.  The project is really different, 
though, from anything I have seen before.  It begs to be integrated with modern 
AI, which has become quite flexible in what you are allowed to call salient, so 
one can search in very open-ended ways.

> I don't know much about coarse-graining organic chemistry simulators.  For 
> comparison, with molecular dynamics a billion atoms is possible (on a budget 
> of a few megawatts), but not for more than tens of nanoseconds.   I've found 
> game physics engines like Bullet Physics are nice for coarse-grained models 
> because they are fast (optimized to graphics processors) and easy to 
> interleave control or detection logic.  However, they couldn't (without more 
> work) decompose the space across memory domains of a cluster. 

Interesting.  I don’t know much about molecular-dynamics simulations, which is 
deeply an expert’s game, though I guess most major universities have somebody 
in chemistry or biochem who specializes in it.  If one is willing to go one 
level out, and ask which questions are hard at the level of network synthesis 
and search, taking reaction primitives as input data, the graph-grammar methods 
are becoming pretty sophisticated.  The best I know of is the current state of 
the project that started with Peter Stadler but is now dispersed across 
German-speaking Europe and Scandinavia:
http://cheminf.imada.sdu.dk/mod/
Much of what makes this a hard and interesting computational project doesn’t 
show if one merely wants to do chemistry.  It comes up because they are trying 
to create a consistent representational system.  This creates difficulties like 
deciding when two things are the same molecule; when two molecules arrived at 
through different pathways are actually isomorphisms of the same label set, 
etc.  In random network-extension algorithms, this entails solving the 
graph-isomorphism problem a very very large number of times, and the underlying 
representational system must be provably well-defined.  It is in coming up with 
representations that are more well-defined than SMILES or INCHI, and 
implementing most-modern isomorphism searches, that these guys are the furthest 
along.  There is also a playground linked from their main page, though I am 
told they recognize their documentation may be a bit off-putting to people not 
used to wading into new systems.  

The current state of the graph-grammar project is several-fold:
1. Bond topology is present, and has been for some time.
2. Simple stereochemistry of carbon is now implemented, and less-simple 
stereochemistry that requires non-local propagation through a molecule to 
determine equivalence of representations is next to come.
3. Stereochemistry of metals, which will be the gateway to crucial mechanisms 
of metal catalysis, is planned.
4. There is a project, privately held, to port the entire Beilstein database of 
reaction mechanisms to graph-grammar representations, after which engines like 
this become an incredible tool.  RIght now the bottleneck is usually manual 
coding of the mechanisms of interest.  
5. There has been some discussion of raising pattern-matching above the level 
of atoms or local clusters, to inductively-defined patterns like crystal faces, 
but no serious attempt to formulate that problem yet.

Even with the limited state of what they can do, they have achieved some 
tolerable comparisons against messy chemical systems, like the 
formaldehyde-addition network known as the “formose network”, and the HCN 
polymerization and hydrolysis system.  Both are famously complicated, and both 
have long-standing interest to Origin of Life people, though their exact 
situation relative to planetary chemistry is easy to argue about.

All best,

Eric




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Re: [FRIAM] Any non-biological complex systems?

[Marcus Daniels]

Eric writes:


"This creates difficulties like deciding when two things are the same molecule; 
when two molecules arrived at through different pathways are actually 
isomorphisms of the same label set, etc.  In random network-extension 
algorithms, this entails solving the graph-isomorphism problem a very very 
large number of times, and the underlying representational system must be 
provably well-defined."


Looks like MØD uses the Boost (C++) graph library in a deep way.  They must 
have thought about parallel approaches, but I suppose it is complicated enough 
already.

Eventually, the D-Wave or another annealer could be a useful tool here...




https://www.nature.com/articles/srep11168




"5. There has been some discussion of raising pattern-matching above the level 
of atoms or local clusters, to inductively-defined patterns like crystal faces, 
but no serious attempt to formulate that problem yet."


..and also for this and the stereochemistry matching.


Anyway, thanks for all that.  It is really interesting..


Marcus


From: Friam  on behalf of Eric Smith 

Sent: Sunday, June 4, 2017 5:10:36 AM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] Any non-biological complex systems?

