Simulated annealing

[Nick Thompson]

Thanks, Jeff.  At LAST I have learned to spell your name correctly.

Help me out here:  is the conversation about Simulated Annealing REALLY the
same conversation as the conversation about Generative Entrenchment?    I
saw the former as a conversation about selection (fitness landscapes) and
the latter as a conversation about inheritance (the possibility of
differential resemblance between parents and offspring).  Obviously both
selection and inheritance are made more troublesome by genetic
entanglements, but are they the same?

Nick.    

Nicholas Thompson
nickthompson at earthlink.net
http://home.earthlink.net/~nickthompson


> [Original Message]
> From: jcschank <jcschank at ucdavis.edu>
> To: David Sloan Wilson <dwilson at binghamton.edu>
> Cc: <ppgb at cam.ac.uk>; <rsokol at clarku.edu>; echarles
<echarles at clarku.edu>; <lrudolph at black.clarku.edu>; Jaan Valsiner
<jvalsiner at clarku.edu>; jogreen <jogreen at clarku.edu>; <friam at redfish.com>;
elescak <elescak at clarku.edu>; <nickthompson at earthlink.net>; Carl Tollander
<carl at plektyx.com>; sbarr <sbarr at clarku.edu>; Gbarker
<Gbarker at bucknell.edu>; <w-wimsatt at uchicago.edu>

