Re: [Polyworld-develop] Spore and Genes

[Andrew <ber...@gm...>]

I think the computational complexity would become overwhelming.  At some
point, its faster to watch evolution take place in a test tube than a ALife
simuation, isn't it?

On Sun, Sep 7, 2008 at 4:05 PM, <la...@us...> wrote:

> At 2:00 AM -0400 9/7/08, Andrew wrote:
> >Spore has been released!  OK, so only a somewhat related peice of news-
> but I think I might be going out to buy it tomorrow assuming I can find a
> copy.  :)  Anyone else psyched about it?
>
> Oh, heck, I sprung for a pre-order of the "Galactic" edition. :)  Not that
> I will have the time or patience to actually do much with it. :(  But I do
> feel compelled to know something about it.
>
> >The real reason I'm posting to the list to just throw out some thoughts of
> mine I've had today regarding some future features of polyworld and the
> related design approaches, specifically (or probably more acurately just a
> working example) related to the critter genome and genes.
>
> By and large I think it's a good, interesting approach to designing such a
> system.  There are some potential gotchas, I think, such as...  How do the
> genes map to the functionalities they imply?  How did the control structure
> (neural network or whatever) get specified?  How did the outputs get
> computed from the inputs and the control structure?  I think there are
> answers to all of these, but they have implications for the design of the
> code.
>
> But, ultimately, the role of genes, sensors, and actuators, while
> extendable, are still entirely defined by the programmer.  (A reasonable
> complaint lodged against Polyworld and all ALife systems to date.)  In the
> end, you might have a more flexibly-programmed Polyworld-like system, but I
> doubt it could ever do anything that Polyworld couldn't.
>
> Of course, the genetics in Polyworld are, at best, a cartoon of biological
> genetics.  Real genes are expressed continuously, in distinct activation
> patterns, in every cell throughout an organism's life.  They regulate and
> are regulated by other genes and epigenetic components (methylation,
> phosphorylation, etc.).  Their products interact in complex ways to produce
> phenotypic form and function.  Their numbers vary across species.
>  Importantly, they can be duplicated through copying errors.  Polyworld's
> genetics are much more Genetic-Algorithm-like, with fixed numbers and fixed
> meanings for the genes, and the genes are only expressed once, at birth,
> then play no further role in the agents' lives.  An almost embarrassing
> simplification, except, fortunately, standard GA approaches have been shown
> to be excellent at exploring complicated high-dimensional spaces, which is
> what I imagine Polyworld to be doing in "neural-architecture space".
>
> By the way, I'll recommend a book that Virgil Griffith recommended to me:
>  Evolving Brains, by John Morgan Allman <
> http://www.amazon.com/dp/0716750767/>.  (Virgil did a lot of work on
> Polyworld with me as an undergrad at IU before going to the computational
> neuroscience program at CalTech, which is where he read this book as part of
> a course, I think.)
>
> FWIW, I've been thinking off and on about a way to write a much more
> open-ended ALife system.  I think the only way for such a system to be truly
> open-ended is for evolution to produce a situation in which one agent *is*
> the ecological niche for another agent.  I.e., there must a way for
> symbiosis and hierarchical self-organization to take place.  I keep coming
> back to one of two approaches.  It's conceivable that one must step all the
> way down to an artificial chemistry in order to produce the desired outcome.
>  But I think it just may be possible to finesse most (but not all)
> artificial chemistry by working predominantly at the level of the cell.
>  Cells would have key aspects of their physiology and behavior determined by
> their genes, of course.  Cell function would be under the control of
> continuously expressing (and re-expressing) genes, plus some signals
> produced by the cells.  Just how open-ended one can be at the cell level is
> unclear, but at least one could build in th
>  e ability to:
>
> *) vary a level of adherence along the cell surface (how exactly this is
> distributed, spatially, I'm not sure yet)
> *) vary a level of wall stiffness/springiness along the cell surface
> (uniform? spatially distributed?)
> *) propagate a signal (the functional equivalent of an axon action
> potential)
> *) receive a signal (the functional equivalent of a synapse)
> *) modulate received signals (what functional form this takes is unclear)
> *) emit chemicals that affect adjacent cells
> *) absorb chemicals through the cell wall
> *) vary permeability to different chemicals in the cell wall
> *) shrink and expand along multiple axes (in response to both genes and
> received signals and chemicals)
>
> These various cell behaviors are necessarily all temporal.  They are all
> derived from the cell's gene expression, but some of them exhibit their own
> temporal behaviors (signal propagation, reception, and modulation, for
> example, but also shrinking and expanding in response to these signals).  I
> think it might be possible to allow arbitrary aggregations of cells this
> way, that could specialize in form and function, incorporate other cells
> into an existing "body", build muscle tissue, build neural tissue, dissolve
> and consume other cells for energy and chemical resources...  In short,
> support symbiosis, hierarchical form and function, and be genuinely
> open-ended.  Yet only the chemical emission and absorption and the cell
> permeability have to drop down to the artificial chemistry level.  All other
> chemistry is finessed.
>
> Okay, I'll shut up now.  I've been thinking about this a fair bit over the
> years, and have made a few notes to myself, but this is the first time I've
> written anything up for anyone else's consumption.  I think I have too much
> to explore with Polyworld to actually do anything with this, but, then
> again, if the right PhD student came along, or someone wanted to pursue it
> as an open source project, or...
>
> One final note:  Even with all that in place, I fear that the mapping from
> gene to low-level cellular expression is too static.  And it's not
> immediately obvious how to allow genes to be duplicated, unless their impact
> on cell function is mediated through an artificial chemistry, which
> introduces all kinds of additional computational overhead and forces a very
> different design aesthetic on the system.  Ah well.  Nothin's easy.
>
> - larryy
>
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