Darwin@Home

[Nick Thompson]

Steve,

Ahhhhh, your mental ship drifts toward the VERY port I predicted it would!
Shazzam!  Kazzook!

But of COURSE NO ORGANISM BY DEFINITION EXISTS IN SUCH A SITUATION.  So,
selection is always taking place in organisms.   And the only thing left
for us to decide is, whether the adapted organism is the one that uses
energy most efficiently or the one that disperses it most rapidly.  

I am forgetting already EVERYTHING you taught me last semester about the
second law.  Drat!

Nick



Nicholas S. Thompson
Professor of Psychology and Ethology
Clark University
[hidden email]
http://home.earthlink.net/~nickthompson/
 [hidden email]


> [Original Message]
> From: Stephen Guerin <[hidden email]>
> To: <[hidden email]>; The Friday Morning Applied Complexity
Coffee Group <[hidden email]>
> Date: 1/11/2005 11:12:31 AM
> Subject: RE: [FRIAM] Darwin@Home
>
> Nick writes:
> >If there are no external constraints to which natural selection is
shaping
> > whatever it is shaping, in what sense does the shapee become "adapted"
> > except in the [now] trivial sense that it is under selection?
>
> I would say if there are no external constraints, there will be no
gradients
> in the environment from which potential organizations could extract work.
> Although the mechanism of natural selection would be present, no
adaptation

> will take place.
>
> -S
>
> ________________________________________________________
> [hidden email] http://www.redfish.com
> office: [phone] 624 Agua Fria Street
> mobile: [phone] Santa Fe, NM 87501
>
> > -----Original Message-----
> > From: Nicholas Thompson [mailto:[hidden email]]
> > Sent: Tuesday, January 11, 2005 9:59 AM
> > To: Russell Standish; The Friday Morning Applied Complexity Coffee Group
> > Cc: Stephen Guerin
> > Subject: Re: [FRIAM] Darwin@Home
> >
> >
> > Hi Everybody,
> >
> > .... but what about the circularity problem posed in my earlier post?

If

> > there are no external constraints to which natural selection is shaping
> > whatever it is shaping, in what sense does the shapee become "adapted"
> > except in the [now] trivial sense that it is under selection?
> >
> > Nick
> >
> >
> >
> >
> > Nicholas S. Thompson
> > Professor of Psychology and Ethology
> > Clark University
> > [hidden email]
> > http://home.earthlink.net/~nickthompson/
> >  [hidden email]
> >
> >
> > > [Original Message]
> > > From: Russell Standish <[hidden email]>
> > > To: <[hidden email]>; The Friday Morning Applied

Complexity

> > Coffee Group <[hidden email]>
> > > Cc: Stephen Guerin <[hidden email]>
> > > Date: 1/11/2005 3:01:04 PM
> > > Subject: Re: [FRIAM] Darwin@Home
> > >
> > > I'm not entirely sure I could give a precise definition of adaption
> > > either, but it is clear that it differs from natural/artificial
> > > selection. The Bedau-Packard activity stats (see the numerous papers
> > > by Mark Bedau et al. on the subject) provides a measure of adaption,
> > > and it is possible for evolutionary systems (systems with variation
> > > and selection) to not experience adaption at all. The classic example
> > > is an evolutionary system operating above the error threshold (aka
> > > mutational meltdown).
> > >
> > > Note that when the concept of fitness is present, adaption is rather
> > > easy to define. However, not all evolutionary systems have a notion of
> > > fitness - in particular most of the interesting ones don't.
> > >
> > >    Cheers
> > >
> > > On Mon, Jan 10, 2005 at 02:19:54PM -0700, Nicholas Thompson wrote:
> > > > Steve,
> > > >
> > > > We must consider if we want the statements
> > > >
> > > > "natural selection begets adaptation"
> > > >
> > > > or
> > > >
> > > > "the adapted organism is favorably selected"
> > > >
> > > > to be analytical or contingent.   I.e., do we want them to be like