Thanks for this Marcus,

> One could imagine coupling a physical simulation to a search procedure for 
> functional behaviors like memories and doorways.   The detection 
> combinatorics would be challenging, assuming the physical simulation were 
> possible at sufficient fidelity, but perhaps could be constrained by virtue 
> of spatial locality.

Yes.  I can’t bring to mind anybody who seems to be doing important work in 
this entirely within simulation, but Leroy Cronin in Glasgow is trying to 
combine highly parallel robot-maintained reaction vessels with pattern-matching 
computation and feedback, so see if he can search for properties and then 
extract chemical mixtures that will instantiate them.
http://www.chem.gla.ac.uk/cronin/
Lee is a handful, and his group is the size of a small town (larger than some 
small towns in NM, I suspect), so one gets the sense of massive seiving for 
most-anything, with the hope that some fraction of that will remain of interest 
for longer than the time Lee is promoting it.  The project is really different, 
though, from anything I have seen before.  It begs to be integrated with modern 
AI, which has become quite flexible in what you are allowed to call salient, so 
one can search in very open-ended ways.

> I don't know much about coarse-graining organic chemistry simulators.  For 
> comparison, with molecular dynamics a billion atoms is possible (on a budget 
> of a few megawatts), but not for more than tens of nanoseconds.   I've found 
> game physics engines like Bullet Physics are nice for coarse-grained models 
> because they are fast (optimized to graphics processors) and easy to 
> interleave control or detection logic.  However, they couldn't (without more 
> work) decompose the space across memory domains of a cluster.

Interesting.  I don’t know much about molecular-dynamics simulations, which is 
deeply an expert’s game, though I guess most major universities have somebody 
in chemistry or biochem who specializes in it.  If one is willing to go one 
level out, and ask which questions are hard at the level of network synthesis 
and search, taking reaction primitives as input data, the graph-grammar methods 
are becoming pretty sophisticated.  The best I know of is the current state of 
the project that started with Peter Stadler but is now dispersed across 
German-speaking Europe and Scandinavia:
http://cheminf.imada.sdu.dk/mod/
Much of what makes this a hard and interesting computational project doesn’t 
show if one merely wants to do chemistry.  It comes up because they are trying 
to create a consistent representational system.  This creates difficulties like 
deciding when two things are the same molecule; when two molecules arrived at 
through different pathways are actually isomorphisms of the same label set, 
etc.  In random network-extension algorithms, this entails solving the 
graph-isomorphism problem a very very large number of times, and the underlying 
representational system must be provably well-defined.  It is in coming up with 
representations that are more well-defined than SMILES or INCHI, and 
implementing most-modern isomorphism searches, that these guys are the furthest 
along.  There is also a playground linked from their main page, though I am 
told they recognize their documentation may be a bit off-putting to people not 
used to wading into new systems.

The current state of the graph-grammar project is several-fold:
1. Bond topology is present, and has been for some time.
2. Simple stereochemistry of carbon is now implemented, and less-simple 
stereochemistry that requires non-local propagation th

Re: [FRIAM] Any non-biological complex systems?

[gepr ⛧]

Excellent typology, Eric. 

1) Memory, 2) doorways, 3) autonomous, 4) model, 5) control system, and 6) 
agency.

It seems 1-2 are about the boundary. 3 is the closure. 4-5 are proto-semantic, 
separating what a thing is from what it means. And 6 is the mechanism for 
ambiguity (symbols, switches, where a thing can mean more than one thing).

re: "a natural sense of a system's own delimitation."  I think you describe it 
well enough when talking about reflectivity. Such a natural boundary must be 
natural to a given sense/perspective. A pre-reflective system's boundary is 
determined in part by its context (since you cited Ashby, H_c >= H_s). But it's 
a much stronger statement to suggest that a boundary can be determined from/by 
the perspective of the bounded.