> Date: 5/21/2006 3:02:09 PM
> Subject: Re: Simulated annealing
>
> If one uses simulated annealing (SA)  all that one is doing is adding
> noise to the system, which decreases as the process cools down.  In
> designing an SA algorithm, there is plenty of latitude in designing the
> percolation process, including mutation and recombination.  Fitness
> functions are defined for specific problems.  The only essential
> feature of an SA is the temperature analogue, so that the system
> bounces around more at the beginning of the selection process.  So, if
> you agree that only the temperature analogue is essential to an SA,
> then any selection process can be implemented in an SA framework.  
> There is one reason not use an SA that I can think of and that is when
> there are other sources of noise in the simulated evolutionary process.
>
> Jeff
> On May 21, 2006, at 10:55 AM, David Sloan Wilson wrote:
>
> > A quick comment about "simulated annealing." If I understand it
> > correctly, it can move a system from smaller to larger basins of
> > attraction, but stability does not equal adaptation. There are some
> > very dysfunctional systems that are also very stable, as we know too
> > well for human social systems. Insofar as the adaptedness of a system
> > and the size its basin of attraction are uncorrelated, simulated
> > annealing will not lead to the evolution of adaptive systems, in
> > contrast to selection among alternative local equilibria.
> >
> > By the way, there is a small literature on this concept in the
> > economic and evolutionary literature under the term   "equilibrium
> > selection."
> >
> > d.
> >
> > On May 21, 2006, at 12:09 PM, lrudolph at meganet.net wrote:
> >
> >> To paraphrase the friend of the Dustin Hoffman character's
> >> parents at the graduation party, "Just two words: simulated
> >> annealing."  Accepting arguendo that "a parameter space with
> >> many local stable equilibria" is the appropriate model, I still don't
> >> see why it can't happen that--even "When a biological system is
> >> in the basin of attraction for a particular local equilibrium" and is
> >> thus "generatively entrenched"--the (metaphorical) heat might
> >> not get turned up and down irregularly, allowing some systems
> >> to jump out of one basin of attraction (when they've been heated
> >> up) and then settle into another more or less nearby basin (when
> >> they cool down).
> >>
> >> I don't know your literature, so for all I know this kind of thing
> >> has been considered and debunked long ago, but my new friends
> >> in the protein-conformation-modelling community seem to be willing
> >> to do S.A. all the time. (I don't know if they claim it's happening
> >> *in
> >> the biological system* where the protein is being assembled; they
> >> may *only* be using it artefactually inside the black-box part of
> >> their model, to get the model out of locally energy-minimizing
> >> conformations that aren't physically realistic so that it can have
> >> a better chance of falling into a more realistic local stable
> >> equilibrium.  But I do know they use it.)
> >>
> >>
> >>> Hi everybody,
> >>>
> >>> Forgive me for casting such a wide net, but we seem to be skating
> >>> very
> >>> close to what Carl Tollander calls "artificial epigenesis and I want
> >>> to
> >>> keep the conversation as open as possible until I see who is
> >>> interested.
> >>>
> >>> David Wilson (attached and below) has taken the discussion in the
> >>> direction
> >>> I hoped it might turn .... that selection might consist of unstable
> >>> relations amongst stable arrays. Everybody is talking as if the
> >>> elements in
> >>> the arrays are genes, but there is no particular reason not to
> >>> include
> >>> epigenetic nodes as well.   The implication for my question on
> >>> inheritance
> >>> is that all the chaos in the genetic-epigenitic system is going on a
> >>> level
> >>> BELOW where selection is going on.  This might seem to beg the
> >>> question
> >>> concerning inheritance ... what "force" holds together the stable
> >>> arrays?
> >>> However, at this early stage of my reading, Wimsatt and Schank seem
> >>> to be
> >>> saying that the stable arrays are high  entropy .. i.e., they hang
> >>> together
> >>> because that's where randomization takes them.
> >>>
> >>> I am very excited about all of this, as you can see, but as you can
> >>> also
> >>> see, I should shut up and go back to reading before I say more.  
> >>> Thanks for
> >>> your patience.  Be sure to read the message below and the attachment
> >>> if you
> >>> are interested.
> >>>
> >>> thanks, all,
> >>>
> >>> Nick
> >>>
> >>> Nicholas Thompson
> >>> nickthompson at earthlink.net
> >>> http://home.earthlink.net/~nickthompson
> >>>
> >>>
> >>>> [Original Message]
> >>>> From: David Sloan Wilson <dwilson at binghamton.edu>
> >>>> To: <nickthompson at earthlink.net>
> >>>> Date: 5/21/2006 8:35:45 AM
> >>>> Subject: Heritability and generative entrenchment
> >>>>
> >>>> Dear Nick,
> >>>>
> >>>> Thanks for your interesting message. I'm sending this reply to you
> >>>> only
> >>>> rather than the whole group--I'll let you be the judge of what the
> >>>> whole group sees and in what manner.
> >>>>
> >>>> Consider a parameter space with many local stable equilibria.  When
> >>>> a
> >>>> biological system is in the basin of attraction for a particular
> >>>> local
> >>>> equilibrium, it is generatively entrenched and here is a problem for
> >>>> heritability. However, there can still be selection among multiple
> >>>> basins of attraction, providing a concept of heritability. I discuss
> >>>> this in the following paper titled "Natural Selection and Complex
> >>>> Systems: a complex interaction."
> >>>>
> >>>>
> >>>
> >>
> >>
> >>
> > David Sloan Wilson
> > Professor, Departments of Biology and Anthropology
> > Binghamton University
> > Binghamton, New York 13902-6000
> > tel: [phone] fax: [phone]
> > dwilson at binghamton.edu
> > http://biology.binghamton.edu/dwilson/
> >
> > Are YOU the kind of person who supports worthy causes? Then consider
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> >
> Jeff Schank 
> Associate Professor
> Department of Psychology
> University of California
> One Shields Ave.
> Davis, CA 95616
>
> Associate Editor, Adaptive Behavior
> Home Page
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> Lab:    [phone]
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> E-mail: jcschank at ucdavis.edu
>
> False facts are highly injurious to the progress of science, for they
> often endure long; but false views, if supported by some evidence, do
> little harm, for every one takes a salutary pleasure in proving their
> falseness: and when this is done, one path towards error is closed and
> the road to truth is often at the same time opened. (p. 909, Darwin,
> 1874, The Descent of Man)

[Jochen Fromm-3]

Perhaps the concept of "canalization" is associated with
"generative entrenchment", whatever this nebulous idea may mean ?
You still have not explained the problem in simple words.
Canalization refers to certain properties of the genotype-phenotype
mapping. Of course this is a complex subject.

Even molecular biologists don't know exactly how the phenotype
arises from the genotype in detail, and I am not an expert in
molecular biology. Do we have an expert here ? According to
the things I have read genetic canalization is defined as the
suppression of phenotypic variation and describes insensitivity
of a character to mutations.

see "Progress on canalization"
http://www.pnas.org/cgi/content/full/99/16/10229

Since Carlos mentioned RBNs (Random Boolean Networks), the
following paper about canalization and self-organization
may be interesting in this context:

"Evolution of Developmental Canalization in Networks of Competing Boolean
Nodes"
Kevin E. Bassler, Choongseop Lee, and Yong Lee
Phys. Rev. Lett. 93, 038101 (2004)
http://link.aps.org/doi/10.1103/PhysRevLett.93.038101

-J.