2 +
> > 2 =
> > > > 4, or do we want them to be like "steve Guerin has a red tie
> > on today."
> > > >
> > > > I prefer them to be contingent, which means of course that is
possible
> > to
> > > > imagine worlds in which natural selection does NOT produce
adaptation
> > and
> > > > worlds in which the adapted organism is NOT favorably.
> > > >
> > > > To make the truth of these statements contingent, adaptation has to
be

> > > > defined in a way that is unconnected with the definition of natural
> > > > selection.  Adaptation cannot be defined as, "Whatever
> > natural selection
> > > > produces."  nor can the adapted organism be defined as that organism
> > that
> > > > has the most offspring.  How can we define adaptation and how can we
> > > > recognize the adapted organism without counting the number of its
> > offspring
> > > >
> > > > To answer this question I think we need to turn to the thinking of a
> > much
> > > > abused and little known author who has defined adaptation as

"natural
> > > > design".  Natural design is, roughly, "whatever properties of nature
> > that
> > > > WOULD lead us to make attributions of intentional design
> > except that we
> > > > know they arent."   What ARE those properties.    A sahib, that is
the
> > > > problem.
> > > > Unfortuately, nobody (except the aforementioned lonely thinker) has
> > given
> > > > this problem any damn thought at all and the lonely thinking has
been
> > too
> > > > stupid to make much progress on it on his own.
> > > >
> > > > I do know, though that a natural selection program that does not
adapt

> > in
> > > > some [other] sense is not doing evolution.
> > > >
> > > > Nick
> > > >
> > > > Nick
> > > >
> > > >
> > > >
> > > > Nicholas S. Thompson
> > > > Professor of Psychology and Ethology
> > > > Clark University
> > > > [hidden email]
> > > > http://home.earthlink.net/~nickthompson/
> > > >  [hidden email]
> > > >
> > > >
> > > > > [Original Message]
> > > > > From: Stephen Guerin <[hidden email]>
> > > > > To: <[hidden email]>; The Friday Morning Applied
> > Complexity
> > > > Coffee Group <[hidden email]>
> > > > > Date: 1/10/2005 1:01:54 PM
> > > > > Subject: RE: [FRIAM] Darwin@Home
> > > > >
> > > > > Nick writes:
> > > > > > Do these models have adaptation?   Most models of this type

that I

> > have
> > > > > > been exposed to  have evolution and natural selection but not
> > > > > > ADAPTATION.
> > > > >
> > > > > Hmm, you may define "adaptation" in a more rigorous way than I.
> > > > >
> > > > > I consider natural selection to be a form of adaptation. Learning
> > during
> > > > an
> > > > > agent's lifetime is another form of adaptation. And, manipulation

of

> > the
> > > > > environment, as in the indirect communication via pheromone
> > fields in
> > ant
> > > > > foraging, to be a third form of adaptation for an agent system.
> > > > >
> > > > > As a generality, I'd say most Alife models primary mechanism of
> > adaptation
> > > > > is natural or artificial selection.
> > > > >
> > > > > However, Larry Yaeger's Polyworld, which is one of the models on

the

> > link,
> > > > > does include non-hereditary adaptation through Hebbian
> > learning. From
> > his
> > > > > paper (http://www.beanblossom.in.us/larryy/Yaeger.ALife3.pdf):
> > > > >
> > > > > "PolyWorld brings together biologically motivated
> > > > > genetics, simple simulated physiologies and metabolisms, Hebbian
> > learning
> > > > in
> > > > > arbitrary neural network
> > > > > architectures, a visual perceptive mechanism, and a suite
> > of primitive
> > > > > behaviors in artificial organisms
> > > > > grounded in an ecology just complex enough to foster speciation

and
> > > > > inter-species competition.
> > > > > Predation, mimicry, sexual reproduction, and even communication
are
> > all
> > > > > supported in a
> > > > > straightforward fashion. The resulting survival strategies, both
> > > > individual
> > > > > and group, are purely
> > > > > emergent, as are the functionalities embodied in their
> > neural network
> > > > > "brains". Complex behaviors
> > > > > resulting from the simulated neural activity are unpredictable,
and