On June 3, 2017 8:53:18 AM PDT, Eric Smith  wrote:
>1. Protected degrees of freedom are a precondition to even the
>possibility of MEMORY.  If you are a mere physical degree of freedom,
>and you are always coupled to your environment, you are nothing
>different than an instant-by-instant reflection of the immediate local
>state of your environment.  All of the later concepts in the list
>require various forms of internal state that have enough insulation to
>be protected from constant harassment.  So where in the physical world
>are suitably decoupled degrees of freedom available to be found?  (Much
>later, to be built, but not yet.)
>
>2. Some kind of dynamical variables need to be capable of being
>couplers that can become DOORWAYS, so that the other DOF are sometimes
>coupled and sometimes not.  A DOF that is always behind a wall (a
>chemical reaction behind such a high energy barrier that it is never
>achieved) can’t remember anything because, although it can certianly
>hold a state, it is never in contact with the environment that would
>imprint anything on that state.  This doesn’t yet talk about how the
>open/close states of the doorway happen, which will determine when and
>what it allows the environment to imprint on the memory variable, and
>for how long that imprint can be held.  Here one can be quite precese
>with examples without invoking biology.  Organic chemistry at low
>energy in water is largely non-active.  Metal centers, particular
>d-block elements, are the major doorways that govern the sectors of
>organic chemistry available to early ocean-rock worlds.  Many enzymes
>still use them in something not too far from a mineral or soluble
>metal-ligand complex state, with a little tuning.  In this case, the
>doorway works just through physical drift.  Molecules free in solution
>are inert; those that bump into a metal can potentially become active;
>when they dissolve and drift on, they become inert again.  This leads
>to a very different set of relations between thermal energy and
>information in reactions, than simple thermally-activated reactions
>among the same species.  Probably one can invoke many other examples.  
>
>3. Some of the internal variables need to be capable of carrying on an
>AUTONOMOUS dynamics or internal process.  I guess a memory variable can
>sit there passively and still, at some level, categorize the way a
>system (set of DOF) responds to an environmental event, but for most of
>the later levels, there needs to be actual internal dynamics.  This in
>itself is not so hard; the world is far from equilibrium in any number
>of dimensions, and for something to be moving in a direction is not
>rare.
>
>4. Internal dynamics can be autonomous, but it isn’t really “about”
>anything unless something about the configuration constitutes a MODEL
>in the sense of Conant and Ashby from old 1950s control theory.  How
>the model is registered, and how reflexive or self-referential the
>internal dynamics needs to be for a meaningful model to be imprinted,
>probably ramify to many differenent questions.  I would of course be
>happy to produce an interesting case of the emergence of any of them.
>
>5. At some stage, a protected internal process of which the state of
>the model is part needs to act back on the doorway, if we are to be
>justified in saying the basic relation of a CONTROL SYSTEM has come
>into existence.  Here again I intend a Conant and Ashby line of
>thought: that “Every good controller “contains? entails?” a model of
>the system controlled.  There has to be some internal state that is
>capable of being in different relations to the state of the world, and
>then the internal dynamics has to take an input from a comparison of
>those two states.  Only if the resulting action feeds back on the
>state, does the system start controlling its own interaction with the
>world (for instance, what gets remembered).
>
>6. The next one is hard for me to say, even at the very low standards
>of the previous five:  I can be a control system with a model of my
>world, even if I have only modest machinery.  A membrane-bound protein
>that lets in some molecules and ignores others, and which is preserved
>in a population through 

[FRIAM] the woman behind the woman

[Marcus Daniels]

She had the right idea about FORMAC.   Only a reality now with systems like 
SymPy 50 years later.   But an evolved FORMAC would have been better, as it 
would have been a high performance numerics language too.


http://www.pl-enthusiast.net/2017/05/24/jean-sammet-a-remembrance/

FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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Re: [FRIAM] Dutch households will use servers to heat their showers for free - The Verge

[Owen Densmore]

Sorta like bitcoin.

On Sat, Jun 3, 2017 at 1:28 PM, Marcus Daniels  wrote:

> Compare with Sequoia's closed loop cooling system
>  @ 3600 gallons per minute.
>
>
> A fast way to heat a swimming pool, at least.
>
>
> A few of these 1 gallon per minute closed loop water cooling systems with
> a radiator is enough to heat the house in winter.   Not the cheapest way
> unless the compute is useful.
>
>
> Marcus
>

FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
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