> > change
> > > > > as natural selection acts over
> > > > > multiple generations."
> > > > >
> > > > > Your point is interesting. I guess what constitutes an
> > Alife model is
> > > > rather
> > > > > fuzzy. In the late 80s and early 90s I'd say ~70% of Alife
> > models had
> > > > GA/GP
> > > > > mechanisms as central components. That said, tangentially related
> > models
> > > > > like flocking, ant foraging models and machine learning models

were

> > also
> > > > > included in the conferences. Since the mid-90s, I think the
> > meaning of
> > > > what
> > > > > constitutes a living system to the Alife community has pushed out
> > from a
> > > > > naive application of neo-darwinist mechanism. Some would
> > argue for the
> > > > > necessary presence of generalized thermodynamic work-cycles for an
> > Alife
> > > > > system to be considered "alive". "Some" being me with a mouse in

my

> > pocket
> > > > > ;-)
> > > > >
> > > > > -S
> > > > > ________________________________________________________
> > > > > [hidden email] http://www.redfish.com
> > > > > office: [phone] 624 Agua Fria Street
> > > > > mobile: [phone] Santa Fe, NM 87501
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: Nicholas Thompson [mailto:[hidden email]]
> > > > > > Sent: Monday, January 10, 2005 11:25 AM
> > > > > > To: [hidden email]
> > > > > > Subject: [FRIAM] RE: Friam Digest, Vol 19, Issue 10
> > > > > >
> > > > > >
> > > > > > Steve,
> > > > > >
> > > > >
> > > > > >
> > > > > > Just being annoying,
> > > > > >
> > > > > > Nick
> > > > > >
> > > > > > Nicholas S. Thompson
> > > > > > Professor of Psychology and Ethology
> > > > > > Clark University
> > > > > > [hidden email]
> > > > > > http://home.earthlink.net/~nickthompson/
> > > > > >  [hidden email]
> > > > > >
> > > > > >
> > > > > > >
> > > > > > >
> > > > > > > Today's Topics:
> > > > > > >
> > > > > > >    1. Darwin@Home (Stephen Guerin)
> > > > > > >
> > > > > > >
> > > > > > >
> > ----------------------------------------------------------------------
> > > > > > >
> > > > > > > Message: 1
> > > > > > > Date: Mon, 10 Jan 2005 00:27:13 -0700
> > > > > > > From: "Stephen Guerin" <[hidden email]>
> > > > > > > Subject: [FRIAM] Darwin@Home
> > > > > > > To: "Friam" <[hidden email]>
> > > > > > > Message-ID:
> > <[hidden email]>
> > > > > > > Content-Type: text/plain; charset="iso-8859-1"
> > > > > > >
> > > > > > > Biota.org is back up and promoting Darwin@Home.
> > > > > > > http://www.darwinathome.org/mission/index.html
> > > > > > >
> > > > > > > Some familiar Alife applications are adapting to it:
> > > > > > >
> > > > > > >   - Fluidium: Gerald De Jong's "tensegrity" structures. Nice
> > example
> > > > of
> > > > > > JOGL
> > > > > > > and webstart
> > > > > > > I believe Owen passed around a link 6 months ago:
> > > > > > > http://fluidiom.sourceforge.net/
> > > > > > >
> > > > > > >   - SodaBot -> SodaRace
> > > > > > >
> > > > > > >   - Larry Yaeger's PolyWorld
> > > > > > >
> > > > > > >   - More at: http://www.darwinathome.org/teams/index.html
> > > > > > >
> > > > > > > -Steve
> > > > > > >
> > > > > > > ________________________________________________________
> > > > > > > [hidden email] http://www.redfish.com
> > > > > > > office: [phone] 624 Agua Fria Street
> > > > > > > mobile: [phone] Santa Fe, NM 87501
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > ------------------------------
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > Friam mailing list
> > > > > > > [hidden email]
> > > > > > > http://redfish.com/mailman/listinfo/friam_redfish.com
> > > > > > >
> > > > > > >
> > > > > > > End of Friam Digest, Vol 19, Issue 10
> > > > > > > *************************************
> > > > > >
> > > > > >
> > > > > >
> > > > > > ============================================================
> > > > > > FRIAM Applied Complexity Group listserv
> > > > > > Meets Fridays 9AM @ Jane's Cafe
> > > > > > Lecture schedule, archives, unsubscribe, etc.:
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> > > > > >
> > > >
> > > >
> > > >
> > > > ============================================================
> > > > FRIAM Applied Complexity Group listserv
> > > > Meets Fridays 9AM @ Jane's Cafe
> > > > Lecture schedule, archives, unsubscribe, etc.:
> > > > http://www.friam.org
> > >
> > > --
> > > *PS: A number of people ask me about the attachment to my email, which
> > > is of type "application/pgp-signature". Don't worry, it is not a
> > > virus. It is an electronic signature, that may be used to verify this
> > > email came from me if you have PGP or GPG installed. Otherwise, you
> > > may safely ignore this attachment.
> > >
> > >
> > ------------------------------------------------------------------
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> > > High Performance Computing Support Unit, Phone [phone]
> > (mobile)
> > > UNSW SYDNEY 2052                     Fax   [phone],
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> [hidden email]
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> > >
> > ------------------------------------------------------------------
> > ----------
> >
> >
> >
> > ============================================================
> > FRIAM Applied Complexity Group listserv
> > Meets Fridays 9AM @ Jane's Cafe
> > Lecture schedule, archives, unsubscribe, etc.:
> > http://www.friam.org
> >
> >

[Katharine Mullen-2]

I was very happy to read the discussion regarding adaptation over the past
few days.

The comment by Russell Standish that "when the concept of fitness is
present, adaption is rather easy to define.  However, not all evolutionary
systems have a notion of fitness - in particular most of the interesting
ones don't" is something I've addressed explicitly in a draft of a paper
which formulates a measure of adaptation as change in Shannon information
between components of a system (e.g., entity and environment).  This sort
of measure connects (via use of entropy in the definition of information)
to the thermodynamic-work-cycles-centric ideas brought up by Carl ... and
as for the "circularity problem" posed by Nick ... Gel-Man has said
``when fitness is emergent, it is not so easy to define without a somewhat
circular argument in which whatever wins is fit by definition, and
whatever is fit is likely to win'' (this quote and a citation are in the
paper).  What's needed to get around the problem is a non-teleological
definition of adaptation, which an information-theoretic measure
provides.  In the same way that information theory allowed communication
to be quantified without reference to semantics, it can allow adaptation
to be quantified without reference to fitness.
The draft of the paper is here (it's just 8 pp):
http://www.nat.vu.nl/~kate/info_adapt2004.ps
http://www.nat.vu.nl/~kate/info_adapt2004.pdf
I'd be interested in any comments!

----
Kate Mullen | [hidden email]
Physics Applied Computer Science Group  | Tel. + 31-(0)20-59 87870
Dept. of Physics and Astronomy          | Fax  + 31-(0)20-44 47992
Vrije Universiteit Amsterdam | http://www.nat.vu.nl/~kate/

[Stephen Guerin]

Thanks, Kate!

Your paper reminds me of some of Chris Adami's work measuring Complexity as
the joint entropy between the system and its environment. Have you seen it?

Here's a powerpoint:
http://www.klab.caltech.edu/~ma/cclub/AdamiCClub.ppt

and a paper:
http://www.klab.caltech.edu/~ma/cclub/Adami2.pdf
ABSTRACT: Arguments for or against a trend in the evolution of complexity
are weakened by the lack of an unambiguous definition of complexity. Such
definitions abound for both dynamical systems and biological organisms, but
have drawbacks of either a conceptual or a practical nature. Physical
complexity, a measure based on automata theory and information theory, is a
simple and intuitive measure of the amount of information that an organism
stores, in its genome, about the environment in which it evolves. It is
argued that physical complexity must increase in molecular evolution of
asexual organisms in a single niche if the environment does not change, due
to natural selection. It is possible that complexity decreases in
co-evolving systems as well as at high mutation rates, in sexual
populations, and in time-dependent landscapes. However, it is reasoned that
these factors usually help, rather than hinder, the evolution of complexity,
and that a theory of physical complexity for coevolving species will reveal
an overall trend towards higher complexity in biological evolution.
BioEssays 24:1085-1094, 2002.
2002 Wiley Periodicals, Inc.

-S

________________________________________________________
[hidden email] http://www.redfish.com
office: [phone] 624 Agua Fria Street
mobile: [phone] Santa Fe, NM 87501

> -----Original Message-----
> From: Katharine Mullen [mailto:[hidden email]]
> Sent: Tuesday, January 11, 2005 2:56 PM
> To: [hidden email]; The Friday Morning Applied Complexity
> Coffee Group
> Cc: Stephen Guerin
> Subject: RE: [FRIAM] Darwin@Home
>
>
> I was very happy to read the discussion regarding adaptation over the past
> few days.
>
> The comment by Russell Standish that "when the concept of fitness is
> present, adaption is rather easy to define.  However, not all evolutionary
> systems have a notion of fitness - in particular most of the interesting
> ones don't" is something I've addressed explicitly in a draft of a paper
> which formulates a measure of adaptation as change in Shannon information
> between components of a system (e.g., entity and environment).  This sort
> of measure connects (via use of entropy in the definition of information)
> to the thermodynamic-work-cycles-centric ideas brought up by Carl ... and
> as for the "circularity problem" posed by Nick ... Gel-Man has said
> ``when fitness is emergent, it is not so easy to define without a somewhat
> circular argument in which whatever wins is fit by definition, and
> whatever is fit is likely to win'' (this quote and a citation are in the
> paper).  What's needed to get around the problem is a non-teleological
> definition of adaptation, which an information-theoretic measure
> provides.  In the same way that information theory allowed communication
> to be quantified without reference to semantics, it can allow adaptation
> to be quantified without reference to fitness.
> The draft of the paper is here (it's just 8 pp):
> http://www.nat.vu.nl/~kate/info_adapt2004.ps
> http://www.nat.vu.nl/~kate/info_adapt2004.pdf
> I'd be interested in any comments!
>
> ----
> Kate Mullen | [hidden email]
> Physics Applied Computer Science Group  | Tel. + 31-(0)20-59 87870
> Dept. of Physics and Astronomy          | Fax  + 31-(0)20-44 47992
> Vrije Universiteit Amsterdam | http://www.nat.vu.nl/~kate/
>
>
>
>
> ============================================================
> FRIAM Applied Complexity Group listserv
> Meets Fridays 9AM @ Jane's Cafe
> Lecture schedule, archives, unsubscribe, etc.:
> http://www.friam.org
>
>

[Katharine Mullen-2]

Stephen,

I have seen Chris Adami's work - he has a good discussion of information
theory and entropy in relation to artificial/biological "life" in his book
"Introduction to Artificial Life".  Somewhat disappointing is that he
doesn't mention the work of Charles Bennett along the same lines in the
review you sent a link to.
http://www.research.ibm.com/people/b/bennetc/chbbib.htm
contains the relevant papers
C.H. Bennett "Information, Dissipation, and the Definition of
Organization", in Emerging Syntheses in Science David Pines ed.,
Santa Fe Institute, pp 297-313 (1985).
Charles H. Bennett, "How to Define Complexity in Physics, and Why,"
in Complexity, Entropy, and the Physics of Information (Wojciech H.
Zurek, Editor), Addison-Wesley, 1990 pp 137-148.


--
Kate Mullen | [hidden email]
Physics Applied Computer Science Group  | Tel. + 31-(0)20-59 87870
Dept. of Physics and Astronomy          | Fax  + 31-(0)20-44 47992
Vrije Universiteit Amsterdam | http://www.nat.vu.nl/~kate/